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 <akus8...@uni.sydney.edu.au> 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.
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