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)
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