trajectory_binding_site_volumes.py Command Help
Command: $SCHRODINGER/run trajectory_binding_site_volumes.py
usage: trajectory_binding_site_volumes.py [-v] [-h]
[-omae <output Maestro file>]
[-ocsv <output CSV file>]
[-superimpose]
[-sitemap_ligand_asl <ASL> | -sitemap_site_asl <ASL> | -sitemap_ligand | -sitemap_all {all,best by Dscore,best by SiteScore}]
[-protein_asl <ASL>]
[-start_frame <int>]
[-num_frames <int>]
[-every_nth <int>]
[-cluster_distance <float>]
[-sitemap_options [...]] [-DEBUG]
[-HOST <hostname>]
[<input file> ...]
{trajectory,structure}
Script for running SiteMap on each frame of a Desmond trajectory or on a series
of structures.
This script runs SiteMap on each frame of a Desmond trajectory or on a series of
structure files or on a multi-structure input file of conformers. The user must
define the input type, and then define how SiteMap should be run. If the script
is run with the -sitemap_ligand_asl option, the ligand will be removed from that
binding site and that site will be characterized by SiteMap in each frame. If
the script is run with the -sitemap_site_asl option, a fake single-atom ligand
will be created at the centroid of this ASL and used by SiteMap to define the
region to be analyzed in each frame. If the script is run with the
-sitemap_ligand option, in each frame the last molecule in the structure will be
treated as the ligand, which will be removed from the binding site before
characterization by SiteMap. And if the -sitemap_all option is used, SiteMap
will be run on the entire structure, and either all results returned, or the
best by Dscore or SiteScore will be returned, as specified.
For example -sitemap_ligand_asl 'res.ptype 478'
Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
<input file> Input file. This can be either a Desmond output cms
file, or one or more structure files.
{trajectory,structure}
Input file format.
options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
-omae <output Maestro file>
Output Maestro file. The Trajectory_frame property in
each SiteMap result ct will specify which frame that
result came from. (If not provided, output file name
will be based on input .cms name).
-ocsv <output CSV file>
Output .csv file with SiteMap properties from each
frame. The Trajectory_frame property in each SiteMap
result ct will specify which frame that result came
from.
-superimpose Superimpose all the structures to the first frame or
structure using the -protein_asl ASL expression.
-sitemap_ligand_asl <ASL>
ASL expression defining the ligand in each structure.
Default="all".
-sitemap_site_asl <ASL>
ASL expression defining residues for the site to
analyze in each structure. Default is sitemap_site_asl
"all".
-sitemap_ligand Treat the last molecule in each structure as the
ligand.
-sitemap_all {all,best by Dscore,best by SiteScore}
Option to run SiteMap on the entire structure and
return either "all" sites or "best by Dscore" or "best
by SiteScore". Default="all".
-protein_asl <ASL> ASL expression defining the protein in the structure.
Default="protein".
-start_frame <int> Index of first frame to process. Default=0.
-num_frames <int> Number of frames to process. Default behavior is to
parse all frames.
-every_nth <int> Process every Nth frame. Default=1.
-cluster_distance <float>
Clustering distance. Default=0.3.
-sitemap_options [ ...]
Additional SiteMap options. These options are given as
a list of "option:value". For example sitebox:6
maxsites:5. Please refer to the SiteMap documentation
for a full description of the available options.
-DEBUG Show details of Job Control operation, turn on SiteMap
verbose mode and retain all intermediate files.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.