[Rdkit-discuss] Using RDKit in PyCharm and Anaconda on Windows

2017-05-30 Thread West, Richard
We're having trouble getting RDKit to work in a PyCharm project using an Anaconda interpreter (Python 2.7), on Windows 8.1. Has anyone had success with this and can guide us? The trouble is we get an ImportError: DLL load failed: The specified module could not be found. when trying to import

[Rdkit-discuss] ReplaceSubstructs changes chirality

2017-05-30 Thread Jan Halborg Jensen
The code below protonates select nitrogen atoms using ReplaceSubstructs but in some cases the chirality is changed, despite the fact that I used MolToSmiles(xx,isomericSmiles=True) Any help appreciated Output C[C@]1(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)N=C(N)OCC1(F)F [NX2;H0] [NH+]

[Rdkit-discuss] FW: ReplaceSubstructs changes chirality

2017-05-30 Thread Jan Halborg Jensen
Also newmol = AllChem.ReplaceSubstructs(m, patt1, patt2, useChirality=True) doesn't help From: Jan Halborg Jensen Sent: Saturday, May 27, 2017 3:11 PM To: rdkit-discuss@lists.sourceforge.net Subject: ReplaceSubstructs changes chirality The code below

[Rdkit-discuss] RemoveHs and [H][*:1] mol

2017-05-30 Thread Pavel Polishchuk
Hello, probably this is a message mainly to developers. I discovered some strange behavior of removeHs function applied for '[H][*:1]' molecule. If I create that mol from smiles, RemoveHs does not remove a single H from the mol: mmm = Chem.MolFromSmiles('[H][*:1]')