Two suggestions:
If you know that residues will always contain one and only one of a
given atom type, then you can just use "count_atoms"
For example:
number=cmd.count_atoms("name ca")
Alternatively, you can have PyMOL create a dictionary of all residues:
import pymol
pymol.stored.dict = {}
iterate (all),stored.dict[(segi,chain,resn,resi)]=1
number= len(pymol.stored.dict)
Your cmd.get_model() approach is fine too. Note that you don't need to
define a selection before using it...
number= len(cmd.get_model("name ca").atom)
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Cameron Mura
> Sent: Wednesday, June 25, 2003 3:39 PM
> To: PyMOL-users@lists.sourceforge.net
> Subject: [PyMOL] extracting number of residues
>
> Hello,
> I'm wondering what's the easiest way to extract the number of residues
> from a PyMOL molecular object?? I need to be able to do this in an
> automated way for a python script I'm writing. I guess a roundabout
way
> would be to define a selection (say "X_ca") from an object ("X"), and
> then use something like this to extract the number of atoms in the
X_ca
> object:
>
> calphas = cmd.get_model("X_ca");
> num_residues = length(calphas.atom);
>
> But, this seems unneccesary? I thought I could load in the chempy
> "models" module and then use its "get_residues()" function, but the
> command fails as follows:
>
> ###
> models.get_residues("all")
> PyMOL>models.get_residues("all")
> Traceback (most recent call last):
> File "modules/pymol/parser.py", line 251, in parse
> exec(com2[nest]+"\n",pymol_names,pymol_names)
> File "<string>", line 1, in ?
> AttributeError: 'module' object has no attribute 'get_residues'
> ###
>
> So, I'm wondering what I'm missing...is there an easy way to do this?
>
> Thanks anyone,
> Cameron
>
>
>
>
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