Fixed biopython bug and fpocket version updated

bioexcel · May 7, 2024 · 307c73a · 307c73a
1 parent 10ff1b1
commit 307c73a
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Showing 6 changed files with 7 additions and 8 deletions.
diff --git a/.github/env.yaml b/.github/env.yaml
@@ -6,6 +6,4 @@ channels:
 dependencies:
   - biobb_common ==4.1.0
   - vina ==1.2.3
-  - fpocket >=3.1.4.2
-  - biopython ==1.81
-
+  - fpocket ==4.1
diff --git a/biobb_vs/fpocket/fpocket_run.py b/biobb_vs/fpocket/fpocket_run.py
@@ -54,7 +54,7 @@ class FPocketRun(BiobbObject):
     Info:
         * wrapped_software:
             * name: fpocket
-            * version: >=3.1.4.2
+            * version: ==4.1
             * license: MIT
         * ontology:
             * name: EDAM

diff --git a/biobb_vs/json_schemas/biobb_vs.json b/biobb_vs/json_schemas/biobb_vs.json
@@ -82,7 +82,7 @@
         "python >=3.8", 
         "biobb_common ==4.1.0", 
         "vina ==1.2.3",
-        "fpocket >=3.1.4.2"
+        "fpocket ==4.1"
     ],
     "keywords" : [
         "virtual screening",

diff --git a/biobb_vs/json_schemas/fpocket_run.json b/biobb_vs/json_schemas/fpocket_run.json
@@ -8,7 +8,7 @@
     "info": {
         "wrapped_software": {
             "name": "fpocket",
-            "version": ">=3.1.4.2",
+            "version": "==4.1",
             "license": "MIT"
         },
         "ontology": {

diff --git a/biobb_vs/utils/common.py b/biobb_vs/utils/common.py
@@ -12,7 +12,8 @@
         import Bio.SubsMat.MatrixInfo
     except ImportError:
         import Bio.Align.substitution_matrices
-    from Bio.Data.SCOPData import protein_letters_3to1 as prot_one_letter
+    # from Bio.Data.SCOPData import protein_letters_3to1 as prot_one_letter
+    from Bio.Data.PDBData import protein_letters_3to1 as prot_one_letter
 
 
 # CHECK PARAMETERS

diff --git a/references.jsonld b/references.jsonld
@@ -22,7 +22,7 @@
       "applicationCategory": "Computational Biology tool",
       "citation": "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-168",
       "license": "https://opensource.org/license/mit",
-      "softwareVersion": "3.1.4.2"
+      "softwareVersion": "4.1"
     }
   ]
 }