There is also declaration of the Python-visible attributes of Atom/Residue/etc. in the source distribution in libs/_chimera/pyinterface. The more convenient way nowadays to get pyinterface is by browsing our SVN repository, i.e. from:

The other thing you might want to know that seems germane to your specific query is that the PDB headers are stored in the pdbHeaders dictionary in Molecule (key: header type [e.g. REMARK], value: list of strings).

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

On Apr 2, 2009, at 1:23 PM, Matthew Dougherty wrote:

I was writing some python code involving PDB data.

looking at pre-existing code involving PDB:

m = om.open(pdb_path, 'PDB')[0]
rlist = m.residues

for r in rlist:

lc = 'monomer residue %d' % (r.id.position)
    if r.isHelix:
        lc += '    HELIX'
    elif r.isSheet:
        lc += '    SHEET'

I was trying to track down the data structure for r/rlist, to see if
there are any other parameters I could use besides isHelix, isSheet,
and id.position.
where would that be located in the Chimera package?

thanks, Matt
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