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

FepLauncher

DesmondJob

FepJob

Task

ForcefieldBuilder

BuildGeometry

AssignForcefield

SystemBuilder

FepMapping

Simulate

Minimize

ReplicaExchange

LambdaHopping

DesmondExtend

Vrun

FepVrun

Reporter

AnalysisJob

TimeSeriesAnalysisJob

MetadynamicsAnalysisJob

SeaJob

MatSciAnalysis
This class sets up and runs automatic analysis for material-science related jobs.

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

Analysis

FepanaJob

FepAnalysis

FepAnalysis2

CalcDdg

FepMapperReport

Trajectory

WaterMap

WaterMapCluster

WaterMapAnaJob

WaterMapPostAnalysis

SolvatePocket

McproStageBase

McproSystemBuilder

McproSimulate

Extern

Trim

Stop

ProteinMutationGenerator

CovalentFepMapper

ProteinFepMapper

FepProteinMapper

FepMapper

LeadOptMap

AlignCore

FepMapperCleanup

Aacg_SiteMap_Multijob
This class runs multiple SiteMap jobs for mixed resolution cosolvent simulations

Functions

concatenate_and_backup(text_fname)

move_to_base_dir(fname, _print, jobname, master_jobname, base_dir)

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 = {"remd": set(["replica_exchange", "l...

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)

Variables Details

PREDEFINED_STAGE_FAMILY

Value:

{"remd": set(["replica_exchange", "lambda_hopping",]), "md": set(["sim
ulate", "replica_exchange", "lambda_hopping",]), "desmond": set(["mini
mize", "simulate", "replica_exchange", "lambda_hopping", "fep_vrun",])
,}

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)