schrodinger.application.desmond.fep_reporter module

class schrodinger.application.desmond.fep_reporter.FEPReportMaker(basename=None, cms_fn=None, tmp_dir=None)

Bases: object

__init__(basename=None, cms_fn=None, tmp_dir=None)

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

get_cms(cms_fn)

try to find cms file

parse_fep_data()

Given an ark object, parse the data

read_FEPSimulation(ark_obj)

read_ProteinInfo(ark_obj)

read_LigandInfo(ark_obj)

read_FEP_REST_energetics(ark_obj)

read_REST_exchanges(ark_obj)

report()

cleanupTempFiles()

init_report()

reportFinalResults()

reportReplicaExchanges()

reportReplicaPairEnergies()

add_replicas_dF_table(ark_obj)

add_overlapEnergyTable(data)

getRESTDensityPlot()

getOverlapEnergyPlot()

getEnergyConvergencePlot()

reportLigandsDetails()

reportProteinDetails()

getSequenceViewerImage(prot_str)

Generate protein sequence image, given a protein structure Returns a platipus image

getTempImageFilename()

getLigandImage(asl_str, lig_num)

get_protein()

reportSimulationDetails()

error(msg)

str(str_in)

This is to remove the “‘s in ARK returned strings enclosed in double quotes

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.fep_reporter', '__init__': <function FEPReportMaker.__init__>, '_load_modules': <function FEPReportMaker._load_modules>, 'get_cms': <function FEPReportMaker.get_cms>, 'parse_fep_data': <function FEPReportMaker.parse_fep_data>, 'read_FEPSimulation': <function FEPReportMaker.read_FEPSimulation>, 'read_ProteinInfo': <function FEPReportMaker.read_ProteinInfo>, 'read_LigandInfo': <function FEPReportMaker.read_LigandInfo>, 'read_FEP_REST_energetics': <function FEPReportMaker.read_FEP_REST_energetics>, 'read_REST_exchanges': <function FEPReportMaker.read_REST_exchanges>, 'report': <function FEPReportMaker.report>, 'cleanupTempFiles': <function FEPReportMaker.cleanupTempFiles>, 'init_report': <function FEPReportMaker.init_report>, 'reportFinalResults': <function FEPReportMaker.reportFinalResults>, 'reportReplicaExchanges': <function FEPReportMaker.reportReplicaExchanges>, 'reportReplicaPairEnergies': <function FEPReportMaker.reportReplicaPairEnergies>, 'add_replicas_dF_table': <function FEPReportMaker.add_replicas_dF_table>, 'add_overlapEnergyTable': <function FEPReportMaker.add_overlapEnergyTable>, 'getRESTDensityPlot': <function FEPReportMaker.getRESTDensityPlot>, 'getOverlapEnergyPlot': <function FEPReportMaker.getOverlapEnergyPlot>, 'getEnergyConvergencePlot': <function FEPReportMaker.getEnergyConvergencePlot>, 'reportLigandsDetails': <function FEPReportMaker.reportLigandsDetails>, 'reportProteinDetails': <function FEPReportMaker.reportProteinDetails>, 'getSequenceViewerImage': <function FEPReportMaker.getSequenceViewerImage>, 'getTempImageFilename': <function FEPReportMaker.getTempImageFilename>, 'getLigandImage': <function FEPReportMaker.getLigandImage>, 'get_protein': <function FEPReportMaker.get_protein>, 'reportSimulationDetails': <function FEPReportMaker.reportSimulationDetails>, 'error': <function FEPReportMaker.error>, 'str': <function FEPReportMaker.str>, '__dict__': <attribute '__dict__' of 'FEPReportMaker' objects>, '__weakref__': <attribute '__weakref__' of 'FEPReportMaker' 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.fep_reporter'

__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)