Merge pull request #6 from nostrumbiodiscovery/devel

Copied supported_aminoacids to prevent modifications during tests

Author: martimunicoy

.github/workflows/conda_deployment.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8]
+        python-version: [3.7, 3.8, 3.9]
     name: Python ${{ matrix.python-version }} at ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2

PPP/__init__.py

@@ -1,4 +1,4 @@
 
 
 
-__version__ = "1.0.7"
+__version__ = "1.0.8"

PPP/adjustments_module.py

@@ -5,7 +5,7 @@
 from PPP.checks_module import CheckClashes
 from PPP.coordinates_module import ChangeResidueCoordinates
 from PPP.global_processes import FindInitialAndFinalResidues
-from PPP.global_variables import protein_atomnames_dictionary, supported_aminoacids, supported_metals
+from PPP.global_variables import protein_atomnames_dictionary, default_supported_aminoacids, supported_metals
 from PPP.program_own_classes import ROTAMERLIB
 
 __author__ = 'jelisa'
@@ -185,8 +185,8 @@ def FixStructureResnames(initial_structure, ligand_chain=False):
     for res in structure.iterResidues():
         resname = res.getResname()
         ligand_structure = None
-        # print ligand_chain == res.getChid(), resname in supported_aminoacids
-        if ligand_chain == res.getChid() and resname in supported_aminoacids:
+
+        if ligand_chain == res.getChid() and resname in default_supported_aminoacids:
             ligand_structure = structure.chain_Z.copy()
         if ligand_structure is not None and ligand_structure.hetero is not None:
             print("INFO: Renaming the ligand to LIG in structure {}".format(initial_structure.getTitle()))

PPP/checks_module.py

@@ -3,7 +3,7 @@
 from prody import Contacts, calcDistance, calcAngle
 
 from PPP.global_processes import FindInitialAndFinalResidues
-from PPP.global_variables import supported_aminoacids, supported_metals, coordination_geometries
+from PPP.global_variables import default_supported_aminoacids, supported_metals, coordination_geometries
 from PPP.program_own_classes import ZMATRIX
 
 __author__ = 'jelisa'
@@ -207,7 +207,7 @@ def CheckStructure(initial_structure, gaps={}, no_gaps={}, charge_terminals=Fals
             residue_atomnames = list(residue.getNames())
             if resname in supported_metals:
                 continue
-            if resname in supported_aminoacids:
+            if resname in default_supported_aminoacids:
                 if charge_terminals:
                     if resnum == initial_residue or resnum in gaps_b:
                         zmatrix = ZMATRIX(resname + 'B')
@@ -438,7 +438,7 @@ def CheckMutation(wt_structure, mutation):
         - valid_resnames_file: the path to the file containing a list with the supported mutations
     """
 
-    if mutation['fin_resname'] not in supported_aminoacids:
+    if mutation['fin_resname'] not in default_supported_aminoacids:
         return False
 
     testing_the_resnum = "resnum {}".format(mutation['resnum'])
@@ -536,7 +536,7 @@ def CheckClashes(mutated_protein, mutation, zmatrix, initial_residue,
             atom2check = mutated_protein.select('index {}'.format(ind))
             atom2check_resname = atom2check.getResnames()[0]
             atom2check_resnum = atom2check.getResnums()[0]
-            if atom2check_resnum == initial_residue and atom2check_resname in supported_aminoacids:
+            if atom2check_resnum == initial_residue and atom2check_resname in default_supported_aminoacids:
                 atom2check_zmatrix = ZMATRIX(atom2check_resname + 'B')
             elif atom2check_resnum == final_residue:
                 atom2check_zmatrix = ZMATRIX(atom2check_resname + 'E')
@@ -583,7 +583,7 @@ def CheckforGaps(structure, max_bond_distance):
             # print residue.getResnum() < previous_residue_number
             if previous_residue_number is not None:
                 # if residue.getResnum() > previous_residue_number + 1:
-                if residue.getResname() in supported_aminoacids:
+                if residue.getResname() in default_supported_aminoacids:
                     if residue.getResname() == 'ACE':
                         try:
                             gaps[chain_id]

PPP/global_processes.py

@@ -1,7 +1,8 @@
+import copy
 import sys
 from argparse import ArgumentParser, RawTextHelpFormatter
 from re import match
-from PPP.global_variables import supported_aminoacids, input_keywords, aminoacids_1letter, aminoacids_3letter
+from PPP.global_variables import default_supported_aminoacids, input_keywords, aminoacids_1letter, aminoacids_3letter
 from PPP import parameters_help
 
 from prody import parsePDB
@@ -79,7 +80,7 @@ def ParseMutations(unprocessed_mutation, structure_filename):
                 final_resname = splitted_mutation[splitted_mutation.index('to') + 1].upper()
         mutation = {'ini_resname': original_resname, "resnum": resnum,
                     "chain": chain, "fin_resname": final_resname}
-        if mutation["fin_resname"] in supported_aminoacids:
+        if mutation["fin_resname"] in default_supported_aminoacids:
             processed_mutations.append(mutation)
             print('a')
         elif mutation["fin_resname"].lower() in input_keywords.keys():
@@ -186,7 +187,7 @@ def FindInitialAndFinalResidues(structure):
     for res in structure.iterResidues():
         resnum = res.getResnum()
         resname = res.getResname()
-        if resname in supported_aminoacids:
+        if resname in default_supported_aminoacids:
             if not first_aa:
                 initial_residue = resnum
                 first_aa = True
@@ -198,6 +199,7 @@ def FindInitialAndFinalResidues(structure):
 
 def PDBwriter(output_file_name, structure, make_unique, residues2remove, no_ter_mkar_for_gaps, no_proteic_ligand=None,
               gaps={}, no_gaps={}, mid_chain_nonstd_residue=[]):
+    supported_aminoacids = copy.copy(default_supported_aminoacids)
     supported_aminoacids.extend(mid_chain_nonstd_residue)
     if '.pdb' not in output_file_name:
         output_file_name += '.pdb'

PPP/global_variables.py

@@ -1,4 +1,4 @@
-supported_aminoacids = ["ALA", "ARG", "ASH", "ASN", "ASP", "CYS", "CYT", "GLH",
+default_supported_aminoacids = ["ALA", "ARG", "ASH", "ASN", "ASP", "CYS", "CYT", "GLH",
                         "GLN", "GLU", "GLY", "HID", "HIE", "HIS", "HIP", "ILE",
                         "LEU", "LYS", "LYN", "MET", "PHE", "PRO", "PTR", "SER", "TRP",
                         "THR", "TYR", "VAL", "ACE", "NMA"]

conda_recipe/meta.yaml

@@ -1,7 +1,7 @@
 # must do conda install -c NostrumBioDiscovery pele_platform 
 package:
   name: pppele
-  version: "1.0.7"
+  version: "1.0.8"
 
 about:
   home: https://github.com/NostrumBioDiscovery/PP