v1.3.2, more reliable conf gen for large mols with random coords

.gitignore

@@ -3,4 +3,4 @@
 /build/
 /db_access/
 /dist/
-/.ipynb_checkpoints/
+/.ipynb_checkpoints/

autoqchem/molecule.py

@@ -23,7 +23,7 @@
 class molecule(object):
     """Wrapper class for molecule"""
 
-    def __init__(self, smiles, num_conf=5, engine='rdkit', rdkit_ff='MMFF94', ob_gen3D_option='best') -> None:
+    def __init__(self, smiles, num_conf=5, engine='rdkit', rdkit_ff='MMFF94', ob_gen3D_option='best', large_mol=False) -> None:
         """Initialize the molecule with a conformational ensemble
 
         :arg smiles: SMILES string
@@ -43,8 +43,8 @@ def __init__(self, smiles, num_conf=5, engine='rdkit', rdkit_ff='MMFF94', ob_gen
             self.elements, \
             self.conformer_coordinates, \
             self.connectivity_matrix, \
-            self.charges = generate_conformations_from_rdkit(smiles=smiles, num_conf=num_conf,
-                                                             rdkit_ff=rdkit_ff)
+            self.charges = generate_conformations_from_rdkit(smiles=smiles, num_conf=num_conf, rdkit_ff=rdkit_ff, large_mol=large_mol)
+
         elif engine == 'openbabel':
             self.elements, \
             self.conformer_coordinates, \

autoqchem/rdkit_utils.py

@@ -106,7 +106,7 @@ def add_conformers_to_rdmol(mol: Chem.Mol, conformer_coordinates: np.ndarray) ->
         mol.AddConformer(conformer, assignId=True)
 
 
-def generate_conformations_from_rdkit(smiles, num_conf, rdkit_ff='MMFF94') -> tuple:
+def generate_conformations_from_rdkit(smiles, num_conf, rdkit_ff, large_mol) -> tuple:
     """Generate conformational ensemble using rdkit
 
     :param smiles: SMILES string
@@ -131,6 +131,8 @@ def generate_conformations_from_rdkit(smiles, num_conf, rdkit_ff='MMFF94') -> tu
     params.ETversion = 2
     params.pruneRmsThresh = 0.35
     params.numThreads = n_threads
+    if large_mol:
+        params.useRandomCoords = True
 
     # embed and optimized conformers
     AllChem.EmbedMultipleConfs(rdmol, num_conf, params)

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='auto-qchem',
-    version='1.3.1',
+    version='1.3.2',
     packages=['autoqchem'],
     data_files=['config.yml'],
     url='https://github.com/doyle-lab-ucla/auto-qchem',