schrodinger.application.desmond.replica_dE module

class schrodinger.application.desmond.replica_dE.replica_energy(rep_number, filename)

Bases: object

__init__(rep_number, filename)

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

getNumber()

getRMin()

getRMax()

getFMin()

getFMax()

getRMean()

getFMean()

getRHistogram(his_min, his_max, nbins)

getFHistogram(his_min, his_max, nbins)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_dE', '__init__': <function replica_energy.__init__>, 'getNumber': <function replica_energy.getNumber>, 'getRMin': <function replica_energy.getRMin>, 'getRMax': <function replica_energy.getRMax>, 'getFMin': <function replica_energy.getFMin>, 'getFMax': <function replica_energy.getFMax>, 'getRMean': <function replica_energy.getRMean>, 'getFMean': <function replica_energy.getFMean>, 'getRHistogram': <function replica_energy.getRHistogram>, 'getFHistogram': <function replica_energy.getFHistogram>, '__dict__': <attribute '__dict__' of 'replica_energy' objects>, '__weakref__': <attribute '__weakref__' of 'replica_energy' 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.replica_dE'

__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.replica_dE.replica_container(basename, energy_output, task_type=None, n_win=12)

Bases: object

__init__(basename, energy_output, task_type=None, n_win=12)

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

read_dE_Replicas()

getReplica(number)

get_nrep()

printInfo()

set_globalMin()

set_globalMax()

getOverlap(irepA, irepB)

export()

process_bennett_log(data)

export_dE_data(data, bennett_dG, bennett_per_replica)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_dE', '__init__': <function replica_container.__init__>, '_setup_fn_template': <function replica_container._setup_fn_template>, '_addReplica': <function replica_container._addReplica>, 'read_dE_Replicas': <function replica_container.read_dE_Replicas>, 'getReplica': <function replica_container.getReplica>, 'get_nrep': <function replica_container.get_nrep>, 'printInfo': <function replica_container.printInfo>, '_getFMin': <function replica_container._getFMin>, '_getRMin': <function replica_container._getRMin>, '_getFMax': <function replica_container._getFMax>, '_getRMax': <function replica_container._getRMax>, 'set_globalMin': <function replica_container.set_globalMin>, 'set_globalMax': <function replica_container.set_globalMax>, 'getOverlap': <function replica_container.getOverlap>, 'export': <function replica_container.export>, 'process_bennett_log': <function replica_container.process_bennett_log>, 'export_dE_data': <function replica_container.export_dE_data>, '__dict__': <attribute '__dict__' of 'replica_container' objects>, '__weakref__': <attribute '__weakref__' of 'replica_container' 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.replica_dE'

__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.replica_dE.replicas_monitor(basename, cfg, task_type)

Bases: object

__init__(basename, cfg, task_type)

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

get_histogram(data)

get_nrep()

export()

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_dE', '__init__': <function replicas_monitor.__init__>, 'get_histogram': <function replicas_monitor.get_histogram>, 'get_nrep': <function replicas_monitor.get_nrep>, 'export': <function replicas_monitor.export>, '__dict__': <attribute '__dict__' of 'replicas_monitor' objects>, '__weakref__': <attribute '__weakref__' of 'replicas_monitor' 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.replica_dE'

__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)