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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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)¶