htmd package

Subpackages

• htmd.adaptive package
  • Submodules
    • htmd.adaptive.adaptive module
      • AdaptiveBase
      • epochSimIndexes()
      • getEpochFromName()
      • reconstructAdaptiveTraj()
    • htmd.adaptive.adaptivebandit module
      • AdaptiveBandit
    • htmd.adaptive.adaptivegoal module
      • AdaptiveGoal
    • htmd.adaptive.adaptivegoaleg module
      • AdaptiveGoalEG
    • htmd.adaptive.adaptiverun module
      • AdaptiveMD
    • htmd.adaptive.util module
      • getEpochSimIdx()
      • getEpochTrajectoryDictionary()
      • getParentSimIdxFrame()
      • updatingMean()
  • Module contents
• htmd.builder package
  • Submodules
    • htmd.builder.amber module
      • build()
      • defaultAmberHome()
      • defaultFf()
      • defaultParam()
      • defaultTopo()
      • htmdAmberHome()
      • listFiles()
    • htmd.builder.builder module
      • BuildError
      • MissingAngleError
      • MissingAtomTypeError
      • MissingBondError
      • MissingParameterError
      • MissingResidueError
      • MissingTorsionError
      • MixedSegmentError
      • ResidueInsertionError
      • convertDisulfide()
      • detectCisPeptideBonds()
      • detectDisulfideBonds()
      • embed()
      • minimalRotation()
      • removeAtomsInHull()
      • removeHET()
      • removeLipidsInProtein()
      • tileMembrane()
    • htmd.builder.charmm module
      • build()
      • combine()
      • defaultParam()
      • defaultStream()
      • defaultTopo()
      • htmdCharmmHome()
      • listFiles()
      • search()
      • split()
    • htmd.builder.ionize module
      • ionize()
      • ionizePlace()
    • htmd.builder.loopmodeler module
      • loopModeller()
    • htmd.builder.noncanonical module
      • parameterizeNonCanonicalResidues()
    • htmd.builder.solvate module
      • solvate()
  • Module contents
• htmd.clustering package
  • Submodules
    • htmd.clustering.kcenters module
      • KCenter
    • htmd.clustering.regular module
      • RegCluster
  • Module contents
• htmd.mdengine package
  • Subpackages
    • htmd.mdengine.acemd package
      • Submodules
      • Module contents
  • Module contents
• htmd.membranebuilder package
  • Submodules
    • htmd.membranebuilder.build_membrane module
      • buildMembrane()
      • listLipids()
      • wrapping_dist_python()
    • htmd.membranebuilder.globalminimization module
      • minimize()
    • htmd.membranebuilder.ljfluid module
      • distributeLipids()
    • htmd.membranebuilder.pdbreporter module
      • PDBReporter
      • PDBxReporter
    • htmd.membranebuilder.ringpenetration module
      • getAllNeighbours()
      • least_square_fit_plane()
      • moveLipidToPos()
      • resolveRingPenetrations()
      • wrap()
    • htmd.membranebuilder.simulate_openmm module
      • equilibrateSystem()
  • Module contents
• htmd.molecule package
  • Submodules
    • htmd.molecule.molecule module
    • htmd.molecule.util module
  • Module contents
• htmd.projections package
  • Submodules
    • htmd.projections.gwpca module
      • GWPCA
    • htmd.projections.kmeanstri module
      • KMeansTri
    • htmd.projections.metric module
      • Metric
    • htmd.projections.metriccoordinate module
    • htmd.projections.metricdihedral module
    • htmd.projections.metricdistance module
    • htmd.projections.metricfluctuation module
    • htmd.projections.metricplumed2 module
    • htmd.projections.metricrmsd module
    • htmd.projections.metricsasa module
    • htmd.projections.metricsecondarystructure module
    • htmd.projections.metricshell module
    • htmd.projections.metricsphericalcoordinate module
    • htmd.projections.metrictmscore module
    • htmd.projections.tica module
      • TICA
  • Module contents
• htmd.protocols package
  • Submodules
    • htmd.protocols.equilibration_v3 module
      • Equilibration
    • htmd.protocols.production_v6 module
      • Production
  • Module contents
• htmd.queues package
  • Submodules
    • htmd.queues.localqueue module
    • htmd.queues.lsfqueue module
    • htmd.queues.pbsqueue module
    • htmd.queues.playqueue module
    • htmd.queues.simqueue module
    • htmd.queues.slurmqueue module
  • Module contents

Submodules

• htmd.config module
  • config()
• htmd.decorators module
• htmd.dock module
  • dock()
• htmd.home module
  • home()
• htmd.kinetics module
  • Kinetics
    • Kinetics.getRates()
    • Kinetics.plotFluxPathways()
    • Kinetics.plotMarkovModel()
    • Kinetics.plotRates()
  • Rates
    • Rates.mfpton
    • Rates.mfptoff
    • Rates.kon
    • Rates.koff
    • Rates.kdeq
    • Rates.g0eq
• htmd.latest module
  • compareVersions()
• htmd.license module
  • check_for_license()
  • htmd_register()
  • htmd_registration()
  • htmd_show_news()
• htmd.metricdata module
  • MetricData
    • MetricData.dat
    • MetricData.ref
    • MetricData.simlist
    • MetricData.fstep
    • MetricData.map
    • MetricData.parent
    • MetricData.St
    • MetricData.K
    • MetricData.N
    • MetricData.Centers
    • MetricData.St
    • MetricData.abs2rel()
    • MetricData.abs2sim()
    • MetricData.aggregateTime
    • MetricData.append()
    • MetricData.bootstrap()
    • MetricData.cluster()
    • MetricData.combine()
    • MetricData.copy()
    • MetricData.dat
    • MetricData.deconcatenate()
    • MetricData.dropDimensions()
    • MetricData.dropFrames()
    • MetricData.dropTraj()
    • MetricData.fromHDF5()
    • MetricData.load()
    • MetricData.map
    • MetricData.numDimensions
    • MetricData.numFrames
    • MetricData.numTrajectories
    • MetricData.plotClusters()
    • MetricData.plotCounts()
    • MetricData.plotTrajSizes()
    • MetricData.ref
    • MetricData.rel2sim()
    • MetricData.sampleClusters()
    • MetricData.sampleRegion()
    • MetricData.save()
    • MetricData.simlist
    • MetricData.splitCols()
    • MetricData.toHDF5()
    • MetricData.trajLengths
  • Trajectory
    • Trajectory.cluster
    • Trajectory.copy()
    • Trajectory.dropFrames()
    • Trajectory.fromHDF5()
    • Trajectory.numDimensions
    • Trajectory.numFrames
    • Trajectory.projection
    • Trajectory.reference
    • Trajectory.toHDF5()
• htmd.metricdatagenerator module
  • MetricDataGenerator
    • MetricDataGenerator.newMetricData()
    • MetricDataGenerator.newTrajectoriesClusterJumping()
    • MetricDataGenerator.newTrajectoriesFiller()
    • MetricDataGenerator.newTrajectoriesMSM()
    • MetricDataGenerator.newTrajectoriesSimple()
    • MetricDataGenerator.parallelTest()
  • abs2rel()
• htmd.model module
  • Model
    • Model.P
    • Model.cktest()
    • Model.cluster_ofmicro
    • Model.copy()
    • Model.createCoreSetModel()
    • Model.createState()
    • Model.eqDistribution()
    • Model.getStates()
    • Model.load()
    • Model.macro_ofcluster
    • Model.macro_ofmicro
    • Model.macronum
    • Model.markovModel()
    • Model.maxConnectedLag()
    • Model.micro_ofcluster
    • Model.micronum
    • Model.plotFES()
    • Model.plotTimescales()
    • Model.sampleStates()
    • Model.save()
    • Model.viewStates()
  • getStateStatistic()
  • macroAccumulate()
• htmd.mutualinformation module
  • MutualInformation
    • MutualInformation.calculate()
    • MutualInformation.loadMI()
    • MutualInformation.saveMI()
    • MutualInformation.save_graphml()
    • MutualInformation.weightGraph()
• htmd.parallelprogress module
  • ParallelExecutor()
• htmd.pathplanning module
  • Tree
    • Tree.addPoint()
  • parallelfunc()
  • raytracing()
  • rrt()
  • rrtstarsmart()
• htmd.session module
  • htmdload()
  • htmdsave()
• htmd.simlist module
  • Frame
    • Frame.frame
    • Frame.piece
    • Frame.sim
  • Sim
    • Sim.simid
    • Sim.parent
    • Sim.input
    • Sim.trajectory
    • Sim.molfile
    • Sim.numframes
    • Sim.copy()
    • Sim.fromHDF5()
    • Sim.toHDF5()
  • simfilter()
  • simlist()
  • simmerge()
• htmd.ui module
• htmd.units module
  • convert()
• htmd.util module
  • assertSameAsReferenceDir()
  • diffMolecules()
  • ensurelist()
  • getPdbStrings()
  • tempname()
  • testDHFR()
• htmd.version module
  • version()
• htmd.versionwarnings module

Module contents