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=2097152, 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.sea.Map object>

MINIMIZE = <schrodinger.utils.sea.sea.Map object>

BROWNIE_MINIMIZE = <schrodinger.utils.sea.sea.Map object>

REMD = <schrodinger.utils.sea.sea.Map object>

META = <schrodinger.utils.sea.sea.Map object>

VRUN = <schrodinger.utils.sea.sea.Map object>

CONCAT = <schrodinger.utils.sea.sea.Map object>

GCMC = <schrodinger.utils.sea.sea.Map object>

VALIDATE_MD = <schrodinger.utils.sea.sea.Map object>

VALIDATE_MINIMIZE = <schrodinger.utils.sea.sea.Map object>

VALIDATE_BROWNIE_MINIMIZE = <schrodinger.utils.sea.sea.Map object>

VALIDATE_REMD = <schrodinger.utils.sea.sea.Map object>

VALIDATE_META = <schrodinger.utils.sea.sea.Map object>

VALIDATE_VRUN = <schrodinger.utils.sea.sea.Map object>

VALIDATE_CONCAT = <schrodinger.utils.sea.sea.Map object>

VALIDATE_GCMC = <schrodinger.utils.sea.sea.Map object>

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>

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)