[Chimera-users] PDB data

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 2 14:29:00 PDT 2009

Hi Matt,
	You can find out about the (C++) attributes/methods of a class by  
using help() in the IDLE interpreter, e.g.:


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:

/trunk/libs/_chimera/pyinterface – Chimera

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  


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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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> Chimera-users at cgl.ucsf.edu
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