schrodinger.application.desmond.fep_scholar_msj_generator module

class schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator(jobname, cd_params, structure_fname, force_field='OPLS_2005', ensemble='NPT', sim_time='5000', rand_seed='2015', complex_box_buffer_width=5.0, trj_interval=24.0)

Bases: object

This class generates master msj file that manages both solvent and complex legs of the FEP simulation.

__init__(jobname, cd_params, structure_fname, force_field='OPLS_2005', ensemble='NPT', sim_time='5000', rand_seed='2015', complex_box_buffer_width=5.0, trj_interval=24.0)

Valid FF : OPLS_2005 CHARMM AMBER

write_complex_msj()

write_solvent_msj()

write_master_msj()

generate_subjob_msj(fname, buffer_width, MSJ_TEMPLATE=None)

generate_master_msj()

modify_multisim_stage(raw)

Method modifies ‘multisim’ stage in the master msj file

get_total_proc()

static set_box_buffer_width(raw, width)

set_ff(raw)

set_lambda_hopping(raw)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.fep_scholar_msj_generator', '__doc__': '\n This class generates master msj file that manages both solvent and complex\n legs of the FEP simulation.\n ', '__init__': <function FEPScholarMsjGenerator.__init__>, 'write_complex_msj': <function FEPScholarMsjGenerator.write_complex_msj>, 'write_solvent_msj': <function FEPScholarMsjGenerator.write_solvent_msj>, 'write_master_msj': <function FEPScholarMsjGenerator.write_master_msj>, 'generate_subjob_msj': <function FEPScholarMsjGenerator.generate_subjob_msj>, 'generate_master_msj': <function FEPScholarMsjGenerator.generate_master_msj>, 'modify_multisim_stage': <function FEPScholarMsjGenerator.modify_multisim_stage>, 'get_total_proc': <function FEPScholarMsjGenerator.get_total_proc>, 'set_box_buffer_width': <staticmethod object>, 'set_ff': <function FEPScholarMsjGenerator.set_ff>, 'set_lambda_hopping': <function FEPScholarMsjGenerator.set_lambda_hopping>, '__dict__': <attribute '__dict__' of 'FEPScholarMsjGenerator' objects>, '__weakref__': <attribute '__weakref__' of 'FEPScholarMsjGenerator' 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.fep_scholar_msj_generator'

__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)