schrodinger.application.desmond.gconfig module¶

Utilities for handling gDesmond config files.

schrodinger.application.desmond.gconfig.add_plugin(desmond_exec, plugin_name, position=None)¶: Wrap config.add_plugin, making sure to place added plugins before GCMC

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, box: List[float])¶

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

Parameters: box – Simulation box dimensions.

class schrodinger.application.desmond.gconfig.LambdaSchedule¶

Bases: object

Base class for lambda schedules.

lambdas: List[float] = []¶

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.ScheduleAngleCorePhysical¶

Bases: schrodinger.application.desmond.gconfig.LambdaSchedule

Schedule for angle_core_physical terms.

lambdas: List[float] = [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]¶

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: List[float] = [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]¶

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: List[float] = [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]¶

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: List[float] = [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]¶

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: List[float] = [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]¶

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.ScheduleLinear¶

Bases: schrodinger.application.desmond.gconfig.LambdaSchedule

Linear lambda schedule.

lambdas: List[float] = [1.0, 0.0]¶

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.set_dpd_params(msj, cfg, ensemble)¶

Set parameters for DPD simulation

Parameters: ensemble (str) – name of the ensemble

schrodinger.application.desmond.gconfig.get_tempearture(msj)¶

get temperature from msj

Return type: float
Returns: temperature

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, previous_posre_scaling, 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
previous_posre_scaling (float or NoneType) – posre_scaling parameter from the previous stage’s config, or None if unknown
restrain (sea.Map) – this stage’s restrain parameter
this_integrator (sea.Map) – this stage’s integrator

Returns

the first restrain parameter and posre scaling factor

schrodinger.application.desmond.gconfig.restrain_force_constant(restraints: schrodinger.utils.sea.sea.Map) → float¶

Get restraints force constant.

Parameters: restraints – the restraints block for a given stage
Returns: the (first) restraint force constant

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