schrodinger.application.vsw.vswinput module

Class for writing VSW (not general Pipeline) input files.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.vsw.vswinput.parse_command_line()

Returns the path to input file, as determined from command line option parser.

class schrodinger.application.vsw.vswinput.VSWWriter(jp=None)

Bases: object

Use writeInputFile() method

__init__(jp=None)

Initialize from parameters dictionary.

writeDockingStage(mode, receptor, input, output, outtype, gencodes_out_set=None, frags=False, recombine=True, unique_field=None)

Writes stage that describes how the docking will be executed.

writeGenConfsStage(receptor_suffix, input, output)

Writes stages that generate MMFFs and OPLS conformers from the input, combine them with the input, and put into output.

writePreFilterStage(input, output, custom_filter_text)

Writes the stage that filters by specified LigFilter criteria

writePrepareStages(lastoutput, recombine)

writeInputFile()

Writes the VSW input file

Raises a RuntimeError on error.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.vsw.vswinput', '__doc__': '\n Use writeInputFile() method\n ', '__init__': <function VSWWriter.__init__>, 'writeDockingStage': <function VSWWriter.writeDockingStage>, 'writeGenConfsStage': <function VSWWriter.writeGenConfsStage>, 'writePreFilterStage': <function VSWWriter.writePreFilterStage>, 'writePrepareStages': <function VSWWriter.writePrepareStages>, 'writeInputFile': <function VSWWriter.writeInputFile>, '__dict__': <attribute '__dict__' of 'VSWWriter' objects>, '__weakref__': <attribute '__weakref__' of 'VSWWriter' 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.vsw.vswinput'

__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)