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

[Elaine Meng]

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
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html

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.