Merge pull request #169 from martimunicoy/mae_compatibility

Mae compatibility

docs/releasehistory.rst

@@ -11,12 +11,17 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 1.4.2 - Compatibility fixes for latest RDKit and Schrodinger versions
 ---------------------------------------------------------------------
 
-This is a micro release of peleffy that fixes several bugs related with latest versions of RDKit and Schrodinger. Affected modules are rotamer libraries, the runner and parser of the ffld server, and the alchemistry package.
+This is a micro release of peleffy that fixes several bugs related with latest versions of RDKit and Schrodinger. Affected modules are rotamer libraries, the runner and parser of the ffld server, and the alchemistry package. It also adds some minor improvements to log handlers.
+
+New features
+""""""""""""
+- `PR #166 <https://github.com/martimunicoy/peleffy/pull/166>`_: New options for log handlers.
 
 Bugfixes
 """"""""
 - `PR #167 <https://github.com/martimunicoy/peleffy/pull/167>`_: Bug fixes for rotamer libraries and affected tests
 - `PR #168 <https://github.com/martimunicoy/peleffy/pull/168>`_: Compatibility changes for the ffld server shipped with latest Schrodinger version
+- `PR #169 <https://github.com/martimunicoy/peleffy/pull/169>`_: Support new RDKit versions.
 
 
 1.4.1 - Bug fixes for heteromolecules extraction

peleffy/data/tests/alchemical_structure.pdb

@@ -34,10 +34,10 @@ CONECT    3   12   13   14
 CONECT    4   15   16   17
 CONECT    5    6   18   19
 CONECT    6    7    7    8
-CONECT   20   21   25
+CONECT   20   21   21   25
 CONECT   21   22   26
-CONECT   22   23   27
+CONECT   22   23   23   27
 CONECT   23   24   28
-CONECT   24   25   29
+CONECT   24   25   25   29
 CONECT   25   30
 END

peleffy/utils/toolkits.py

@@ -957,6 +957,10 @@ def alchemical_combination(self, mol1, mol2, atom_mapping,
         for atom in mol_combo.GetAtoms():
             atom.SetIsAromatic(False)
 
+        # Sanitize it
+        Chem.SanitizeMol(mol_combo,
+                         Chem.SANITIZE_ALL ^ Chem.SANITIZE_KEKULIZE ^ Chem.SANITIZE_SETAROMATICITY)
+
         return mol_combo
 
 

peleffy/utils/utils.py

@@ -314,7 +314,7 @@ def parse_charges_from_mae(path, parameters):
     import re
 
     # Read external file containing the partial charges information
-    params_info, params_list = ([] for i in range(2))
+    params_info, params_list = ([], [])
     copy = False
     with open(path, 'r') as file:
         for line in file.readlines():
@@ -333,15 +333,21 @@ def parse_charges_from_mae(path, parameters):
         params_list = [l.replace('"', '').split() for l in params_list[1:-1]]
 
     # Get the index of the atom name and charge from the parameter's list
-    idx_charges, idx_atom_name = (None for i in range(2))
+    idx_charges, idx_atom_name = (None, None)
     for idx, line in enumerate(params_info):
+        # Get PDB atom name
         if 's_m_pdb_atom_name' in line:
             idx_atom_name = idx
+
+        # Get precomputed charges
         if 'r_m_charge1' in line:
             idx_charges = idx
-    if idx_charges is None or idx_atom_name is None:
-        raise ValueError(
-            " {} does not contain charges information. ".format(path))
+
+    if idx_charges is None:
+        raise ValueError(f"{path} does not contain charges information")
+
+    if idx_atom_name is None:
+        raise ValueError(f"{path} does not contain PDB atom names information")
 
     # Creates a charges by atom name dictionary
     d = {}