Dear Greg, I noticed the following peculiarities - not sure if it's a bug or a feature. 1) When assembling a fragment like this CN(=O)=O (a nitro group), mol->addAtom(new Atom(7)); mol->addAtom(new Atom(8)); mol->addAtom(new Atom(8)); mol->addAtom(new Atom(6)); mol->addBond(0,1,Bond::DOUBLE); mol->addBond(0,2,Bond::DOUBLE); mol->addBond(0,3,Bond::SINGLE);
it automatically gets converted to C[N+](=O)[O-] Not exactly what I have entered, though equivalent? 2) If I designate a bond as aromatic and it's not in a ring, the Sanitization procedure throws an exception - not a desired behavior for me, as I would like to have an opportunity to clear up AROMATIC flag from non-ring bonds (if it gets there by mistake), but I cannot perceive ring bonds before sanitization. So it's somewhat like chicken-and-eggs problem. [02:42:01] Kekulization somehow did not convert bond 2 terminate called after throwing an instance of 'RDKit::MolSanitizeException' what(): N5RDKit20MolSanitizeExceptionE Aborted Other than that I'm happy to inform you that I have added the support for RDKIT to OSRA and the upcoming release will give users a choice of whether to compile with OpenBabel or RDKit as a molecular back-end. Best regards, Igor -- Igor Filippov [Contr] <[email protected]>
