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'
__init__(jobname, leg='complex', stage='9')

Initialize self. See help(type(self)) for accurate signature.

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()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.title_to_hex', '__doc__': '\n ', 'ANALYSIS_DIR_NAME': 'analysis', '__init__': <function Analysis.__init__>, 'load_graph': <function Analysis.load_graph>, 'create_workdir': <function Analysis.create_workdir>, 'extract_trajectories': <function Analysis.extract_trajectories>, 'rename_cms_title': <function Analysis.rename_cms_title>, 'create_soft_links': <function Analysis.create_soft_links>, 'gzip_it': <function Analysis.gzip_it>, 'analyze_it': <function Analysis.analyze_it>, '__dict__': <attribute '__dict__' of 'Analysis' objects>, '__weakref__': <attribute '__weakref__' of 'Analysis' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.title_to_hex'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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