schrodinger.application.desmond.title_to_hex module

This is the script displays ligand title to hex map Copyright Schrodinger, LLC. All rights reserved.

This map can be displayed by using the –pkl_name option before launching to see what edges in the graph are available for extension.

$SCHRODINGER/run title_to_hex.py –pkl_name <pkl_file>

To copy the trajectories for the end point windows (0, 11) for the complex simulations you would run

$SCHRODINGER/run title_to_hex.py –pkl_name <pkl_file> –jobname <jobname> –analysis

This will produce a directory called analysis with soft links using the actual ligand titles to the cms files. The titles which will be displayed in the workspace and project table have been renamed with the ligand titles. All you need to do is load a cms file and then click on the “T” to view the trajectory in the project table.

To also copy the solvent sims provide the additional argument –both

schrodinger.application.desmond.title_to_hex.show_hex_id_title_id_map(pkl_name)

Will display the hex_id title_id map for a pkl :return : True if it successfully read the pkl :rtype : False

class schrodinger.application.desmond.title_to_hex.Analysis(jobname, leg='complex', stage='9')

Bases: object

ANALYSIS_DIR_NAME = 'analysis'
load_graph(pkl_fname)

load graph from pkl

create_workdir()

Create a analysis dir

extract_trajectories()

dir structure before unziping /scr/pierce/benzi_series_2005/benzi_2005_3

file structure to unzip benzi_2005_504a987_ac53848_complex_9-out.tgz

dir structure /scr/pierce/benzi_series_2005/benzi_2005_3/benzi_2005_3a3d3bf_504a987_complex_fep1/benzi_2005_3a3d3bf_504a987_complex_9

rename_cms_title(new_fname, hex)

Will rename the cms title from hex to title

Creates softlinks to files using titles instead of hex ids

gzip_it()
analyze_it()
schrodinger.application.desmond.title_to_hex.parse_it()

This will parse the command line

schrodinger.application.desmond.title_to_hex.main()

Script to launch jobs