schrodinger.application.watermap.watermap_inp module

This is a class that generates watermap input files and runs them through jobcontrol. This also supports all the options in GUI.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.watermap.watermap_inp.print_deprecate(option, opt, value, parser)

class schrodinger.application.watermap.watermap_inp.WaterMapInput(protein_st, ligand_st, **kwargs)

Bases: object

__init__(protein_st, ligand_st, **kwargs)

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

update(**kwargs)

updates states of options

reorder_solute(st)

reorder atoms so that the very first atom is located close to origin to prevent solute to be shifted to other images.

createTip4pFfio(ct)

make_canonical_solvent(st)

Fix atomic order to O H H

prepareStructures()

Prepare -solute, -protein, -ligand.mae files.

writeMSJ()

Write multisim file

write(jobname, suffix='maegz', hostname=None, cpus=None)

Call all write functions

Parameters:

• jobname (str) – The name of the job in the command example
• suffix (str) – The file extension for the input file
• hostname (str) – The name of the host in the command example
• cpus (int) – The number of cpus in the command example

run(jobname, host, cpu)

Run WaterMap Job

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.watermap.watermap_inp', '__init__': <function WaterMapInput.__init__>, 'update': <function WaterMapInput.update>, 'reorder_solute': <function WaterMapInput.reorder_solute>, 'createTip4pFfio': <function WaterMapInput.createTip4pFfio>, 'make_canonical_solvent': <function WaterMapInput.make_canonical_solvent>, 'prepareStructures': <function WaterMapInput.prepareStructures>, '_writeStructures': <function WaterMapInput._writeStructures>, 'writeMSJ': <function WaterMapInput.writeMSJ>, 'write': <function WaterMapInput.write>, 'run': <function WaterMapInput.run>, '__dict__': <attribute '__dict__' of 'WaterMapInput' objects>, '__weakref__': <attribute '__weakref__' of 'WaterMapInput' objects>, '__doc__': None})

__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.watermap.watermap_inp'

__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.watermap.watermap_inp.main(opt)