schrodinger.application.desmond.config module

Utilities for handling Desmond config files.

Copyright Schrodinger, LLC. All rights reserved.

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
schrodinger.application.desmond.config.has_plugin(desmond_exec, plugin_name)
schrodinger.application.desmond.config.add_plugin(desmond_exec, plugin_name, position=None)
schrodinger.application.desmond.config.remove_plugin(desmond_exec, plugin_name)
schrodinger.application.desmond.config.get_homebox(box, cpu_top)
schrodinger.application.desmond.config.is_triclinic_box(box)
schrodinger.application.desmond.config.optimize_key(msj, cfg, model)

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

schrodinger.application.desmond.config.parse_lambda(s)
schrodinger.application.desmond.config.lambda_type(lambda_)
schrodinger.application.desmond.config.num_lambda_window(lambda_)
schrodinger.application.desmond.config.get_fep_lambda_schedule(lambda_, fep_type)
class schrodinger.application.desmond.config.DEFAULT_SETTING

Bases: object

MD = <schrodinger.utils.sea.Map object>
MINIMIZE = <schrodinger.utils.sea.Map object>
BROWNIE_MINIMIZE = <schrodinger.utils.sea.Map object>
REMD = <schrodinger.utils.sea.Map object>
META = <schrodinger.utils.sea.Map object>
VRUN = <schrodinger.utils.sea.Map object>
CONCAT = <schrodinger.utils.sea.Map object>
GCMC = <schrodinger.utils.sea.Map object>
VALIDATE_MD = <schrodinger.utils.sea.Map object>
VALIDATE_MINIMIZE = <schrodinger.utils.sea.Map object>
VALIDATE_BROWNIE_MINIMIZE = <schrodinger.utils.sea.Map object>
VALIDATE_REMD = <schrodinger.utils.sea.Map object>
VALIDATE_META = <schrodinger.utils.sea.Map object>
VALIDATE_VRUN = <schrodinger.utils.sea.Map object>
VALIDATE_CONCAT = <schrodinger.utils.sea.Map object>
VALIDATE_GCMC = <schrodinger.utils.sea.Map object>
__init__

Initialize self. See help(type(self)) for accurate signature.

schrodinger.application.desmond.config.get_default_setting(msj)
schrodinger.application.desmond.config.tag_sim_map(map, sim_tag_spec, **kwargs)
class schrodinger.application.desmond.config.TagSpec(tag, remove_keys=())

Bases: object

Represents a tag and its associated keys

__init__(tag, remove_keys=())

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.config.TAG_SPECS

Bases: object

md = <schrodinger.application.desmond.config.TagSpec object>
minimize = <schrodinger.application.desmond.config.TagSpec object>
brownie_minimize = <schrodinger.application.desmond.config.TagSpec object>
remd = <schrodinger.application.desmond.config.TagSpec object>
meta = <schrodinger.application.desmond.config.TagSpec object>
vrun = <schrodinger.application.desmond.config.TagSpec object>
concat = <schrodinger.application.desmond.config.TagSpec object>
gcmc = <schrodinger.application.desmond.config.TagSpec object>
__init__

Initialize self. See help(type(self)) for accurate signature.

schrodinger.application.desmond.config.is_minimize(msj)
schrodinger.application.desmond.config.is_remd(msj)
schrodinger.application.desmond.config.is_meta(msj)
schrodinger.application.desmond.config.is_vrun(msj)
schrodinger.application.desmond.config.is_concat(msj)
schrodinger.application.desmond.config.is_gcmc(msj)
schrodinger.application.desmond.config.is_fep(msj)
schrodinger.application.desmond.config.get_exec(msj, cfg)
schrodinger.application.desmond.config.get_exec_name(msj)
schrodinger.application.desmond.config.num_replica(msj, model, printer=None)
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

schrodinger.application.desmond.config.num_cpu(msj)
schrodinger.application.desmond.config.get_fep_lambdas(n_win, fep_type, scheme)

return default lambdas

schrodinger.application.desmond.config.get_ensemble_class_method(msj)
schrodinger.application.desmond.config.get_simbox_output_filename(msj)

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

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

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

schrodinger.application.desmond.config.get_fep_output_filename(msj)
schrodinger.application.desmond.config.gen_temperature_for_solute_tempering(setting, model, base_temp, asl, printer=None)
schrodinger.application.desmond.config.gen_replica(msj, model=None)
schrodinger.application.desmond.config.get_replica_setting(msj)
schrodinger.application.desmond.config.msj2cfg(msj, cfg, model, macro=None, is_gdesmond=False)
schrodinger.application.desmond.config.translate_output_file_names_helper(msj, macro_dict)
schrodinger.application.desmond.config.translate_output_file_names(msj, macro_dict, num_replica=1)
schrodinger.application.desmond.config.canonicalize(msj)