schrodinger.application.desmond.simulation_block_data module¶
Block data calculation script.
For a MD Simulation, calculates properties from log, energy and simbox files Calculates block averages of properties in energy file.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.desmond.simulation_block_data.print_usage(text=None)¶
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class
schrodinger.application.desmond.simulation_block_data.Array_Prop¶ Bases:
object-
__init__()¶
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prop_value= []¶
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get_prop_value()¶
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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.simulation_block_data', '__doc__': '\n\n ', 'prop_value': [], '__init__': <function Array_Prop.__init__>, 'get_prop_value': <function Array_Prop.get_prop_value>, '__dict__': <attribute '__dict__' of 'Array_Prop' objects>, '__weakref__': <attribute '__weakref__' of 'Array_Prop' 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.simulation_block_data'¶
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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.simulation_block_data.calc_block_average(ene_fname, prop_list, sba_fname, start_line, time_column=0, start_time=0.0, block_length=10.0)¶
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schrodinger.application.desmond.simulation_block_data.get_listof_props_ene(ene_fname)¶ Given a .ene file, parse the ]header and get a list of properties.
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schrodinger.application.desmond.simulation_block_data.get_print_simbox_data(simbox_fname, sba_fname)¶ Given a simbox.dat file, parse the file and print simulation box details in the sba file.
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schrodinger.application.desmond.simulation_block_data.get_top_level_props(ene_fname)¶ Given a .ene file, parse the header and get top level props. Print those in sba file.
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schrodinger.application.desmond.simulation_block_data.get_log_props(log_fname)¶ Given a .log file, parse the header and determine if it completed okay.
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schrodinger.application.desmond.simulation_block_data.parse_sba(sba_fname)¶ Given name of a sba file name find all blocks except time and job details and return their average, sd and slope.
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schrodinger.application.desmond.simulation_block_data.get_block_summary(inp_content, start_index, stop_index)¶ From block content get averages, sd, slope and units. Return them as dictionary.