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
Unimplemented stage.

DesmondJob

FepJob

Task

BuildGeometry

AssignForcefield

SystemBuilder

Simulate

Minimize

ReplicaExchange

LambdaHopping

Vrun

FepVrun

Reporter

AnalysisJob

TimeSeriesAnalysisJob

MetadynamicsAnalysisJob

SeaJob

Analysis

FepanaJob

FepAnalysis

Trajectory

WaterMap

WaterMapCluster

WaterMapAnaJob

WaterMapPostAnalysis

SolvatePocket

McproStageBase

McproSystemBuilder

McproSimulate

Extern

Trim

Stop

Functions

all_stage_family()

_xchk_check_stage_family(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'])}

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)