schrodinger.application.desmond.rest_inp module

It prepares or runs a REST MD job.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.rest_inp.get_rest_input(model, jobname, host, **kwargs)

Function to prepare rest input.

Parameters:

• structure (Structure or cms.Cms) – Structure to apply rest hot region.
• jobname (str) – jobname
• hostname (str) – hostname
• kwargs (dict) – dictionary to set options

Return type:

tuple

Returns:

A tuple composed of (structure, msj, command)

schrodinger.application.desmond.rest_inp.add_rest_region(model, **kwargs)

Function to add rest region.

Parameters:

• structure (Structure or cms.Cms) – Structure to apply rest hot region.
• kwargs (dict) – dictionary to set options

Return type:

tuple

Returns:

A tuple composed of (structure, msj) msj only has “replica_exchange” stage

schrodinger.application.desmond.rest_inp.get_rest_region(model)

class schrodinger.application.desmond.rest_inp.RestInput(model, **kwargs)

Bases: object

__init__(model, **kwargs)

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

update(**kwargs)

updates states of options

prepare_structure()

Set hot region

prepare_msj()

Prepare multisim file

prepare_command(jobname, host, msj_fname, mae_fname)

Prepare command line

write(jobname, host)

writes msj and mae files

run(jobname, host)

Run MD REST Job

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.rest_inp', '__init__': <function RestInput.__init__>, 'update': <function RestInput.update>, 'prepare_structure': <function RestInput.prepare_structure>, 'prepare_msj': <function RestInput.prepare_msj>, 'prepare_command': <function RestInput.prepare_command>, 'write': <function RestInput.write>, 'run': <function RestInput.run>, '__dict__': <attribute '__dict__' of 'RestInput' objects>, '__weakref__': <attribute '__weakref__' of 'RestInput' 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_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.rest_inp'

__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)