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-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.14&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.0&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;, &#34;duration&#34;: &#34;00:01:11&#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_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:11&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:14:05,429 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.1.0\n2024-05-07 08:14:05,430 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_ac/ef701d95-2ebe-4faf-aafd-e6f49d7788ec\n2024-05-07 08:14:05,430 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_ac/ef701d95-2ebe-4faf-aafd-e6f49d7788ec/acpype.params.pdb -b BBB.WrhXuN -n 0\n\n2024-05-07 08:15:16,125 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:15:16,125 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.WrhXuN.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 11s\n\n2024-05-07 08:15:16,127 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod succesfully created\n2024-05-07 08:15:16,128 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.prmtop succesfully created\n2024-05-07 08:15:16,128 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd succesfully created\n2024-05-07 08:15:16,129 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.lib succesfully created\n2024-05-07 08:15:16,130 [MainThread  ] [INFO ]  Removed temporary folder: BBB.WrhXuN.acpype\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.lib\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.prmtop\nComparing: \n        File_A: /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.frcmod\n        File_A hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.inpcrd\n        File_A hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_ac/ef701d95-2ebe-4faf-aafd-e6f49d7788ec\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_ac/ef701d95-2ebe-4faf-aafd-e6f49d7788ec/acpype.params.pdb -b BBB.WrhXuN -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.WrhXuN.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 11s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.prmtop succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.lib succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 Removed temporary folder: BBB.WrhXuN.acpype\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;, &#34;duration&#34;: &#34;00:01:10&#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_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:15:16,214 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.1.0\n2024-05-07 08:15:16,215 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_cns/b9e8d3c4-81e7-4f59-a489-a669011be7e8\n2024-05-07 08:15:16,215 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_cns/b9e8d3c4-81e7-4f59-a489-a669011be7e8/acpype.params.pdb -b BBB.XiKoVJ -n 0\n\n2024-05-07 08:16:26,508 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:16:26,508 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.XiKoVJ.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\n2024-05-07 08:16:26,510 [MainThread  ] [INFO ]  Files: BBB.XiKoVJ.acpype/BBB.XiKoVJ_CNS.inp\n2024-05-07 08:16:26,510 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.inp succesfully created\n2024-05-07 08:16:26,510 [MainThread  ] [INFO ]  Files: BBB.XiKoVJ.acpype/BBB.XiKoVJ_CNS.par\n2024-05-07 08:16:26,510 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.par succesfully created\n2024-05-07 08:16:26,511 [MainThread  ] [INFO ]  Files: BBB.XiKoVJ.acpype/BBB.XiKoVJ_CNS.top\n2024-05-07 08:16:26,511 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.top succesfully created\n2024-05-07 08:16:26,512 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.pdb succesfully created\n2024-05-07 08:16:26,543 [MainThread  ] [INFO ]  Removed temporary folder: BBB.XiKoVJ.acpype\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_cns/output.par\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_cns/output.inp\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_cns/output.inp\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.cns.inp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_cns/b9e8d3c4-81e7-4f59-a489-a669011be7e8\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_cns/b9e8d3c4-81e7-4f59-a489-a669011be7e8/acpype.params.pdb -b BBB.XiKoVJ -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.XiKoVJ.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Files: BBB.XiKoVJ.acpype/BBB.XiKoVJ_CNS.inp\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.inp succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Files: BBB.XiKoVJ.acpype/BBB.XiKoVJ_CNS.par\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.par succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Files: BBB.XiKoVJ.acpype/BBB.XiKoVJ_CNS.top\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.top succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.pdb succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Removed temporary folder: BBB.XiKoVJ.acpype\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;, &#34;duration&#34;: &#34;00:01:10&#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_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:16:26,613 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.1.0\n2024-05-07 08:16:26,613 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx/01d7889c-1b41-4f73-a3ff-6d65cb855d7c\n2024-05-07 08:16:26,613 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_gmx/01d7889c-1b41-4f73-a3ff-6d65cb855d7c/acpype.params.pdb -b BBB.zFaXmu -n 0\n\n2024-05-07 08:17:36,646 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:17:36,646 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.zFaXmu.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\n2024-05-07 08:17:36,648 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\n2024-05-07 08:17:36,649 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top succesfully created\n2024-05-07 08:17:36,650 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.itp\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx/01d7889c-1b41-4f73-a3ff-6d65cb855d7c\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_gmx/01d7889c-1b41-4f73-a3ff-6d65cb855d7c/acpype.params.pdb -b BBB.zFaXmu -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.zFaXmu.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;, &#34;duration&#34;: &#34;00:01:10&#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_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:17:36,740 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.1.0\n2024-05-07 08:17:36,740 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx_opls/16e4e0f9-300b-4f15-a813-2d7c5ae23755\n2024-05-07 08:17:36,740 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_gmx_opls/16e4e0f9-300b-4f15-a813-2d7c5ae23755/acpype.params.pdb -b BBB.PHhGPF -n 0\n\n2024-05-07 08:18:47,048 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:18:47,052 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.PHhGPF.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\n2024-05-07 08:18:47,053 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\n2024-05-07 08:18:47,055 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.opls.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx_opls/16e4e0f9-300b-4f15-a813-2d7c5ae23755\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_gmx_opls/16e4e0f9-300b-4f15-a813-2d7c5ae23755/acpype.params.pdb -b BBB.PHhGPF -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.PHhGPF.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;480 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_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;480 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 -----------------------------\n2024-05-07 08:18:47,126 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.1.0\n2024-05-07 08:18:47,126 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03\n2024-05-07 08:18:47,126 [MainThread  ] [INFO ]  reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03/output.pdb\n\n2024-05-07 08:18:47,536 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:18:47,537 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n2024-05-07 08:18:47,538 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/reduce_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:33 reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03/output.pdb\n\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/reduce_add_hydrogens/4cad0903-6edd-4993-9106-80368c2e5c03&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;79 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_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;79 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 -----------------------------\n2024-05-07 08:18:47,607 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.1.0\n2024-05-07 08:18:47,608 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7\n2024-05-07 08:18:47,608 [MainThread  ] [INFO ]  reduce -Trim /tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7/output.pdb\n\n2024-05-07 08:18:47,618 [MainThread  ] [INFO ]  Exit code 255\n\n2024-05-07 08:18:47,618 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nChecking if empty file: /tmp/biobb/unitests_19/reduce_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:33 reduce -Trim /tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7/output.pdb\n\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 255\n\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_remove_hydrogens/092c0ef7-f9ef-4edd-8bbf-2f3150aba8a7/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;208 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_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;208 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 -----------------------------\n2024-05-07 08:18:47,688 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.1.0\n2024-05-07 08:18:47,688 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.no.H.pdb to /tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0\n2024-05-07 08:18:47,689 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0/output.pdb --gen3d -p 7.4\n\n2024-05-07 08:18:47,827 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:18:47,828 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-05-07 08:18:47,828 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.no.H.pdb to /tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0/output.pdb --gen3d -p 7.4\n\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_add_hydrogens/c21e6400-aea8-4f6d-835f-993fb578afc0&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;, &#34;duration&#34;: &#34;97 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_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;97 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 -----------------------------\n2024-05-07 08:18:47,897 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_convert Version: 4.1.0\n2024-05-07 08:18:47,898 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.smi to /tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342\n2024-05-07 08:18:47,898 [MainThread  ] [INFO ]  obabel -ismi /tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342/babel.smi -omol2 -O/tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342/output.mol2 --gen2d -p 7.4 -r\n\n2024-05-07 08:18:47,925 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:18:47,926 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-05-07 08:18:47,926 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_convert/output.mol2\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_convert Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.smi to /tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:cmd_wrapper.py:33 obabel -ismi /tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342/babel.smi -omol2 -O/tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342/output.mol2 --gen2d -p 7.4 -r\n\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_convert/7c61aa88-42bc-44fc-82dd-2512cad64342&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;, &#34;duration&#34;: &#34;154 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_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;154 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 -----------------------------\n2024-05-07 08:18:47,996 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_minimize Version: 4.1.0\n2024-05-07 08:18:47,996 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.minimize.pdb to /tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7\n2024-05-07 08:18:47,997 [MainThread  ] [INFO ]  obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7/output.pdb\n\n2024-05-07 08:18:48,079 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:18:48,079 [MainThread  ] [INFO ]  \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.047836seconds. Iterations per second: 3219.33\n\n2024-05-07 08:18:48,080 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_minimize/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_19/babel_minimize/output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/babel/ref_babel.minimize.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3\n     Atoms ALIGNED in PDB_B: 3\n     RMS: 0.0021526397693638504\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_minimize Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.minimize.pdb to /tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:33 obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7/output.pdb\n\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.err:cmd_wrapper.py:60 \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.047836seconds. Iterations per second: 3219.33\n\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_minimize/5b1078e1-370a-456f-9174-c8c75df7d5b7&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;236 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_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;236 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 -----------------------------\n2024-05-07 08:18:48,152 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.1.0\n2024-05-07 08:18:48,152 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.H.pdb to /tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a\n2024-05-07 08:18:48,152 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a/babel.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a/output.pdb --gen3d -d -p 7.4\n\n2024-05-07 08:18:48,319 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:18:48,319 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-05-07 08:18:48,319 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.H.pdb to /tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a/babel.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a/output.pdb --gen3d -d -p 7.4\n\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_remove_hydrogens/8c3b32f1-4ab9-4f60-9f83-cd61abe1224a&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\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;3.8.19&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.10&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.0&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;, &#34;duration&#34;: &#34;00:01:10&#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_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:21:11,565 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.1.0\n2024-05-07 08:21:11,565 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_ac/b13c467f-171d-4156-84db-5fd3d66b917e\n2024-05-07 08:21:11,565 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_ac/b13c467f-171d-4156-84db-5fd3d66b917e/acpype.params.pdb -b BBB.wwziNv -n 0\n\n2024-05-07 08:22:21,550 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:22:21,550 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.wwziNv.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\n2024-05-07 08:22:21,552 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod succesfully created\n2024-05-07 08:22:21,554 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.prmtop succesfully created\n2024-05-07 08:22:21,554 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd succesfully created\n2024-05-07 08:22:21,555 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_ac/output.lib succesfully created\n2024-05-07 08:22:21,556 [MainThread  ] [INFO ]  Removed temporary folder: BBB.wwziNv.acpype\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.lib\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_ac/output.prmtop\nComparing: \n        File_A: /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.frcmod\n        File_A hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.inpcrd\n        File_A hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_ac/b13c467f-171d-4156-84db-5fd3d66b917e\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_ac/b13c467f-171d-4156-84db-5fd3d66b917e/acpype.params.pdb -b BBB.wwziNv -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.wwziNv.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.frcmod succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.prmtop succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.inpcrd succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_ac/output.lib succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:390 Removed temporary folder: BBB.wwziNv.acpype\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;, &#34;duration&#34;: &#34;00:01:09&#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_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:09&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:22:21,650 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.1.0\n2024-05-07 08:22:21,650 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_cns/ada297b9-2097-4e0e-8c23-c5ee901d83e4\n2024-05-07 08:22:21,650 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_cns/ada297b9-2097-4e0e-8c23-c5ee901d83e4/acpype.params.pdb -b BBB.uwFu6X -n 0\n\n2024-05-07 08:23:30,957 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:23:30,958 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.uwFu6X.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\n2024-05-07 08:23:30,961 [MainThread  ] [INFO ]  Files: BBB.uwFu6X.acpype/BBB.uwFu6X_CNS.top\n2024-05-07 08:23:30,961 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.top succesfully created\n2024-05-07 08:23:30,962 [MainThread  ] [INFO ]  Files: BBB.uwFu6X.acpype/BBB.uwFu6X_CNS.inp\n2024-05-07 08:23:30,962 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.inp succesfully created\n2024-05-07 08:23:30,962 [MainThread  ] [INFO ]  Files: BBB.uwFu6X.acpype/BBB.uwFu6X_CNS.par\n2024-05-07 08:23:30,962 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.par succesfully created\n2024-05-07 08:23:30,963 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_cns/output.pdb succesfully created\n2024-05-07 08:23:30,965 [MainThread  ] [INFO ]  Removed temporary folder: BBB.uwFu6X.acpype\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_cns/output.par\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_cns/output.inp\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_cns/output.inp\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.cns.inp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_cns/ada297b9-2097-4e0e-8c23-c5ee901d83e4\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_cns/ada297b9-2097-4e0e-8c23-c5ee901d83e4/acpype.params.pdb -b BBB.uwFu6X -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.uwFu6X.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Files: BBB.uwFu6X.acpype/BBB.uwFu6X_CNS.top\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.top succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Files: BBB.uwFu6X.acpype/BBB.uwFu6X_CNS.inp\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.inp succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Files: BBB.uwFu6X.acpype/BBB.uwFu6X_CNS.par\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.par succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_cns/output.pdb succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:390 Removed temporary folder: BBB.uwFu6X.acpype\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;, &#34;duration&#34;: &#34;00:01:09&#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_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:09&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:23:31,043 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.1.0\n2024-05-07 08:23:31,043 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx/9f7cb0cd-05a8-4a35-a921-4ba245bd2bca\n2024-05-07 08:23:31,043 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_gmx/9f7cb0cd-05a8-4a35-a921-4ba245bd2bca/acpype.params.pdb -b BBB.7Q0K0I -n 0\n\n2024-05-07 08:24:40,431 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:24:40,432 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.7Q0K0I.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\n2024-05-07 08:24:40,434 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\n2024-05-07 08:24:40,435 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top succesfully created\n2024-05-07 08:24:40,435 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.itp\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx/9f7cb0cd-05a8-4a35-a921-4ba245bd2bca\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_gmx/9f7cb0cd-05a8-4a35-a921-4ba245bd2bca/acpype.params.pdb -b BBB.7Q0K0I -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.7Q0K0I.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.top succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;, &#34;duration&#34;: &#34;00:01:09&#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_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:09&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 08:24:40,510 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.1.0\n2024-05-07 08:24:40,510 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx_opls/691ae200-5388-47db-98a8-4fc5926aa617\n2024-05-07 08:24:40,511 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_19/acpype_params_gmx_opls/691ae200-5388-47db-98a8-4fc5926aa617/acpype.params.pdb -b BBB.RfFt2Y -n 0\n\n2024-05-07 08:25:49,753 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:25:49,753 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.RfFt2Y.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\n2024-05-07 08:25:49,756 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\n2024-05-07 08:25:49,757 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp\nChecking if empty file: /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.opls.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_19/acpype_params_gmx_opls/691ae200-5388-47db-98a8-4fc5926aa617\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_19/acpype_params_gmx_opls/691ae200-5388-47db-98a8-4fc5926aa617/acpype.params.pdb -b BBB.RfFt2Y -n 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.RfFt2Y.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\nINFO     /tmp/biobb/unitests_19/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:390 File /tmp/biobb/unitests_19/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;541 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_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;541 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 -----------------------------\n2024-05-07 08:25:49,834 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.1.0\n2024-05-07 08:25:49,835 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd\n2024-05-07 08:25:49,835 [MainThread  ] [INFO ]  reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd/output.pdb\n\n2024-05-07 08:25:50,301 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:25:50,302 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n2024-05-07 08:25:50,302 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/reduce_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:33 reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd/output.pdb\n\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nINFO     /tmp/biobb/unitests_19/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/reduce_add_hydrogens/1e91349e-e3c3-42ed-a09c-022eea221cfd&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;86 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_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;86 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 -----------------------------\n2024-05-07 08:25:50,376 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.1.0\n2024-05-07 08:25:50,376 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3\n2024-05-07 08:25:50,377 [MainThread  ] [INFO ]  reduce -Trim /tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3/output.pdb\n\n2024-05-07 08:25:50,391 [MainThread  ] [INFO ]  Exit code 255\n\n2024-05-07 08:25:50,391 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nChecking if empty file: /tmp/biobb/unitests_19/reduce_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:33 reduce -Trim /tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3/output.pdb\n\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 255\n\nINFO     /tmp/biobb/unitests_19/reduce_remove_hydrogens/reduce_remove_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_19/reduce_remove_hydrogens/5b9a0601-f01f-43f2-9ef2-8674e1b6e9a3/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;250 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_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;250 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 -----------------------------\n2024-05-07 08:25:50,466 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.1.0\n2024-05-07 08:25:50,466 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.no.H.pdb to /tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80\n2024-05-07 08:25:50,467 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80/output.pdb --gen3d -p 7.4\n\n2024-05-07 08:25:50,642 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:25:50,642 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-05-07 08:25:50,643 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.no.H.pdb to /tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80/output.pdb --gen3d -p 7.4\n\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_19/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_add_hydrogens/19904d8d-5626-4423-8a1a-c46a7aca1a80&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;, &#34;duration&#34;: &#34;109 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_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;109 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 -----------------------------\n2024-05-07 08:25:50,720 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_convert Version: 4.1.0\n2024-05-07 08:25:50,721 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.smi to /tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c\n2024-05-07 08:25:50,721 [MainThread  ] [INFO ]  obabel -ismi /tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c/babel.smi -omol2 -O/tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c/output.mol2 --gen2d -p 7.4 -r\n\n2024-05-07 08:25:50,753 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:25:50,753 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-05-07 08:25:50,754 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_convert/output.mol2\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_convert Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.smi to /tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:cmd_wrapper.py:33 obabel -ismi /tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c/babel.smi -omol2 -O/tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c/output.mol2 --gen2d -p 7.4 -r\n\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_19/babel_convert/babel_convert_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_convert/24b86ced-7975-4aaa-94c2-e34d3b8f386c&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;, &#34;duration&#34;: &#34;176 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_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;176 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 -----------------------------\n2024-05-07 08:25:50,830 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_minimize Version: 4.1.0\n2024-05-07 08:25:50,831 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.minimize.pdb to /tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5\n2024-05-07 08:25:50,831 [MainThread  ] [INFO ]  obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5/output.pdb\n\n2024-05-07 08:25:50,928 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:25:50,928 [MainThread  ] [INFO ]  \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.054608seconds. Iterations per second: 2820.1\n\n2024-05-07 08:25:50,929 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_minimize/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_19/babel_minimize/output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/babel/ref_babel.minimize.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3\n     Atoms ALIGNED in PDB_B: 3\n     RMS: 0.0021526397693638504\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_minimize Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.minimize.pdb to /tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:33 obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5/output.pdb\n\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.err:cmd_wrapper.py:60 \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.054608seconds. Iterations per second: 2820.1\n\nINFO     /tmp/biobb/unitests_19/babel_minimize/babel_minimize_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_minimize/829ec9f0-840f-4889-bd3d-4aca984cffa5&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;256 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_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;256 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 -----------------------------\n2024-05-07 08:25:51,004 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.1.0\n2024-05-07 08:25:51,005 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.H.pdb to /tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344\n2024-05-07 08:25:51,005 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344/babel.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344/output.pdb --gen3d -d -p 7.4\n\n2024-05-07 08:25:51,190 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 08:25:51,190 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-05-07 08:25:51,191 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_19/babel_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:390 Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.1.0\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babel/babel.H.pdb to /tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344/babel.H.pdb -opdb -O/tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344/output.pdb --gen3d -d -p 7.4\n\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_19/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_19/babel_remove_hydrogens/7e29b2f2-97b0-4816-a51b-820074a86344&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_19\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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