Thank you! That answers my question. I agree that an OBAtom::GetAtomID() would
be a useful addition. -JB
________________________________________
From: Stefano Forli <fo...@scripps.edu>
Sent: Friday, February 24, 2017 4:22:42 PM
To: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] determine in code the pdb atom name of an OBAtom
Hi John,
you didn't specify which language you're using, but in Python you can get it
with
something like this:
=================
import pybel
ob = pybel.ob
import sys
mol = pybel.readfile('mol2', sys.argv[1]).next()
obmol = mol.OBMol
for res in ob.OBResidueIter(obmol):
for atom in ob.OBResidueAtomIter(res):
atName = res.GetAtomID(atom)
print "Atom name:", atName # i.e., CA
=================
Every once in a while this question pops in the mailing list. Does any of the
main
developers think that there would be some use for a dedicated function at the
atom
level?Maybe mapping the same residue function to the OBAtom object?, something
like:
OBAtom::GetAtomID()
S
On 02/24/2017 02:14 PM, John Baxter wrote:
> Hello, openbabel-discuss!
>
> For a project I need to be able to tell which atom of a protein residue is
> the carbon alpha atom (" CA " in a PDB file). I can't figure out how to query
> an OBAtom for this data; is there a way to do this?
>
> Thank you very much.
> -John Baxter
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--
Stefano Forli, PhD
Assistant Professor of ISCB
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112A
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: fo...@scripps.edu
http://www.scripps.edu/~forli/
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