Hi Alexandre,
assuming that I now understand what you want to do, you could extract/process
each
separate ligand generating individuals OBMol objects, then you can combine them
into a
single molecule, i.e. (Python):
full = openbabel.OBMol()
for frag in fragments:
full += frag
full.ConnectTheDots() # perceive existing bonds by distance
See here [1] for references.
Best,
S
[1] http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml
On 11/21/2015 08:45 AM, Alexandre Fassio wrote:
> Hi Stefano,
>
> Thanks for the reply.
>
> However, my problem is a bit different. It's more related to how to convert
> a PDB to Mol2 considering the covalent bonds between the ligands and/or how
> to get a SDF that represents a set of ligands covalently bonded.
>
> Anyway, thank you.
>
> best wishes.
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659064.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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--
Stefano Forli, PhD
Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: [email protected]
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