Jim,
I don't know which language you are using, but in Python I do it by iterating
the atoms in
a given residue, then using them as argument for the GetAtomID() method of the
residue.
=================
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
=================
Not exactly the most straightforward way, but I couldn't find any better, and
it works for me.
Hope this helps,
S
On 07/17/2014 02:40 PM, Jim Parker wrote:
> Hello,
> I would like to read and modify the atom names from a .mol2 file.
>
> I have been working through the tutorials and documentation for the API, and
> I can read in the file, and write a file, and I see that the names are parsed
> correctly in
> the output file, so I'm confident that the OBMol object has the information,
> but I'm
> confused as to where I can find it.
>
> I assumed it would be in each OBAtom object, but the only string value is
> .GetTtitle() and
> .SetTitle() but those are blank.
> I've tried Google and searches on this mailing list.
> There is an old post
> http://sourceforge.net/p/openbabel/mailman/openbabel-devel/thread/caokanmena-r1f+n_ggvn00lj_cegtvydmxzcxaado1d+spg...@mail.gmail.com/
>
> for .cif formats involving OBPairData, but there is no "_atom_site_label"
> found for my
> molecule.
>
> Just trying to find out where that information is stored.
> Any help would be appreciated.
>
> Cheers,
> --Jim
>
--
Stefano Forli, PhD
Staff Scientist
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: (858) 784-2055
fax: (858) 784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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