schrodinger.application.canvas.r_group_dee module¶
R-Group Analysis Dead End elimination
-
class
schrodinger.application.canvas.r_group_dee.
SimulatedAnnealing
(energy_matrix, sa_seed=None, t_factor=None, tmax_mult=None)¶ Bases:
object
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static
getChoiceSpectrum
(choices)¶
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__init__
(energy_matrix, sa_seed=None, t_factor=None, tmax_mult=None)¶ Initializer for simulated annealing class.
Parameters: - energy_matrix (
DEE_EnergyMatrix
) – precalculated pairwise matrix used by SA. - sa_seed (float) – SA random number generator seed
- t_fac – Factor (<1) by which T will be multiplied at each T change
- tmax_mult (float) – Factor by which no. of st. will be multiplied to get starting T
- energy_matrix (
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run
()¶
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is_another_best_config
(solution)¶
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new_best
(energy, solution)¶
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report_t
(t, start_E, end_E, tsteps, totalCnt, acceptCnt)¶
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getNewSolution
(solution_old)¶
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neighbor
(solution)¶
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new_temperature
(old_t)¶
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boltzmann_probability
(e_old, e_new, t)¶
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getBestMatch
()¶
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__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.canvas.r_group_dee', 'getChoiceSpectrum': <staticmethod object>, '__init__': <function SimulatedAnnealing.__init__>, 'run': <function SimulatedAnnealing.run>, 'is_another_best_config': <function SimulatedAnnealing.is_another_best_config>, 'new_best': <function SimulatedAnnealing.new_best>, 'report_t': <function SimulatedAnnealing.report_t>, 'getNewSolution': <function SimulatedAnnealing.getNewSolution>, 'neighbor': <function SimulatedAnnealing.neighbor>, 'new_temperature': <function SimulatedAnnealing.new_temperature>, 'boltzmann_probability': <function SimulatedAnnealing.boltzmann_probability>, 'getBestMatch': <function SimulatedAnnealing.getBestMatch>, '__dict__': <attribute '__dict__' of 'SimulatedAnnealing' objects>, '__weakref__': <attribute '__weakref__' of 'SimulatedAnnealing' objects>, '__doc__': None})¶
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__dir__
() → list¶ default dir() implementation
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__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.canvas.r_group_dee'¶
-
__ne__
¶ Return self!=value.
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__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).
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__weakref__
¶ list of weak references to the object (if defined)
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static
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class
schrodinger.application.canvas.r_group_dee.
DEE_Backtracking
(energy_matrix)¶ Bases:
object
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__init__
(energy_matrix)¶ Initialize self. See help(type(self)) for accurate signature.
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minimize
()¶
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backtrack
(solution)¶
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reject
(solution)¶
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accept
(solution)¶
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first
(solution)¶
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next
(solution)¶
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output
(solution)¶
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getBestMatch
()¶
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__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.canvas.r_group_dee', '__init__': <function DEE_Backtracking.__init__>, 'minimize': <function DEE_Backtracking.minimize>, 'backtrack': <function DEE_Backtracking.backtrack>, 'reject': <function DEE_Backtracking.reject>, 'accept': <function DEE_Backtracking.accept>, 'first': <function DEE_Backtracking.first>, 'next': <function DEE_Backtracking.next>, 'output': <function DEE_Backtracking.output>, 'getBestMatch': <function DEE_Backtracking.getBestMatch>, '__dict__': <attribute '__dict__' of 'DEE_Backtracking' objects>, '__weakref__': <attribute '__weakref__' of 'DEE_Backtracking' 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.canvas.r_group_dee'¶
-
__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.canvas.r_group_dee.
DEE_EnergyMatrix
(choices, uij)¶ Bases:
object
-
__init__
(choices, uij)¶ Initialize self. See help(type(self)) for accurate signature.
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numPos
()¶
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numChoices
()¶
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calculateEnergy
(solution)¶
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calculateEnergyDifference
(solution_old, e_old, istruct, solution_new)¶
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initialSolution
()¶
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checkSolution
(solution)¶
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convertSolution
(solution)¶
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applyEnergyFilter
(solution, current_energy)¶
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eliminateSingles
()¶
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eliminatePairs
()¶
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applyGoldsteinSingles
(k, a, b)¶
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__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.canvas.r_group_dee', '__init__': <function DEE_EnergyMatrix.__init__>, 'numPos': <function DEE_EnergyMatrix.numPos>, 'numChoices': <function DEE_EnergyMatrix.numChoices>, 'calculateEnergy': <function DEE_EnergyMatrix.calculateEnergy>, 'calculateEnergyDifference': <function DEE_EnergyMatrix.calculateEnergyDifference>, 'initialSolution': <function DEE_EnergyMatrix.initialSolution>, 'checkSolution': <function DEE_EnergyMatrix.checkSolution>, 'convertSolution': <function DEE_EnergyMatrix.convertSolution>, 'applyEnergyFilter': <function DEE_EnergyMatrix.applyEnergyFilter>, 'eliminateSingles': <function DEE_EnergyMatrix.eliminateSingles>, 'eliminatePairs': <function DEE_EnergyMatrix.eliminatePairs>, 'applyGoldsteinSingles': <function DEE_EnergyMatrix.applyGoldsteinSingles>, '__dict__': <attribute '__dict__' of 'DEE_EnergyMatrix' objects>, '__weakref__': <attribute '__weakref__' of 'DEE_EnergyMatrix' 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.canvas.r_group_dee'¶
-
__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)
-
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schrodinger.application.canvas.r_group_dee.
main
()¶