Yes it recognizes it, when I check the binary in my unzip directory,
however, it does not.
19:21:35 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ obabel -H pdb
Protein Data Bank format
Read Options e.g. -as
s Output single bonds only
b Disable bonding entirely
c Ignore CONECT records
Specification at: http://www.wwpdb.org/docs.html
19:21:39 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ ./obabel -H pdb
Format type: was not recognized
On Tue, Sep 6, 2011 at 7:07 PM, Noel O'Boyle <[email protected]> wrote:
> Does "obabel -H pdb" show the PDB format?
>
> On 6 September 2011 07:16, Daniel Sindhikara <[email protected]> wrote:
> > Hello,
> > After a long hiatus I got back on this project. After following the
> > instructions I successfully installed openbabel/pybel.
> > However, when I tried testing the program I got a funny error, "pdb is
> not a
> > recognised OpenBabel format".
> >
> > Enthought Python Distribution -- www.enthought.com
> > Version: 7.1-1 (64-bit)
> >
> > Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul 3 2011, 15:56:02)
> > [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> > Type "packages", "demo" or "enthought" for more information.
> >>>> import pybel as pb
> >>>> testmolecule = pb.readfile("pdb","mai.pdb").next()
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > File
> >
> "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
> > line 90, in readfile
> > raise ValueError("%s is not a recognised OpenBabel format" % format)
> > ValueError: pdb is not a recognised OpenBabel format
> >
> >
> > Further, checking the formats variable:
> >>>> pb.informats
> > {}
> >
> > It was empty.
> > Any clues into why this would happen?
> >
> > Thanks in advance!
> > -Dan
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: [email protected]
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> >
> >
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>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: [email protected]
Website: http://sites.google.com/site/dansindhikara/
--
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