htmd package#
Subpackages#
- htmd.adaptive package
- htmd.builder package
- Submodules
- htmd.builder.amber module
- 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
- htmd.builder.ionize module
- htmd.builder.loopmodeler module
- htmd.builder.noncanonical module
- htmd.builder.solvate module
- Module contents
- Submodules
- htmd.clustering package
- htmd.mdengine package
- htmd.membranebuilder package
- htmd.molecule package
- htmd.projections package
- Submodules
- htmd.projections.gwpca module
- htmd.projections.kmeanstri module
- htmd.projections.metric module
- 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
- Module contents
- Submodules
- htmd.protocols package
- htmd.queues package
Submodules#
- htmd.config module
- htmd.decorators module
- htmd.dock module
- htmd.home module
- htmd.kinetics module
- htmd.latest module
- htmd.license module
- 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
- htmd.metricdatagenerator module
- 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
- htmd.parallelprogress module
- htmd.pathplanning module
- htmd.session module
- htmd.simlist module
- htmd.ui module
- htmd.units module
- htmd.util module
- htmd.version module
- htmd.versionwarnings module