Dear All,
I'm generating conformation of a molecule:
C1C2C3OC3C1C13OC21C1CC3C2OC21
This molecule has many chiral centers and 10 possible isomers.
EmbedMolecule command of RDKit_2015_03_1 can generate every isomer but
RDKit_2016_09_3 fails in 9 of 10.
For example,
RDKit_2015_03_1
---------------------------------
>>> mol=Chem.MolFromSmiles('C1[C@H]2[C@@H]3O[C@@H]3[C@@H]1[C@@]13O[C@@]21[C@@H]1C[C@H]3[C@@H]2O[C@@H]21')
>>> Chem.FindMolChiralCenters( copy(m), includeUnassigned=True )
[(1, 'S'), (2, 'S'), (4, 'R'), (5, 'R'), (6, 'R'), (8, 'R'), (9, 'R'), (11,
'S'), (12, 'S'), (14, 'R')]
>>> m=Chem.AddHs(mol)
>>> AllChem.EmbedMolecule( m, randomSeed = 256, maxAttempts = 1, clearConfs =
>>> False )
0
---------------------------------
RDKit_2016_09_3
---------------------------------
>>> mol=Chem.MolFromSmiles('C1[C@H]2[C@@H]3O[C@@H]3[C@@H]1[C@@]13O[C@@]21[C@@H]1C[C@H]3[C@@H]2O[C@@H]21')
>>> m=Chem.AddHs(mol)
>>> Chem.FindMolChiralCenters( copy(m), includeUnassigned=True )
[(1, 'S'), (2, 'S'), (4, 'R'), (5, 'R'), (6, 'R'), (8, 'R'), (9, 'R'), (11,
'S'), (12, 'S'), (14, 'R')]
>>> AllChem.EmbedMolecule( m, randomSeed = 256, maxAttempts = 100, clearConfs =
>>> False )
-1
---------------------------------
Two chiral centers in this molecule are stereo-dependent (6th and 8th atoms).
Conformation of molecule without assignment for these atoms can be generated,
but the chiralities remain unassigned.
RDKit_2016_09_3
---------------------------------
>>> mol=Chem.MolFromSmiles('C1[C@H]2[C@@H]3O[C@@H]3[C@@H]1C13OC21[C@@H]1C[C@H]3[C@@H]2O[C@@H]21')
>>> Chem.FindMolChiralCenters( copy(m), includeUnassigned=True )
[(1, 'S'), (2, 'S'), (4, 'R'), (5, 'R'), (6, '?'), (8, '?'), (9, 'R'), (11,
'S'), (12, 'S'), (14, 'R')]
>>> m=Chem.AddHs(mol)
>>> AllChem.EmbedMolecule( m, randomSeed = 256, maxAttempts = 100, clearConfs =
>>> False )
0
>>> Chem.AssignAtomChiralTagsFromStructure(m)
>>> Chem.FindMolChiralCenters( copy(m), includeUnassigned=True )
[(1, 'S'), (2, 'S'), (4, 'R'), (5, 'R'), (6, '?'), (8, '?'), (9, 'S'), (11,
'R'), (12, 'S'), (14, 'R')]
>>> opt = AllChem.UFFOptimizeMolecule( m, maxIters = 10000, confId=0)
>>> ff = AllChem.UFFGetMoleculeForceField( m, confId = 0 )
>>> ff.Minimize()
0
>>> Chem.AssignAtomChiralTagsFromStructure(m)
>>> Chem.FindMolChiralCenters( copy(m), includeUnassigned=True )
[(1, 'S'), (2, 'S'), (4, 'R'), (5, 'R'), (6, '?'), (8, '?'), (9, 'R'), (11,
'S'), (12, 'S'), (14, 'R')]
---------------------------------
How can I assign chiralities of these atoms in RDKit_2016_09_3?
Regards,
Rintarou
------------------------------------------------------------
Suzuki, Rintarou
National Agriculture and Food Research Organization
Tsukuba, Japan
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