schrodinger.application.desmond.restraint module¶

Restraint generation for cross-CT terms and all terms supported by desmond backend, including alchemical terms.

Either a single term or a generator can be used. For single term, each selection corresponds to a single atom.

Two kinds of generators are implemented now:

product: The product of all selections is used to generate all: the terms. Use case is to keep alchemical ions way from places they may get stuck.
connected: One selection is evaluated to generate terms for bond, angle: and torsion. Use case is the alchemical restraints on protein conformations.

Reference distance, angle and torsion values are computed for generated terms. For alchemical terms, reference coordinates saved previously will be used for these calculations if avaialble.

class schrodinger.application.desmond.restraint.GeneratorTypes(PRODUCT, CONNECTED)¶

Bases: tuple

CONNECTED¶: Alias for field number 1

PRODUCT¶: Alias for field number 0

__add__¶: Return self+value.

__class__¶: alias of builtins.type

__contains__¶: Return key in self.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getitem__¶: Return self[key].

__getnewargs__()¶: Return self as a plain tuple. Used by copy and pickle.

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__¶: Implement iter(self).

__le__¶: Return self<=value.

__len__¶: Return len(self).

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.desmond.restraint'¶

__mul__¶: Return self*value.n

__ne__¶: Return self!=value.

static __new__(_cls, PRODUCT, CONNECTED)¶: Create new instance of GeneratorTypes(PRODUCT, CONNECTED)

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__()¶: Return a nicely formatted representation string

__rmul__¶: Return self*value.

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__slots__ = ()¶

__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).

count(value) → integer -- return number of occurrences of value¶

index(value[, start[, stop]]) → integer -- return first index of value.¶: Raises ValueError if the value is not present.

schrodinger.application.desmond.restraint.is_position_restraint(table_name)¶

schrodinger.application.desmond.restraint.is_alchemical(table_name)¶

schrodinger.application.desmond.restraint.get_encoded_restraints(cms_sys)¶

Get encoded restraints from cms

Return type:	`str`

schrodinger.application.desmond.restraint.set_encoded_restraints(cms_sys, restr)¶

Store restraints in cms_sys object.

class schrodinger.application.desmond.restraint.RestraintBuilder(res_spec, cms_sys)¶

Bases: object

__init__(res_spec, cms_sys)¶

Parameters:	res_spec (`sea.List`) – all restraint terms to be added cms_sys (`cms.Cms`) – cms object for molecules

addRestraints()¶: Add all restraint terms to the cms object passed in the constructor. This should be the only function called to process all the restraints specified

getEncoded()¶

Return type:	`str`

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.restraint', '__init__': <function RestraintBuilder.__init__>, '_addAllPosreTerms': <function RestraintBuilder._addAllPosreTerms>, '_addOneTerm': <function RestraintBuilder._addOneTerm>, '_addTermFromGenerator': <function RestraintBuilder._addTermFromGenerator>, 'addRestraints': <function RestraintBuilder.addRestraints>, 'getEncoded': <function RestraintBuilder.getEncoded>, 'getJson': <function RestraintBuilder.getJson>, '__dict__': <attribute '__dict__' of 'RestraintBuilder' objects>, '__weakref__': <attribute '__weakref__' of 'RestraintBuilder' 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).