schrodinger.application.desmond.config module¶
Utilities for handling Desmond config files.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.desmond.config.
extract_cfg
(cpt_fname, min_size=1048576, return_raw=False)¶ Extracts the extended ark content from a checkpoint file. This function returns a `sea.Map’ object or None if parsing fails.
- The ark as represented by the string contains the following values:
- argv : the argument vector
- boot_timestamp : the boot time for the program
- chemical_time : chemical time in pico seconds
- config : the ark file
- threader_size : the number of threads
- version : the desmond version
- world_size : the number of processors
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schrodinger.application.desmond.config.
has_plugin
(desmond_exec, plugin_name)¶
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schrodinger.application.desmond.config.
add_plugin
(desmond_exec, plugin_name, position=None)¶
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schrodinger.application.desmond.config.
remove_plugin
(desmond_exec, plugin_name)¶
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schrodinger.application.desmond.config.
get_homebox
(box, cpu_top)¶
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schrodinger.application.desmond.config.
is_triclinic_box
(box)¶
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schrodinger.application.desmond.config.
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.config.
parse_lambda
(s)¶
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schrodinger.application.desmond.config.
lambda_type
(lambda_)¶
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schrodinger.application.desmond.config.
num_lambda_window
(lambda_)¶
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schrodinger.application.desmond.config.
get_fep_lambda_schedule
(lambda_, fep_type)¶
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class
schrodinger.application.desmond.config.
DEFAULT_SETTING
¶ Bases:
object
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MD
= <schrodinger.utils.sea.Map object>¶
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MINIMIZE
= <schrodinger.utils.sea.Map object>¶
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BROWNIE_MINIMIZE
= <schrodinger.utils.sea.Map object>¶
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REMD
= <schrodinger.utils.sea.Map object>¶
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META
= <schrodinger.utils.sea.Map object>¶
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VRUN
= <schrodinger.utils.sea.Map object>¶
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CONCAT
= <schrodinger.utils.sea.Map object>¶
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GCMC
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_MD
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_MINIMIZE
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_BROWNIE_MINIMIZE
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_REMD
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_META
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_VRUN
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_CONCAT
= <schrodinger.utils.sea.Map object>¶
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VALIDATE_GCMC
= <schrodinger.utils.sea.Map object>¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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schrodinger.application.desmond.config.
get_default_setting
(msj)¶
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schrodinger.application.desmond.config.
tag_sim_map
(map, sim_tag_spec, **kwargs)¶
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class
schrodinger.application.desmond.config.
TagSpec
(tag, remove_keys=())¶ Bases:
object
Represents a tag and its associated keys
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__init__
(tag, remove_keys=())¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.config.
TAG_SPECS
¶ Bases:
object
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md
= <schrodinger.application.desmond.config.TagSpec object>¶
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minimize
= <schrodinger.application.desmond.config.TagSpec object>¶
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brownie_minimize
= <schrodinger.application.desmond.config.TagSpec object>¶
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remd
= <schrodinger.application.desmond.config.TagSpec object>¶
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meta
= <schrodinger.application.desmond.config.TagSpec object>¶
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vrun
= <schrodinger.application.desmond.config.TagSpec object>¶
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concat
= <schrodinger.application.desmond.config.TagSpec object>¶
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gcmc
= <schrodinger.application.desmond.config.TagSpec object>¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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schrodinger.application.desmond.config.
is_minimize
(msj)¶
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schrodinger.application.desmond.config.
is_remd
(msj)¶
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schrodinger.application.desmond.config.
is_meta
(msj)¶
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schrodinger.application.desmond.config.
is_vrun
(msj)¶
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schrodinger.application.desmond.config.
is_concat
(msj)¶
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schrodinger.application.desmond.config.
is_gcmc
(msj)¶
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schrodinger.application.desmond.config.
is_fep
(msj)¶
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schrodinger.application.desmond.config.
get_exec
(msj, cfg)¶
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schrodinger.application.desmond.config.
get_exec_name
(msj)¶
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schrodinger.application.desmond.config.
num_replica
(msj, model, printer=None)¶
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schrodinger.application.desmond.config.
get_rest_replica
(atom_selection='atom.i_rest_hotregion 1', exchange_probability=0.3, n_replica=2)¶ Return REST-specific replicas :rtype:
sea.Map
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schrodinger.application.desmond.config.
num_cpu
(msj)¶
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schrodinger.application.desmond.config.
get_fep_lambdas
(n_win, fep_type, scheme)¶ return default lambdas
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schrodinger.application.desmond.config.
get_ensemble_class_method
(msj)¶
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schrodinger.application.desmond.config.
get_simbox_output_filename
(msj)¶ Returns ‘None’ if the simbox_output plugin is turned off.
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schrodinger.application.desmond.config.
get_energy_group_output_filename
(msj)¶ Returns ‘None’ if the energy_groups plugin is turned off.
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schrodinger.application.desmond.config.
get_fep_output_filename
(msj)¶
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schrodinger.application.desmond.config.
gen_temperature_for_solute_tempering
(setting, model, base_temp, asl, printer=None)¶
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schrodinger.application.desmond.config.
gen_replica
(msj, model=None)¶
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schrodinger.application.desmond.config.
get_replica_setting
(msj)¶
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schrodinger.application.desmond.config.
msj2cfg
(msj, cfg, model, macro=None, is_gdesmond=False)¶
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schrodinger.application.desmond.config.
translate_output_file_names_helper
(msj, macro_dict)¶
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schrodinger.application.desmond.config.
translate_output_file_names
(msj, macro_dict, num_replica=1)¶
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schrodinger.application.desmond.config.
canonicalize
(msj)¶