diff --git a/coverage/class_index.html b/coverage/class_index.html
index 17a0e41..7572dca 100644
--- a/coverage/class_index.html
+++ b/coverage/class_index.html
@@ -11,7 +11,7 @@
 <header>
     <div class="content">
         <h1>Coverage report:
-            <span class="pc_cov">76%</span>
+            <span class="pc_cov">75%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -55,7 +55,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
 </header>
@@ -91,10 +91,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_d938f4eecb54a579_common_py.html">biobb_pmx/pmxbiobb/common.py</a></td>
                 <td class="name left"><a href="z_d938f4eecb54a579_common_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>22</td>
-                <td>4</td>
+                <td>31</td>
+                <td>12</td>
                 <td>0</td>
-                <td class="right" data-ratio="18 22">82%</td>
+                <td class="right" data-ratio="19 31">61%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_d938f4eecb54a579_pmxanalyse_py.html#t14">biobb_pmx/pmxbiobb/pmxanalyse.py</a></td>
@@ -129,8 +129,8 @@ <h2>
                 <td class="right" data-ratio="17 37">46%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t16">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t16"><data value='Pmxcreate_top'>Pmxcreate_top</data></a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t18">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t18"><data value='Pmxcreate_top'>Pmxcreate_top</data></a></td>
                 <td>57</td>
                 <td>2</td>
                 <td>0</td>
@@ -333,10 +333,10 @@ <h2>
             <tr class="total">
                 <td class="name left">Total</td>
                 <td class="name left">&nbsp;</td>
-                <td>776</td>
-                <td>186</td>
+                <td>785</td>
+                <td>194</td>
                 <td>0</td>
-                <td class="right" data-ratio="590 776">76%</td>
+                <td class="right" data-ratio="591 785">75%</td>
             </tr>
         </tfoot>
     </table>
@@ -348,7 +348,7 @@ <h2>
     <div class="content">
         <p>
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index 6a9818b..ded6202 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
-<coverage version="7.6.4" timestamp="1730734712479" lines-valid="776" lines-covered="590" line-rate="0.7603" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+<coverage version="7.6.4" timestamp="1731601477868" lines-valid="785" lines-covered="591" line-rate="0.7529" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.4 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
@@ -19,7 +19,7 @@
 				</class>
 			</classes>
 		</package>
-		<package name="biobb_pmx.pmxbiobb" line-rate="0.7289" branch-rate="0" complexity="0">
+		<package name="biobb_pmx.pmxbiobb" line-rate="0.7209" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="biobb_pmx/pmxbiobb/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
@@ -35,31 +35,40 @@
 						<line number="10" hits="1"/>
 					</lines>
 				</class>
-				<class name="common.py" filename="biobb_pmx/pmxbiobb/common.py" complexity="0" line-rate="0.8182" branch-rate="0">
+				<class name="common.py" filename="biobb_pmx/pmxbiobb/common.py" complexity="0" line-rate="0.6129" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="3" hits="1"/>
 						<line number="4" hits="1"/>
-						<line number="7" hits="1"/>
-						<line number="10" hits="1"/>
-						<line number="11" hits="1"/>
-						<line number="13" hits="1"/>
-						<line number="14" hits="0"/>
-						<line number="15" hits="0"/>
-						<line number="16" hits="1"/>
-						<line number="17" hits="1"/>
-						<line number="18" hits="1"/>
-						<line number="19" hits="1"/>
-						<line number="20" hits="1"/>
-						<line number="21" hits="1"/>
-						<line number="22" hits="1"/>
-						<line number="23" hits="0"/>
-						<line number="24" hits="1"/>
-						<line number="25" hits="1"/>
-						<line number="26" hits="0"/>
-						<line number="28" hits="1"/>
-						<line number="29" hits="1"/>
-						<line number="31" hits="1"/>
+						<line number="6" hits="1"/>
+						<line number="60" hits="1"/>
+						<line number="65" hits="1"/>
+						<line number="67" hits="1"/>
+						<line number="68" hits="0"/>
+						<line number="69" hits="0"/>
+						<line number="70" hits="1"/>
+						<line number="71" hits="1"/>
+						<line number="72" hits="1"/>
+						<line number="73" hits="1"/>
+						<line number="74" hits="1"/>
+						<line number="75" hits="1"/>
+						<line number="76" hits="1"/>
+						<line number="77" hits="0"/>
+						<line number="78" hits="1"/>
+						<line number="79" hits="1"/>
+						<line number="80" hits="0"/>
+						<line number="83" hits="1"/>
+						<line number="84" hits="1"/>
+						<line number="86" hits="1"/>
+						<line number="90" hits="1"/>
+						<line number="101" hits="0"/>
+						<line number="102" hits="0"/>
+						<line number="104" hits="0"/>
+						<line number="106" hits="0"/>
+						<line number="109" hits="0"/>
+						<line number="110" hits="0"/>
+						<line number="113" hits="0"/>
+						<line number="115" hits="0"/>
 					</lines>
 				</class>
 				<class name="pmxanalyse.py" filename="biobb_pmx/pmxbiobb/pmxanalyse.py" complexity="0" line-rate="0.7563" branch-rate="0">
@@ -316,92 +325,92 @@
 				<class name="pmxcreate_top.py" filename="biobb_pmx/pmxbiobb/pmxcreate_top.py" complexity="0" line-rate="0.8488" branch-rate="0">
 					<methods/>
 					<lines>
-						<line number="4" hits="1"/>
 						<line number="5" hits="1"/>
 						<line number="6" hits="1"/>
 						<line number="7" hits="1"/>
 						<line number="8" hits="1"/>
 						<line number="9" hits="1"/>
 						<line number="10" hits="1"/>
-						<line number="11" hits="1"/>
 						<line number="12" hits="1"/>
 						<line number="13" hits="1"/>
-						<line number="16" hits="1"/>
-						<line number="65" hits="1"/>
+						<line number="14" hits="1"/>
+						<line number="15" hits="1"/>
+						<line number="18" hits="1"/>
 						<line number="67" hits="1"/>
-						<line number="70" hits="1"/>
-						<line number="71" hits="1"/>
-						<line number="74" hits="1"/>
-						<line number="80" hits="1"/>
-						<line number="81" hits="1"/>
+						<line number="75" hits="1"/>
+						<line number="78" hits="1"/>
+						<line number="79" hits="1"/>
 						<line number="82" hits="1"/>
-						<line number="83" hits="1"/>
-						<line number="86" hits="1"/>
-						<line number="87" hits="1"/>
-						<line number="88" hits="1"/>
-						<line number="89" hits="1"/>
 						<line number="91" hits="1"/>
-						<line number="92" hits="0"/>
+						<line number="92" hits="1"/>
 						<line number="93" hits="1"/>
-						<line number="96" hits="1"/>
+						<line number="94" hits="1"/>
 						<line number="97" hits="1"/>
+						<line number="98" hits="1"/>
 						<line number="99" hits="1"/>
 						<line number="100" hits="1"/>
-						<line number="104" hits="1"/>
-						<line number="105" hits="0"/>
-						<line number="106" hits="1"/>
-						<line number="108" hits="1"/>
+						<line number="105" hits="1"/>
+						<line number="106" hits="0"/>
 						<line number="111" hits="1"/>
-						<line number="112" hits="1"/>
 						<line number="114" hits="1"/>
 						<line number="115" hits="1"/>
-						<line number="116" hits="1"/>
 						<line number="117" hits="1"/>
-						<line number="119" hits="1"/>
-						<line number="120" hits="1"/>
-						<line number="121" hits="1"/>
+						<line number="118" hits="1"/>
 						<line number="122" hits="1"/>
+						<line number="123" hits="0"/>
 						<line number="124" hits="1"/>
-						<line number="128" hits="1"/>
+						<line number="126" hits="1"/>
+						<line number="129" hits="1"/>
 						<line number="130" hits="1"/>
 						<line number="132" hits="1"/>
+						<line number="135" hits="1"/>
 						<line number="136" hits="1"/>
 						<line number="137" hits="1"/>
 						<line number="139" hits="1"/>
-						<line number="141" hits="1"/>
+						<line number="142" hits="1"/>
 						<line number="143" hits="1"/>
 						<line number="144" hits="1"/>
 						<line number="146" hits="1"/>
-						<line number="147" hits="1"/>
-						<line number="148" hits="1"/>
-						<line number="149" hits="1"/>
+						<line number="150" hits="1"/>
 						<line number="152" hits="1"/>
-						<line number="153" hits="1"/>
-						<line number="155" hits="1"/>
-						<line number="156" hits="1"/>
-						<line number="157" hits="1"/>
+						<line number="154" hits="1"/>
 						<line number="158" hits="1"/>
-						<line number="160" hits="1"/>
+						<line number="159" hits="1"/>
+						<line number="161" hits="1"/>
+						<line number="163" hits="1"/>
+						<line number="165" hits="1"/>
 						<line number="166" hits="1"/>
 						<line number="168" hits="1"/>
 						<line number="169" hits="1"/>
+						<line number="170" hits="1"/>
 						<line number="171" hits="1"/>
-						<line number="172" hits="1"/>
+						<line number="174" hits="1"/>
 						<line number="175" hits="1"/>
+						<line number="179" hits="1"/>
 						<line number="180" hits="1"/>
-						<line number="185" hits="1"/>
-						<line number="187" hits="0"/>
-						<line number="189" hits="0"/>
-						<line number="192" hits="0"/>
-						<line number="193" hits="0"/>
-						<line number="194" hits="0"/>
-						<line number="195" hits="0"/>
-						<line number="197" hits="0"/>
-						<line number="198" hits="0"/>
-						<line number="199" hits="0"/>
-						<line number="202" hits="0"/>
-						<line number="207" hits="1"/>
-						<line number="208" hits="0"/>
+						<line number="181" hits="1"/>
+						<line number="182" hits="1"/>
+						<line number="184" hits="1"/>
+						<line number="190" hits="1"/>
+						<line number="192" hits="1"/>
+						<line number="193" hits="1"/>
+						<line number="195" hits="1"/>
+						<line number="196" hits="1"/>
+						<line number="199" hits="1"/>
+						<line number="209" hits="1"/>
+						<line number="218" hits="1"/>
+						<line number="220" hits="0"/>
+						<line number="224" hits="0"/>
+						<line number="232" hits="0"/>
+						<line number="233" hits="0"/>
+						<line number="238" hits="0"/>
+						<line number="243" hits="0"/>
+						<line number="249" hits="0"/>
+						<line number="250" hits="0"/>
+						<line number="251" hits="0"/>
+						<line number="254" hits="0"/>
+						<line number="262" hits="1"/>
+						<line number="263" hits="0"/>
 					</lines>
 				</class>
 				<class name="pmxgentop.py" filename="biobb_pmx/pmxbiobb/pmxgentop.py" complexity="0" line-rate="0.7368" branch-rate="0">
diff --git a/coverage/coveragebadge.svg b/coverage/coveragebadge.svg
index 6b439cb..ed64b91 100644
--- a/coverage/coveragebadge.svg
+++ b/coverage/coveragebadge.svg
@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="116" height="20" role="img" aria-label="Coverage: 76.03%"><title>Coverage: 76.03%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="116" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="63" height="20" fill="#555"/><rect x="63" width="53" height="20" fill="#97ca00"/><rect width="116" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="325" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="530">Coverage</text><text x="325" y="140" transform="scale(.1)" fill="#fff" textLength="530">Coverage</text><text aria-hidden="true" x="885" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">76.03%</text><text x="885" y="140" transform="scale(.1)" fill="#fff" textLength="430">76.03%</text></g></svg>
\ No newline at end of file
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="116" height="20" role="img" aria-label="Coverage: 75.29%"><title>Coverage: 75.29%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="116" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="63" height="20" fill="#555"/><rect x="63" width="53" height="20" fill="#97ca00"/><rect width="116" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="325" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="530">Coverage</text><text x="325" y="140" transform="scale(.1)" fill="#fff" textLength="530">Coverage</text><text aria-hidden="true" x="885" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">75.29%</text><text x="885" y="140" transform="scale(.1)" fill="#fff" textLength="430">75.29%</text></g></svg>
\ No newline at end of file
diff --git a/coverage/function_index.html b/coverage/function_index.html
index c6a5524..a98e2ac 100644
--- a/coverage/function_index.html
+++ b/coverage/function_index.html
@@ -11,7 +11,7 @@
 <header>
     <div class="content">
         <h1>Coverage report:
-            <span class="pc_cov">76%</span>
+            <span class="pc_cov">75%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -55,7 +55,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
 </header>
@@ -89,20 +89,28 @@ <h2>
                 <td class="right" data-ratio="9 9">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_d938f4eecb54a579_common_py.html#t10">biobb_pmx/pmxbiobb/common.py</a></td>
-                <td class="name left"><a href="z_d938f4eecb54a579_common_py.html#t10"><data value='create_mutations_file'>create_mutations_file</data></a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_common_py.html#t60">biobb_pmx/pmxbiobb/common.py</a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_common_py.html#t60"><data value='create_mutations_file'>create_mutations_file</data></a></td>
                 <td>18</td>
                 <td>4</td>
                 <td>0</td>
                 <td class="right" data-ratio="14 18">78%</td>
             </tr>
+            <tr class="region">
+                <td class="name left"><a href="z_d938f4eecb54a579_common_py.html#t90">biobb_pmx/pmxbiobb/common.py</a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_common_py.html#t90"><data value='from_string_to_list'>_from_string_to_list</data></a></td>
+                <td>8</td>
+                <td>8</td>
+                <td>0</td>
+                <td class="right" data-ratio="0 8">0%</td>
+            </tr>
             <tr class="region">
                 <td class="name left"><a href="z_d938f4eecb54a579_common_py.html">biobb_pmx/pmxbiobb/common.py</a></td>
                 <td class="name left"><a href="z_d938f4eecb54a579_common_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>4</td>
+                <td>5</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="4 4">100%</td>
+                <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_d938f4eecb54a579_pmxanalyse_py.html#t78">biobb_pmx/pmxbiobb/pmxanalyse.py</a></td>
@@ -185,32 +193,32 @@ <h2>
                 <td class="right" data-ratio="16 17">94%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t65">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t65"><data value='init__'>Pmxcreate_top.__init__</data></a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t67">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t67"><data value='init__'>Pmxcreate_top.__init__</data></a></td>
                 <td>17</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="16 17">94%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t100">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t100"><data value='launch'>Pmxcreate_top.launch</data></a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t118">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t118"><data value='launch'>Pmxcreate_top.launch</data></a></td>
                 <td>40</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="39 40">98%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t175">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t175"><data value='pmxcreate_top'>pmxcreate_top</data></a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t199">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t199"><data value='pmxcreate_top'>pmxcreate_top</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t185">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
-                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t185"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_d938f4eecb54a579_pmxcreate_top_py.html#t218">biobb_pmx/pmxbiobb/pmxcreate_top.py</a></td>
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     </div>
 </footer>
diff --git a/coverage/z_bf2f27f5e62eb5d4_test_pmxanalyse_py.html b/coverage/z_bf2f27f5e62eb5d4_test_pmxanalyse_py.html
index f8c6f48..b181a76 100644
--- a/coverage/z_bf2f27f5e62eb5d4_test_pmxanalyse_py.html
+++ b/coverage/z_bf2f27f5e62eb5d4_test_pmxanalyse_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_bf2f27f5e62eb5d4_test_pmxatom_mapping_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <h2>
             <a class="nav" href="z_bf2f27f5e62eb5d4_test_pmxatom_mapping_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_bf2f27f5e62eb5d4_test_pmxatom_mapping_py.html b/coverage/z_bf2f27f5e62eb5d4_test_pmxatom_mapping_py.html
index c563de7..835f62b 100644
--- a/coverage/z_bf2f27f5e62eb5d4_test_pmxatom_mapping_py.html
+++ b/coverage/z_bf2f27f5e62eb5d4_test_pmxatom_mapping_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_bf2f27f5e62eb5d4_test_pmxcreate_top_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -107,7 +107,7 @@ <h2>
             <a class="nav" href="z_bf2f27f5e62eb5d4_test_pmxcreate_top_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
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 </footer>
diff --git a/coverage/z_bf2f27f5e62eb5d4_test_pmxcreate_top_py.html b/coverage/z_bf2f27f5e62eb5d4_test_pmxcreate_top_py.html
index 24662e2..c5689a1 100644
--- a/coverage/z_bf2f27f5e62eb5d4_test_pmxcreate_top_py.html
+++ b/coverage/z_bf2f27f5e62eb5d4_test_pmxcreate_top_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_bf2f27f5e62eb5d4_test_pmxgentop_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -105,7 +105,7 @@ <h2>
             <a class="nav" href="z_bf2f27f5e62eb5d4_test_pmxgentop_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
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 </footer>
diff --git a/coverage/z_bf2f27f5e62eb5d4_test_pmxgentop_py.html b/coverage/z_bf2f27f5e62eb5d4_test_pmxgentop_py.html
index 73ecd08..269d4fd 100644
--- a/coverage/z_bf2f27f5e62eb5d4_test_pmxgentop_py.html
+++ b/coverage/z_bf2f27f5e62eb5d4_test_pmxgentop_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_bf2f27f5e62eb5d4_test_pmxligand_hybrid_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_bf2f27f5e62eb5d4_test_pmxligand_hybrid_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_bf2f27f5e62eb5d4_test_pmxligand_hybrid_py.html b/coverage/z_bf2f27f5e62eb5d4_test_pmxligand_hybrid_py.html
index 0562b7b..2769b7d 100644
--- a/coverage/z_bf2f27f5e62eb5d4_test_pmxligand_hybrid_py.html
+++ b/coverage/z_bf2f27f5e62eb5d4_test_pmxligand_hybrid_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_bf2f27f5e62eb5d4_test_pmxmerge_ff_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -111,7 +111,7 @@ <h2>
             <a class="nav" href="z_bf2f27f5e62eb5d4_test_pmxmerge_ff_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
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 </footer>
diff --git a/coverage/z_bf2f27f5e62eb5d4_test_pmxmerge_ff_py.html b/coverage/z_bf2f27f5e62eb5d4_test_pmxmerge_ff_py.html
index 0a96bfa..757d35b 100644
--- a/coverage/z_bf2f27f5e62eb5d4_test_pmxmerge_ff_py.html
+++ b/coverage/z_bf2f27f5e62eb5d4_test_pmxmerge_ff_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_bf2f27f5e62eb5d4_test_pmxmutate_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -107,7 +107,7 @@ <h2>
             <a class="nav" href="z_bf2f27f5e62eb5d4_test_pmxmutate_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
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     </div>
 </footer>
diff --git a/coverage/z_bf2f27f5e62eb5d4_test_pmxmutate_py.html b/coverage/z_bf2f27f5e62eb5d4_test_pmxmutate_py.html
index d830693..b8614dc 100644
--- a/coverage/z_bf2f27f5e62eb5d4_test_pmxmutate_py.html
+++ b/coverage/z_bf2f27f5e62eb5d4_test_pmxmutate_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -105,7 +105,7 @@ <h2>
             <a class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
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 </footer>
diff --git a/coverage/z_d938f4eecb54a579___init___py.html b/coverage/z_d938f4eecb54a579___init___py.html
index 6a8b8a4..77fa99a 100644
--- a/coverage/z_d938f4eecb54a579___init___py.html
+++ b/coverage/z_d938f4eecb54a579___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_d938f4eecb54a579_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -99,7 +99,7 @@ <h2>
             <a class="nav" href="z_d938f4eecb54a579_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_d938f4eecb54a579_common_py.html b/coverage/z_d938f4eecb54a579_common_py.html
index 7359554..e53b0c0 100644
--- a/coverage/z_d938f4eecb54a579_common_py.html
+++ b/coverage/z_d938f4eecb54a579_common_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_pmx/pmxbiobb/common.py: 82%</title>
+    <title>Coverage for biobb_pmx/pmxbiobb/common.py: 61%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_pmx/pmxbiobb/common.py</b>:
-            <span class="pc_cov">82%</span>
+            <span class="pc_cov">61%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,9 +54,9 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">22 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">18<span class="text"> run</span></button>
-            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">4<span class="text"> missing</span></button>
+            <span class="text">31 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">19<span class="text"> run</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">12<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
         <p class="text">
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_d938f4eecb54a579_pmxanalyse_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -80,37 +80,121 @@ <h2>
     </div>
 </header>
 <main id="source">
-    <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="str">""" Common functions for package biobb_pmx.pmx """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="str">"""Common functions for package biobb_pmx.pmx"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="key">import</span> <span class="nam">re</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Union</span><span class="op">,</span> <span class="nam">Iterable</span><span class="op">,</span> <span class="nam">Mapping</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Iterable</span><span class="op">,</span> <span class="nam">Mapping</span><span class="op">,</span> <span class="nam">Optional</span><span class="op">,</span> <span class="nam">Union</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="nam">MUTATION_DICT</span> <span class="op">=</span> <span class="op">{</span><span class="str">'ALA'</span><span class="op">:</span> <span class="str">'A'</span><span class="op">,</span> <span class="str">'ARG'</span><span class="op">:</span> <span class="str">'R'</span><span class="op">,</span> <span class="str">'ASN'</span><span class="op">:</span> <span class="str">'N'</span><span class="op">,</span> <span class="str">'ASP'</span><span class="op">:</span> <span class="str">'D'</span><span class="op">,</span> <span class="str">'ASPH'</span><span class="op">:</span> <span class="str">'B'</span><span class="op">,</span> <span class="str">'ASPP'</span><span class="op">:</span> <span class="str">'B'</span><span class="op">,</span> <span class="str">'ASH'</span><span class="op">:</span> <span class="str">'B'</span><span class="op">,</span> <span class="str">'CYS'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span> <span class="str">'CYS2'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span> <span class="str">'CYN'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span> <span class="str">'CYX'</span><span class="op">:</span> <span class="str">'CX'</span><span class="op">,</span> <span class="str">'CYM'</span><span class="op">:</span> <span class="str">'CM'</span><span class="op">,</span> <span class="str">'CYSH'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span> <span class="str">'GLU'</span><span class="op">:</span> <span class="str">'E'</span><span class="op">,</span> <span class="str">'GLUH'</span><span class="op">:</span> <span class="str">'J'</span><span class="op">,</span> <span class="str">'GLUP'</span><span class="op">:</span> <span class="str">'J'</span><span class="op">,</span> <span class="str">'GLH'</span><span class="op">:</span> <span class="str">'J'</span><span class="op">,</span> <span class="str">'GLN'</span><span class="op">:</span> <span class="str">'Q'</span><span class="op">,</span> <span class="str">'GLY'</span><span class="op">:</span> <span class="str">'G'</span><span class="op">,</span> <span class="str">'HIS'</span><span class="op">:</span> <span class="str">'H'</span><span class="op">,</span> <span class="str">'HIE'</span><span class="op">:</span> <span class="str">'X'</span><span class="op">,</span> <span class="str">'HISE'</span><span class="op">:</span> <span class="str">'X'</span><span class="op">,</span> <span class="str">'HSE'</span><span class="op">:</span> <span class="str">'X'</span><span class="op">,</span> <span class="str">'HIP'</span><span class="op">:</span> <span class="str">'Z'</span><span class="op">,</span> <span class="str">'HSP'</span><span class="op">:</span> <span class="str">'Z'</span><span class="op">,</span> <span class="str">'HISH'</span><span class="op">:</span> <span class="str">'Z'</span><span class="op">,</span> <span class="str">'HID'</span><span class="op">:</span> <span class="str">'H'</span><span class="op">,</span> <span class="str">'HSD'</span><span class="op">:</span> <span class="str">'H'</span><span class="op">,</span> <span class="str">'ILE'</span><span class="op">:</span> <span class="str">'I'</span><span class="op">,</span> <span class="str">'LEU'</span><span class="op">:</span> <span class="str">'L'</span><span class="op">,</span> <span class="str">'LYS'</span><span class="op">:</span> <span class="str">'K'</span><span class="op">,</span> <span class="str">'LYSH'</span><span class="op">:</span> <span class="str">'K'</span><span class="op">,</span> <span class="str">'LYP'</span><span class="op">:</span> <span class="str">'K'</span><span class="op">,</span> <span class="str">'LYN'</span><span class="op">:</span> <span class="str">'O'</span><span class="op">,</span> <span class="str">'LSN'</span><span class="op">:</span> <span class="str">'O'</span><span class="op">,</span> <span class="str">'MET'</span><span class="op">:</span> <span class="str">'M'</span><span class="op">,</span> <span class="str">'PHE'</span><span class="op">:</span> <span class="str">'F'</span><span class="op">,</span> <span class="str">'PRO'</span><span class="op">:</span> <span class="str">'P'</span><span class="op">,</span> <span class="str">'SER'</span><span class="op">:</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'SP1'</span><span class="op">:</span> <span class="str">'SP1'</span><span class="op">,</span> <span class="str">'SP2'</span><span class="op">:</span> <span class="str">'SP2'</span><span class="op">,</span> <span class="str">'THR'</span><span class="op">:</span> <span class="str">'T'</span><span class="op">,</span> <span class="str">'TRP'</span><span class="op">:</span> <span class="str">'W'</span><span class="op">,</span> <span class="str">'TYR'</span><span class="op">:</span> <span class="str">'Y'</span><span class="op">,</span> <span class="str">'VAL'</span><span class="op">:</span> <span class="str">'V'</span><span class="op">,</span> <span class="str">'A'</span><span class="op">:</span> <span class="str">'A'</span><span class="op">,</span> <span class="str">'T'</span><span class="op">:</span> <span class="str">'T'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span> <span class="str">'G'</span><span class="op">:</span> <span class="str">'G'</span><span class="op">,</span> <span class="str">'U'</span><span class="op">:</span> <span class="str">'U'</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">def</span> <span class="nam">create_mutations_file</span><span class="op">(</span><span class="nam">input_mutations_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">mutation_list</span><span class="op">:</span> <span class="nam">Union</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">Iterable</span><span class="op">[</span><span class="nam">str</span><span class="op">]</span><span class="op">]</span><span class="op">,</span> <span class="nam">mutation_dict</span><span class="op">:</span> <span class="nam">Mapping</span><span class="op">)</span> <span class="op">-></span> <span class="nam">str</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">    <span class="key">try</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">        <span class="com"># Check if self.mutation_list is a string</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">        <span class="nam">mutation_list</span> <span class="op">=</span> <span class="nam">mutation_list</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">','</span><span class="op">)</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">    <span class="key">except</span> <span class="nam">AttributeError</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">        <span class="key">pass</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">    <span class="nam">pattern</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">r"(?P&lt;chain>[a-zA-Z])*:?(?P&lt;resnum>\d+)(?P&lt;mt>[a-zA-Z0-9]+)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">    <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">input_mutations_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">mut_file</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">        <span class="key">for</span> <span class="nam">mut</span> <span class="key">in</span> <span class="nam">mutation_list</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">            <span class="nam">match</span> <span class="op">=</span> <span class="nam">pattern</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="nam">mut</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">            <span class="key">if</span> <span class="nam">match</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">                <span class="nam">mut_groups_dict</span> <span class="op">=</span> <span class="nam">match</span><span class="op">.</span><span class="nam">groupdict</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">                <span class="key">if</span> <span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'chain'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">                    <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'chain'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">                <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'resnum'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t">                <span class="key">if</span> <span class="key">not</span> <span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'mt'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span><span class="op">.</span><span class="nam">upper</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">mutation_dict</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t">                    <span class="key">raise</span> <span class="nam">TypeError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t">                        <span class="str">f"{mut_groups_dict.get('mt','').upper()} is not a valid AA code or NA code. Possible values are {mutation_dict.keys()}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t">                <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">mutation_dict</span><span class="op">[</span><span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'mt'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span><span class="op">.</span><span class="nam">upper</span><span class="op">(</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t">                <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t">    <span class="key">return</span> <span class="nam">input_mutations_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="nam">MUTATION_DICT</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">    <span class="str">"ALA"</span><span class="op">:</span> <span class="str">"A"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">    <span class="str">"ARG"</span><span class="op">:</span> <span class="str">"R"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">    <span class="str">"ASN"</span><span class="op">:</span> <span class="str">"N"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">    <span class="str">"ASP"</span><span class="op">:</span> <span class="str">"D"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">    <span class="str">"ASPH"</span><span class="op">:</span> <span class="str">"B"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">    <span class="str">"ASPP"</span><span class="op">:</span> <span class="str">"B"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">    <span class="str">"ASH"</span><span class="op">:</span> <span class="str">"B"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">    <span class="str">"CYS"</span><span class="op">:</span> <span class="str">"C"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">    <span class="str">"CYS2"</span><span class="op">:</span> <span class="str">"C"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">    <span class="str">"CYN"</span><span class="op">:</span> <span class="str">"C"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">    <span class="str">"CYX"</span><span class="op">:</span> <span class="str">"CX"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">    <span class="str">"CYM"</span><span class="op">:</span> <span class="str">"CM"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"CYSH"</span><span class="op">:</span> <span class="str">"C"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">    <span class="str">"GLU"</span><span class="op">:</span> <span class="str">"E"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">    <span class="str">"GLUH"</span><span class="op">:</span> <span class="str">"J"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">    <span class="str">"GLUP"</span><span class="op">:</span> <span class="str">"J"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">    <span class="str">"GLH"</span><span class="op">:</span> <span class="str">"J"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">    <span class="str">"GLN"</span><span class="op">:</span> <span class="str">"Q"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t">    <span class="str">"GLY"</span><span class="op">:</span> <span class="str">"G"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t">    <span class="str">"HIS"</span><span class="op">:</span> <span class="str">"H"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t">    <span class="str">"HIE"</span><span class="op">:</span> <span class="str">"X"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t">    <span class="str">"HISE"</span><span class="op">:</span> <span class="str">"X"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t">    <span class="str">"HSE"</span><span class="op">:</span> <span class="str">"X"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t">    <span class="str">"HIP"</span><span class="op">:</span> <span class="str">"Z"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t">    <span class="str">"HSP"</span><span class="op">:</span> <span class="str">"Z"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t">    <span class="str">"HISH"</span><span class="op">:</span> <span class="str">"Z"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t">    <span class="str">"HID"</span><span class="op">:</span> <span class="str">"H"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t">    <span class="str">"HSD"</span><span class="op">:</span> <span class="str">"H"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">    <span class="str">"ILE"</span><span class="op">:</span> <span class="str">"I"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">    <span class="str">"LEU"</span><span class="op">:</span> <span class="str">"L"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t">    <span class="str">"LYS"</span><span class="op">:</span> <span class="str">"K"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">    <span class="str">"LYSH"</span><span class="op">:</span> <span class="str">"K"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">    <span class="str">"LYP"</span><span class="op">:</span> <span class="str">"K"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">    <span class="str">"LYN"</span><span class="op">:</span> <span class="str">"O"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">    <span class="str">"LSN"</span><span class="op">:</span> <span class="str">"O"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t">    <span class="str">"MET"</span><span class="op">:</span> <span class="str">"M"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">    <span class="str">"PHE"</span><span class="op">:</span> <span class="str">"F"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">    <span class="str">"PRO"</span><span class="op">:</span> <span class="str">"P"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t">    <span class="str">"SER"</span><span class="op">:</span> <span class="str">"S"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t">    <span class="str">"SP1"</span><span class="op">:</span> <span class="str">"SP1"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t">    <span class="str">"SP2"</span><span class="op">:</span> <span class="str">"SP2"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t">    <span class="str">"THR"</span><span class="op">:</span> <span class="str">"T"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t">    <span class="str">"TRP"</span><span class="op">:</span> <span class="str">"W"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t">    <span class="str">"TYR"</span><span class="op">:</span> <span class="str">"Y"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t">    <span class="str">"VAL"</span><span class="op">:</span> <span class="str">"V"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t">    <span class="str">"A"</span><span class="op">:</span> <span class="str">"A"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t">    <span class="str">"T"</span><span class="op">:</span> <span class="str">"T"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t">    <span class="str">"C"</span><span class="op">:</span> <span class="str">"C"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t">    <span class="str">"G"</span><span class="op">:</span> <span class="str">"G"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t">    <span class="str">"U"</span><span class="op">:</span> <span class="str">"U"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="key">def</span> <span class="nam">create_mutations_file</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">    <span class="nam">input_mutations_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">    <span class="nam">mutation_list</span><span class="op">:</span> <span class="nam">Union</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">Iterable</span><span class="op">[</span><span class="nam">str</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">    <span class="nam">mutation_dict</span><span class="op">:</span> <span class="nam">Mapping</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">str</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">try</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="com"># Check if self.mutation_list is a string</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">mutation_list</span> <span class="op">=</span> <span class="nam">mutation_list</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">","</span><span class="op">)</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">    <span class="key">except</span> <span class="nam">AttributeError</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="key">pass</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">    <span class="nam">pattern</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">r"(?P&lt;chain>[a-zA-Z])*:?(?P&lt;resnum>\d+)(?P&lt;mt>[a-zA-Z0-9]+)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">    <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">input_mutations_path</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">mut_file</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="key">for</span> <span class="nam">mut</span> <span class="key">in</span> <span class="nam">mutation_list</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="nam">match</span> <span class="op">=</span> <span class="nam">pattern</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="nam">mut</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="key">if</span> <span class="nam">match</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="nam">mut_groups_dict</span> <span class="op">=</span> <span class="nam">match</span><span class="op">.</span><span class="nam">groupdict</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="key">if</span> <span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"chain"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                    <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"chain"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span> <span class="op">+</span> <span class="str">" "</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"resnum"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span> <span class="op">+</span> <span class="str">" "</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="key">if</span> <span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"mt"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">.</span><span class="nam">upper</span><span class="op">(</span><span class="op">)</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">mutation_dict</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                    <span class="key">raise</span> <span class="nam">TypeError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                        <span class="str">f"{mut_groups_dict.get('mt','').upper()} is not a valid AA code or NA code. Possible values are {mutation_dict.keys()}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">mutation_dict</span><span class="op">[</span><span class="nam">mut_groups_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"mt"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">.</span><span class="nam">upper</span><span class="op">(</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="nam">mut_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">    <span class="key">return</span> <span class="nam">input_mutations_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t"><span class="com"># TODO: Move this function to biobb_common.tools.file_utils</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t"><span class="key">def</span> <span class="nam">_from_string_to_list</span><span class="op">(</span><span class="nam">input_data</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">Union</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">list</span><span class="op">[</span><span class="nam">str</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="op">-></span> <span class="nam">list</span><span class="op">[</span><span class="nam">str</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t"><span class="str">    Converts a string to a list, splitting by commas or spaces. If the input is already a list, returns it as is.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t"><span class="str">    Returns an empty list if input_data is None.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t"><span class="str">    Parameters:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t"><span class="str">        input_data (str, list, or None): The string, list, or None value to convert.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t"><span class="str">    Returns:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t"><span class="str">        list: A list of string elements or an empty list if input_data is None.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="key">if</span> <span class="nam">input_data</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="key">return</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">    <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">input_data</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># If input is already a list, return it</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="key">return</span> <span class="nam">input_data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">    <span class="com"># If input is a string, determine the delimiter based on presence of commas</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">    <span class="nam">delimiter</span> <span class="op">=</span> <span class="str">","</span> <span class="key">if</span> <span class="str">","</span> <span class="key">in</span> <span class="nam">input_data</span> <span class="key">else</span> <span class="str">" "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">    <span class="nam">items</span> <span class="op">=</span> <span class="nam">input_data</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">delimiter</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">    <span class="com"># Remove whitespace from each item and ignore empty strings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">    <span class="nam">processed_items</span> <span class="op">=</span> <span class="op">[</span><span class="nam">item</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span> <span class="key">for</span> <span class="nam">item</span> <span class="key">in</span> <span class="nam">items</span> <span class="key">if</span> <span class="nam">item</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">    <span class="key">return</span> <span class="nam">processed_items</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -120,7 +204,7 @@ <h2>
             <a class="nav" href="z_d938f4eecb54a579_pmxanalyse_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_d938f4eecb54a579_pmxanalyse_py.html b/coverage/z_d938f4eecb54a579_pmxanalyse_py.html
index 2dc7024..33c385d 100644
--- a/coverage/z_d938f4eecb54a579_pmxanalyse_py.html
+++ b/coverage/z_d938f4eecb54a579_pmxanalyse_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_d938f4eecb54a579_pmxatom_mapping_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -342,7 +342,7 @@ <h2>
             <a class="nav" href="z_d938f4eecb54a579_pmxatom_mapping_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
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     </div>
 </footer>
diff --git a/coverage/z_d938f4eecb54a579_pmxatom_mapping_py.html b/coverage/z_d938f4eecb54a579_pmxatom_mapping_py.html
index 594616f..d1fa60e 100644
--- a/coverage/z_d938f4eecb54a579_pmxatom_mapping_py.html
+++ b/coverage/z_d938f4eecb54a579_pmxatom_mapping_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_d938f4eecb54a579_pmxcreate_top_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -379,7 +379,7 @@ <h2>
             <a class="nav" href="z_d938f4eecb54a579_pmxcreate_top_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_d938f4eecb54a579_pmxcreate_top_py.html b/coverage/z_d938f4eecb54a579_pmxcreate_top_py.html
index 18ce0b7..3f39672 100644
--- a/coverage/z_d938f4eecb54a579_pmxcreate_top_py.html
+++ b/coverage/z_d938f4eecb54a579_pmxcreate_top_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_d938f4eecb54a579_pmxgentop_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -83,211 +83,266 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the PMX create_top class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">os</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">sys</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span><span class="op">,</span> <span class="nam">PurePath</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">import</span> <span class="nam">os</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">shutil</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">file_utils</span> <span class="key">as</span> <span class="nam">fu</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">class</span> <span class="nam">Pmxcreate_top</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="str">    | biobb_pmx Pmxcreate_top</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    | Wrapper class for the `PMX create_top &lt;https://github.com/deGrootLab/pmx>`_ module.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | Create a complete ligand topology file from two input topology files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_topology1_path (str): Path to the input topology file 1. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_topology2_path (str): Path to the input topology file 2. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_topology_path (str): Path to the complete ligand topology file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand_top.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        properties (dic):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **force_field** (*str*) - ("amber99sb-star-ildn-mut.ff") Force-field to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **water** (*str*) - ("tip3p") Water model to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **system_name** (*str*) - ("Pmx topology") System name to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **mols** (*list*) - ([['Protein',1],['Ligand',1]]) Molecules to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None)  Path to the binary executable of your container.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **container_image** (*str*) - (None) Container Image identifier.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ("/inout") Path to an internal directory in the container.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            from biobb_pmx.pmxbiobb.pmxcreate_top import pmxcreate_top</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'remove_tmp' : True</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            pmxcreate_top(input_topology1_path='/path/to/myTopology1.itp',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                    input_topology2_path='/path/to/myTopology2.itp',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                    output_topology_path='/path/to/myMergedTopology.zip',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                    properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: PMX create_top</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * version: >=1.0.1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">sys</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span><span class="op">,</span> <span class="nam">PurePath</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">file_utils</span> <span class="key">as</span> <span class="nam">fu</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">class</span> <span class="nam">Pmxcreate_top</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_pmx Pmxcreate_top</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Wrapper class for the `PMX create_top &lt;https://github.com/deGrootLab/pmx>`_ module.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Create a complete ligand topology file from two input topology files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_topology1_path (str): Path to the input topology file 1. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_topology2_path (str): Path to the input topology file 2. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_topology_path (str): Path to the complete ligand topology file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand_top.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        properties (dic):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **force_field** (*str*) - ("amber99sb-star-ildn-mut.ff") Force-field to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **water** (*str*) - ("tip3p") Water model to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **system_name** (*str*) - ("Pmx topology") System name to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **mols** (*list*) - ([['Protein',1],['Ligand',1]]) Molecules to be included in the generated topology.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None)  Path to the binary executable of your container.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **container_image** (*str*) - (None) Container Image identifier.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ("/inout") Path to an internal directory in the container.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            from biobb_pmx.pmxbiobb.pmxcreate_top import pmxcreate_top</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                'remove_tmp' : True</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">            pmxcreate_top(input_topology1_path='/path/to/myTopology1.itp',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                    input_topology2_path='/path/to/myTopology2.itp',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                    output_topology_path='/path/to/myMergedTopology.zip',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                    properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * name: PMX create_top</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * version: >=1.0.1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_topology1_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_topology2_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_topology_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                 <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span><span class="str">"input_topology1_path"</span><span class="op">:</span> <span class="nam">input_topology1_path</span><span class="op">,</span> <span class="str">"input_topology2_path"</span><span class="op">:</span> <span class="nam">input_topology2_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_topology_path"</span><span class="op">:</span> <span class="nam">output_topology_path</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'force_field'</span><span class="op">,</span> <span class="str">"amber99sb-star-ildn-mut.ff"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">water</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'water'</span><span class="op">,</span> <span class="str">"tip3p"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">system_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'system_name'</span><span class="op">,</span> <span class="str">"Pmx topology"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">mols</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'mols'</span><span class="op">,</span> <span class="op">[</span><span class="op">[</span><span class="str">'Protein'</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="op">[</span><span class="str">'Ligand'</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="com"># Properties common in all PMX BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'gmx_lib'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="key">and</span> <span class="nam">os</span><span class="op">.</span><span class="nam">environ</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'CONDA_PREFIX'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">            <span class="nam">python_version</span> <span class="op">=</span> <span class="str">f"{sys.version_info.major}.{sys.version_info.minor}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">environ</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'CONDA_PREFIX'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">f"lib/python{python_version}/site-packages/pmx/data/mutff/"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'container_path'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="str">'/usr/local/'</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"lib/python3.7/site-packages/pmx/data/mutff/"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'pmx'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="str">"""Execute the :class:`Pmxcreate_top &lt;pmx.pmxcreate_top.Pmxcreate_top>` pmx.pmxcreate_top.Pmxcreate_top object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t"><span class="com">#        os.chdir("/Users/hospital/BioBB/Notebooks_dev/biobb_wf_pmx_tutorial_ligands/biobb_wf_pmx_tutorial/notebooks")</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Running create_top from pmx package...\n'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">itp</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">basename</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">normpath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_topology1_path"</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s itp file in temporary folder'</span> <span class="op">%</span> <span class="nam">itp</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">itp_local</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">PurePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">itp</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_topology1_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">itp_local</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">itp2</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">basename</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">normpath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_topology2_path"</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s itp file in temporary folder'</span> <span class="op">%</span> <span class="nam">itp2</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">itp2_local</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">PurePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">itp2</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_topology2_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">itp2_local</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">top_local</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">PurePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"topology.top"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="nam">self</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">input_topology1_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">input_topology2_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">output_topology_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">    <span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">"input_topology1_path"</span><span class="op">:</span> <span class="nam">input_topology1_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">"input_topology2_path"</span><span class="op">:</span> <span class="nam">input_topology2_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_topology_path"</span><span class="op">:</span> <span class="nam">output_topology_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"force_field"</span><span class="op">,</span> <span class="str">"amber99sb-star-ildn-mut.ff"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">water</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"water"</span><span class="op">,</span> <span class="str">"tip3p"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">system_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"system_name"</span><span class="op">,</span> <span class="str">"Pmx topology"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">mols</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"mols"</span><span class="op">,</span> <span class="op">[</span><span class="op">[</span><span class="str">"Protein"</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="op">[</span><span class="str">"Ligand"</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># Properties common in all PMX BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"gmx_lib"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="key">and</span> <span class="nam">os</span><span class="op">.</span><span class="nam">environ</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"CONDA_PREFIX"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">            <span class="nam">python_version</span> <span class="op">=</span> <span class="str">f"{sys.version_info.major}.{sys.version_info.minor}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">environ</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"CONDA_PREFIX"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">                    <span class="str">f"lib/python{python_version}/site-packages/pmx/data/mutff/"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"container_path"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">gmx_lib</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">                    <span class="nam">Path</span><span class="op">(</span><span class="str">"/usr/local/"</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">                        <span class="str">"lib/python3.7/site-packages/pmx/data/mutff/"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"binary_path"</span><span class="op">,</span> <span class="str">"pmx"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="str">"""Execute the :class:`Pmxcreate_top &lt;pmx.pmxcreate_top.Pmxcreate_top>` pmx.pmxcreate_top.Pmxcreate_top object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="com">#        os.chdir("/Users/hospital/BioBB/Notebooks_dev/biobb_wf_pmx_tutorial_ligands/biobb_wf_pmx_tutorial/notebooks")</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="com"># _create_top function, taken from the pmx AZ tutorial:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="com"># https://github.com/deGrootLab/pmx/blob/develop/tutorials/AZtutorial.py</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">fp</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">top_local</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># BioBB signature</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"; Topology generated by the BioBB pmxcreate_top building block\n\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># ff itp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s/forcefield.itp"\n\n'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># additional itp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="com"># for i in self.itps:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="com">#    fp.write('#include "%s"\n' % i)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s"\n'</span> <span class="op">%</span> <span class="nam">itp</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s"\n\n'</span> <span class="op">%</span> <span class="nam">itp2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="com"># water itp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s/%s.itp"\n'</span> <span class="op">%</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">water</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># ions</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s/ions.itp"\n\n'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># system</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'[ system ]\n'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'{0}\n\n'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">system_name</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># molecules</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'[ molecules ]\n'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">for</span> <span class="nam">mol</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">mols</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'%s %s\n'</span> <span class="op">%</span> <span class="op">(</span><span class="nam">mol</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">mol</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># zip topology</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">current_cwd</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">top_final</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">PurePath</span><span class="op">(</span><span class="nam">current_cwd</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_topology_path"</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Compressing topology to: %s'</span> <span class="op">%</span> <span class="nam">top_final</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">zip_top</span><span class="op">(</span><span class="nam">zip_file</span><span class="op">=</span><span class="nam">top_final</span><span class="op">,</span> <span class="nam">top_file</span><span class="op">=</span><span class="str">"topology.top"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">current_cwd</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Exit code 0\n'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="com"># self.run_biobb()</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t"><span class="key">def</span> <span class="nam">pmxcreate_top</span><span class="op">(</span><span class="nam">input_topology1_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_topology2_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_topology_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">                  <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">    <span class="str">"""Execute the :class:`Pmxcreate_top &lt;pmx.pmxcreate_top.Pmxcreate_top>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;pmx.pmxmcreate_top.Pmxmcreate_top.launch> method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="key">return</span> <span class="nam">Pmxcreate_top</span><span class="op">(</span><span class="nam">input_topology1_path</span><span class="op">=</span><span class="nam">input_topology1_path</span><span class="op">,</span> <span class="nam">input_topology2_path</span><span class="op">=</span><span class="nam">input_topology2_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">                         <span class="nam">output_topology_path</span><span class="op">=</span><span class="nam">output_topology_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">                         <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Running create_top from pmx package...\n"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Creating %s temporary folder"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">itp</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">basename</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">normpath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_topology1_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Creating %s itp file in temporary folder"</span> <span class="op">%</span> <span class="nam">itp</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">itp_local</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">PurePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">itp</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_topology1_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">itp_local</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">itp2</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">basename</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">normpath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_topology2_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Creating %s itp file in temporary folder"</span> <span class="op">%</span> <span class="nam">itp2</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">itp2_local</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">PurePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">itp2</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_topology2_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">itp2_local</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">top_local</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">PurePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"topology.top"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># _create_top function, taken from the pmx AZ tutorial:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># https://github.com/deGrootLab/pmx/blob/develop/tutorials/AZtutorial.py</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">fp</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">top_local</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># BioBB signature</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"; Topology generated by the BioBB pmxcreate_top building block\n\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># ff itp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s/forcefield.itp"\n\n'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># additional itp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="com"># for i in self.itps:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="com">#    fp.write('#include "%s"\n' % i)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s"\n'</span> <span class="op">%</span> <span class="nam">itp</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s"\n\n'</span> <span class="op">%</span> <span class="nam">itp2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="com"># water itp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s/%s.itp"\n'</span> <span class="op">%</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">water</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="com"># ions</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'#include "%s/ions.itp"\n\n'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">force_field</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="com"># system</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"[ system ]\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"{0}\n\n"</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">system_name</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="com"># molecules</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"[ molecules ]\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">for</span> <span class="nam">mol</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">mols</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">fp</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"%s %s\n"</span> <span class="op">%</span> <span class="op">(</span><span class="nam">mol</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">mol</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">fp</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="com"># zip topology</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">current_cwd</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">top_final</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">PurePath</span><span class="op">(</span><span class="nam">current_cwd</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_topology_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Compressing topology to: %s"</span> <span class="op">%</span> <span class="nam">top_final</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">zip_top</span><span class="op">(</span><span class="nam">zip_file</span><span class="op">=</span><span class="nam">top_final</span><span class="op">,</span> <span class="nam">top_file</span><span class="op">=</span><span class="str">"topology.top"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">current_cwd</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">"Run PMX create_top module"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'-c'</span><span class="op">,</span> <span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_topology1_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Path to the input topology file 1"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_topology2_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Path to the input topology file 2"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_topology_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Path to the complete ligand topology file"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">pmxcreate_top</span><span class="op">(</span><span class="nam">input_topology1_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_topology1_path</span><span class="op">,</span> <span class="nam">input_topology2_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_topology2_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">                  <span class="nam">output_topology_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_topology_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                  <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Exit code 0\n"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="com"># self.run_biobb()</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t"><span class="key">def</span> <span class="nam">pmxcreate_top</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">input_topology1_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="nam">input_topology2_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">output_topology_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="str">"""Execute the :class:`Pmxcreate_top &lt;pmx.pmxcreate_top.Pmxcreate_top>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;pmx.pmxmcreate_top.Pmxmcreate_top.launch> method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="key">return</span> <span class="nam">Pmxcreate_top</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">input_topology1_path</span><span class="op">=</span><span class="nam">input_topology1_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">input_topology2_path</span><span class="op">=</span><span class="nam">input_topology2_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">output_topology_path</span><span class="op">=</span><span class="nam">output_topology_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Run PMX create_top module"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="str">"--input_topology1_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Path to the input topology file 1"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="str">"--input_topology2_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Path to the input topology file 2"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="str">"--output_topology_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Path to the complete ligand topology file"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">    <span class="nam">pmxcreate_top</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">input_topology1_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_topology1_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">input_topology2_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_topology2_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">output_topology_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_topology_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -297,7 +352,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
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--- a/coverage/z_d938f4eecb54a579_pmxgentop_py.html
+++ b/coverage/z_d938f4eecb54a579_pmxgentop_py.html
@@ -65,7 +65,7 @@ <h2>
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+            created at 2024-11-14 16:24 +0000
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+            created at 2024-11-14 16:24 +0000
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index 14b9e55..f1dc919 100644
--- a/coverage/z_d938f4eecb54a579_pmxligand_hybrid_py.html
+++ b/coverage/z_d938f4eecb54a579_pmxligand_hybrid_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_d938f4eecb54a579_pmxmerge_ff_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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+            created at 2024-11-14 16:24 +0000
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-            created at 2024-11-04 15:38 +0000
+            created at 2024-11-14 16:24 +0000
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index 7c4c7d6..f520810 100644
--- a/coverage/z_d938f4eecb54a579_pmxmerge_ff_py.html
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@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_d938f4eecb54a579_pmxmutate_py.html">&#xbb; next</a>
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&amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame99/dhdl99.xvg&amp;#x27;]\n2024-11-04 15:38:00,262 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_B.zip\n2024-11-04 15:38:00,262 [MainThread  ] [INFO ]  to:\n2024-11-04 15:38:00,262 [MainThread  ] [INFO ]  [&amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame10/dhdl10.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame11/dhdl11.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame12/dhdl12.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame13/dhdl13.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame14/dhdl14.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame15/dhdl15.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame16/dhdl16.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame17/dhdl17.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame18/dhdl18.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame19/dhdl19.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame2/dhdl2.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame20/dhdl20.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame21/dhdl21.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame22/dhdl22.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame23/dhdl23.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame24/dhdl24.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame25/dhdl25.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame26/dhdl26.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame27/dhdl27.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame28/dhdl28.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame29/dhdl29.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame3/dhdl3.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame30/dhdl30.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame31/dhdl31.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame32/dhdl32.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame33/dhdl33.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame34/dhdl34.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame35/dhdl35.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame36/dhdl36.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame37/dhdl37.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame38/dhdl38.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame39/dhdl39.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame4/dhdl4.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame40/dhdl40.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame41/dhdl41.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame42/dhdl42.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame43/dhdl43.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame44/dhdl44.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame45/dhdl45.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame46/dhdl46.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame47/dhdl47.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame48/dhdl48.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame49/dhdl49.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame5/dhdl5.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame50/dhdl50.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame51/dhdl51.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame52/dhdl52.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame53/dhdl53.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame54/dhdl54.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame55/dhdl55.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame56/dhdl56.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame57/dhdl57.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame58/dhdl58.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame59/dhdl59.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame6/dhdl6.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame60/dhdl60.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame61/dhdl61.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame62/dhdl62.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame63/dhdl63.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame64/dhdl64.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame65/dhdl65.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame66/dhdl66.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame67/dhdl67.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame68/dhdl68.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame69/dhdl69.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame7/dhdl7.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame99/dhdl99.xvg&amp;#x27;]\n2024-11-04 15:38:00,264 [MainThread  ] [INFO ]  pmx analyse -fA f823099f-c416-460e-aacd-ead30d8ebe03/frame0/dhdl0.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame1/dhdl1.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame10/dhdl10.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame11/dhdl11.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame12/dhdl12.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame13/dhdl13.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame14/dhdl14.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame15/dhdl15.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame16/dhdl16.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame17/dhdl17.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame18/dhdl18.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame19/dhdl19.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame2/dhdl2.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame20/dhdl20.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame21/dhdl21.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame22/dhdl22.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame23/dhdl23.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame24/dhdl24.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame25/dhdl25.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame26/dhdl26.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame27/dhdl27.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame28/dhdl28.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame29/dhdl29.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame3/dhdl3.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame30/dhdl30.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame31/dhdl31.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame32/dhdl32.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame33/dhdl33.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame34/dhdl34.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame35/dhdl35.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame36/dhdl36.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame37/dhdl37.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame38/dhdl38.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame39/dhdl39.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame4/dhdl4.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame40/dhdl40.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame41/dhdl41.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame42/dhdl42.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame43/dhdl43.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame44/dhdl44.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame45/dhdl45.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame46/dhdl46.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame47/dhdl47.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame48/dhdl48.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame49/dhdl49.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame5/dhdl5.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame50/dhdl50.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame51/dhdl51.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame52/dhdl52.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame53/dhdl53.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame54/dhdl54.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame55/dhdl55.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame56/dhdl56.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame57/dhdl57.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame58/dhdl58.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame59/dhdl59.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame6/dhdl6.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame60/dhdl60.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame61/dhdl61.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame62/dhdl62.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame63/dhdl63.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame64/dhdl64.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame65/dhdl65.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame66/dhdl66.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame67/dhdl67.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame68/dhdl68.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame69/dhdl69.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame7/dhdl7.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame70/dhdl70.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame71/dhdl71.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame72/dhdl72.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame73/dhdl73.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame74/dhdl74.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame75/dhdl75.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame76/dhdl76.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame77/dhdl77.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame78/dhdl78.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame79/dhdl79.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame8/dhdl8.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame80/dhdl80.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame81/dhdl81.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame82/dhdl82.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame83/dhdl83.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame84/dhdl84.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame85/dhdl85.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame86/dhdl86.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame87/dhdl87.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame88/dhdl88.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame89/dhdl89.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame9/dhdl9.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame90/dhdl90.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame91/dhdl91.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame92/dhdl92.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame93/dhdl93.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame94/dhdl94.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame95/dhdl95.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame96/dhdl96.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame97/dhdl97.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame98/dhdl98.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame99/dhdl99.xvg -fB b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame0/dhdl0.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame1/dhdl1.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame10/dhdl10.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame11/dhdl11.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame12/dhdl12.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame13/dhdl13.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame14/dhdl14.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame15/dhdl15.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame16/dhdl16.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame17/dhdl17.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame18/dhdl18.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame19/dhdl19.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame2/dhdl2.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame20/dhdl20.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame21/dhdl21.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame22/dhdl22.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame23/dhdl23.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame24/dhdl24.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame25/dhdl25.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame26/dhdl26.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame27/dhdl27.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame28/dhdl28.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame29/dhdl29.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame3/dhdl3.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame30/dhdl30.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame31/dhdl31.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame32/dhdl32.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame33/dhdl33.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame34/dhdl34.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame35/dhdl35.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame36/dhdl36.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame37/dhdl37.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame38/dhdl38.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame39/dhdl39.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame4/dhdl4.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame40/dhdl40.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame41/dhdl41.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame42/dhdl42.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame43/dhdl43.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame44/dhdl44.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame45/dhdl45.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame46/dhdl46.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame47/dhdl47.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame48/dhdl48.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame49/dhdl49.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame5/dhdl5.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame50/dhdl50.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame51/dhdl51.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame52/dhdl52.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame53/dhdl53.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame54/dhdl54.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame55/dhdl55.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame56/dhdl56.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame57/dhdl57.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame58/dhdl58.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame59/dhdl59.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame6/dhdl6.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame60/dhdl60.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame61/dhdl61.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame62/dhdl62.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame63/dhdl63.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame64/dhdl64.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame65/dhdl65.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame66/dhdl66.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame67/dhdl67.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame68/dhdl68.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame69/dhdl69.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame7/dhdl7.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame70/dhdl70.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame71/dhdl71.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame72/dhdl72.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame73/dhdl73.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame74/dhdl74.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame75/dhdl75.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame76/dhdl76.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame77/dhdl77.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame78/dhdl78.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame79/dhdl79.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame8/dhdl8.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame80/dhdl80.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame81/dhdl81.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame82/dhdl82.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame83/dhdl83.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame84/dhdl84.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame85/dhdl85.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame86/dhdl86.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame87/dhdl87.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame88/dhdl88.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame89/dhdl89.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame9/dhdl9.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame90/dhdl90.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame91/dhdl91.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame92/dhdl92.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame93/dhdl93.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame94/dhdl94.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame95/dhdl95.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame96/dhdl96.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame97/dhdl97.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame98/dhdl98.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame99/dhdl99.xvg -o /tmp/biobb/unitests_35/pmxanalyse/sandbox_3e64acc8-0ece-421d-a41c-a0c310a3fae7/result.txt -w /tmp/biobb/unitests_35/pmxanalyse/sandbox_3e64acc8-0ece-421d-a41c-a0c310a3fae7/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\n2024-11-04 15:38:12,402 [MainThread  ] [INFO ]  Executing: pmx analyse -fA f823099f-c416-460e-aacd-ead30d8ebe03/frame0/dhdl0.xvg f823099f-c...\n2024-11-04 15:38:12,403 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:38:12,403 [MainThread  ] [INFO ]  \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: f823099f-c416-460e-aacd-ead30d8ebe03/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame1/dhdl1.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame2/dhdl2.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame3/dhdl3.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame4/dhdl4.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame5/dhdl5.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame6/dhdl6.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame7/dhdl7.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame8/dhdl8.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame9/dhdl9.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame10/dhdl10.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame11/dhdl11.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame12/dhdl12.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame13/dhdl13.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame14/dhdl14.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame15/dhdl15.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame16/dhdl16.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame17/dhdl17.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame18/dhdl18.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame19/dhdl19.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame20/dhdl20.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame21/dhdl21.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame22/dhdl22.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame23/dhdl23.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame24/dhdl24.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame25/dhdl25.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame26/dhdl26.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame27/dhdl27.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame28/dhdl28.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame29/dhdl29.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame30/dhdl30.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame31/dhdl31.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame32/dhdl32.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame33/dhdl33.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame34/dhdl34.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame35/dhdl35.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame36/dhdl36.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame37/dhdl37.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame38/dhdl38.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame39/dhdl39.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame40/dhdl40.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame41/dhdl41.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame42/dhdl42.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame43/dhdl43.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame44/dhdl44.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame45/dhdl45.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame46/dhdl46.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame47/dhdl47.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame48/dhdl48.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame49/dhdl49.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame50/dhdl50.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame51/dhdl51.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame52/dhdl52.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame53/dhdl53.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame54/dhdl54.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame55/dhdl55.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame56/dhdl56.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame57/dhdl57.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame58/dhdl58.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame59/dhdl59.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame60/dhdl60.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame61/dhdl61.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame62/dhdl62.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame63/dhdl63.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame64/dhdl64.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame65/dhdl65.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame66/dhdl66.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame67/dhdl67.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame68/dhdl68.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame69/dhdl69.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame70/dhdl70.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame71/dhdl71.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame72/dhdl72.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame73/dhdl73.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame74/dhdl74.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame75/dhdl75.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame76/dhdl76.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame77/dhdl77.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame78/dhdl78.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame79/dhdl79.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame80/dhdl80.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame81/dhdl81.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame82/dhdl82.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame83/dhdl83.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame84/dhdl84.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame85/dhdl85.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame86/dhdl86.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame87/dhdl87.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame88/dhdl88.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame89/dhdl89.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame90/dhdl90.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame91/dhdl91.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame92/dhdl92.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame93/dhdl93.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame94/dhdl94.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame95/dhdl95.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame96/dhdl96.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame97/dhdl97.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame98/dhdl98.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame1/dhdl1.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame2/dhdl2.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame3/dhdl3.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame4/dhdl4.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame5/dhdl5.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame6/dhdl6.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame7/dhdl7.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame8/dhdl8.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame9/dhdl9.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame10/dhdl10.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame11/dhdl11.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame12/dhdl12.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame13/dhdl13.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame14/dhdl14.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame15/dhdl15.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame16/dhdl16.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame17/dhdl17.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame18/dhdl18.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame19/dhdl19.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame20/dhdl20.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame21/dhdl21.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame22/dhdl22.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame23/dhdl23.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame24/dhdl24.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame25/dhdl25.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame26/dhdl26.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame27/dhdl27.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame28/dhdl28.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame29/dhdl29.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame30/dhdl30.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame31/dhdl31.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame32/dhdl32.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame33/dhdl33.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame34/dhdl34.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame35/dhdl35.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame36/dhdl36.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame37/dhdl37.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame38/dhdl38.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame39/dhdl39.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame40/dhdl40.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame41/dhdl41.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame42/dhdl42.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame43/dhdl43.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame44/dhdl44.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame45/dhdl45.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame46/dhdl46.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame47/dhdl47.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame48/dhdl48.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame49/dhdl49.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame50/dhdl50.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame51/dhdl51.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame52/dhdl52.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame53/dhdl53.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame54/dhdl54.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame55/dhdl55.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame56/dhdl56.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame57/dhdl57.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame58/dhdl58.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame59/dhdl59.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame60/dhdl60.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame61/dhdl61.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame62/dhdl62.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame63/dhdl63.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame64/dhdl64.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame65/dhdl65.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame66/dhdl66.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame67/dhdl67.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame68/dhdl68.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame69/dhdl69.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame70/dhdl70.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame71/dhdl71.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame72/dhdl72.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame73/dhdl73.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame74/dhdl74.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame75/dhdl75.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame76/dhdl76.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame77/dhdl77.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame78/dhdl78.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame79/dhdl79.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame80/dhdl80.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame81/dhdl81.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame82/dhdl82.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame83/dhdl83.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame84/dhdl84.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame85/dhdl85.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame86/dhdl86.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame87/dhdl87.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame88/dhdl88.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame89/dhdl89.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame90/dhdl90.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame91/dhdl91.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame92/dhdl92.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame93/dhdl93.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame94/dhdl94.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame95/dhdl95.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame96/dhdl96.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame97/dhdl97.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame98/dhdl98.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std Err): iteration 20/100\r  Bootstrap (Std Err): iteration 21/100\r  Bootstrap (Std Err): iteration 22/100\r  Bootstrap (Std Err): iteration 23/100\r  Bootstrap (Std Err): iteration 24/100\r  Bootstrap (Std Err): iteration 25/100\r  Bootstrap (Std Err): iteration 26/100\r  Bootstrap (Std Err): iteration 27/100\r  Bootstrap 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Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.42 kJ/mol\n  CGI: Std Err (bootstrap) =     0.35 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 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38/100\r  Bootstrap (Std Err): iteration 39/100\r  Bootstrap (Std Err): iteration 40/100\r  Bootstrap (Std Err): iteration 41/100\r  Bootstrap (Std Err): iteration 42/100\r  Bootstrap (Std Err): iteration 43/100\r  Bootstrap (Std Err): iteration 44/100\r  Bootstrap (Std Err): iteration 45/100\r  Bootstrap (Std Err): iteration 46/100\r  Bootstrap (Std Err): iteration 47/100\r  Bootstrap (Std Err): iteration 48/100\r  Bootstrap (Std Err): iteration 49/100\r  Bootstrap (Std Err): iteration 50/100\r  Bootstrap (Std Err): iteration 51/100\r  Bootstrap (Std Err): iteration 52/100\r  Bootstrap (Std Err): iteration 53/100\r  Bootstrap (Std Err): iteration 54/100\r  Bootstrap (Std Err): iteration 55/100\r  Bootstrap (Std Err): iteration 56/100\r  Bootstrap (Std Err): iteration 57/100\r  Bootstrap (Std Err): iteration 58/100\r  Bootstrap (Std Err): iteration 59/100\r  Bootstrap (Std Err): iteration 60/100\r  Bootstrap (Std Err): iteration 61/100\r  Bootstrap (Std Err): iteration 62/100\r  Bootstrap (Std Err): iteration 63/100\r  Bootstrap (Std Err): iteration 64/100\r  Bootstrap (Std Err): iteration 65/100\r  Bootstrap (Std Err): iteration 66/100\r  Bootstrap (Std Err): iteration 67/100\r  Bootstrap (Std Err): iteration 68/100\r  Bootstrap (Std Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.60 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.60 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\n2024-11-04 15:38:12,427 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxanalyse/sandbox_3e64acc8-0ece-421d-a41c-a0c310a3fae7&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1&amp;#x27;]\n2024-11-04 15:38:12,427 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxanalyse/result.txt\nChecking if empty file: /tmp/biobb/unitests_35/pmxanalyse/plot.png\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_35/pmxanalyse/plot.png\n     IMAGE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_plot.png\n     IMAGE_A HASH: ffdfe78183a7f7df SIZE: 64 bits\n     IMAGE_B HASH: ffdfe78183a7f7df SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call 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&amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03/frame99/dhdl99.xvg&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_B.zip\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:174 [&amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame10/dhdl10.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame11/dhdl11.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame12/dhdl12.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame13/dhdl13.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame14/dhdl14.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame15/dhdl15.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame16/dhdl16.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame17/dhdl17.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame18/dhdl18.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame19/dhdl19.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame2/dhdl2.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame20/dhdl20.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame21/dhdl21.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame22/dhdl22.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame23/dhdl23.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame24/dhdl24.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame25/dhdl25.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame26/dhdl26.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame27/dhdl27.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame28/dhdl28.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame29/dhdl29.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame3/dhdl3.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame30/dhdl30.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame31/dhdl31.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame32/dhdl32.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame33/dhdl33.xvg&amp;#x27;, 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&amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame46/dhdl46.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame47/dhdl47.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame48/dhdl48.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame49/dhdl49.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame5/dhdl5.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame50/dhdl50.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame51/dhdl51.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame52/dhdl52.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame53/dhdl53.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame54/dhdl54.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame55/dhdl55.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame56/dhdl56.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame57/dhdl57.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame58/dhdl58.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame59/dhdl59.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame6/dhdl6.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame60/dhdl60.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame61/dhdl61.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame62/dhdl62.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame63/dhdl63.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame64/dhdl64.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame65/dhdl65.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame66/dhdl66.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame67/dhdl67.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame68/dhdl68.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame69/dhdl69.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame7/dhdl7.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame99/dhdl99.xvg&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:63 pmx analyse -fA f823099f-c416-460e-aacd-ead30d8ebe03/frame0/dhdl0.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame1/dhdl1.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame10/dhdl10.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame11/dhdl11.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame12/dhdl12.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame13/dhdl13.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame14/dhdl14.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame15/dhdl15.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame16/dhdl16.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame17/dhdl17.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame18/dhdl18.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame19/dhdl19.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame2/dhdl2.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame20/dhdl20.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame21/dhdl21.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame22/dhdl22.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame23/dhdl23.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame24/dhdl24.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame25/dhdl25.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame26/dhdl26.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame27/dhdl27.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame28/dhdl28.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame29/dhdl29.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame3/dhdl3.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame30/dhdl30.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame31/dhdl31.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame32/dhdl32.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame33/dhdl33.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame34/dhdl34.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame35/dhdl35.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame36/dhdl36.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame37/dhdl37.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame38/dhdl38.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame39/dhdl39.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame4/dhdl4.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame40/dhdl40.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame41/dhdl41.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame42/dhdl42.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame43/dhdl43.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame44/dhdl44.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame45/dhdl45.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame46/dhdl46.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame47/dhdl47.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame48/dhdl48.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame49/dhdl49.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame5/dhdl5.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame50/dhdl50.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame51/dhdl51.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame52/dhdl52.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame53/dhdl53.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame54/dhdl54.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame55/dhdl55.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame56/dhdl56.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame57/dhdl57.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame58/dhdl58.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame59/dhdl59.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame6/dhdl6.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame60/dhdl60.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame61/dhdl61.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame62/dhdl62.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame63/dhdl63.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame64/dhdl64.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame65/dhdl65.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame66/dhdl66.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame67/dhdl67.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame68/dhdl68.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame69/dhdl69.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame7/dhdl7.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame70/dhdl70.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame71/dhdl71.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame72/dhdl72.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame73/dhdl73.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame74/dhdl74.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame75/dhdl75.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame76/dhdl76.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame77/dhdl77.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame78/dhdl78.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame79/dhdl79.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame8/dhdl8.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame80/dhdl80.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame81/dhdl81.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame82/dhdl82.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame83/dhdl83.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame84/dhdl84.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame85/dhdl85.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame86/dhdl86.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame87/dhdl87.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame88/dhdl88.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame89/dhdl89.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame9/dhdl9.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame90/dhdl90.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame91/dhdl91.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame92/dhdl92.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame93/dhdl93.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame94/dhdl94.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame95/dhdl95.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame96/dhdl96.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame97/dhdl97.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame98/dhdl98.xvg f823099f-c416-460e-aacd-ead30d8ebe03/frame99/dhdl99.xvg -fB b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame0/dhdl0.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame1/dhdl1.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame10/dhdl10.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame11/dhdl11.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame12/dhdl12.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame13/dhdl13.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame14/dhdl14.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame15/dhdl15.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame16/dhdl16.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame17/dhdl17.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame18/dhdl18.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame19/dhdl19.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame2/dhdl2.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame20/dhdl20.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame21/dhdl21.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame22/dhdl22.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame23/dhdl23.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame24/dhdl24.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame25/dhdl25.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame26/dhdl26.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame27/dhdl27.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame28/dhdl28.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame29/dhdl29.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame3/dhdl3.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame30/dhdl30.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame31/dhdl31.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame32/dhdl32.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame33/dhdl33.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame34/dhdl34.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame35/dhdl35.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame36/dhdl36.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame37/dhdl37.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame38/dhdl38.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame39/dhdl39.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame4/dhdl4.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame40/dhdl40.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame41/dhdl41.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame42/dhdl42.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame43/dhdl43.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame44/dhdl44.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame45/dhdl45.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame46/dhdl46.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame47/dhdl47.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame48/dhdl48.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame49/dhdl49.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame5/dhdl5.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame50/dhdl50.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame51/dhdl51.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame52/dhdl52.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame53/dhdl53.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame54/dhdl54.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame55/dhdl55.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame56/dhdl56.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame57/dhdl57.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame58/dhdl58.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame59/dhdl59.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame6/dhdl6.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame60/dhdl60.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame61/dhdl61.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame62/dhdl62.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame63/dhdl63.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame64/dhdl64.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame65/dhdl65.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame66/dhdl66.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame67/dhdl67.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame68/dhdl68.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame69/dhdl69.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame7/dhdl7.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame70/dhdl70.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame71/dhdl71.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame72/dhdl72.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame73/dhdl73.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame74/dhdl74.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame75/dhdl75.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame76/dhdl76.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame77/dhdl77.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame78/dhdl78.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame79/dhdl79.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame8/dhdl8.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame80/dhdl80.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame81/dhdl81.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame82/dhdl82.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame83/dhdl83.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame84/dhdl84.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame85/dhdl85.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame86/dhdl86.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame87/dhdl87.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame88/dhdl88.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame89/dhdl89.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame9/dhdl9.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame90/dhdl90.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame91/dhdl91.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame92/dhdl92.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame93/dhdl93.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame94/dhdl94.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame95/dhdl95.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame96/dhdl96.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame97/dhdl97.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame98/dhdl98.xvg b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame99/dhdl99.xvg -o /tmp/biobb/unitests_35/pmxanalyse/sandbox_3e64acc8-0ece-421d-a41c-a0c310a3fae7/result.txt -w /tmp/biobb/unitests_35/pmxanalyse/sandbox_3e64acc8-0ece-421d-a41c-a0c310a3fae7/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:36 Executing: pmx analyse -fA f823099f-c416-460e-aacd-ead30d8ebe03/frame0/dhdl0.xvg f823099f-c...\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:41 \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: f823099f-c416-460e-aacd-ead30d8ebe03/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame1/dhdl1.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame2/dhdl2.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame3/dhdl3.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame4/dhdl4.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame5/dhdl5.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame6/dhdl6.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame7/dhdl7.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame8/dhdl8.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame9/dhdl9.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame10/dhdl10.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame11/dhdl11.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame12/dhdl12.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame13/dhdl13.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame14/dhdl14.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame15/dhdl15.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame16/dhdl16.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame17/dhdl17.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame18/dhdl18.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame19/dhdl19.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame20/dhdl20.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame21/dhdl21.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame22/dhdl22.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame23/dhdl23.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame24/dhdl24.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame25/dhdl25.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame26/dhdl26.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame27/dhdl27.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame28/dhdl28.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame29/dhdl29.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame30/dhdl30.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame31/dhdl31.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame32/dhdl32.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame33/dhdl33.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame34/dhdl34.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame35/dhdl35.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame36/dhdl36.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame37/dhdl37.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame38/dhdl38.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame39/dhdl39.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame40/dhdl40.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame41/dhdl41.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame42/dhdl42.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame43/dhdl43.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame44/dhdl44.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame45/dhdl45.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame46/dhdl46.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame47/dhdl47.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame48/dhdl48.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame49/dhdl49.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame50/dhdl50.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame51/dhdl51.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame52/dhdl52.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame53/dhdl53.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame54/dhdl54.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame55/dhdl55.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame56/dhdl56.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame57/dhdl57.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame58/dhdl58.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame59/dhdl59.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame60/dhdl60.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame61/dhdl61.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame62/dhdl62.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame63/dhdl63.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame64/dhdl64.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame65/dhdl65.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame66/dhdl66.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame67/dhdl67.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame68/dhdl68.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame69/dhdl69.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame70/dhdl70.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame71/dhdl71.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame72/dhdl72.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame73/dhdl73.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame74/dhdl74.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame75/dhdl75.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame76/dhdl76.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame77/dhdl77.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame78/dhdl78.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame79/dhdl79.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame80/dhdl80.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame81/dhdl81.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame82/dhdl82.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame83/dhdl83.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame84/dhdl84.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame85/dhdl85.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame86/dhdl86.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame87/dhdl87.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame88/dhdl88.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame89/dhdl89.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame90/dhdl90.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame91/dhdl91.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame92/dhdl92.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame93/dhdl93.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame94/dhdl94.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame95/dhdl95.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame96/dhdl96.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame97/dhdl97.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame98/dhdl98.xvg\r    Reading f823099f-c416-460e-aacd-ead30d8ebe03/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame1/dhdl1.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame2/dhdl2.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame3/dhdl3.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame4/dhdl4.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame5/dhdl5.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame6/dhdl6.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame7/dhdl7.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame8/dhdl8.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame9/dhdl9.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame10/dhdl10.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame11/dhdl11.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame12/dhdl12.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame13/dhdl13.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame14/dhdl14.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame15/dhdl15.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame16/dhdl16.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame17/dhdl17.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame18/dhdl18.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame19/dhdl19.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame20/dhdl20.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame21/dhdl21.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame22/dhdl22.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame23/dhdl23.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame24/dhdl24.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame25/dhdl25.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame26/dhdl26.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame27/dhdl27.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame28/dhdl28.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame29/dhdl29.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame30/dhdl30.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame31/dhdl31.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame32/dhdl32.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame33/dhdl33.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame34/dhdl34.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame35/dhdl35.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame36/dhdl36.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame37/dhdl37.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame38/dhdl38.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame39/dhdl39.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame40/dhdl40.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame41/dhdl41.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame42/dhdl42.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame43/dhdl43.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame44/dhdl44.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame45/dhdl45.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame46/dhdl46.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame47/dhdl47.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame48/dhdl48.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame49/dhdl49.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame50/dhdl50.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame51/dhdl51.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame52/dhdl52.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame53/dhdl53.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame54/dhdl54.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame55/dhdl55.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame56/dhdl56.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame57/dhdl57.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame58/dhdl58.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame59/dhdl59.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame60/dhdl60.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame61/dhdl61.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame62/dhdl62.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame63/dhdl63.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame64/dhdl64.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame65/dhdl65.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame66/dhdl66.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame67/dhdl67.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame68/dhdl68.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame69/dhdl69.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame70/dhdl70.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame71/dhdl71.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame72/dhdl72.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame73/dhdl73.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame74/dhdl74.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame75/dhdl75.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame76/dhdl76.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame77/dhdl77.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame78/dhdl78.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame79/dhdl79.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame80/dhdl80.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame81/dhdl81.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame82/dhdl82.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame83/dhdl83.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame84/dhdl84.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame85/dhdl85.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame86/dhdl86.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame87/dhdl87.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame88/dhdl88.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame89/dhdl89.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame90/dhdl90.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame91/dhdl91.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame92/dhdl92.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame93/dhdl93.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame94/dhdl94.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame95/dhdl95.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame96/dhdl96.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame97/dhdl97.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame98/dhdl98.xvg\r    Reading b5eb410a-9b77-45ef-a734-5558b01c7eb1/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std Err): iteration 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Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  CGI: Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.42 kJ/mol\n  CGI: Std Err (bootstrap) =     0.35 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap 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-0.23\n  BAR: Conv Std Err (bootstrap) =     0.05\n\n --------------------------------------------------------\n             Jarzynski estimator     \n --------------------------------------------------------\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std 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Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.60 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.60 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxanalyse/sandbox_3e64acc8-0ece-421d-a41c-a0c310a3fae7&amp;#x27;, &amp;#x27;f823099f-c416-460e-aacd-ead30d8ebe03&amp;#x27;, &amp;#x27;b5eb410a-9b77-45ef-a734-5558b01c7eb1&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:38:13,096 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\n2024-11-04 15:38:13,096 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7 directory successfully created\n2024-11-04 15:38:13,096 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7\n2024-11-04 15:38:13,097 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7\n2024-11-04 15:38:13,097 [MainThread  ] [INFO ]  pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/lig2.pdb -o1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/pairs1.dat -o2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/pairs2.dat -log /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/atom_mapping.log --d 0.05\n\n2024-11-04 15:38:17,568 [MainThread  ] [INFO ]  Executing: pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a...\n2024-11-04 15:38:17,568 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:38:17,568 [MainThread  ] [INFO ]  atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\n2024-11-04 15:38:17,570 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7&amp;#x27;]\n2024-11-04 15:38:17,570 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxatom_mapping/pairs1.dat\nChecking if empty file: /tmp/biobb/unitests_35/pmxatom_mapping/pairs2.dat\nComparing: \n        File_A: /tmp/biobb/unitests_35/pmxatom_mapping/pairs1.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs1.dat\n        File_A hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\n        File_B hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_35/pmxatom_mapping/pairs2.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs2.dat\n        File_A hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n        File_B hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:63 pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/lig2.pdb -o1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/pairs1.dat -o2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/pairs2.dat -log /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7/atom_mapping.log --d 0.05\n\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:36 Executing: pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a...\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:41 atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxatom_mapping/sandbox_0d200882-a69a-4ff9-873b-44607f18b3f7&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;, &#34;duration&#34;: &#34;44 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;44 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:38:17,605 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\n2024-11-04 15:38:17,605 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2 directory successfully created\n2024-11-04 15:38:17,605 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2\n2024-11-04 15:38:17,606 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2\n2024-11-04 15:38:17,606 [MainThread  ] [INFO ]  Running create_top from pmx package...\n\n2024-11-04 15:38:17,606 [MainThread  ] [INFO ]  Creating f7660375-60e7-4590-9ba4-5e31dcc7ae39 temporary folder\n2024-11-04 15:38:17,606 [MainThread  ] [INFO ]  Creating topo1.itp itp file in temporary folder\n2024-11-04 15:38:17,606 [MainThread  ] [INFO ]  Creating topo2.itp itp file in temporary folder\n2024-11-04 15:38:17,606 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\n2024-11-04 15:38:17,607 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-04 15:38:17,608 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-04 15:38:17,608 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-04 15:38:17,608 [MainThread  ] [INFO ]  Adding:\n2024-11-04 15:38:17,608 [MainThread  ] [INFO ]  [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-04 15:38:17,609 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\n2024-11-04 15:38:17,609 [MainThread  ] [INFO ]  Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-04 15:38:17,609 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-04 15:38:17,609 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2&amp;#x27;]\n2024-11-04 15:38:17,609 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopo.zip\nComparing TOP/ITP:\n     FILE_A: 82577af3-00d4-4126-80db-834f0d97127e/topo1.itp\n     FILE_B: 216bf159-62f0-4b0d-b40b-1096aa8378f4/topo1.itp\nComparing TOP/ITP:\n     FILE_A: 82577af3-00d4-4126-80db-834f0d97127e/topo2.itp\n     FILE_B: 216bf159-62f0-4b0d-b40b-1096aa8378f4/topo2.itp\nComparing TOP/ITP:\n     FILE_A: 82577af3-00d4-4126-80db-834f0d97127e/topology.top\n     FILE_B: 216bf159-62f0-4b0d-b40b-1096aa8378f4/topology.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Running create_top from pmx package...\n\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating f7660375-60e7-4590-9ba4-5e31dcc7ae39 temporary folder\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo1.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo2.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:149 [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:150 to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxcreate_top/sandbox_10ab79f9-2f24-4bba-bf40-2698f51148f2&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;, &#34;duration&#34;: &#34;00:00:06&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:06&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:38:17,649 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\n2024-11-04 15:38:17,649 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxgentop/sandbox_35e1c2a7-d81b-4e09-9ce6-b534183d378c directory successfully created\n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  to:\n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  [&amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Ion.itp&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Ion.itp&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  Unzipping: \n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  To: \n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top\n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Ion.itp\n2024-11-04 15:38:17,651 [MainThread  ] [INFO ]  3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Protein_chain_A.itp\n2024-11-04 15:38:17,652 [MainThread  ] [INFO ]  3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Ion.itp\n2024-11-04 15:38:17,652 [MainThread  ] [INFO ]  3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Protein_chain_A.itp\n2024-11-04 15:38:17,652 [MainThread  ] [INFO ]  unique_dir_output_file: aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top\n2024-11-04 15:38:17,652 [MainThread  ] [INFO ]  pmx gentop -o aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top\n\n2024-11-04 15:38:23,391 [MainThread  ] [INFO ]  Executing: pmx gentop -o aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top -ff amber99...\n2024-11-04 15:38:23,391 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:38:23,391 [MainThread  ] [INFO ]  \nlog_&amp;gt; Reading input top file &amp;quot;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\n2024-11-04 15:38:23,392 [MainThread  ] [INFO ]  Check if aca938de-3e49-4524-883b-7b0ca441f487/p2g_Protein_chain_A.itp exists\n2024-11-04 15:38:23,393 [MainThread  ] [INFO ]  Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Protein_chain_A.itp to: aca938de-3e49-4524-883b-7b0ca441f487\n2024-11-04 15:38:23,393 [MainThread  ] [INFO ]  Check if aca938de-3e49-4524-883b-7b0ca441f487/p2g_Ion.itp exists\n2024-11-04 15:38:23,393 [MainThread  ] [INFO ]  Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Ion.itp to: aca938de-3e49-4524-883b-7b0ca441f487\n2024-11-04 15:38:23,393 [MainThread  ] [INFO ]  Check if aca938de-3e49-4524-883b-7b0ca441f487/p2g.top exists\n2024-11-04 15:38:23,394 [MainThread  ] [INFO ]  Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top to: aca938de-3e49-4524-883b-7b0ca441f487\n2024-11-04 15:38:23,394 [MainThread  ] [INFO ]  Check if aca938de-3e49-4524-883b-7b0ca441f487/posre_Protein_chain_A.itp exists\n2024-11-04 15:38:23,394 [MainThread  ] [INFO ]  Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Protein_chain_A.itp to: aca938de-3e49-4524-883b-7b0ca441f487\n2024-11-04 15:38:23,394 [MainThread  ] [INFO ]  Check if aca938de-3e49-4524-883b-7b0ca441f487/posre_Ion.itp exists\n2024-11-04 15:38:23,394 [MainThread  ] [INFO ]  Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Ion.itp to: aca938de-3e49-4524-883b-7b0ca441f487\n2024-11-04 15:38:23,394 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\n2024-11-04 15:38:23,395 [MainThread  ] [INFO ]  Ignored file aca938de-3e49-4524-883b-7b0ca441f487/amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-04 15:38:23,404 [MainThread  ] [INFO ]  Ignored file aca938de-3e49-4524-883b-7b0ca441f487/amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-04 15:38:23,404 [MainThread  ] [INFO ]  Ignored file aca938de-3e49-4524-883b-7b0ca441f487/amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-04 15:38:23,406 [MainThread  ] [INFO ]  Adding:\n2024-11-04 15:38:23,406 [MainThread  ] [INFO ]  [&amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-04 15:38:23,406 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\n2024-11-04 15:38:23,432 [MainThread  ] [INFO ]  Removed: [&amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top&amp;#x27;]\n2024-11-04 15:38:23,433 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mut_gmx_hybrid_top.zip\nComparing TOP/ITP:\n     FILE_A: d1a81100-9339-4587-a960-2ab7033ffcef/pmx_p2g_Ion.itp\n     FILE_B: f0c72d88-aa44-4b30-9512-fe9fb3caf5cf/pmx_p2g_Ion.itp\nComparing TOP/ITP:\n     FILE_A: d1a81100-9339-4587-a960-2ab7033ffcef/pmx_p2g_Protein_chain_A.itp\n     FILE_B: f0c72d88-aa44-4b30-9512-fe9fb3caf5cf/pmx_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: d1a81100-9339-4587-a960-2ab7033ffcef/pmxgentop_p2g.top\n     FILE_B: f0c72d88-aa44-4b30-9512-fe9fb3caf5cf/pmxgentop_p2g.top\nComparing TOP/ITP:\n     FILE_A: d1a81100-9339-4587-a960-2ab7033ffcef/posre_Ion.itp\n     FILE_B: f0c72d88-aa44-4b30-9512-fe9fb3caf5cf/posre_Ion.itp\nComparing TOP/ITP:\n     FILE_A: d1a81100-9339-4587-a960-2ab7033ffcef/posre_Protein_chain_A.itp\n     FILE_B: f0c72d88-aa44-4b30-9512-fe9fb3caf5cf/posre_Protein_chain_A.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxgentop/sandbox_35e1c2a7-d81b-4e09-9ce6-b534183d378c directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:174 [&amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Ion.itp&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Ion.itp&amp;#x27;, &amp;#x27;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Ion.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Ion.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 unique_dir_output_file: aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:63 pmx gentop -o aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top\n\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:36 Executing: pmx gentop -o aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top -ff amber99...\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:41 \nlog_&amp;gt; Reading input top file &amp;quot;3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if aca938de-3e49-4524-883b-7b0ca441f487/p2g_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Protein_chain_A.itp to: aca938de-3e49-4524-883b-7b0ca441f487\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if aca938de-3e49-4524-883b-7b0ca441f487/p2g_Ion.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g_Ion.itp to: aca938de-3e49-4524-883b-7b0ca441f487\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if aca938de-3e49-4524-883b-7b0ca441f487/p2g.top exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/p2g.top to: aca938de-3e49-4524-883b-7b0ca441f487\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if aca938de-3e49-4524-883b-7b0ca441f487/posre_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Protein_chain_A.itp to: aca938de-3e49-4524-883b-7b0ca441f487\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if aca938de-3e49-4524-883b-7b0ca441f487/posre_Ion.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 3ae8cd66-8984-44cb-a5d0-7e38fb67d7cc/posre_Ion.itp to: aca938de-3e49-4524-883b-7b0ca441f487\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file aca938de-3e49-4524-883b-7b0ca441f487/amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file aca938de-3e49-4524-883b-7b0ca441f487/amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file aca938de-3e49-4524-883b-7b0ca441f487/amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:149 [&amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:150 to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Removed: [&amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/posre_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;aca938de-3e49-4524-883b-7b0ca441f487/pmxgentop_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:38:23,640 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\n2024-11-04 15:38:23,641 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471 directory successfully created\n2024-11-04 15:38:23,641 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\n2024-11-04 15:38:23,641 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\n2024-11-04 15:38:23,641 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\n2024-11-04 15:38:23,642 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\n2024-11-04 15:38:23,642 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\n2024-11-04 15:38:23,642 [MainThread  ] [INFO ]  pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig2.pdb -itp1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig1.itp -itp2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig2.itp -pairs /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/myPairs1.dat -oA /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridStruct1.pdb -oB /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridStruct2.pdb -oitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridTopo.itp -offitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridAtomTypes.itp -log /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/ligand_hybrid.log --fit --d 0.05\n\n2024-11-04 15:38:25,358 [MainThread  ] [INFO ]  Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a2...\n2024-11-04 15:38:25,359 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:38:25,359 [MainThread  ] [INFO ]  ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridAtomTypes.itp&amp;quot;\n\n2024-11-04 15:38:25,360 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471&amp;#x27;]\n2024-11-04 15:38:25,361 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct1.pdb\nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct2.pdb\nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridTopo.itp\nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridAtomTypes.itp\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct1.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 3.850114164176677e-15\n     RMS_CUTOFF: 1\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct2.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure2.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 0.1872943529544109\n     RMS_CUTOFF: 1\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopology.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridAtomTypes.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridAtomTypes.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:63 pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig2.pdb -itp1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig1.itp -itp2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig2.itp -pairs /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/myPairs1.dat -oA /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridStruct1.pdb -oB /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridStruct2.pdb -oitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridTopo.itp -offitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridAtomTypes.itp -log /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/ligand_hybrid.log --fit --d 0.05\n\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:36 Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a2...\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:41 ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471/hybridAtomTypes.itp&amp;quot;\n\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_d3e81d68-a270-463f-b63b-71d39a17b471&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;, &#34;duration&#34;: &#34;34 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;34 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:38:25,409 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\n2024-11-04 15:38:25,409 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1 directory successfully created\n2024-11-04 15:38:25,409 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1\n2024-11-04 15:38:25,409 [MainThread  ] [INFO ]  Creating c7e27b44-0f18-4d96-83c8-e54a4ea068b9 temporary folder\n2024-11-04 15:38:25,410 [MainThread  ] [INFO ]  Extracting: /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1/itps_to_merge.zip\n2024-11-04 15:38:25,410 [MainThread  ] [INFO ]  to:\n2024-11-04 15:38:25,410 [MainThread  ] [INFO ]  [&amp;#x27;c7e27b44-0f18-4d96-83c8-e54a4ea068b9/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;c7e27b44-0f18-4d96-83c8-e54a4ea068b9/lig1ffMOL.itp&amp;#x27;, &amp;#x27;c7e27b44-0f18-4d96-83c8-e54a4ea068b9/lig2ffMOL.itp&amp;#x27;]\n2024-11-04 15:38:25,411 [MainThread  ] [INFO ]  Running merge_FF_files from pmx package...\n\n2024-11-04 15:38:25,411 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-04 15:38:25,411 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1&amp;#x27;]\n2024-11-04 15:38:25,412 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxmerge_ff/hybridTopo.itp\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_35/pmxmerge_ff/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mergedTopology.itp\n     SIZE_A: 1468 bytes\n     SIZE_B: 1468 bytes\n     TOLERANCE: 1.0%, Low: 1453.32 bytes, High: 1482.68 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Creating c7e27b44-0f18-4d96-83c8-e54a4ea068b9 temporary folder\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:172 Extracting: /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1/itps_to_merge.zip\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:174 [&amp;#x27;c7e27b44-0f18-4d96-83c8-e54a4ea068b9/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;c7e27b44-0f18-4d96-83c8-e54a4ea068b9/lig1ffMOL.itp&amp;#x27;, &amp;#x27;c7e27b44-0f18-4d96-83c8-e54a4ea068b9/lig2ffMOL.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Running merge_FF_files from pmx package...\n\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmerge_ff/sandbox_7512f53d-e70f-485f-ac50-c7afe0bb64f1&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:38:25,443 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\n2024-11-04 15:38:25,443 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28 directory successfully created\n2024-11-04 15:38:25,446 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28\n2024-11-04 15:38:25,446 [MainThread  ] [INFO ]  pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28/frameA0.pdb -o /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28/output_structure.pdb -ff amber99sb-star-ildn-mut --script 38f2c614-6376-4357-ba38-465d986252f1/mutations.txt\n\n2024-11-04 15:38:28,540 [MainThread  ] [INFO ]  Executing: pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b...\n2024-11-04 15:38:28,540 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:38:28,540 [MainThread  ] [INFO ]  log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\n2024-11-04 15:38:28,543 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28&amp;#x27;]\n2024-11-04 15:38:28,544 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxmutate/output_structure.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_35/pmxmutate/output_structure.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_output_structure.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 11092\n     Atoms ALIGNED in PDB_B: 11092\n     RMS: 2.2084949513674e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:63 pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28/frameA0.pdb -o /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28/output_structure.pdb -ff amber99sb-star-ildn-mut --script 38f2c614-6376-4357-ba38-465d986252f1/mutations.txt\n\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:36 Executing: pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b...\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:41 log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmutate/sandbox_3ad12ea5-2435-4fe6-926c-b0cef53e0d28&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.15&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.3&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_pmx/test/unitests/test_pmx/test_pmxanalyse.py::TestPmxanalyse::test_pmxanalyse&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxanalyse.py::TestPmxanalyse::test_pmxanalyse&#34;, &#34;duration&#34;: &#34;00:00:13&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxanalyse.py::TestPmxanalyse::test_pmxanalyse&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:13&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-14 16:22:18,812 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxanalyse Version: 4.2.1\n2024-11-14 16:22:18,813 [MainThread  ] [INFO ]  /tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3 directory successfully created\n2024-11-14 16:22:19,078 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_A.zip\n2024-11-14 16:22:19,079 [MainThread  ] [INFO ]  to:\n2024-11-14 16:22:19,079 [MainThread  ] [INFO ]  [&amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101/frame10/dhdl10.xvg&amp;#x27;, 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&amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame99/dhdl99.xvg&amp;#x27;]\n2024-11-14 16:22:19,348 [MainThread  ] [INFO ]  pmx analyse -fA 2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame1/dhdl1.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame10/dhdl10.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame11/dhdl11.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame12/dhdl12.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame13/dhdl13.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame14/dhdl14.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame15/dhdl15.xvg 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2d4db6a9-3201-4354-940f-503bcb0a7101/frame78/dhdl78.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame79/dhdl79.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame8/dhdl8.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame80/dhdl80.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame81/dhdl81.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame82/dhdl82.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame83/dhdl83.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame84/dhdl84.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame85/dhdl85.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame86/dhdl86.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame87/dhdl87.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame88/dhdl88.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame89/dhdl89.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame9/dhdl9.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame90/dhdl90.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame91/dhdl91.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame92/dhdl92.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame93/dhdl93.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame94/dhdl94.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame95/dhdl95.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame96/dhdl96.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame97/dhdl97.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame98/dhdl98.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame99/dhdl99.xvg -fB 08500195-f31b-4abe-82ac-b98599b2ae17/frame0/dhdl0.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame1/dhdl1.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame10/dhdl10.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame11/dhdl11.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame12/dhdl12.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame13/dhdl13.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame14/dhdl14.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame15/dhdl15.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame16/dhdl16.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame17/dhdl17.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame18/dhdl18.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame19/dhdl19.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame2/dhdl2.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame20/dhdl20.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame21/dhdl21.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame22/dhdl22.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame23/dhdl23.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame24/dhdl24.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame25/dhdl25.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame26/dhdl26.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame27/dhdl27.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame28/dhdl28.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame29/dhdl29.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame3/dhdl3.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame30/dhdl30.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame31/dhdl31.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame32/dhdl32.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame33/dhdl33.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame34/dhdl34.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame35/dhdl35.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame36/dhdl36.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame37/dhdl37.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame38/dhdl38.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame39/dhdl39.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame4/dhdl4.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame40/dhdl40.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame41/dhdl41.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame42/dhdl42.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame43/dhdl43.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame44/dhdl44.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame45/dhdl45.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame46/dhdl46.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame47/dhdl47.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame48/dhdl48.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame49/dhdl49.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame5/dhdl5.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame50/dhdl50.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame51/dhdl51.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame52/dhdl52.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame53/dhdl53.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame54/dhdl54.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame55/dhdl55.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame56/dhdl56.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame57/dhdl57.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame58/dhdl58.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame59/dhdl59.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame6/dhdl6.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame60/dhdl60.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame61/dhdl61.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame62/dhdl62.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame63/dhdl63.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame64/dhdl64.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame65/dhdl65.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame66/dhdl66.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame67/dhdl67.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame68/dhdl68.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame69/dhdl69.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame7/dhdl7.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame70/dhdl70.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame71/dhdl71.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame72/dhdl72.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame73/dhdl73.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame74/dhdl74.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame75/dhdl75.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame76/dhdl76.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame77/dhdl77.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame78/dhdl78.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame79/dhdl79.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame8/dhdl8.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame80/dhdl80.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame81/dhdl81.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame82/dhdl82.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame83/dhdl83.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame84/dhdl84.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame85/dhdl85.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame86/dhdl86.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame87/dhdl87.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame88/dhdl88.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame89/dhdl89.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame9/dhdl9.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame90/dhdl90.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame91/dhdl91.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame92/dhdl92.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame93/dhdl93.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame94/dhdl94.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame95/dhdl95.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame96/dhdl96.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame97/dhdl97.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame98/dhdl98.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame99/dhdl99.xvg -o /tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3/result.txt -w /tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\n2024-11-14 16:22:30,883 [MainThread  ] [INFO ]  Executing: pmx analyse -fA 2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg 2d4db6a9-3...\n2024-11-14 16:22:30,884 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-14 16:22:30,884 [MainThread  ] [INFO ]  \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame1/dhdl1.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame2/dhdl2.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame3/dhdl3.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame4/dhdl4.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame5/dhdl5.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame6/dhdl6.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame7/dhdl7.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame8/dhdl8.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame9/dhdl9.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame10/dhdl10.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame11/dhdl11.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame12/dhdl12.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame13/dhdl13.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame14/dhdl14.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame15/dhdl15.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame16/dhdl16.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame17/dhdl17.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame18/dhdl18.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame19/dhdl19.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame20/dhdl20.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame21/dhdl21.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame22/dhdl22.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame23/dhdl23.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame24/dhdl24.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame25/dhdl25.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame26/dhdl26.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame27/dhdl27.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame28/dhdl28.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame29/dhdl29.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame30/dhdl30.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame31/dhdl31.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame32/dhdl32.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame33/dhdl33.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame34/dhdl34.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame35/dhdl35.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame36/dhdl36.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame37/dhdl37.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame38/dhdl38.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame39/dhdl39.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame40/dhdl40.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame41/dhdl41.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame42/dhdl42.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame43/dhdl43.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame44/dhdl44.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame45/dhdl45.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame46/dhdl46.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame47/dhdl47.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame48/dhdl48.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame49/dhdl49.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame50/dhdl50.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame51/dhdl51.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame52/dhdl52.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame53/dhdl53.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame54/dhdl54.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame55/dhdl55.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame56/dhdl56.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame57/dhdl57.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame58/dhdl58.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame59/dhdl59.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame60/dhdl60.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame61/dhdl61.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame62/dhdl62.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame63/dhdl63.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame64/dhdl64.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame65/dhdl65.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame66/dhdl66.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame67/dhdl67.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame68/dhdl68.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame69/dhdl69.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame70/dhdl70.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame71/dhdl71.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame72/dhdl72.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame73/dhdl73.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame74/dhdl74.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame75/dhdl75.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame76/dhdl76.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame77/dhdl77.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame78/dhdl78.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame79/dhdl79.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame80/dhdl80.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame81/dhdl81.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame82/dhdl82.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame83/dhdl83.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame84/dhdl84.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame85/dhdl85.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame86/dhdl86.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame87/dhdl87.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame88/dhdl88.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame89/dhdl89.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame90/dhdl90.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame91/dhdl91.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame92/dhdl92.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame93/dhdl93.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame94/dhdl94.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame95/dhdl95.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame96/dhdl96.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame97/dhdl97.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame98/dhdl98.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 08500195-f31b-4abe-82ac-b98599b2ae17/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame1/dhdl1.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame2/dhdl2.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame3/dhdl3.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame4/dhdl4.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame5/dhdl5.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame6/dhdl6.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame7/dhdl7.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame8/dhdl8.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame9/dhdl9.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame10/dhdl10.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame11/dhdl11.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame12/dhdl12.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame13/dhdl13.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame14/dhdl14.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame15/dhdl15.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame16/dhdl16.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame17/dhdl17.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame18/dhdl18.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame19/dhdl19.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame20/dhdl20.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame21/dhdl21.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame22/dhdl22.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame23/dhdl23.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame24/dhdl24.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame25/dhdl25.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame26/dhdl26.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame27/dhdl27.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame28/dhdl28.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame29/dhdl29.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame30/dhdl30.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame31/dhdl31.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame32/dhdl32.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame33/dhdl33.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame34/dhdl34.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame35/dhdl35.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame36/dhdl36.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame37/dhdl37.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame38/dhdl38.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame39/dhdl39.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame40/dhdl40.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame41/dhdl41.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame42/dhdl42.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame43/dhdl43.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame44/dhdl44.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame45/dhdl45.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame46/dhdl46.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame47/dhdl47.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame48/dhdl48.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame49/dhdl49.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame50/dhdl50.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame51/dhdl51.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame52/dhdl52.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame53/dhdl53.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame54/dhdl54.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame55/dhdl55.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame56/dhdl56.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame57/dhdl57.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame58/dhdl58.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame59/dhdl59.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame60/dhdl60.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame61/dhdl61.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame62/dhdl62.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame63/dhdl63.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame64/dhdl64.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame65/dhdl65.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame66/dhdl66.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame67/dhdl67.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame68/dhdl68.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame69/dhdl69.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame70/dhdl70.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame71/dhdl71.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame72/dhdl72.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame73/dhdl73.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame74/dhdl74.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame75/dhdl75.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame76/dhdl76.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame77/dhdl77.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame78/dhdl78.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame79/dhdl79.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame80/dhdl80.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame81/dhdl81.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame82/dhdl82.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame83/dhdl83.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame84/dhdl84.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame85/dhdl85.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame86/dhdl86.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame87/dhdl87.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame88/dhdl88.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame89/dhdl89.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame90/dhdl90.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame91/dhdl91.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame92/dhdl92.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame93/dhdl93.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame94/dhdl94.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame95/dhdl95.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame96/dhdl96.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame97/dhdl97.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame98/dhdl98.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std Err): iteration 20/100\r  Bootstrap (Std Err): iteration 21/100\r  Bootstrap (Std Err): iteration 22/100\r  Bootstrap (Std Err): iteration 23/100\r  Bootstrap (Std Err): iteration 24/100\r  Bootstrap (Std Err): iteration 25/100\r  Bootstrap (Std Err): iteration 26/100\r  Bootstrap (Std Err): iteration 27/100\r  Bootstrap 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iteration 52/100\r  Bootstrap (Std Err): iteration 53/100\r  Bootstrap (Std Err): iteration 54/100\r  Bootstrap (Std Err): iteration 55/100\r  Bootstrap (Std Err): iteration 56/100\r  Bootstrap (Std Err): iteration 57/100\r  Bootstrap (Std Err): iteration 58/100\r  Bootstrap (Std Err): iteration 59/100\r  Bootstrap (Std Err): iteration 60/100\r  Bootstrap (Std Err): iteration 61/100\r  Bootstrap (Std Err): iteration 62/100\r  Bootstrap (Std Err): iteration 63/100\r  Bootstrap (Std Err): iteration 64/100\r  Bootstrap (Std Err): iteration 65/100\r  Bootstrap (Std Err): iteration 66/100\r  Bootstrap (Std Err): iteration 67/100\r  Bootstrap (Std Err): iteration 68/100\r  Bootstrap (Std Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  CGI: Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.42 kJ/mol\n  CGI: Std Err (bootstrap) =     0.44 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 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Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ: dG Forward =    10.24 kJ/mol\n  JARZ: dG Reverse =    20.82 kJ/mol\n  JARZ: dG Mean    =    15.53 kJ/mol\n  JARZ: Std Err Forward (bootstrap) =     0.47 kJ/mol\n  JARZ: Std Err Reverse (bootstrap) =     3.05 kJ/mol\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  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Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.62 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.69 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\n2024-11-14 16:22:30,908 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3&amp;#x27;, &amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17&amp;#x27;]\n2024-11-14 16:22:30,908 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_50/pmxanalyse/result.txt\nChecking if empty file: /tmp/biobb/unitests_50/pmxanalyse/plot.png\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_50/pmxanalyse/plot.png\n     IMAGE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_plot.png\n     IMAGE_A HASH: ffdfe78183a7f7df SIZE: 64 bits\n     IMAGE_B HASH: ffdfe78183a7f7df SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxanalyse Version: 4.2.1\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:file_utils.py:82 /tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3 directory successfully created\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_A.zip\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:file_utils.py:174 [&amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101/frame10/dhdl10.xvg&amp;#x27;, 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&amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame46/dhdl46.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame47/dhdl47.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame48/dhdl48.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame49/dhdl49.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame5/dhdl5.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame50/dhdl50.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame51/dhdl51.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame52/dhdl52.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame53/dhdl53.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame54/dhdl54.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame55/dhdl55.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame56/dhdl56.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame57/dhdl57.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame58/dhdl58.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame59/dhdl59.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame6/dhdl6.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame60/dhdl60.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame61/dhdl61.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame62/dhdl62.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame63/dhdl63.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame64/dhdl64.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame65/dhdl65.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame66/dhdl66.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame67/dhdl67.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame68/dhdl68.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame69/dhdl69.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame7/dhdl7.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17/frame99/dhdl99.xvg&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:63 pmx analyse -fA 2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame1/dhdl1.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame10/dhdl10.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame11/dhdl11.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame12/dhdl12.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame13/dhdl13.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame14/dhdl14.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame15/dhdl15.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame16/dhdl16.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame17/dhdl17.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame18/dhdl18.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame19/dhdl19.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame2/dhdl2.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame20/dhdl20.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame21/dhdl21.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame22/dhdl22.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame23/dhdl23.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame24/dhdl24.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame25/dhdl25.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame26/dhdl26.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame27/dhdl27.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame28/dhdl28.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame29/dhdl29.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame3/dhdl3.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame30/dhdl30.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame31/dhdl31.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame32/dhdl32.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame33/dhdl33.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame34/dhdl34.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame35/dhdl35.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame36/dhdl36.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame37/dhdl37.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame38/dhdl38.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame39/dhdl39.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame4/dhdl4.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame40/dhdl40.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame41/dhdl41.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame42/dhdl42.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame43/dhdl43.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame44/dhdl44.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame45/dhdl45.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame46/dhdl46.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame47/dhdl47.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame48/dhdl48.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame49/dhdl49.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame5/dhdl5.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame50/dhdl50.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame51/dhdl51.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame52/dhdl52.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame53/dhdl53.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame54/dhdl54.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame55/dhdl55.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame56/dhdl56.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame57/dhdl57.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame58/dhdl58.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame59/dhdl59.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame6/dhdl6.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame60/dhdl60.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame61/dhdl61.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame62/dhdl62.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame63/dhdl63.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame64/dhdl64.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame65/dhdl65.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame66/dhdl66.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame67/dhdl67.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame68/dhdl68.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame69/dhdl69.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame7/dhdl7.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame70/dhdl70.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame71/dhdl71.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame72/dhdl72.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame73/dhdl73.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame74/dhdl74.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame75/dhdl75.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame76/dhdl76.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame77/dhdl77.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame78/dhdl78.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame79/dhdl79.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame8/dhdl8.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame80/dhdl80.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame81/dhdl81.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame82/dhdl82.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame83/dhdl83.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame84/dhdl84.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame85/dhdl85.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame86/dhdl86.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame87/dhdl87.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame88/dhdl88.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame89/dhdl89.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame9/dhdl9.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame90/dhdl90.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame91/dhdl91.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame92/dhdl92.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame93/dhdl93.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame94/dhdl94.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame95/dhdl95.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame96/dhdl96.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame97/dhdl97.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame98/dhdl98.xvg 2d4db6a9-3201-4354-940f-503bcb0a7101/frame99/dhdl99.xvg -fB 08500195-f31b-4abe-82ac-b98599b2ae17/frame0/dhdl0.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame1/dhdl1.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame10/dhdl10.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame11/dhdl11.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame12/dhdl12.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame13/dhdl13.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame14/dhdl14.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame15/dhdl15.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame16/dhdl16.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame17/dhdl17.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame18/dhdl18.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame19/dhdl19.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame2/dhdl2.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame20/dhdl20.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame21/dhdl21.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame22/dhdl22.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame23/dhdl23.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame24/dhdl24.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame25/dhdl25.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame26/dhdl26.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame27/dhdl27.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame28/dhdl28.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame29/dhdl29.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame3/dhdl3.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame30/dhdl30.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame31/dhdl31.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame32/dhdl32.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame33/dhdl33.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame34/dhdl34.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame35/dhdl35.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame36/dhdl36.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame37/dhdl37.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame38/dhdl38.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame39/dhdl39.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame4/dhdl4.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame40/dhdl40.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame41/dhdl41.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame42/dhdl42.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame43/dhdl43.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame44/dhdl44.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame45/dhdl45.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame46/dhdl46.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame47/dhdl47.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame48/dhdl48.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame49/dhdl49.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame5/dhdl5.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame50/dhdl50.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame51/dhdl51.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame52/dhdl52.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame53/dhdl53.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame54/dhdl54.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame55/dhdl55.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame56/dhdl56.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame57/dhdl57.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame58/dhdl58.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame59/dhdl59.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame6/dhdl6.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame60/dhdl60.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame61/dhdl61.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame62/dhdl62.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame63/dhdl63.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame64/dhdl64.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame65/dhdl65.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame66/dhdl66.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame67/dhdl67.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame68/dhdl68.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame69/dhdl69.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame7/dhdl7.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame70/dhdl70.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame71/dhdl71.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame72/dhdl72.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame73/dhdl73.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame74/dhdl74.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame75/dhdl75.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame76/dhdl76.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame77/dhdl77.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame78/dhdl78.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame79/dhdl79.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame8/dhdl8.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame80/dhdl80.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame81/dhdl81.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame82/dhdl82.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame83/dhdl83.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame84/dhdl84.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame85/dhdl85.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame86/dhdl86.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame87/dhdl87.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame88/dhdl88.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame89/dhdl89.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame9/dhdl9.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame90/dhdl90.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame91/dhdl91.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame92/dhdl92.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame93/dhdl93.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame94/dhdl94.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame95/dhdl95.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame96/dhdl96.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame97/dhdl97.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame98/dhdl98.xvg 08500195-f31b-4abe-82ac-b98599b2ae17/frame99/dhdl99.xvg -o /tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3/result.txt -w /tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:36 Executing: pmx analyse -fA 2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg 2d4db6a9-3...\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:41 \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 2d4db6a9-3201-4354-940f-503bcb0a7101/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame1/dhdl1.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame2/dhdl2.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame3/dhdl3.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame4/dhdl4.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame5/dhdl5.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame6/dhdl6.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame7/dhdl7.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame8/dhdl8.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame9/dhdl9.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame10/dhdl10.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame11/dhdl11.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame12/dhdl12.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame13/dhdl13.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame14/dhdl14.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame15/dhdl15.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame16/dhdl16.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame17/dhdl17.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame18/dhdl18.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame19/dhdl19.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame20/dhdl20.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame21/dhdl21.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame22/dhdl22.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame23/dhdl23.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame24/dhdl24.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame25/dhdl25.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame26/dhdl26.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame27/dhdl27.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame28/dhdl28.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame29/dhdl29.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame30/dhdl30.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame31/dhdl31.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame32/dhdl32.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame33/dhdl33.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame34/dhdl34.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame35/dhdl35.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame36/dhdl36.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame37/dhdl37.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame38/dhdl38.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame39/dhdl39.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame40/dhdl40.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame41/dhdl41.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame42/dhdl42.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame43/dhdl43.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame44/dhdl44.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame45/dhdl45.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame46/dhdl46.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame47/dhdl47.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame48/dhdl48.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame49/dhdl49.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame50/dhdl50.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame51/dhdl51.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame52/dhdl52.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame53/dhdl53.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame54/dhdl54.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame55/dhdl55.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame56/dhdl56.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame57/dhdl57.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame58/dhdl58.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame59/dhdl59.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame60/dhdl60.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame61/dhdl61.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame62/dhdl62.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame63/dhdl63.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame64/dhdl64.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame65/dhdl65.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame66/dhdl66.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame67/dhdl67.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame68/dhdl68.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame69/dhdl69.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame70/dhdl70.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame71/dhdl71.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame72/dhdl72.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame73/dhdl73.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame74/dhdl74.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame75/dhdl75.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame76/dhdl76.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame77/dhdl77.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame78/dhdl78.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame79/dhdl79.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame80/dhdl80.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame81/dhdl81.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame82/dhdl82.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame83/dhdl83.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame84/dhdl84.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame85/dhdl85.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame86/dhdl86.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame87/dhdl87.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame88/dhdl88.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame89/dhdl89.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame90/dhdl90.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame91/dhdl91.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame92/dhdl92.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame93/dhdl93.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame94/dhdl94.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame95/dhdl95.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame96/dhdl96.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame97/dhdl97.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame98/dhdl98.xvg\r    Reading 2d4db6a9-3201-4354-940f-503bcb0a7101/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 08500195-f31b-4abe-82ac-b98599b2ae17/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame1/dhdl1.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame2/dhdl2.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame3/dhdl3.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame4/dhdl4.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame5/dhdl5.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame6/dhdl6.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame7/dhdl7.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame8/dhdl8.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame9/dhdl9.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame10/dhdl10.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame11/dhdl11.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame12/dhdl12.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame13/dhdl13.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame14/dhdl14.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame15/dhdl15.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame16/dhdl16.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame17/dhdl17.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame18/dhdl18.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame19/dhdl19.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame20/dhdl20.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame21/dhdl21.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame22/dhdl22.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame23/dhdl23.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame24/dhdl24.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame25/dhdl25.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame26/dhdl26.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame27/dhdl27.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame28/dhdl28.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame29/dhdl29.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame30/dhdl30.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame31/dhdl31.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame32/dhdl32.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame33/dhdl33.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame34/dhdl34.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame35/dhdl35.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame36/dhdl36.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame37/dhdl37.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame38/dhdl38.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame39/dhdl39.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame40/dhdl40.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame41/dhdl41.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame42/dhdl42.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame43/dhdl43.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame44/dhdl44.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame45/dhdl45.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame46/dhdl46.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame47/dhdl47.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame48/dhdl48.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame49/dhdl49.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame50/dhdl50.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame51/dhdl51.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame52/dhdl52.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame53/dhdl53.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame54/dhdl54.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame55/dhdl55.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame56/dhdl56.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame57/dhdl57.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame58/dhdl58.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame59/dhdl59.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame60/dhdl60.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame61/dhdl61.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame62/dhdl62.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame63/dhdl63.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame64/dhdl64.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame65/dhdl65.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame66/dhdl66.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame67/dhdl67.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame68/dhdl68.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame69/dhdl69.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame70/dhdl70.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame71/dhdl71.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame72/dhdl72.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame73/dhdl73.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame74/dhdl74.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame75/dhdl75.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame76/dhdl76.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame77/dhdl77.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame78/dhdl78.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame79/dhdl79.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame80/dhdl80.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame81/dhdl81.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame82/dhdl82.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame83/dhdl83.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame84/dhdl84.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame85/dhdl85.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame86/dhdl86.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame87/dhdl87.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame88/dhdl88.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame89/dhdl89.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame90/dhdl90.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame91/dhdl91.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame92/dhdl92.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame93/dhdl93.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame94/dhdl94.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame95/dhdl95.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame96/dhdl96.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame97/dhdl97.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame98/dhdl98.xvg\r    Reading 08500195-f31b-4abe-82ac-b98599b2ae17/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std Err): iteration 20/100\r  Bootstrap (Std Err): iteration 21/100\r  Bootstrap (Std Err): iteration 22/100\r  Bootstrap (Std Err): iteration 23/100\r  Bootstrap (Std Err): iteration 24/100\r  Bootstrap (Std Err): iteration 25/100\r  Bootstrap (Std Err): iteration 26/100\r  Bootstrap (Std Err): iteration 27/100\r  Bootstrap (Std Err): iteration 28/100\r  Bootstrap (Std Err): iteration 29/100\r  Bootstrap (Std Err): iteration 30/100\r  Bootstrap (Std Err): iteration 31/100\r  Bootstrap (Std Err): iteration 32/100\r  Bootstrap (Std Err): iteration 33/100\r  Bootstrap (Std Err): iteration 34/100\r  Bootstrap (Std Err): iteration 35/100\r  Bootstrap (Std Err): iteration 36/100\r  Bootstrap (Std Err): iteration 37/100\r  Bootstrap (Std Err): iteration 38/100\r  Bootstrap (Std Err): iteration 39/100\r  Bootstrap (Std Err): iteration 40/100\r  Bootstrap (Std Err): iteration 41/100\r  Bootstrap (Std Err): iteration 42/100\r  Bootstrap (Std Err): iteration 43/100\r  Bootstrap (Std Err): iteration 44/100\r  Bootstrap (Std Err): iteration 45/100\r  Bootstrap (Std Err): iteration 46/100\r  Bootstrap (Std Err): iteration 47/100\r  Bootstrap (Std Err): iteration 48/100\r  Bootstrap (Std Err): iteration 49/100\r  Bootstrap (Std Err): iteration 50/100\r  Bootstrap (Std Err): iteration 51/100\r  Bootstrap (Std Err): iteration 52/100\r  Bootstrap (Std Err): iteration 53/100\r  Bootstrap (Std Err): iteration 54/100\r  Bootstrap (Std Err): iteration 55/100\r  Bootstrap (Std Err): iteration 56/100\r  Bootstrap (Std Err): iteration 57/100\r  Bootstrap (Std Err): iteration 58/100\r  Bootstrap (Std Err): iteration 59/100\r  Bootstrap (Std Err): iteration 60/100\r  Bootstrap (Std Err): iteration 61/100\r  Bootstrap (Std Err): iteration 62/100\r  Bootstrap (Std Err): iteration 63/100\r  Bootstrap (Std Err): iteration 64/100\r  Bootstrap (Std Err): iteration 65/100\r  Bootstrap (Std Err): iteration 66/100\r  Bootstrap (Std Err): iteration 67/100\r  Bootstrap (Std Err): iteration 68/100\r  Bootstrap (Std Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  CGI: Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.42 kJ/mol\n  CGI: Std Err (bootstrap) =     0.44 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std Err): iteration 20/100\r  Bootstrap (Std Err): iteration 21/100\r  Bootstrap (Std Err): iteration 22/100\r  Bootstrap (Std Err): iteration 23/100\r  Bootstrap (Std Err): iteration 24/100\r  Bootstrap (Std Err): iteration 25/100\r  Bootstrap (Std Err): iteration 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-0.23\n  BAR: Conv Std Err (bootstrap) =     0.05\n\n --------------------------------------------------------\n             Jarzynski estimator     \n --------------------------------------------------------\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std 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Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.62 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.69 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxanalyse/sandbox_49133bc4-ed42-48f4-851f-76607fed5cb3&amp;#x27;, &amp;#x27;2d4db6a9-3201-4354-940f-503bcb0a7101&amp;#x27;, &amp;#x27;08500195-f31b-4abe-82ac-b98599b2ae17&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxanalyse/pmxanalyse_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_50\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;, &#34;duration&#34;: &#34;00:00:04&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:04&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-14 16:22:31,557 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\n2024-11-14 16:22:31,557 [MainThread  ] [INFO ]  /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08 directory successfully created\n2024-11-14 16:22:31,557 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08\n2024-11-14 16:22:31,557 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08\n2024-11-14 16:22:31,558 [MainThread  ] [INFO ]  pmx atomMapping -i1 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/lig1.pdb -i2 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/lig2.pdb -o1 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/pairs1.dat -o2 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/pairs2.dat -log /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/atom_mapping.log --d 0.05\n\n2024-11-14 16:22:35,982 [MainThread  ] [INFO ]  Executing: pmx atomMapping -i1 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c...\n2024-11-14 16:22:35,982 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-14 16:22:35,982 [MainThread  ] [INFO ]  atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\n2024-11-14 16:22:35,983 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08&amp;#x27;]\n2024-11-14 16:22:35,984 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_50/pmxatom_mapping/pairs1.dat\nChecking if empty file: /tmp/biobb/unitests_50/pmxatom_mapping/pairs2.dat\nComparing: \n        File_A: /tmp/biobb/unitests_50/pmxatom_mapping/pairs1.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs1.dat\n        File_A hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\n        File_B hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_50/pmxatom_mapping/pairs2.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs2.dat\n        File_A hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n        File_B hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:82 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08 directory successfully created\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:63 pmx atomMapping -i1 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/lig1.pdb -i2 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/lig2.pdb -o1 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/pairs1.dat -o2 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/pairs2.dat -log /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08/atom_mapping.log --d 0.05\n\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:36 Executing: pmx atomMapping -i1 /tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c...\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:41 atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxatom_mapping/sandbox_b5405ab5-c72c-44c6-9a58-4f69837cda08&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_50\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;, &#34;duration&#34;: &#34;43 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;43 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-14 16:22:36,018 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\n2024-11-14 16:22:36,018 [MainThread  ] [INFO ]  /tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b directory successfully created\n2024-11-14 16:22:36,018 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b\n2024-11-14 16:22:36,019 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b\n2024-11-14 16:22:36,019 [MainThread  ] [INFO ]  Running create_top from pmx package...\n\n2024-11-14 16:22:36,019 [MainThread  ] [INFO ]  Creating 303f9a3e-9f82-4cef-a362-0c43bf406258 temporary folder\n2024-11-14 16:22:36,019 [MainThread  ] [INFO ]  Creating topo1.itp itp file in temporary folder\n2024-11-14 16:22:36,019 [MainThread  ] [INFO ]  Creating topo2.itp itp file in temporary folder\n2024-11-14 16:22:36,020 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_50/pmxcreate_top/topo.zip\n2024-11-14 16:22:36,020 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-14 16:22:36,021 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-14 16:22:36,021 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-14 16:22:36,021 [MainThread  ] [INFO ]  Adding:\n2024-11-14 16:22:36,021 [MainThread  ] [INFO ]  [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-14 16:22:36,022 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_50/pmxcreate_top/topo.zip\n2024-11-14 16:22:36,022 [MainThread  ] [INFO ]  Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-14 16:22:36,022 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-14 16:22:36,022 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b&amp;#x27;]\n2024-11-14 16:22:36,022 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_50/pmxcreate_top/topo.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_50/pmxcreate_top/topo.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopo.zip\nComparing TOP/ITP:\n     FILE_A: 9432ad13-3a5f-4ed3-a725-1479952c50a2/topo1.itp\n     FILE_B: c5e6f9e5-8930-4342-99b5-7be672a65c3b/topo1.itp\nComparing TOP/ITP:\n     FILE_A: 9432ad13-3a5f-4ed3-a725-1479952c50a2/topo2.itp\n     FILE_B: c5e6f9e5-8930-4342-99b5-7be672a65c3b/topo2.itp\nComparing TOP/ITP:\n     FILE_A: 9432ad13-3a5f-4ed3-a725-1479952c50a2/topology.top\n     FILE_B: c5e6f9e5-8930-4342-99b5-7be672a65c3b/topology.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:82 /tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b directory successfully created\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Running create_top from pmx package...\n\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating 303f9a3e-9f82-4cef-a362-0c43bf406258 temporary folder\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo1.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo2.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_50/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:149 [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:150 to: /tmp/biobb/unitests_50/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxcreate_top/sandbox_e3ff752a-fd07-4b64-8bb4-21a16bd08b1b&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_50\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;, &#34;duration&#34;: &#34;00:01:48&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:48&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-14 16:22:36,061 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\n2024-11-14 16:22:36,061 [MainThread  ] [INFO ]  /tmp/biobb/unitests_50/pmxgentop/sandbox_c1489164-18de-428e-9ac3-2c3ee34755c4 directory successfully created\n2024-11-14 16:22:36,063 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-14 16:22:36,063 [MainThread  ] [INFO ]  to:\n2024-11-14 16:22:36,063 [MainThread  ] [INFO ]  [&amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Ion.itp&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Ion.itp&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-14 16:22:36,063 [MainThread  ] [INFO ]  Unzipping: \n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  To: \n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top\n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Ion.itp\n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Protein_chain_A.itp\n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Ion.itp\n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Protein_chain_A.itp\n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  unique_dir_output_file: 36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top\n2024-11-14 16:22:36,064 [MainThread  ] [INFO ]  pmx gentop -o 36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top\n\n2024-11-14 16:24:23,569 [MainThread  ] [INFO ]  Executing: pmx gentop -o 36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top -ff amber99...\n2024-11-14 16:24:23,569 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-14 16:24:23,570 [MainThread  ] [INFO ]  \nlog_&amp;gt; Reading input top file &amp;quot;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_50/pmxgentop/36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_50/pmxgentop/36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\n2024-11-14 16:24:23,698 [MainThread  ] [INFO ]  Check if 36630fb4-8942-4748-8651-120f3bd93540/p2g_Protein_chain_A.itp exists\n2024-11-14 16:24:23,699 [MainThread  ] [INFO ]  Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Protein_chain_A.itp to: 36630fb4-8942-4748-8651-120f3bd93540\n2024-11-14 16:24:23,699 [MainThread  ] [INFO ]  Check if 36630fb4-8942-4748-8651-120f3bd93540/p2g_Ion.itp exists\n2024-11-14 16:24:23,699 [MainThread  ] [INFO ]  Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Ion.itp to: 36630fb4-8942-4748-8651-120f3bd93540\n2024-11-14 16:24:23,700 [MainThread  ] [INFO ]  Check if 36630fb4-8942-4748-8651-120f3bd93540/p2g.top exists\n2024-11-14 16:24:23,700 [MainThread  ] [INFO ]  Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top to: 36630fb4-8942-4748-8651-120f3bd93540\n2024-11-14 16:24:23,700 [MainThread  ] [INFO ]  Check if 36630fb4-8942-4748-8651-120f3bd93540/posre_Protein_chain_A.itp exists\n2024-11-14 16:24:23,700 [MainThread  ] [INFO ]  Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Protein_chain_A.itp to: 36630fb4-8942-4748-8651-120f3bd93540\n2024-11-14 16:24:23,701 [MainThread  ] [INFO ]  Check if 36630fb4-8942-4748-8651-120f3bd93540/posre_Ion.itp exists\n2024-11-14 16:24:23,702 [MainThread  ] [INFO ]  Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Ion.itp to: 36630fb4-8942-4748-8651-120f3bd93540\n2024-11-14 16:24:23,702 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_50/pmxgentop/output_topology.zip\n2024-11-14 16:24:23,702 [MainThread  ] [INFO ]  Ignored file 36630fb4-8942-4748-8651-120f3bd93540/amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-14 16:24:23,716 [MainThread  ] [INFO ]  Ignored file 36630fb4-8942-4748-8651-120f3bd93540/amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-14 16:24:23,717 [MainThread  ] [INFO ]  Ignored file 36630fb4-8942-4748-8651-120f3bd93540/amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-14 16:24:23,719 [MainThread  ] [INFO ]  Adding:\n2024-11-14 16:24:23,719 [MainThread  ] [INFO ]  [&amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-14 16:24:23,720 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_50/pmxgentop/output_topology.zip\n2024-11-14 16:24:23,729 [MainThread  ] [INFO ]  Removed: [&amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top&amp;#x27;]\n2024-11-14 16:24:23,729 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_50/pmxgentop/output_topology.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_50/pmxgentop/output_topology.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mut_gmx_hybrid_top.zip\nComparing TOP/ITP:\n     FILE_A: 6b55a42b-0f4e-46a4-beea-711bedac270e/pmx_p2g_Ion.itp\n     FILE_B: 4075b03c-7424-4e49-a4ec-b313e7b88242/pmx_p2g_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 6b55a42b-0f4e-46a4-beea-711bedac270e/pmx_p2g_Protein_chain_A.itp\n     FILE_B: 4075b03c-7424-4e49-a4ec-b313e7b88242/pmx_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: 6b55a42b-0f4e-46a4-beea-711bedac270e/pmxgentop_p2g.top\n     FILE_B: 4075b03c-7424-4e49-a4ec-b313e7b88242/pmxgentop_p2g.top\nComparing TOP/ITP:\n     FILE_A: 6b55a42b-0f4e-46a4-beea-711bedac270e/posre_Ion.itp\n     FILE_B: 4075b03c-7424-4e49-a4ec-b313e7b88242/posre_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 6b55a42b-0f4e-46a4-beea-711bedac270e/posre_Protein_chain_A.itp\n     FILE_B: 4075b03c-7424-4e49-a4ec-b313e7b88242/posre_Protein_chain_A.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:82 /tmp/biobb/unitests_50/pmxgentop/sandbox_c1489164-18de-428e-9ac3-2c3ee34755c4 directory successfully created\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:174 [&amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Ion.itp&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Ion.itp&amp;#x27;, &amp;#x27;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:256 ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:256 ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Ion.itp\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:256 ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:256 ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Ion.itp\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:256 ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 unique_dir_output_file: 36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:63 pmx gentop -o 36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top\n\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:36 Executing: pmx gentop -o 36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top -ff amber99...\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:41 \nlog_&amp;gt; Reading input top file &amp;quot;ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_50/pmxgentop/36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_50/pmxgentop/36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 36630fb4-8942-4748-8651-120f3bd93540/p2g_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Protein_chain_A.itp to: 36630fb4-8942-4748-8651-120f3bd93540\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 36630fb4-8942-4748-8651-120f3bd93540/p2g_Ion.itp exists\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g_Ion.itp to: 36630fb4-8942-4748-8651-120f3bd93540\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 36630fb4-8942-4748-8651-120f3bd93540/p2g.top exists\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/p2g.top to: 36630fb4-8942-4748-8651-120f3bd93540\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 36630fb4-8942-4748-8651-120f3bd93540/posre_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Protein_chain_A.itp to: 36630fb4-8942-4748-8651-120f3bd93540\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 36630fb4-8942-4748-8651-120f3bd93540/posre_Ion.itp exists\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying ddbdfe6e-ae6e-4eff-acc8-5d42ef09e04a/posre_Ion.itp to: 36630fb4-8942-4748-8651-120f3bd93540\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_50/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 36630fb4-8942-4748-8651-120f3bd93540/amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 36630fb4-8942-4748-8651-120f3bd93540/amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 36630fb4-8942-4748-8651-120f3bd93540/amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:149 [&amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:150 to: /tmp/biobb/unitests_50/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409 Removed: [&amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/posre_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;36630fb4-8942-4748-8651-120f3bd93540/pmxgentop_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxgentop/pmxgentop_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_50\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-14 16:24:23,971 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\n2024-11-14 16:24:23,972 [MainThread  ] [INFO ]  /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974 directory successfully created\n2024-11-14 16:24:23,972 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\n2024-11-14 16:24:23,972 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\n2024-11-14 16:24:23,973 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\n2024-11-14 16:24:23,973 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\n2024-11-14 16:24:23,973 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\n2024-11-14 16:24:23,974 [MainThread  ] [INFO ]  pmx ligandHybrid -i1 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig1.pdb -i2 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig2.pdb -itp1 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig1.itp -itp2 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig2.itp -pairs /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/myPairs1.dat -oA /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridStruct1.pdb -oB /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridStruct2.pdb -oitp /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridTopo.itp -offitp /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridAtomTypes.itp -log /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/ligand_hybrid.log --fit --d 0.05\n\n2024-11-14 16:24:25,872 [MainThread  ] [INFO ]  Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-65...\n2024-11-14 16:24:25,872 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-14 16:24:25,873 [MainThread  ] [INFO ]  ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridAtomTypes.itp&amp;quot;\n\n2024-11-14 16:24:25,874 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974&amp;#x27;]\n2024-11-14 16:24:25,875 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridStruct1.pdb\nChecking if empty file: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridStruct2.pdb\nChecking if empty file: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridTopo.itp\nChecking if empty file: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridAtomTypes.itp\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridStruct1.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 3.850114164176677e-15\n     RMS_CUTOFF: 1\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridStruct2.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure2.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 0.1872943529544109\n     RMS_CUTOFF: 1\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopology.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_50/pmxligand_hybrid/hybridAtomTypes.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridAtomTypes.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:82 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974 directory successfully created\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:63 pmx ligandHybrid -i1 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig1.pdb -i2 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig2.pdb -itp1 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig1.itp -itp2 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig2.itp -pairs /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/myPairs1.dat -oA /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridStruct1.pdb -oB /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridStruct2.pdb -oitp /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridTopo.itp -offitp /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridAtomTypes.itp -log /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/ligand_hybrid.log --fit --d 0.05\n\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:36 Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-65...\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:41 ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974/hybridAtomTypes.itp&amp;quot;\n\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxligand_hybrid/sandbox_b9381830-651e-43e7-97fb-1b0da5a78974&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_50\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;, &#34;duration&#34;: &#34;33 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;33 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-14 16:24:25,919 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\n2024-11-14 16:24:25,919 [MainThread  ] [INFO ]  /tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81 directory successfully created\n2024-11-14 16:24:25,919 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81\n2024-11-14 16:24:25,919 [MainThread  ] [INFO ]  Creating 878f82ad-a655-4672-8d58-3216d688f7f7 temporary folder\n2024-11-14 16:24:25,920 [MainThread  ] [INFO ]  Extracting: /tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81/itps_to_merge.zip\n2024-11-14 16:24:25,920 [MainThread  ] [INFO ]  to:\n2024-11-14 16:24:25,920 [MainThread  ] [INFO ]  [&amp;#x27;878f82ad-a655-4672-8d58-3216d688f7f7/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;878f82ad-a655-4672-8d58-3216d688f7f7/lig1ffMOL.itp&amp;#x27;, &amp;#x27;878f82ad-a655-4672-8d58-3216d688f7f7/lig2ffMOL.itp&amp;#x27;]\n2024-11-14 16:24:25,921 [MainThread  ] [INFO ]  Running merge_FF_files from pmx package...\n\n2024-11-14 16:24:25,921 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-14 16:24:25,921 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81&amp;#x27;]\n2024-11-14 16:24:25,922 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_50/pmxmerge_ff/hybridTopo.itp\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_50/pmxmerge_ff/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mergedTopology.itp\n     SIZE_A: 1468 bytes\n     SIZE_B: 1468 bytes\n     TOLERANCE: 1.0%, Low: 1453.32 bytes, High: 1482.68 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:82 /tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81 directory successfully created\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Creating 878f82ad-a655-4672-8d58-3216d688f7f7 temporary folder\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:172 Extracting: /tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81/itps_to_merge.zip\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:174 [&amp;#x27;878f82ad-a655-4672-8d58-3216d688f7f7/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;878f82ad-a655-4672-8d58-3216d688f7f7/lig1ffMOL.itp&amp;#x27;, &amp;#x27;878f82ad-a655-4672-8d58-3216d688f7f7/lig2ffMOL.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Running merge_FF_files from pmx package...\n\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxmerge_ff/sandbox_c6b3ec1a-918d-45bd-80b9-550af7a20a81&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_50\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-14 16:24:25,953 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\n2024-11-14 16:24:25,953 [MainThread  ] [INFO ]  /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10 directory successfully created\n2024-11-14 16:24:25,956 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10\n2024-11-14 16:24:25,956 [MainThread  ] [INFO ]  pmx mutate -f /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10/frameA0.pdb -o /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10/output_structure.pdb -ff amber99sb-star-ildn-mut --script ffad79b3-17aa-4233-8769-4ad6810283ef/mutations.txt\n\n2024-11-14 16:24:28,830 [MainThread  ] [INFO ]  Executing: pmx mutate -f /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b...\n2024-11-14 16:24:28,966 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-14 16:24:28,966 [MainThread  ] [INFO ]  log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\n2024-11-14 16:24:28,970 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10&amp;#x27;]\n2024-11-14 16:24:28,970 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_50/pmxmutate/output_structure.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_50/pmxmutate/output_structure.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_output_structure.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 11092\n     Atoms ALIGNED in PDB_B: 11092\n     RMS: 2.2084949513674e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:file_utils.py:82 /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10 directory successfully created\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:63 pmx mutate -f /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10/frameA0.pdb -o /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10/output_structure.pdb -ff amber99sb-star-ildn-mut --script ffad79b3-17aa-4233-8769-4ad6810283ef/mutations.txt\n\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:36 Executing: pmx mutate -f /tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b...\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:41 log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_50/pmxmutate/sandbox_e86a2994-9488-4d03-962b-b741dafe9f10&amp;#x27;]\nINFO     /tmp/biobb/unitests_50/pmxmutate/pmxmutate_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_50\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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