Hi, I've found this (http://code.google.com/p/rdkit/wiki/Generating3DCoordinates) wiki page suggesting how to compute 3D coordinates:
from rdkit import Chem from rdkit.Chem import AllChem m = Chem.MolFromSmiles('c1ccccc1C(=O)O') AllChem.EmbedMolecule(m) # the molecule now has a crude conformation, clean it up: AllChem.UFFOptimizeMolecule(m) On the other hand, "Getting started document" describes this differently: AllChem.EmbedMolecule(m2)AllChem.UFFOptimizeMolecule(m2) In the meantime, someone suggested that I should call: Chem.AddHs(m) Before calculating 3D properties. So what is an ultimate way of doing this? Lets assume I already have rdkit molecule: m = Chem.MolFromSmiles('Cc1ccccc1') or: m = Chem.MolFromMolFile('data/input.mol') what should I do with 'm' to compute 3D coordinates? Also, once we have MMFF implemented in rdkit, is there any benefit of using UFF (apart from maybe backwards compatibility, as this is a new feature)? Is UFF significantly faster then MMFF? Kind regards, Michał Nowotka
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss