schrodinger.application.desmond.fep_reporter module¶

class schrodinger.application.desmond.fep_reporter.FEPReportMaker(basename=None, cms_fn=None, tmp_dir=None)[source]¶

Bases: object

__init__(basename=None, cms_fn=None, tmp_dir=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

get_cms(cms_fn)[source]¶: try to find cms file

parse_fep_data()[source]¶: Given an ark object, parse the data

read_FEPSimulation(ark_obj)[source]¶

read_ProteinInfo(ark_obj)[source]¶

read_LigandInfo(ark_obj)[source]¶

read_FEP_REST_energetics(ark_obj)[source]¶

read_REST_exchanges(ark_obj)[source]¶

report()[source]¶

cleanupTempFiles()[source]¶

init_report()[source]¶

reportFinalResults()[source]¶

reportReplicaExchanges()[source]¶

reportReplicaPairEnergies()[source]¶

add_replicas_dF_table(ark_obj)[source]¶

add_overlapEnergyTable(data)[source]¶

getRESTDensityPlot()[source]¶

getOverlapEnergyPlot()[source]¶

getEnergyConvergencePlot()[source]¶

reportLigandsDetails()[source]¶

reportProteinDetails()[source]¶

getSequenceViewerImage(prot_str)[source]¶: Generate protein sequence image, given a protein structure Returns a platipus image

getTempImageFilename()[source]¶

getLigandImage(asl_str, lig_num)[source]¶

get_protein()[source]¶

reportSimulationDetails()[source]¶

error(msg)[source]¶

str(str_in)[source]¶: This is to remove the “‘s in ARK returned strings enclosed in double quotes