schrodinger.application.desmond.packages.energygroup module

exception schrodinger.application.desmond.packages.energygroup.EnergyGroupError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.energygroup', '__weakref__': <attribute '__weakref__' of 'EnergyGroupError' 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.packages.energygroup'
__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.packages.energygroup.EnergyGroupBase

Bases: object

Its subclasses work with EnergyFacade to perform energy group calculations.

The subclass instance should have the following public attributes: - key: immutable and iterable. It is used as the key to retrieve

calculation result from cache in EnergyFacade
  • kwargs: dict. It is the keyword arguments for get_energies.

Its roles include: - store and validate the parameters - retrieve result from the cache in EnergyFacade

getResult(result)

Retrieve and format the result from the cache in EnergyFacade

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.energygroup', '__doc__': '\n Its subclasses work with `EnergyFacade` to perform energy group calculations.\n\n The subclass instance should have the following public attributes:\n - `key`: immutable and iterable. It is used as the key to retrieve\n calculation result from cache in `EnergyFacade`\n - `kwargs`: `dict`. It is the keyword arguments for `get_energies`.\n\n Its roles include:\n - store and validate the parameters\n - retrieve result from the cache in `EnergyFacade`\n ', 'getResult': <function EnergyGroupBase.getResult>, '__dict__': <attribute '__dict__' of 'EnergyGroupBase' objects>, '__weakref__': <attribute '__weakref__' of 'EnergyGroupBase' 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.packages.energygroup'
__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.packages.energygroup.Energy(_, molecule_number, type, type2)

Bases: schrodinger.application.desmond.packages.energygroup.EnergyGroupBase

Analyzer for energy group calculation with single molecule selection. The pre-defined energy groups are (see COMPONENT_LIST)

  1. Selected molecule
  2. All atoms - group 1, 3, 4, 5
  3. Solute atoms - group 1
  4. Membrane atoms - group 1
  5. Solvent atoms - group 1
TYPE_MAP = {'Angle': 'angle', 'Bond': 'stretch', 'Coulomb': 'elec', 'Torsion': 'dihedral', 'Total': 'Total', 'vdW': 'vdw'}
COMPONENT_LIST = ['Self', 'Other', 'Solute', 'Membrane', 'Solvent']
__init__(_, molecule_number, type, type2)
Parameters:
  • _ – it is a place holder for cms_model
  • molecule_number (int) – index of the molecule
  • type (str) – pre-defined energy type, see TYPE_MAP
  • type2 (str) – pre-defined atom group, see COMPONENT_LIST
getResult(result)
Returns:frame-by-frame result of the type energy (see TYPE_MAP) of the atom group type2 (see COMPONENT_LIST)
Return type:a list of `float`s
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.energygroup', '__doc__': '\n Analyzer for energy group calculation with single molecule selection. The\n pre-defined energy groups are (see COMPONENT_LIST)\n 1. Selected molecule\n 2. All atoms - group 1, 3, 4, 5\n 3. Solute atoms - group 1\n 4. Membrane atoms - group 1\n 5. Solvent atoms - group 1\n ', 'TYPE_MAP': {'Coulomb': 'elec', 'vdW': 'vdw', 'Bond': 'stretch', 'Angle': 'angle', 'Torsion': 'dihedral', 'Total': 'Total'}, 'COMPONENT_LIST': ['Self', 'Other', 'Solute', 'Membrane', 'Solvent'], '__init__': <function Energy.__init__>, 'getResult': <function Energy.getResult>})
__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.packages.energygroup'
__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.packages.energygroup.InteractionEnergy(_, asl1, asl2)

Bases: schrodinger.application.desmond.packages.energygroup.EnergyGroupBase

Analyzer for interaction energy group calculation.

__init__(_, asl1, asl2)
Parameters:
  • asl1 (str) – atom selection for group 1
  • asl2 (str) – atom selection for group 2
getResult(result)
Returns:frame-by-frame result of the electric and van der Walls energies (both non-bonded and pair) between the two groups
Return type:a list of `tuple`s. Each tuple contains two `float`s
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.energygroup', '__doc__': '\n Analyzer for interaction energy group calculation.\n ', '__init__': <function InteractionEnergy.__init__>, 'getResult': <function InteractionEnergy.getResult>})
__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.packages.energygroup'
__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.packages.energygroup.Bulk(cms_model, type)

Bases: schrodinger.application.desmond.packages.energygroup.EnergyGroupBase

Analyzer for material science energy group calculation

MAX_GROUPS = 870
OPTIONS = {'DENSITY', 'PRESSURE_TENSOR', 'COHES_E', 'SOL_PARAM', 'SPECIFIC_HEAT', 'VOLUME', 'HEAT_VAP', 'INTRA_E', 'TOTAL_E'}
__init__(cms_model, type)

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

getResult(result)

Retrieve and format the result from the cache in EnergyFacade

getCfgParams(cfg_file)
Parameters:cfg_file – path to the simulation configuration file
parseEnergies(tmp_dir, num_groups)

Parse results of material science energy group calculaiton

Return type:dict
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.energygroup', '__doc__': '\n Analyzer for material science energy group calculation\n ', 'MAX_GROUPS': 870, 'OPTIONS': {'DENSITY', 'PRESSURE_TENSOR', 'COHES_E', 'SOL_PARAM', 'SPECIFIC_HEAT', 'VOLUME', 'HEAT_VAP', 'INTRA_E', 'TOTAL_E'}, '__init__': <function Bulk.__init__>, 'getResult': <function Bulk.getResult>, 'getCfgParams': <function Bulk.getCfgParams>, '_reduceEnergies': <function Bulk._reduceEnergies>, '_calcSpecHeat': <function Bulk._calcSpecHeat>, '_calcSpecHeatNVE': <function Bulk._calcSpecHeatNVE>, '_getResultsForLastNPercent': <function Bulk._getResultsForLastNPercent>, 'parseEnergies': <function Bulk.parseEnergies>})
__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.packages.energygroup'
__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.packages.energygroup.SliceParams(first, interval, last)

Bases: tuple

__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.packages.energygroup'
__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, first, interval, last)

Create new instance of SliceParams(first, interval, last)

__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
first

Alias for field number 0

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

interval

Alias for field number 1

last

Alias for field number 2

class schrodinger.application.desmond.packages.energygroup.EnergyComponent

Bases: object

Class for storing different energy components

add(term, val)
elec
vdw
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.energygroup', '__doc__': '\n Class for storing different energy components\n ', 'add': <function EnergyComponent.add>, 'elec': <property object>, 'vdw': <property object>, '__dict__': <attribute '__dict__' of 'EnergyComponent' objects>, '__weakref__': <attribute '__weakref__' of 'EnergyComponent' 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.packages.energygroup'
__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.packages.energygroup.temp_dir()
schrodinger.application.desmond.packages.energygroup.get_energies(sim_cfg, tr_path, cms_model, slicing, mol_num=None, asls=None, groups=None, max_groups=870, parse=<function _parse_energies>)

Calculate energies between groups of atoms specified by ASL selections, list of list of AIDs, or molecule number. Note there should be no overlap between any pair of the atom groups.

Parameters:parse (callable) – parser for the energy-group output data file
Return type:(c{list} of c{float}s, c{list} of EnergyComponent)
Returns:simulation times, and various energies for each frame

See EnergyFacade for other arguments

class schrodinger.application.desmond.packages.energygroup.EnergyFacade(sim_cfg, tr_path, cms_model, slicing)

Bases: object

A helper class to manage energy group calculations. Different energy group calculations have different input/output formats. All these details are hidden by using this class and the subclasses of EnergyGroupBase.

To get full control over the energy group calculation, call get_energies directly.

__init__(sim_cfg, tr_path, cms_model, slicing)
Parameters:
  • sim_cfg (str or None) – Path to Desmond simulaiton configuration.
  • tr_path (str) – Path to trajectory folder
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.energygroup', '__doc__': '\n A helper class to manage energy group calculations. Different energy group\n calculations have different input/output formats. All these details are\n hidden by using this class and the subclasses of `EnergyGroupBase`.\n\n To get full control over the energy group calculation, call `get_energies`\n directly.\n ', '__init__': <function EnergyFacade.__init__>, 'get': <function EnergyFacade.get>, '__dict__': <attribute '__dict__' of 'EnergyFacade' objects>, '__weakref__': <attribute '__weakref__' of 'EnergyFacade' 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.packages.energygroup'
__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)

get(ene)