schrodinger.application.desmond.gconfig module¶
Utilities for handling gDesmond config files.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.desmond.gconfig.
real_to_int
(val)¶ round up to the closest integer when the difference is less than 1e-7
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schrodinger.application.desmond.gconfig.
optimize_key
(msj, cfg, model)¶ Optimizes the simulation parameters in ‘cfg’, where ‘cfg’ must represent a complete config file.
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class
schrodinger.application.desmond.gconfig.
LambdaSchedule
¶ Bases:
object
Base class for lambda schedules.
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lambdas
= []¶
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classmethod
schedule
(n_win: int) → List[float]¶ Return schedule with the desired number of windows.
This method constructs a piecewise linear spline interpolator of the prototype lambda schedule and evaluates it on the specified number of windows to obtain the new lambda schedule.
Parameters: n_win – Number of lambda windows to use. Returns: New lambda schedule.
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__annotations__
= {'lambdas': typing.List[float]}¶
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.gconfig', '__annotations__': {'lambdas': typing.List[float]}, '__doc__': 'Base class for lambda schedules.', 'lambdas': [], 'schedule': <classmethod object>, '__dict__': <attribute '__dict__' of 'LambdaSchedule' objects>, '__weakref__': <attribute '__weakref__' of 'LambdaSchedule' objects>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
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__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
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__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.
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__le__
¶ Return self<=value.
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__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.gconfig'¶
-
__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).
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__weakref__
¶ list of weak references to the object (if defined)
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class
schrodinger.application.desmond.gconfig.
ScheduleAngleCorePhysical
¶ Bases:
schrodinger.application.desmond.gconfig.LambdaSchedule
Schedule for angle_core_physical terms.
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lambdas
= [1.0, 0.8, 0.6, 0.35, 0.2, 0.1, 0.03, 0.01, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]¶
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__annotations__
= {'lambdas': typing.List[float]}¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.gconfig', '__doc__': 'Schedule for angle_core_physical terms.', 'lambdas': [1.0, 0.8, 0.6, 0.35, 0.2, 0.1, 0.03, 0.01, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]})¶
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__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
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__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
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__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.
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__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.gconfig'¶
-
__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).
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__weakref__
¶ list of weak references to the object (if defined)
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classmethod
schedule
(n_win: int) → List[float]¶ Return schedule with the desired number of windows.
This method constructs a piecewise linear spline interpolator of the prototype lambda schedule and evaluates it on the specified number of windows to obtain the new lambda schedule.
Parameters: n_win – Number of lambda windows to use. Returns: New lambda schedule.
-
-
class
schrodinger.application.desmond.gconfig.
ScheduleAngleCoreDummy
¶ Bases:
schrodinger.application.desmond.gconfig.LambdaSchedule
Schedule for angle_core_dummy terms.
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lambdas
= [1.0, 0.8, 0.65, 0.5, 0.4, 0.3, 0.2, 0.16, 0.12, 0.08, 0.04, 0.01, 0.0, 0.0, 0.0, 0.0]¶
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__annotations__
= {'lambdas': typing.List[float]}¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.gconfig', '__doc__': 'Schedule for angle_core_dummy terms.', 'lambdas': [1.0, 0.8, 0.65, 0.5, 0.4, 0.3, 0.2, 0.16, 0.12, 0.08, 0.04, 0.01, 0.0, 0.0, 0.0, 0.0]})¶
-
__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.gconfig'¶
-
__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)
-
classmethod
schedule
(n_win: int) → List[float]¶ Return schedule with the desired number of windows.
This method constructs a piecewise linear spline interpolator of the prototype lambda schedule and evaluates it on the specified number of windows to obtain the new lambda schedule.
Parameters: n_win – Number of lambda windows to use. Returns: New lambda schedule.
-
-
class
schrodinger.application.desmond.gconfig.
ScheduleBondCorePhysical
¶ Bases:
schrodinger.application.desmond.gconfig.LambdaSchedule
Schedule for bond_core_physical terms.
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lambdas
= [1.0, 0.3, 0.1, 0.05, 0.03, 0.01, 0.002, 0.001, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]¶
-
__annotations__
= {'lambdas': typing.List[float]}¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.gconfig', '__doc__': 'Schedule for bond_core_physical terms.', 'lambdas': [1.0, 0.3, 0.1, 0.05, 0.03, 0.01, 0.002, 0.001, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]})¶
-
__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.gconfig'¶
-
__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)
-
classmethod
schedule
(n_win: int) → List[float]¶ Return schedule with the desired number of windows.
This method constructs a piecewise linear spline interpolator of the prototype lambda schedule and evaluates it on the specified number of windows to obtain the new lambda schedule.
Parameters: n_win – Number of lambda windows to use. Returns: New lambda schedule.
-
-
class
schrodinger.application.desmond.gconfig.
ScheduleBondCoreDummy
¶ Bases:
schrodinger.application.desmond.gconfig.LambdaSchedule
Schedule for bond_core_dummy terms.
-
lambdas
= [1.0, 0.6, 0.35, 0.22, 0.18, 0.14, 0.12, 0.11, 0.09, 0.08, 0.06, 0.02, 0.005, 0.0, 0.0, 0.0]¶
-
__annotations__
= {'lambdas': typing.List[float]}¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.gconfig', '__doc__': 'Schedule for bond_core_dummy terms.', 'lambdas': [1.0, 0.6, 0.35, 0.22, 0.18, 0.14, 0.12, 0.11, 0.09, 0.08, 0.06, 0.02, 0.005, 0.0, 0.0, 0.0]})¶
-
__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.gconfig'¶
-
__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)
-
classmethod
schedule
(n_win: int) → List[float]¶ Return schedule with the desired number of windows.
This method constructs a piecewise linear spline interpolator of the prototype lambda schedule and evaluates it on the specified number of windows to obtain the new lambda schedule.
Parameters: n_win – Number of lambda windows to use. Returns: New lambda schedule.
-
-
class
schrodinger.application.desmond.gconfig.
ScheduleAngleAttachment
¶ Bases:
schrodinger.application.desmond.gconfig.LambdaSchedule
Schedule for angle_attachment terms.
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lambdas
= [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.95, 0.9, 0.85, 0.8, 0.75, 0.6, 0.35, 0.1, 0.0]¶
-
__annotations__
= {'lambdas': typing.List[float]}¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.gconfig', '__doc__': 'Schedule for angle_attachment terms.', 'lambdas': [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.95, 0.9, 0.85, 0.8, 0.75, 0.6, 0.35, 0.1, 0.0]})¶
-
__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.gconfig'¶
-
__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)
-
classmethod
schedule
(n_win: int) → List[float]¶ Return schedule with the desired number of windows.
This method constructs a piecewise linear spline interpolator of the prototype lambda schedule and evaluates it on the specified number of windows to obtain the new lambda schedule.
Parameters: n_win – Number of lambda windows to use. Returns: New lambda schedule.
-
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schrodinger.application.desmond.gconfig.
get_ensemble_class_method
(msj)¶
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schrodinger.application.desmond.gconfig.
get_simbox_output_filename
(msj)¶ Returns ‘None’ if the simbox_output plugin is turned off.
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schrodinger.application.desmond.gconfig.
get_energy_group_output_filename
(msj)¶ Returns ‘None’ if the energy_groups plugin is turned off.
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schrodinger.application.desmond.gconfig.
get_fep_output_filename
(msj)¶
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schrodinger.application.desmond.gconfig.
gen_temperature_for_solute_tempering
(setting, model, base_temp, asl, printer=None)¶
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schrodinger.application.desmond.gconfig.
gen_replica
(msj, model=None)¶
-
schrodinger.application.desmond.gconfig.
get_replica_setting
(msj)¶
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schrodinger.application.desmond.gconfig.
concatenate_cfgs
(simulate_cfgs, base_cfg)¶ Create a single backend config file from a list of simulate configs created from the simulate block of a concatenate front-end config and the backend config created from the rest of the concatenate front-end config.
Parameters: - simulate_cfgs (
list
ofsea.Map
) – The list of backend config files created from the simulate block of a concatenate front-end config - base_cfg (
sea.Map
) – The backend config file created from a concatenate front-end config, with its simulate block removed.
Returns: A copy of the base concatenate config with the information from the simulate configs merged in.
Return type: sea.Map
- simulate_cfgs (
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schrodinger.application.desmond.gconfig.
set_relative_restrain_scaling
(first_restrain, restrain, this_integrator)¶ Set each integrator’s posre_scaling attribute to the ratio between the desired restraint force constant and the first force constant. This allows us to modulate the restraint force constant between concatenate stages.
Parameters: - first_restrain (
sea.Map
) – the restrain parameter from the first stage’s config, or None if updating the first stage - restrain (
sea.Map
) – this stage’s restrain parameter - this_integrator (
sea.Map
) – this stage’s integrator
Returns: the first restrain parameter and the first force constant
- first_restrain (
-
schrodinger.application.desmond.gconfig.
restrain_force_constant
(restrain)¶ Get the force constant for a restrain parameter
Parameters: restrain ( sea.Map
) – the restrain block for a given stage
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schrodinger.application.desmond.gconfig.
msj2cfg
(msj, cfg, model, macro=None)¶