Hi, this was the result of a bug in the way the conformation was copied from the first molecule to the new one. I just checked in a fix (https://github.com/rdkit/rdkit/issues/584)
Best, -greg On Wed, Aug 26, 2015 at 11:54 AM, Jose Manuel < [email protected]> wrote: > #/usr/bin/env python > > from rdkit import Chem, rdBase > > # define test molecule > molblock="""TEST_INPUT > RDKit 2D > > 5 5 0 0 0 0 0 0 0 0999 V2000 > -0.1105 -0.5357 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > -0.7779 -1.0207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.5230 -1.8052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.3020 -1.8052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.5569 -1.0207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 > 2 3 1 0 > 3 4 1 0 > 4 5 1 0 > 1 5 1 0 > M END > > $$ > """ > > print rdBase.rdkitVersion > > print molblock # RDKIT 2D > > # renumber test molecule by canonical atom rank > mol = Chem.MolFromMolBlock(molblock) > order_c = list(Chem.CanonicalRankAtoms(mol, breakTies=True, > includeChirality=True)) > mol_c = Chem.RenumberAtoms(mol,order_c) > mol_c.SetProp("_Name", "TEST_OUTPUT") > > # check result > print Chem.MolToMolBlock(mol_c) # RDKIT 3D! >
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