schrodinger.application.desmond.system_builder_util module

The script truncates protein beyond truncate_distance from ligand atoms, restrain remaining protein heavy atoms beyond restrain_distance from ligand atoms, and solvate it by solvent_buffer distance. The truncation is done by residue based ASL.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.system_builder_util.DesmondBoxSize(**kwargs)

Bases: object

__init__(**kwargs)

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

update(**kwargs)

getStructureSize(st)

Returns the a, b, & c absolute coordinates, even when the user specified buffer distances Returns None if there are no atoms in the Workspace

getBoxVectors(st)

Returns the vectors representing the box. Origin is the back face bottom left. Returns None on error (after displaying a dialog box)

calculateVolume(st)

Will return 0 on error (after showing dialog)

findMinVolume(st)

translateCentroidToOrigin(strucs)

minimizeVolume(strucs)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.system_builder_util', '__init__': <function DesmondBoxSize.__init__>, 'update': <function DesmondBoxSize.update>, 'getStructureSize': <function DesmondBoxSize.getStructureSize>, 'getBoxVectors': <function DesmondBoxSize.getBoxVectors>, 'calculateVolume': <function DesmondBoxSize.calculateVolume>, 'findMinVolume': <function DesmondBoxSize.findMinVolume>, 'translateCentroidToOrigin': <function DesmondBoxSize.translateCentroidToOrigin>, 'minimizeVolume': <function DesmondBoxSize.minimizeVolume>, '__dict__': <attribute '__dict__' of 'DesmondBoxSize' objects>, '__weakref__': <attribute '__weakref__' of 'DesmondBoxSize' 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.desmond.system_builder_util'

__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.system_builder_util.truncateProtein(protein_st, ligand_st, retain_ligand=False, truncate_distance=0, restrain_distance=-1)

Parameters:restrain_distance – -1 means no restrain, 0 means restrain all atoms

schrodinger.application.desmond.system_builder_util.truncate_solvate_protein(opt)

schrodinger.application.desmond.system_builder_util.find_equivalent_st(my_st, st_list, pname)

Find a equivalent st of my_st from iterable st_list Copy the pname values to ‘r_ffio_custom_charge’ of my_st