schrodinger.application.desmond.systype module

Facilities for detecting type of model systems.

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.application.desmond.systype.UnknownAppError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', '__weakref__': <attribute '__weakref__' of 'UnknownAppError' 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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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).

__setstate__()

__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).

__suppress_context__

__traceback__

__weakref__

list of weak references to the object (if defined)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.desmond.systype.UnknownRuleError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', '__weakref__': <attribute '__weakref__' of 'UnknownRuleError' 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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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).

__setstate__()

__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).

__suppress_context__

__traceback__

__weakref__

list of weak references to the object (if defined)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.desmond.systype.FormatError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', '__weakref__': <attribute '__weakref__' of 'FormatError' 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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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).

__setstate__()

__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).

__suppress_context__

__traceback__

__weakref__

list of weak references to the object (if defined)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.desmond.systype.DetectionError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', '__weakref__': <attribute '__weakref__' of 'DetectionError' 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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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).

__setstate__()

__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).

__suppress_context__

__traceback__

__weakref__

list of weak references to the object (if defined)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.desmond.systype.TyperBase

Bases: object

typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}

NAME = 'generic'

RULE = {}

STRING = {None: ''}

static prepare(*arg, **kwarg)

static check_rule(systype, rule)

static detect(struc, filename)

static has_rule(rule)

static get_trait(struc)

__class__

alias of _TypeBaseMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', 'typer_cls': {'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}, 'NAME': 'generic', 'RULE': {}, 'STRING': {None: ''}, 'prepare': <staticmethod object>, 'check_rule': <staticmethod object>, 'detect': <staticmethod object>, 'has_rule': <staticmethod object>, 'get_trait': <staticmethod object>, '__dict__': <attribute '__dict__' of 'TyperBase' objects>, '__weakref__': <attribute '__weakref__' of 'TyperBase' 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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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)

class schrodinger.application.desmond.systype.DesmondTyper

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'desmond'

UNKNOWN = 0

MATURE_REGULAR = 101

MATURE_FEP = 102

MATURE_AFEP = 103

RAW_REGULAR = 201

RAW_FEP = 202

RAW_AFEP = 203

STRING = {101: 'a mature model system created for regular molecular dynamics simulations', 102: 'a mature model system created for FEP calculations', 103: 'a mature model system created for absolute FEP calculations', 201: 'a raw geometry for regular molecular dynamics simulations', 202: 'raw geometries created for FEP calculations', 203: 'raw geometries created for absolute FEP calculations'}

RULE = {'afep': [103, 203], 'auto': [101, 102, 103, 201, 202, 203], 'fep': [102, 103, 202, 203], 'mature': [101, 102, 103], 'mature_afep': [103], 'mature_fep': [102, 103], 'mature_regular': [101, 103], 'raw': [201, 202, 203], 'raw_afep': [203], 'raw_fep': [202, 203], 'raw_regular': [201, 203], 'regular': [101, 103, 201, 203]}

static detect(struc, filename)

static has_rule(rule)

static check_rule(systype, rule)

static check_system(struc, filename, rule)

static get_trait(struc)

__class__

alias of _TypeBaseMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', 'NAME': 'desmond', 'UNKNOWN': 0, 'MATURE_REGULAR': 101, 'MATURE_FEP': 102, 'MATURE_AFEP': 103, 'RAW_REGULAR': 201, 'RAW_FEP': 202, 'RAW_AFEP': 203, 'STRING': {101: 'a mature model system created for regular molecular dynamics simulations', 102: 'a mature model system created for FEP calculations', 103: 'a mature model system created for absolute FEP calculations', 201: 'a raw geometry for regular molecular dynamics simulations', 202: 'raw geometries created for FEP calculations', 203: 'raw geometries created for absolute FEP calculations'}, 'RULE': {'mature_regular': [101, 103], 'mature_fep': [102, 103], 'mature_afep': [103], 'mature': [101, 102, 103], 'raw_regular': [201, 203], 'raw_fep': [202, 203], 'raw_afep': [203], 'raw': [201, 202, 203], 'regular': [101, 103, 201, 203], 'fep': [102, 103, 202, 203], 'afep': [103, 203], 'auto': [101, 102, 103, 201, 202, 203]}, 'detect': <staticmethod object>, 'has_rule': <staticmethod object>, 'check_rule': <staticmethod object>, 'check_system': <staticmethod object>, 'get_trait': <staticmethod object>})

__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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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)

static prepare(*arg, **kwarg)

typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}

class schrodinger.application.desmond.systype.McproTyper

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'mcpro'

UNKNOWN = 0

RAW_REGULAR = 201

RAW_FEP = 202

STRING = {201: 'a raw geometry for regular monte carlo simulations', 202: 'raw geometries created for FEP calculations'}

RULE = {'auto': [202, 201], 'fep': [202], 'raw': [202, 201], 'raw_fep': [202], 'raw_regular': [201], 'regular': [201]}

static detect(struc, filename)

static has_rule(rule)

static check_rule(systype, rule)

static check_system(struc, filename, rule)

static get_trait(struc)

__class__

alias of _TypeBaseMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', 'NAME': 'mcpro', 'UNKNOWN': 0, 'RAW_REGULAR': 201, 'RAW_FEP': 202, 'STRING': {201: 'a raw geometry for regular monte carlo simulations', 202: 'raw geometries created for FEP calculations'}, 'RULE': {'raw_regular': [201], 'raw_fep': [202], 'raw': [202, 201], 'regular': [201], 'fep': [202], 'auto': [202, 201]}, 'detect': <staticmethod object>, 'has_rule': <staticmethod object>, 'check_rule': <staticmethod object>, 'check_system': <staticmethod object>, 'get_trait': <staticmethod object>})

__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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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)

static prepare(*arg, **kwarg)

typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}

class schrodinger.application.desmond.systype.WatermapTyper

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'watermap'

RAW_REGULAR = 201

STRING = {201: 'a raw geometry for regular watermap jobs'}

RULE = {'': [201], 'regular': [201]}

static detect(struc, filename)

static has_rule(rule)

static check_rule(systype, rule)

static check_system(struc, filename, rule)

static get_trait(struc)

static prepare(stage, filename)

__class__

alias of _TypeBaseMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', 'NAME': 'watermap', 'RAW_REGULAR': 201, 'STRING': {201: 'a raw geometry for regular watermap jobs'}, 'RULE': {'regular': [201], '': [201]}, 'detect': <staticmethod object>, 'has_rule': <staticmethod object>, 'check_rule': <staticmethod object>, 'check_system': <staticmethod object>, 'get_trait': <staticmethod object>, 'prepare': <staticmethod object>})

__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__

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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.systype'

__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)

typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}

class schrodinger.application.desmond.systype.SysType(typer_rule=None)

Bases: object

__init__(typer_rule=None)

check_system(filename)

get_trait(filename)

prepare(*arg, **kwarg)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.systype', '__doc__': '\n\n ', '__init__': <function SysType.__init__>, 'check_system': <function SysType.check_system>, 'get_trait': <function SysType.get_trait>, 'prepare': <function SysType.prepare>, '__dict__': <attribute '__dict__' of 'SysType' objects>, '__weakref__': <attribute '__weakref__' of 'SysType' 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.desmond.systype'

__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)