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>

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_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>

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.config', '__doc__': '\n\n ', 'MD': <schrodinger.utils.sea.Map object>, '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_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>, '__dict__': <attribute '__dict__' of 'DEFAULT_SETTING' objects>, '__weakref__': <attribute '__weakref__' of 'DEFAULT_SETTING' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.config'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.config', '__doc__': '\n Represents a tag and its associated keys\n ', '__init__': <function TagSpec.__init__>, '__dict__': <attribute '__dict__' of 'TagSpec' objects>, '__weakref__': <attribute '__weakref__' of 'TagSpec' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.config'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.config.TAG_SPECS

Bases: object

md = <schrodinger.application.desmond.config.TagSpec object>

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>

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.config', 'md': <schrodinger.application.desmond.config._create_tag_when_needed object>, 'minimize': <schrodinger.application.desmond.config._create_tag_when_needed object>, 'remd': <schrodinger.application.desmond.config._create_tag_when_needed object>, 'meta': <schrodinger.application.desmond.config._create_tag_when_needed object>, 'vrun': <schrodinger.application.desmond.config._create_tag_when_needed object>, 'concat': <schrodinger.application.desmond.config._create_tag_when_needed object>, 'gcmc': <schrodinger.application.desmond.config._create_tag_when_needed object>, '__dict__': <attribute '__dict__' of 'TAG_SPECS' objects>, '__weakref__': <attribute '__weakref__' of 'TAG_SPECS' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.config'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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)