Python Module Index

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	`htmd`
	`htmd.adaptive`
	`htmd.adaptive.adaptive`
	`htmd.adaptive.adaptivegoal`
	`htmd.adaptive.adaptivegoaleg`
	`htmd.adaptive.adaptiverun`
	`htmd.apps`
	`htmd.apps.acemd`
	`htmd.apps.pmemd`
	`htmd.builder`
	`htmd.builder.amber`
	`htmd.builder.builder`
	`htmd.builder.charmm`
	`htmd.builder.ionize`
	`htmd.builder.loopmodeler`
	`htmd.builder.preparation`
	`htmd.builder.preparationdata`
	`htmd.builder.solvate`
	`htmd.charge`
	`htmd.charge.charge`
	`htmd.charge.compare`
	`htmd.charge.esp`
	`htmd.clustering`
	`htmd.clustering.kcenters`
	`htmd.clustering.regular`
	`htmd.config`
	`htmd.decorators`
	`htmd.dock`
	`htmd.ffevaluation`
	`htmd.ffevaluation.ffevaluate`
	`htmd.ffevaluation.test_ffevaluate`
	`htmd.home`
	`htmd.kinetics`
	`htmd.kineticshmm`
	`htmd.latest`
	`htmd.membranebuilder`
	`htmd.membranebuilder.build_membrane`
	`htmd.membranebuilder.globalminimization`
	`htmd.membranebuilder.ljfluid`
	`htmd.membranebuilder.pdbreporter`
	`htmd.membranebuilder.ringpenetration`
	`htmd.membranebuilder.simulate_openmm`
	`htmd.metricdata`
	`htmd.model`
	`htmd.modelhmm`
	`htmd.molecule`
	`htmd.molecule.crystalpacking`
	`htmd.molecule.graphalignment`
	`htmd.molecule.hhblitsprofile`
	`htmd.molecule.molecule`
	`htmd.molecule.pdbx`
	`htmd.molecule.pdbx.reader`
	`htmd.molecule.pdbx.reader.PdbxContainers`
	`htmd.molecule.pdbx.reader.PdbxParser`
	`htmd.molecule.pdbx.reader.PdbxReader`
	`htmd.molecule.pdbx.tests`
	`htmd.molecule.pdbx.tests.PdbxReaderTests`
	`htmd.molecule.pdbx.tests.PdbxReadWriteTests`
	`htmd.molecule.pdbx.tests.PdbxWriterTests`
	`htmd.molecule.pdbx.writer`
	`htmd.molecule.pdbx.writer.PdbxWriter`
	`htmd.molecule.pka`
	`htmd.molecule.readers`
	`htmd.molecule.support`
	`htmd.molecule.util`
	`htmd.molecule.vdw`
	`htmd.molecule.vmdparser`
	`htmd.molecule.voxeldescriptors`
	`htmd.molecule.wrap`
	`htmd.molecule.writers`
	`htmd.mutualinformation`
	`htmd.numbautil`
	`htmd.parallelprogress`
	`htmd.parameterization`
	`htmd.parameterization.cli`
	`htmd.parameterization.detect`
	`htmd.parameterization.dihedral`
	`htmd.parameterization.fftype`
	`htmd.parameterization.parameterset`
	`htmd.parameterization.readers`
	`htmd.parameterization.test`
	`htmd.parameterization.util`
	`htmd.parameterization.writers`
	`htmd.pathplanning`
	`htmd.projections`
	`htmd.projections.gwpca`
	`htmd.projections.kmeanstri`
	`htmd.projections.metric`
	`htmd.projections.metriccoordinate`
	`htmd.projections.metricdihedral`
	`htmd.projections.metricdistance`
	`htmd.projections.metricfluctuation`
	`htmd.projections.metricnull`
	`htmd.projections.metricplumed2`
	`htmd.projections.metricrmsd`
	`htmd.projections.metricsasa`
	`htmd.projections.metricsecondarystructure`
	`htmd.projections.metricshell`
	`htmd.projections.metricsphericalcoordinate`
	`htmd.projections.metrictmscore`
	`htmd.projections.projection`
	`htmd.projections.tica`
	`htmd.projections.util`
	`htmd.protocols`
	`htmd.protocols.equilibration_v1`
	`htmd.protocols.equilibration_v2`
	`htmd.protocols.oldprotocolinterface`
	`htmd.protocols.pmemdequilibration`
	`htmd.protocols.pmemdproduction`
	`htmd.protocols.production_v1`
	`htmd.protocols.production_v2`
	`htmd.protocols.production_v3`
	`htmd.protocols.production_v4`
	`htmd.protocols.production_v5`
	`htmd.protocols.production_v6`
	`htmd.qm`
	`htmd.qm.base`
	`htmd.qm.custom`
	`htmd.qm.fake`
	`htmd.qm.gaussian`
	`htmd.qm.psi4`
	`htmd.qm.test`
	`htmd.queues`
	`htmd.queues.acecloudqueue`
	`htmd.queues.localqueue`
	`htmd.queues.lsfqueue`
	`htmd.queues.pbsqueue`
	`htmd.queues.simqueue`
	`htmd.queues.slurmqueue`
	`htmd.rotationmatrix`
	`htmd.session`
	`htmd.simlist`
	`htmd.smallmol`
	`htmd.smallmol.chemlab`
	`htmd.smallmol.chemlab.builder`
	`htmd.smallmol.chemlab.periodictable`
	`htmd.smallmol.molvstautomer`
	`htmd.smallmol.smallmol`
	`htmd.smallmol.tautomers`
	`htmd.smallmol.test_chemlab`
	`htmd.smallmol.test_smallmol`
	`htmd.smallmol.test_smallmollib`
	`htmd.smallmol.test_tools`
	`htmd.smallmol.tools`
	`htmd.smallmol.tools.clustering`
	`htmd.smallmol.util`
	`htmd.ui`
	`htmd.units`
	`htmd.util`
	`htmd.version`
	`htmd.vmdgraphics`
	`htmd.vmdviewer`