On 13/07/2012 14:46, scott_m wrote:
> Thanks for the reply but that doesn't seem to be working for me (code below).
> If I just want to get a rough set of coordinates, what should I do? I see
> that gen3d (see link below) does a weighted rotor search as part of the
> process of making 3d coords but I wanted to just get the 3d coords and
> specify my own weighted rotor search conditions.
But you have to start with something. gen3D is quite quick. See my reply
to James Jack on how it is used in C++. The python would be similar.
Chris
>
> mol = openbabel.OBMol()
> cv = openbabel.OBConversion()
> cv.SetInAndOutFormats('smi', outfile_type)
> cv.ReadString(mol, smiles_string)
> mol.AddHydrogens()
> ff = openbabel.OBForceField.FindForceField("MMFF94")
> ff.GetCoordinates(mol)
>
> gen3d source code:
> http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/trunk/src/ops/gen3d.cpp?revision=4307&view=markup
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
