schrodinger.application.desmond.gconfig module

Utilities for handling gDesmond config files.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.gconfig.real_to_int(val)

round up to the closest integer when the difference is less than 1e-7

schrodinger.application.desmond.gconfig.optimize_key(msj, cfg, model)

Optimizes the simulation parameters in ‘cfg’, where ‘cfg’ must represent a complete config file.

class schrodinger.application.desmond.gconfig.LambdaSchedule

Bases: object

Base class for lambda schedules.

lambdas = []

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.

__annotations__ = {'lambdas': typing.List[float]}

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__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>})

__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)

class schrodinger.application.desmond.gconfig.ScheduleAngleCorePhysical

Bases: schrodinger.application.desmond.gconfig.LambdaSchedule

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]

__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]})

__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.ScheduleAngleCoreDummy

Bases: schrodinger.application.desmond.gconfig.LambdaSchedule

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]

__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.

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.

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.

schrodinger.application.desmond.gconfig.get_ensemble_class_method(msj)

schrodinger.application.desmond.gconfig.get_simbox_output_filename(msj)

Returns ‘None’ if the simbox_output plugin is turned off.

schrodinger.application.desmond.gconfig.get_energy_group_output_filename(msj)

Returns ‘None’ if the energy_groups plugin is turned off.

schrodinger.application.desmond.gconfig.get_fep_output_filename(msj)

schrodinger.application.desmond.gconfig.gen_temperature_for_solute_tempering(setting, model, base_temp, asl, printer=None)

schrodinger.application.desmond.gconfig.gen_replica(msj, model=None)

schrodinger.application.desmond.gconfig.get_replica_setting(msj)

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 of sea.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

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

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

schrodinger.application.desmond.gconfig.msj2cfg(msj, cfg, model, macro=None)