Package schrodinger :: Package application :: Package desmond :: Module stage

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Module stage

Various multisim concrete stage classes.

Copyright Schrodinger, LLC. All rights reserved.

Classes

Primer

Concluder
This stage does not create any jobs for the 'cmj.QUEUE'.

Multisim

DesmondJob

FepJob

Task

ForcefieldBuilder

BuildGeometry

AssignForcefield

SystemBuilder

FepMapping

Simulate

Minimize

ReplicaExchange

LambdaHopping

DesmondExtend

Vrun

FepVrun

Reporter

AnalysisJob

TimeSeriesAnalysisJob

MetadynamicsAnalysisJob

SeaJob

PLAnalysis
This class sets up and runs automatic analsyis for protein-ligand complex

Analysis

FepanaJob

FepAnalysis

FepAnalysis2

CalcDdg

FepMapperReport

Trajectory

WaterMap

WaterMapCluster

WaterMapAnaJob

WaterMapPostAnalysis

SolvatePocket

McproStageBase

McproSystemBuilder

McproSimulate

Extern

Trim

Stop

CovMapper

FepMapper

LeadOptMap

AlignCore

Functions

concatenate_and_backup(text_fname)

all_stage_family()

_xchk_check_stage_family(map, valid, ev, prefix)

_xchk_check_box_size(map, valid, ev, prefix)

_xchk_check_restrain(map, valid, ev, prefix)

_xchk_multisim_file_exists(map, valid, ev, prefix)

systrait_is(stage, map_msj, arg)

systype_is(stage, map_msj, arg)

has_file(stage, map_msj, arg)

has_dir(stage, map_msj, arg)

is_debugging(stage, map_msj, arg)

Variables

PREDEFINED_STAGE_FAMILY = {'desmond': set(['fep_vrun', 'lambda...

STAGE_FAMILY = None
hash(x)

stage = cmj.StageBase()

job0 = DesmondJob("", None, None, None, None, None, stage, Non...

job = FepJob(None, None, None, None, None, None, "", None, Non...

job_copy = copy.deepcopy(job)

__package__ = 'schrodinger.application.desmond'

Variables Details

PREDEFINED_STAGE_FAMILY

Value:

{'desmond': set(['fep_vrun',
                 'lambda_hopping',
                 'minimize',
                 'replica_exchange',
                 'simulate']),
 'md': set(['lambda_hopping', 'replica_exchange', 'simulate']),
 'remd': set(['lambda_hopping', 'replica_exchange'])}

job0

Value:

DesmondJob("", None, None, None, None, None, stage, None, None)

job

Value:

FepJob(None, None, None, None, None, None, "", None, None, None, None,
 job0, stage, None, None)