Added stereochemistry removal

Author: OliverBScott

scaffoldgraph/core/graph.py

@@ -11,7 +11,7 @@
 from loguru import logger
 from networkx import DiGraph
 from rdkit import RDLogger
-from rdkit.Chem import rdMolHash, MolToSmiles
+from rdkit.Chem import rdMolHash, MolToSmiles, rdmolops
 from rdkit.Chem.rdMolDescriptors import CalcNumRings
 
 from scaffoldgraph.io import *
@@ -66,6 +66,7 @@ def _construct(self, molecules, ring_cutoff=10, progress=False, annotate=True):
                 name = molecule.GetProp('_Name')
                 logger.warning(f'Molecule {name} filtered (> {ring_cutoff} rings)')
                 continue
+            rdmolops.RemoveStereochemistry(molecule)
             scaffold = Scaffold(get_murcko_scaffold(molecule))
             if scaffold:  # Checks that a scaffold has at least 1 atom
                 if annotate:

scaffoldgraph/tree.py

@@ -3,6 +3,7 @@
 """
 
 from rdkit import RDLogger
+from rdkit.Chem import rdmolops
 
 from .core import ScaffoldGraph, Scaffold, MurckoRingFragmenter
 from .core.fragment import get_murcko_scaffold
@@ -64,6 +65,7 @@ def tree_frags_from_mol(mol, prioritization_rules=None):
 
     rdlogger.setLevel(4)
     scaffold = Scaffold(get_murcko_scaffold(mol))
+    rdmolops.RemoveStereochemistry(scaffold.mol)
     parents = [scaffold]
     fragmenter = MurckoRingFragmenter(use_scheme_4=True)
     rules = prioritization_rules if prioritization_rules else original_ruleset