schrodinger.application.desmond.config module¶

Utilities for handling Desmond config files.

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)¶

schrodinger.application.desmond.config.get_msj_backend(msj, default=None)¶: Get reference to the ‘backend’ map from the msj map.

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>¶

REINIT = <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_REINIT = <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=())¶

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>¶

reinit = <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_reinit(msj)¶: Does msj require the “reinit” app?

schrodinger.application.desmond.config.is_concat(msj)¶

schrodinger.application.desmond.config.is_gcmc(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_updated_msj_block(msj, key, default_settings)¶

Get msj block for given key

NOTE: Here, the assumption is that no other code depends on msj being updated, we can return a block without side effects on the msj. This is implemented as msj block should be kept independent and not updated. Please see RB https://reviewboard.schrodinger.com/r/70593/. However, if this option is impossible to maintain, we should implement the other option suggested in RB.

Parameters

msj (sea.Map) – msj block
key (str) – name of the key
default_settings (sea.Map) – default setting for the given key

schrodinger.application.desmond.config.get_ensemble(msj)¶

Get ensemble name from msj block

Parameters: msj (sea.Map) – msj block
Return str: name of the ensemble

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)¶