schrodinger.application.desmond.fep_reporter module¶
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class
schrodinger.application.desmond.fep_reporter.
FEPReportMaker
(basename=None, cms_fn=None, tmp_dir=None)¶ Bases:
object
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__init__
(basename=None, cms_fn=None, tmp_dir=None)¶ Initialize self. See help(type(self)) for accurate signature.
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get_cms
(cms_fn)¶ try to find cms file
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parse_fep_data
()¶ Given an ark object, parse the data
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read_FEPSimulation
(ark_obj)¶
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read_ProteinInfo
(ark_obj)¶
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read_LigandInfo
(ark_obj)¶
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read_FEP_REST_energetics
(ark_obj)¶
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read_REST_exchanges
(ark_obj)¶
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report
()¶
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cleanupTempFiles
()¶
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init_report
()¶
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reportFinalResults
()¶
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reportReplicaExchanges
()¶
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reportReplicaPairEnergies
()¶
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add_replicas_dF_table
(ark_obj)¶
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add_overlapEnergyTable
(data)¶
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getRESTDensityPlot
()¶
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getOverlapEnergyPlot
()¶
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getEnergyConvergencePlot
()¶
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reportLigandsDetails
()¶
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reportProteinDetails
()¶
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getSequenceViewerImage
(prot_str)¶ Generate protein sequence image, given a protein structure Returns a platipus image
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getTempImageFilename
()¶
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getLigandImage
(asl_str, lig_num)¶
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get_protein
()¶
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reportSimulationDetails
()¶
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error
(msg)¶
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str
(str_in)¶ This is to remove the “‘s in ARK returned strings enclosed in double quotes
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