schrodinger.infra.fast3d module

Fast3D wrappers

schrodinger.infra.fast3d.new_instancemethod(func, inst, cls)
class schrodinger.infra.fast3d.SwigPyIterator(*args, **kwargs)

Bases: object

thisown

The membership flag

__init__(*args, **kwargs)

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

__repr__()
__swig_destroy__()
__iter__()
__add__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__init__': <function SwigPyIterator.__init__>, '__repr__': <function _swig_repr>, '__swig_destroy__': <built-in function delete_SwigPyIterator>, '__iter__': <function SwigPyIterator.__iter__>, '__dict__': <attribute '__dict__' of 'SwigPyIterator' objects>, '__weakref__': <attribute '__weakref__' of 'SwigPyIterator' objects>, '__doc__': None, 'value': <instancemethod SwigPyIterator_value>, 'incr': <instancemethod SwigPyIterator_incr>, 'decr': <instancemethod SwigPyIterator_decr>, 'distance': <instancemethod SwigPyIterator_distance>, 'equal': <instancemethod SwigPyIterator_equal>, 'copy': <instancemethod SwigPyIterator_copy>, 'next': <instancemethod SwigPyIterator_next>, '__next__': <instancemethod SwigPyIterator___next__>, 'previous': <instancemethod SwigPyIterator_previous>, 'advance': <instancemethod SwigPyIterator_advance>, '__eq__': <instancemethod SwigPyIterator___eq__>, '__ne__': <instancemethod SwigPyIterator___ne__>, '__iadd__': <instancemethod SwigPyIterator___iadd__>, '__isub__': <instancemethod SwigPyIterator___isub__>, '__add__': <instancemethod SwigPyIterator___add__>, '__sub__': <instancemethod SwigPyIterator___sub__>})
__dir__() → list

default dir() implementation

__eq__()
__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__iadd__()
__init_subclass__()

This method is called when a class is subclassed.

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

__isub__()
__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.infra.fast3d'
__ne__()
__new__()

Create and return a new object. See help(type) for accurate signature.

__next__()
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__sub__()
__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)

advance()
copy()
decr()
distance()
equal()
incr()
next()
previous()
value()
class schrodinger.infra.fast3d.intvector(*args)

Bases: object

thisown

The membership flag

__repr__()
__iter__()
__init__(*args)

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

__swig_destroy__()
__bool__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__delitem__()
__delslice__()
__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__iter__': <function intvector.__iter__>, '__init__': <function intvector.__init__>, '__swig_destroy__': <built-in function delete_intvector>, '__dict__': <attribute '__dict__' of 'intvector' objects>, '__weakref__': <attribute '__weakref__' of 'intvector' objects>, '__doc__': None, 'iterator': <instancemethod intvector_iterator>, '__nonzero__': <instancemethod intvector___nonzero__>, '__bool__': <instancemethod intvector___bool__>, '__len__': <instancemethod intvector___len__>, '__getslice__': <instancemethod intvector___getslice__>, '__setslice__': <instancemethod intvector___setslice__>, '__delslice__': <instancemethod intvector___delslice__>, '__delitem__': <instancemethod intvector___delitem__>, '__getitem__': <instancemethod intvector___getitem__>, '__setitem__': <instancemethod intvector___setitem__>, 'pop': <instancemethod intvector_pop>, 'append': <instancemethod intvector_append>, 'empty': <instancemethod intvector_empty>, 'size': <instancemethod intvector_size>, 'swap': <instancemethod intvector_swap>, 'begin': <instancemethod intvector_begin>, 'end': <instancemethod intvector_end>, 'rbegin': <instancemethod intvector_rbegin>, 'rend': <instancemethod intvector_rend>, 'clear': <instancemethod intvector_clear>, 'get_allocator': <instancemethod intvector_get_allocator>, 'pop_back': <instancemethod intvector_pop_back>, 'erase': <instancemethod intvector_erase>, 'push_back': <instancemethod intvector_push_back>, 'front': <instancemethod intvector_front>, 'back': <instancemethod intvector_back>, 'assign': <instancemethod intvector_assign>, 'resize': <instancemethod intvector_resize>, 'insert': <instancemethod intvector_insert>, 'reserve': <instancemethod intvector_reserve>, 'capacity': <instancemethod intvector_capacity>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__()
__getslice__()
__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.

__len__()
__lt__

Return self<value.

__module__ = 'schrodinger.infra.fast3d'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__nonzero__()
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__setitem__()
__setslice__()
__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)

append()
assign()
back()
begin()
capacity()
clear()
empty()
end()
erase()
front()
get_allocator()
insert()
iterator()
pop()
pop_back()
push_back()
rbegin()
rend()
reserve()
resize()
size()
swap()
class schrodinger.infra.fast3d.stringvector(*args)

Bases: object

thisown

The membership flag

__repr__()
__iter__()
__init__(*args)

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

__swig_destroy__()
__bool__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__delitem__()
__delslice__()
__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__iter__': <function stringvector.__iter__>, '__init__': <function stringvector.__init__>, '__swig_destroy__': <built-in function delete_stringvector>, '__dict__': <attribute '__dict__' of 'stringvector' objects>, '__weakref__': <attribute '__weakref__' of 'stringvector' objects>, '__doc__': None, 'iterator': <instancemethod stringvector_iterator>, '__nonzero__': <instancemethod stringvector___nonzero__>, '__bool__': <instancemethod stringvector___bool__>, '__len__': <instancemethod stringvector___len__>, '__getslice__': <instancemethod stringvector___getslice__>, '__setslice__': <instancemethod stringvector___setslice__>, '__delslice__': <instancemethod stringvector___delslice__>, '__delitem__': <instancemethod stringvector___delitem__>, '__getitem__': <instancemethod stringvector___getitem__>, '__setitem__': <instancemethod stringvector___setitem__>, 'pop': <instancemethod stringvector_pop>, 'append': <instancemethod stringvector_append>, 'empty': <instancemethod stringvector_empty>, 'size': <instancemethod stringvector_size>, 'swap': <instancemethod stringvector_swap>, 'begin': <instancemethod stringvector_begin>, 'end': <instancemethod stringvector_end>, 'rbegin': <instancemethod stringvector_rbegin>, 'rend': <instancemethod stringvector_rend>, 'clear': <instancemethod stringvector_clear>, 'get_allocator': <instancemethod stringvector_get_allocator>, 'pop_back': <instancemethod stringvector_pop_back>, 'erase': <instancemethod stringvector_erase>, 'push_back': <instancemethod stringvector_push_back>, 'front': <instancemethod stringvector_front>, 'back': <instancemethod stringvector_back>, 'assign': <instancemethod stringvector_assign>, 'resize': <instancemethod stringvector_resize>, 'insert': <instancemethod stringvector_insert>, 'reserve': <instancemethod stringvector_reserve>, 'capacity': <instancemethod stringvector_capacity>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__()
__getslice__()
__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.

__len__()
__lt__

Return self<value.

__module__ = 'schrodinger.infra.fast3d'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__nonzero__()
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__setitem__()
__setslice__()
__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)

append()
assign()
back()
begin()
capacity()
clear()
empty()
end()
erase()
front()
get_allocator()
insert()
iterator()
pop()
pop_back()
push_back()
rbegin()
rend()
reserve()
resize()
size()
swap()
class schrodinger.infra.fast3d.Engine(*args)

Bases: object

thisown

The membership flag

__repr__()
__init__(*args)

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

__swig_destroy__()
static dataDir()
static isFragmentLibraryFile()
static defaultRepositories()
static defaultCustomRepository()
FROZEN_ATOMS_PROPERTY_NAME = 's_f3d_frozen_atoms'
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__init__': <function Engine.__init__>, '__swig_destroy__': <built-in function delete_Engine>, 'dataDir': <staticmethod object>, 'isFragmentLibraryFile': <staticmethod object>, 'defaultRepositories': <staticmethod object>, 'defaultCustomRepository': <staticmethod object>, '__dict__': <attribute '__dict__' of 'Engine' objects>, '__weakref__': <attribute '__weakref__' of 'Engine' objects>, '__doc__': None, 'appendRepository': <instancemethod Engine_appendRepository>, 'invertNitrogens': <instancemethod Engine_invertNitrogens>, 'disallowCisAmides': <instancemethod Engine_disallowCisAmides>, 'setDesiredNumberOfConformers': <instancemethod Engine_setDesiredNumberOfConformers>, 'disableDuplicatesElimination': <instancemethod Engine_disableDuplicatesElimination>, 'autoIncreaseThreshold': <instancemethod Engine_autoIncreaseThreshold>, 'stereo': <instancemethod Engine_stereo>, 'run': <instancemethod Engine_run>, 'partition': <instancemethod Engine_partition>, 'FROZEN_ATOMS_PROPERTY_NAME': 's_f3d_frozen_atoms'})
__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.infra.fast3d'
__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

__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)

appendRepository()
autoIncreaseThreshold()
disableDuplicatesElimination()
disallowCisAmides()
invertNitrogens()
partition()
run()
setDesiredNumberOfConformers()
stereo()
class schrodinger.infra.fast3d.SingleConformerEngine(*args)

Bases: object

thisown

The membership flag

__repr__()
__init__(*args)

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

__swig_destroy__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__init__': <function SingleConformerEngine.__init__>, '__swig_destroy__': <built-in function delete_SingleConformerEngine>, '__dict__': <attribute '__dict__' of 'SingleConformerEngine' objects>, '__weakref__': <attribute '__weakref__' of 'SingleConformerEngine' objects>, '__doc__': None, 'stereo': <instancemethod SingleConformerEngine_stereo>, 'run': <instancemethod SingleConformerEngine_run>})
__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.infra.fast3d'
__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

__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)

run()
stereo()
class schrodinger.infra.fast3d.Volumizer(*args)

Bases: object

thisown

The membership flag

__repr__()
__init__(*args)

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

static defaultConfig()
static newForMaestro()
__swig_destroy__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__init__': <function Volumizer.__init__>, 'defaultConfig': <staticmethod object>, 'newForMaestro': <staticmethod object>, '__swig_destroy__': <built-in function delete_Volumizer>, '__dict__': <attribute '__dict__' of 'Volumizer' objects>, '__weakref__': <attribute '__weakref__' of 'Volumizer' objects>, '__doc__': None, 'run': <instancemethod Volumizer_run>, 'ffldVersion': <instancemethod Volumizer_ffldVersion>, 'dielectricConstant': <instancemethod Volumizer_dielectricConstant>, 'skipCM1A': <instancemethod Volumizer_skipCM1A>})
__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.infra.fast3d'
__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

__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)

dielectricConstant()
ffldVersion()
run()
skipCM1A()
class schrodinger.infra.fast3d.LigPrep3Volumizer(*args)

Bases: schrodinger.infra.fast3d.Volumizer

thisown

The membership flag

__repr__()
__init__(*args)

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

__swig_destroy__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__init__': <function LigPrep3Volumizer.__init__>, '__swig_destroy__': <built-in function delete_LigPrep3Volumizer>, '__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.infra.fast3d'
__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

__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)

static defaultConfig()
dielectricConstant()
ffldVersion()
static newForMaestro()
run()
skipCM1A()
class schrodinger.infra.fast3d.Generalizer(addBuiltinRules: bool = True)

Bases: object

thisown

The membership flag

__repr__()
__init__(addBuiltinRules: bool = True)

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

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__init__': <function Generalizer.__init__>, '__swig_destroy__': <built-in function delete_Generalizer>, '__dict__': <attribute '__dict__' of 'Generalizer' objects>, '__weakref__': <attribute '__weakref__' of 'Generalizer' objects>, '__doc__': None, 'appendRule': <instancemethod Generalizer_appendRule>, 'generalize': <instancemethod Generalizer_generalize>})
__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.infra.fast3d'
__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

__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).

__swig_destroy__()
__weakref__

list of weak references to the object (if defined)

appendRule()
generalize()
class schrodinger.infra.fast3d.Canonicalizer(*args)

Bases: object

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.fast3d', 'thisown': <property object>, '__repr__': <function _swig_repr>, '__init__': <function Canonicalizer.__init__>, '__swig_destroy__': <built-in function delete_Canonicalizer>, '__dict__': <attribute '__dict__' of 'Canonicalizer' objects>, '__weakref__': <attribute '__weakref__' of 'Canonicalizer' objects>, '__doc__': None, 'canonicalizePositions': <instancemethod Canonicalizer_canonicalizePositions>, 'canonicalize': <instancemethod Canonicalizer_canonicalize>})
__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.infra.fast3d'
__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

__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)

canonicalize()
canonicalizePositions()
thisown

The membership flag

__repr__()
__init__(*args)

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

__swig_destroy__()