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