On Dec 9, 2016, at 9:50 PM, Brian Kelley wrote: > >>> from rdkit import Chem > >>> m = Chem.MolFromSmiles("F/C=C/F") > >>> for bond in m.GetBonds(): > ... print bond.GetStereo() > ... > STEREONONE > STEREOE > STEREONONE > > However, setting bond stereo doesn't appear to be exposed.
I thought I knew a way to change it, via GetBondDir()/SetBondDir() on the directional bonds. It doesn't seem to work. First, get the existing bond directions: >>> from rdkit import Chem >>> mol = Chem.MolFromSmiles("F/C=C/F") >>> for bond in mol.GetBonds(): ... print(bond.GetBondDir()) ... ENDUPRIGHT NONE ENDUPRIGHT I'll change the first "/" to a "\" (That's "\\" when escaped for a normal Python string.) >>> mol.GetBondWithIdx(0) <rdkit.Chem.rdchem.Bond object at 0x10fe26600> >>> mol.GetBondWithIdx(0).GetBondDir() rdkit.Chem.rdchem.BondDir.ENDUPRIGHT >>> mol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.ENDDOWNRIGHT) If I generate the SMILES I see the old "F/C=C/F" instead of the new direction. I need to clear internal computed properties when I make structure edits: >>> Chem.MolToSmiles(mol, isomericSmiles=True) 'F/C=C/F' >>> mol.ClearComputedProps() >>> Chem.MolToSmiles(mol, isomericSmiles=True) 'F/C=C\\F' I'll set the directions to "NONE" and clear computed properties. The SMILES is correct: >>> mol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.NONE) >>> mol.GetBondWithIdx(2).SetBondDir(Chem.BondDir.NONE) >>> mol.ClearComputedProps() >>> Chem.MolToSmiles(mol, isomericSmiles=True) 'FC=CF' although the stereo setting is unchanged: >>> for bond in mol.GetBonds(): ... print(bond.GetStereo()) ... STEREONONE STEREOE STEREONONE I expected it to give me all STEREONONEs, as if it were the same as the following: >>> mol2 = Chem.MolFromSmiles("FC=CF") >>> for bond in mol2.GetBonds(): ... print(bond.GetStereo()) ... STEREONONE STEREONONE STEREONONE Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/xeonphi _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss