Merge pull request #179 from shreesowndarya/shree_changes

Update master
jvalegre · Oct 25, 2023 · 1c47f34 · 1c47f34
2 parents fc59088 + b158c24
commit 1c47f34
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Showing 2 changed files with 16 additions and 4 deletions.
diff --git a/aqme/qprep.py b/aqme/qprep.py
@@ -75,6 +75,7 @@
 )
 from aqme.csearch.crest import xyzall_2_xyz
 from pathlib import Path
+from rdkit import Chem
 
 
 class qprep:
@@ -186,6 +187,7 @@ def __init__(self, create_dat=True, **kwargs):
                     sdf_files.append(f"{file.split('.pdb')[0]}.sdf")
 
                 else:
+
                     sdf_files.append(file)
 
                 for sdf_file in sdf_files:
@@ -445,11 +447,15 @@ def qprep_coords(self, file, mol, file_format):
                 try:
                     charge = int(mol.GetProp("Real charge"))
                 except KeyError:
-                    pass
+                    charge = Chem.GetFormalCharge(mol)
                 try:
                     mult = int(mol.GetProp("Mult"))
                 except KeyError:
-                    pass
+                    NumRadicalElectrons = 0
+                    for Atom in mol.GetAtoms():
+                        NumRadicalElectrons += Atom.GetNumRadicalElectrons()
+                    TotalElectronicSpin = NumRadicalElectrons / 2
+                    mult = int((2 * TotalElectronicSpin) + 1)
 
             elif file_format in ["log", "out"]:
                 # detect QM program and number of atoms

diff --git a/tests/test_qprep.py b/tests/test_qprep.py
@@ -191,9 +191,15 @@ def test_QPREP_analysis(test_type, init_folder, target_folder, restore_folder):
 
                 assert outlines[8].strip() == line_8
                 assert outlines[10].strip() == line_10
-            
+
             assert outlines[2].strip() == line_2
-            assert outlines[6].strip() == line_6
+            if init_folder == "pdb_files":
+                line_6 = "-2 1"
+                assert outlines[6].strip() == line_6
+            else:
+                assert outlines[6].strip() == line_6
+
+
 
     elif test_type == "charge_mult":
         if init_folder == "json_files":