Re: [PyMOL] Performing backend calculations within PyMOL

[Thomas H. <tho...@sc...>]

Hi Ali,

I would typically use a temporary object for that, which is loaded into the work space but never rendered:

def intra_rms_tempobj(filename):
    from pymol import cmd
    tmpname = cmd.get_unused_name('_tmpobj')
    cmd.load(filename, tmpname, zoom=0)
    try:
        return cmd.intra_rms(tmpname)
    finally:
        cmd.delete(tmpname)

It's also possible to create a new instance of the PyMOL backend, this is probably closer to what you were looking for:

def intra_rms_tempinstance(filename):
    import pymol2
    with pymol2.PyMOL() as p:
        p.cmd.load(filename)
        return p.cmd.intra_rms('*')

See also:
https://pymolwiki.org/index.php/Launching_From_a_Script#Independent_PyMOL_Instances_.28Context_Manager.29

Cheers,
  Thomas


> On May 3, 2019, at 2:24 AM, Ali Kusay <aku...@un...> wrote:
> 
> I have noticed that PyMOL can be used to perform fast calculations by using it in command line or through something like Jupyter notebook since it doesn’t have to worry about the graphical geometries. I am curious if this can be performed within the PyMOL program itself. For example, loading the python interpreter in PyMOL and using it load a multistate object and calculate RMSD through intra_fit without actually loading the object in the work space. I would appreciate your help, this would be immensely time saving for larger proteins while providing the convince of not having to leave the program.
>  
> Kin regards,
>  
> Ali Kusay
> PhD student 
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.