Hi Michal,
Well, if you have your 3D coordinates as a PDB file, you can read them in
with the new PDB parser and assign the bond orders based on a template
(generated from the SMILES of your molecule):
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
I don't know if this is what you were looking for.
Best,
Sereina
2013/11/4 Michal Krompiec <[email protected]>
> Hello,
> Is it possible to construct a Mol (or EditableMol) object out of a
> list of 3D coordinates? I am trying to write a bridge between cclib
> and RDKit, and I need a function to convert 3D geometries to SDF.
> Thanks,
> Michal
>
>
> ------------------------------------------------------------------------------
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
