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.
add_plugin
(desmond_exec, plugin_name, position=None)¶ Wrap config.add_plugin, making sure to place added plugins before GCMC
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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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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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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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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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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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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]¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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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class
schrodinger.application.desmond.gconfig.
ScheduleBondCoreDummy
¶ Bases:
schrodinger.application.desmond.gconfig.LambdaSchedule
Schedule for bond_core_dummy terms.
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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]¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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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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]¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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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class
schrodinger.application.desmond.gconfig.
ScheduleLinear
¶ Bases:
schrodinger.application.desmond.gconfig.LambdaSchedule
Linear lambda schedule.
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lambdas
= [1.0, 0.0]¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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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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)¶
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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 (
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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)¶