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

[frames] | no frames]

Module stage

Various multisim concrete stage classes.

Copyright Schrodinger, LLC. All rights reserved.

Classes

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

AlignCore

Analysis

AnalysisJob

AssignForcefield

BuildGeometry

CalcDdg

ConcatParam

Concatenate

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

CovalentFepMapper

DesmondExtend

DesmondJob

Extern

FepAnalysis

FepAnalysis2

FepJob

FepLauncher

FepMapper

FepMapperCleanup

FepMapperReport

FepMapping

FepProteinMapper

FepTypes
FepTypes(PRM_STABILITY, PROTEIN_SELECTIVITY, COVALENT_LIGAND, SMALL_MOLECULE, METALLOPROTEIN)

FepVrun

FepanaJob

ForcefieldBuilder

LambdaHopping

LeadOptMap

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

McproSimulate

McproStageBase

McproSystemBuilder

MetadynamicsAnalysisJob

Minimize

Multisim

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

Primer

ProteinFepMapper

ProteinMutationGenerator

ReplicaExchange

Reporter

SeaJob

Simulate

SolvatePocket

Stop

SystemBuilder

Task

TimeSeriesAnalysisJob

Trajectory

Trim

VacuumReport

Vrun

WaterMap

WaterMapAnaJob

WaterMapCluster

WaterMapPostAnalysis

Functions

_xchk_check_box_size(map, valid, ev, prefix)

_xchk_check_restrain(map, valid, ev, prefix)

_xchk_check_stage_family(map, valid, ev, prefix)

_xchk_multisim_file_exists(map, valid, ev, prefix)

all_stage_family()

backup_trajectories(fname)

concatenate_and_backup(text_fname)

concatenate_trajectories(trajectories)

has_dir(stage, map_msj, arg)

has_file(stage, map_msj, arg)

is_debugging(stage, map_msj, arg)

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

systrait_is(stage, map_msj, arg)

systype_is(stage, map_msj, arg)

Variables

FEP_TYPES = FepTypes(PRM_STABILITY='prm_stability', PROTEIN_SE...

PREDEFINED_STAGE_FAMILY = {'desmond': set(['concatenate', 'fep...

STAGE_FAMILY = None
hash(x)

__package__ = 'schrodinger.application.desmond'

Variables Details

FEP_TYPES

Value:

FepTypes(PRM_STABILITY='prm_stability', PROTEIN_SELECTIVITY='protein_s
electivity', COVALENT_LIGAND='covalent_ligand', SMALL_MOLECULE='small_
molecule', METALLOPROTEIN='metalloprotein')

PREDEFINED_STAGE_FAMILY

Value:

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