Hello Greg,
and hello to all other developers.
Thanks for this nice package that i enjoy and i love a lot!!! So.. i’ve noticed
maybe a bug in the stereocenter preservation when more conformer are generated
with “EmbedMultipleConfs”
Here my example with a simple steroid alpha cortolone.
Is it normal? or there is something wrong?
Best regards
GMR
from rdkit import Chem
from rdkit.Chem import AllChem
m =
Chem.MolFromSmiles("C1C[C@H](C[C@@H]2[C@]1([C@@H]1[C@@H](CC2)[C@H]2[C@](CC1=O)([C@](CC2)([C@@H](O)CO)O)C)C)O")
mchirality = Chem.FindMolChiralCenters(m)
AllChem.EmbedMultipleConfs(m, 300)
example = Chem.SDWriter("Example.sdf")
for i in range(m.GetNumConformers()):
Chem.AssignAtomChiralTagsFromStructure(m, confId=i)
AllChem.UFFOptimizeMolecule(m,confId=i)
example.write(m, confId=i)
example.flush()
suppl = Chem.SDMolSupplier("Example.sdf")
for molid in range(len(suppl)):
confchirality = Chem.FindMolChiralCenters(suppl[molid])
problems = False
for i in range(len(confchirality)):
if mchirality[i] == confchirality[i]:
continue
else:
problems = True
break
if problems == True:
print "Warning Different Chirality in Conformer %d" % molid
print mchirality
print confchirality
print "-"*100
else:
continue
Warning Different Chirality in Conformer 25
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 44
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 67
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 87
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 95
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 100
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'S'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 101
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 102
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'S'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 108
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 114
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 144
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 149
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 166
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 170
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 174
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 196
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 214
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 240
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 251
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 252
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 260
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 286
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15,
'R'), (18, 'S')]
----------------------------------------------------------------------------------------------------
Warning Different Chirality in Conformer 297
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'R'), (18, 'S')]
[(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15,
'S'), (18, 'S')]
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles("C1C[C@H](C[C@@H]2[C@]1([C@@H]1[C@@H](CC2)[C@H]2[C@](CC1=O)([C@](CC2)([C@@H](O)CO)O)C)C)O")
mchirality = Chem.FindMolChiralCenters(m)
AllChem.EmbedMultipleConfs(m, 300)
example = Chem.SDWriter("Example.sdf")
for i in range(m.GetNumConformers()):
Chem.AssignAtomChiralTagsFromStructure(m, confId=i)
AllChem.UFFOptimizeMolecule(m,confId=i)
example.write(m, confId=i)
example.flush()
suppl = Chem.SDMolSupplier("Example.sdf")
for molid in range(len(suppl)):
confchirality = Chem.FindMolChiralCenters(suppl[molid])
problems = False
for i in range(len(confchirality)):
if mchirality[i] == confchirality[i]:
continue
else:
problems = True
break
if problems == True:
print "Warning Different Chirality in Conformer %d" % molid
print mchirality
print confchirality
print "-"*100
else:
continue
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