[Chimera-users] python code to loop over molecules

Eric Pettersen pett at cgl.ucsf.edu
Mon May 3 09:57:46 PDT 2021

Hi Julian,
	It would seem that the first thing to do would be to get a list of the poses in order.  This gets a list of the currently open models:

	import chimera
	models = chimera.openModels.list()

To extract the poses in order, the crucial information to know is that each model has an id and subid attribute, so each pose will have and id of 1.  To get a list of them in order then is:

	poses = sorted([m for m in models if m.id <http://m.id/> == 1], key=lambda m: m.subid)

Then the number of poses is obviously len(poses).  For most of the additional things you mentioned, the easiest thing to do is run the equivalent command, e.g.:

	from chimera import runCommand as run
	for pose in poses:
		run("color red %s" % pose)

This may be all you need.  But the run() call doesn't return any values, so for instance if you need to do different things in the Python code depending on how many hydrogen bonds a pose forms, then you would have to call the underlying Python routine, which does return values.  That particular call is FindHBond.findHBonds(models).  I can expand on that if you need that kind of info.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On May 3, 2021, at 5:10 AM, Julian Tirado-Rives <julian.tirado-rives at yale.edu> wrote:
> Dear Chimera (and ChimeraX) team:
>    I need to find some python example or code snippet capable of
> looping over all the molecules in a particular model and do some actions
> separately in each one.
>     In our research we use several different docking programs and other
> ways of generating poses of protein-ligand complexes, and using several
> different programs to analyze them gets quite complicated. Instead,
> we've found that the easiest way is to generate from each code, or using
> conversion utilities such as babel, a pdb file of the host and a sdf or
> mol2 file containing all the ligand poses and read them into chimera.
> An excellent program, by the way. We use it all the time.
>    I would love to automate the process even further by doing all the
> coloring, rendering, Hydrogen Bond and contact analysis, etc. in Python
> rather than manually. I have been trying to do this, but have not found a way to do the following:
> If we have, for instance, the host in model #0, and the ligand poses in model #1 (#1.1, #1.2, ..., #1.N):
> - Get from chimera the number of molecules in model #1 (e.g what is N)
> - loop from the first #1.1 to the last #1.N molecule
> - do some cations there (e.g select, color, find HB's, etc)
>   I think this should be a problem other people have encountered and
> solved  before, but I have not been able to find an example in your
> depository, the mailing lists, or even the book ... I would appreciate
> your input.
> Thanks for your help, and for an excellent program!
>                                             - Julian -
> -- 
>  -----------------------------------------------------------------
> | Julian Tirado-Rives      |                                      |
> | Department of Chemistry  | Phone: (203)432-3356                 |
> | Yale University          | Fax:   (203)432-6144                 |
> | P. O. Box 208107         | email:  Julian.Tirado-Rives at yale.edu |
> | New Haven, CT 06520-8107 |                                      |
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