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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss