Hi Michal, JP gave a good answer already, I'll just add a few things.
First: thanks for pointing out the missing call to AddHs in the documentation. I've fixed that. On Sat, Apr 5, 2014 at 1:35 PM, Michał Nowotka <mmm...@gmail.com> wrote: > 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) > > Those are the same, right? 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? > > JP's answer was good. If you want a single 3D conformation you should AddHs, Embed, and Optimize. If you don't want the Hs in the final molecule, you can RemoveHs after the optimization. > 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? > > MMFF tends to generate better geometries (for some definition of better), UFF tends to be faster and will work for almost any molecule. There are many molecules where MMFF parameters are missing and you will have to use UFF. -greg
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
