[Chimera-users] [chimera-dev] list of atoms attributes

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 1 12:18:41 PDT 2008

A delayed addendum...
Some attributes are not included in the Programmer's Guide lists or  
what you get from help() in IDLE:

atoms:  areaSAS, areaSES, bfactor, charge, occupancy, serialNumber

residues:  areaSAS, areaSES, isHet (the latter is in help but not the  
current Prog. Guide list)

molecule models:  display (not in Prog. Guide list for Molecule  
because inherited from Model)

Some attributes do not come from the C++ layer, and some do not exist  
until you do something particular in Chimera (areaSAS and areaSES are  
assigned when molecular surface is generated; charge is assigned when  
Add Charge is used; etc.).  Also, new attributes you have created  
with Define Attribute are not listed.  Generally the Render/Select by  
Attribute tool will list these atom and residue attributes, however.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

Fri Feb 22 13:07:42 PST 2008 Eric Pettersen wrote:
> dir(a) will list the attributes of 'a'.  help(a) will produce
> documentation for the attributes of 'a' that come from the C++ layer
> (but not ones that were added in the Python layer).  'a' could be a
> class rather than an instance.  For example, help(chimera.Atom) lists
> the methods/attributes of Atom and provides some info about them.
> 	We do what we can to keep the programmer's guide up to date, but for
> attributes (since they get added/changed pretty frequently) it is
> better to query with help()/dir() than to fall back on the relatively
> static programmer's guide documentation.

On Feb 22, 2008, at 1:36 PM, Tom Goddard wrote:
> The Chimera programming reference manual is automatically generated  
> from
> the code and says  little about what the available methods and
> attributes do.  But it does at least name them.   Here are the web  
> pages
> for Atom, Residue and Molecule:
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/ 
> generated/_chimera/__init__/Atom.html
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/ 
> generated/_chimera/__init__/Residue.html
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/ 
> generated/_chimera/__init__/Molecule.html
> I found this looking in the programmer's reference guide, under module
> _chimera, and scroll to the end of that long page for links to the
> different kinds of objects.

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