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
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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
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class
schrodinger.application.desmond.title_to_hex.
Analysis
(jobname, leg='complex', stage='9')¶ Bases:
object
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ANALYSIS_DIR_NAME
= 'analysis'¶
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__init__
(jobname, leg='complex', stage='9')¶ Initialize self. See help(type(self)) for accurate signature.
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load_graph
(pkl_fname)¶ load graph from pkl
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create_workdir
()¶ Create a analysis dir
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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
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rename_cms_title
(new_fname, hex)¶ Will rename the cms title from hex to title
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create_soft_links
()¶ Creates softlinks to files using titles instead of hex ids
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gzip_it
()¶
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analyze_it
()¶
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__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>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
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__ge__
¶ Return self>=value.
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__getattribute__
¶ Return getattr(self, name).
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__gt__
¶ Return self>value.
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__hash__
¶ Return hash(self).
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__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
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__le__
¶ Return self<=value.
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__lt__
¶ Return self<value.
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__module__
= 'schrodinger.application.desmond.title_to_hex'¶
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__ne__
¶ Return self!=value.
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__new__
()¶ Create and return a new object. See help(type) for accurate signature.
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__repr__
¶ Return repr(self).
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__setattr__
¶ Implement setattr(self, name, value).
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__sizeof__
() → int¶ size of object in memory, in bytes
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__str__
¶ Return str(self).
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__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).
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__weakref__
¶ list of weak references to the object (if defined)
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schrodinger.application.desmond.title_to_hex.
parse_it
()¶ This will parse the command line
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schrodinger.application.desmond.title_to_hex.
main
()¶ Script to launch jobs