Index

_

__call__() (htmd.smallmol.molvstautomer.TautomerEnumerator method) (htmd.smallmol.tautomers.TautomerCanonicalizer method)

__getitem__() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method)

A

abs2rel() (htmd.metricdata.MetricData method) abs2sim() (htmd.metricdata.MetricData method) AceCloudQueue (class in htmd.queues.acecloudqueue) Acemd (class in htmd.apps.acemd) AdaptiveBase (class in htmd.adaptive.adaptive) AdaptiveGoal (class in htmd.adaptive.adaptivegoal) AdaptiveGoalEG (class in htmd.adaptive.adaptivegoaleg) AdaptiveMD (class in htmd.adaptive.adaptiverun) add() (htmd.molecule.molecule.Representations method) addCleanup() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) addConstraint() (htmd.protocols.equilibration_v1.Equilibration method) (htmd.protocols.equilibration_v2.Equilibration method) (htmd.protocols.production_v5.Production method) (htmd.protocols.production_v6.Production method) addHydrogens() (htmd.smallmol.chemlab.builder.Builder method) addPoint() (htmd.pathplanning.Tree method) addTypeEqualityFunc() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) aggregateTime (htmd.metricdata.MetricData attribute) align() (htmd.molecule.molecule.Molecule method) alignBySequence() (htmd.molecule.molecule.Molecule method) alignMol() (in module htmd.smallmol.util) altloc (htmd.molecule.molecule.Molecule attribute) angles (htmd.molecule.molecule.Molecule attribute) append() (htmd.metricdata.MetricData method) (htmd.molecule.molecule.Molecule method) (htmd.molecule.molecule.Representations method) (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) appendAttribute() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) appendAttributeExtendRows() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) appendFrames() (htmd.molecule.molecule.Molecule method) appendSmallLib() (htmd.smallmol.smallmol.SmallMolLib method) appendSmallMol() (htmd.smallmol.smallmol.SmallMolLib method) apply_bounds (htmd.charge.esp.ESP attribute) args (htmd.builder.builder.BuildError attribute) (htmd.builder.builder.MissingAngleError attribute) (htmd.builder.builder.MissingAtomTypeError attribute) (htmd.builder.builder.MissingBondError attribute) (htmd.builder.builder.MissingParameterError attribute) (htmd.builder.builder.MissingTorsionError attribute) (htmd.builder.builder.MixedSegmentError attribute) (htmd.builder.builder.ResidueInsertionError attribute) (htmd.builder.builder.UnknownResidueError attribute) (htmd.molecule.molecule.TopologyInconsistencyError attribute) (htmd.molecule.pdbx.reader.PdbxParser.PdbxError attribute) (htmd.molecule.pdbx.reader.PdbxParser.SyntaxError attribute) (htmd.molecule.pdbx.reader.PdbxReader.PdbxError attribute) (htmd.molecule.pdbx.reader.PdbxReader.SyntaxError attribute) (htmd.molecule.pdbx.writer.PdbxWriter.PdbxError attribute) (htmd.molecule.readers.FormatError attribute) (htmd.molecule.readers.TopologyInconsistencyError attribute) (htmd.queues.simqueue.InProgressError attribute) (htmd.queues.simqueue.ProjectNotExistError attribute) (htmd.queues.simqueue.RetrieveError attribute) (htmd.queues.simqueue.SubmitError attribute) args() (htmd.protocols.oldprotocolinterface.BinaryValidator method) (htmd.protocols.oldprotocolinterface.BooleanValidator method) (htmd.protocols.oldprotocolinterface.ClassValidator method) (htmd.protocols.oldprotocolinterface.DictionaryValidator method) (htmd.protocols.oldprotocolinterface.FileValidator method) (htmd.protocols.oldprotocolinterface.FunctionValidator method) (htmd.protocols.oldprotocolinterface.ListListValidator method) (htmd.protocols.oldprotocolinterface.ListValidator method) (htmd.protocols.oldprotocolinterface.ObjectValidator method) (htmd.protocols.oldprotocolinterface.StringValidator method) (htmd.protocols.oldprotocolinterface.TimestepValidator method) assert_() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertAlmostEquals() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertCountEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertDictContainsSubset() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertDictEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertEquals() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertFalse() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertGreater() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertGreaterEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertIn() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertIs() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertIsInstance() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) 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method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertIsNot() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) 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(htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertLess() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertLessEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method)

assertListAlmostEqual() (htmd.parameterization.fftype.TestFftypeGAFF method) assertListEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertLogs() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertMultiLineEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) 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(htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertNotAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) 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(htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertNotRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertNotRegexpMatches() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertRaises() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertRaisesRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertRaisesRegexp() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertRegexpMatches() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertSameAsReferenceDir() (in module htmd.util) assertSequenceEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertSetEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertTrue() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertTupleEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertWarns() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) assertWarnsRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) atominfo (htmd.molecule.readers.Topology attribute) atoms (htmd.smallmol.tautomers.Fragment attribute) atomselect() (htmd.molecule.molecule.Molecule method) atomtype (htmd.molecule.molecule.Molecule attribute) attributePart() (htmd.molecule.pdbx.reader.PdbxContainers.CifName static method) autoSegment() (in module htmd.builder.builder) autoSegment2() (in module htmd.builder.builder)

B

basis (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) BASIS_SETS (htmd.qm.base.QMBase attribute) (htmd.qm.FakeQM attribute) (htmd.qm.FakeQM2 attribute) (htmd.qm.Gaussian attribute) (htmd.qm.Psi4 attribute) (htmd.qm.custom.CustomQM attribute) (htmd.qm.fake.FakeQM attribute) (htmd.qm.fake.FakeQM2 attribute) (htmd.qm.gaussian.Gaussian attribute) (htmd.qm.psi4.Psi4 attribute) beta (htmd.molecule.molecule.Molecule attribute) BinaryValidator (class in htmd.protocols.oldprotocolinterface)

BINCOORread() (in module htmd.molecule.readers) BINCOORwrite() (in module htmd.molecule.writers) BONDMAP (htmd.smallmol.molvstautomer.TautomerTransform attribute) bonds (htmd.molecule.molecule.Molecule attribute) bondtype (htmd.molecule.molecule.Molecule attribute) BooleanValidator (class in htmd.protocols.oldprotocolinterface) bootstrap() (htmd.metricdata.MetricData method) boundingBox() (in module htmd.molecule.util) box (htmd.molecule.molecule.Molecule attribute) boxangles (htmd.molecule.molecule.Molecule attribute) build() (in module htmd.builder.amber) (in module htmd.builder.charmm) Builder (class in htmd.smallmol.chemlab.builder) BuildError buildMembrane() (in module htmd.membranebuilder.build_membrane)

C

calculate() (htmd.ffevaluation.ffevaluate.FFEvaluate method) (htmd.mutualinformation.MutualInformation method) calculateAngle() (in module htmd.smallmol.util) calculateEnergies() (htmd.ffevaluation.ffevaluate.FFEvaluate method) calculateSets() (in module htmd.ffevaluation.ffevaluate) canonicalize() (htmd.smallmol.tautomers.TautomerCanonicalizer method) categoryPart() (htmd.molecule.pdbx.reader.PdbxContainers.CifName static method) center() (htmd.molecule.molecule.Molecule method) centerFrames (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) Centers (htmd.metricdata.MetricData attribute) centreOfMass() (in module htmd.parameterization.util) chain (htmd.molecule.molecule.Molecule attribute) charge (htmd.molecule.molecule.Molecule attribute) (htmd.qm.QMResult attribute) (htmd.qm.base.QMResult attribute) ChargeComparison (class in htmd.charge.compare) CHARGEMAP (htmd.smallmol.molvstautomer.TautomerTransform attribute) checkTruncations() (in module htmd.molecule.writers) chi1() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) chi2() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) chi3() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) chi4() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) chi5() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) CifName (class in htmd.molecule.pdbx.reader.PdbxContainers) cktest() (htmd.model.Model method) ClassValidator (class in htmd.protocols.oldprotocolinterface) close() (htmd.vmdviewer.VMD method) cluster (htmd.metricdata.Trajectory attribute) cluster() (htmd.metricdata.MetricData method) (in module htmd.smallmol.tools.clustering) cluster_centers (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) cluster_centers_ (htmd.clustering.regular.RegCluster attribute) cluster_ofmicro (htmd.model.Model attribute) clusterSize (htmd.clustering.regular.RegCluster attribute) clusterSize_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) combine() (htmd.metricdata.MetricData method) (in module htmd.builder.charmm) compareEnergies() (in module htmd.ffevaluation.test_ffevaluate) compareForces() (in module htmd.ffevaluation.test_ffevaluate) compareGraphs() (in module htmd.molecule.graphalignment) compareVersions() (in module htmd.latest) completed() (htmd.vmdviewer.VMD method) compute_paths() (htmd.smallmol.tautomers.MolFragmenter method) compute_score() (htmd.smallmol.tautomers.TautomerCanonicalizer method) config() (in module htmd.config) connected_component_subgraphs() (in module htmd.parameterization.detect) connection (htmd.smallmol.tautomers.Fragment attribute) construct() (htmd.molecule.readers.MolFactory static method) contactVecToMatrix() (in module htmd.projections.metricdistance) ContainerBase (class in htmd.molecule.pdbx.reader.PdbxContainers) convert() (in module htmd.units) convertDisulfide() (in module htmd.builder.builder) convertProjectionToDataFrame() (in module htmd.projections.util) convertToString() (in module htmd.smallmol.util) coords (htmd.molecule.molecule.Molecule attribute) (htmd.qm.QMResult attribute) (htmd.qm.base.QMResult attribute) copy() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) (htmd.model.Model method) (htmd.molecule.molecule.Molecule method) (htmd.projections.metriccoordinate.MetricCoordinate method) (htmd.projections.metricdihedral.MetricDihedral method) (htmd.projections.metricdistance.MetricDistance method) (htmd.projections.metricdistance.MetricSelfDistance method) (htmd.projections.metricfluctuation.MetricFluctuation method) (htmd.projections.metricnull.MetricNull method) (htmd.projections.metricplumed2.MetricPlumed2 method) (htmd.projections.metricrmsd.MetricRmsd method) (htmd.projections.metricsasa.MetricSasa method) (htmd.projections.metricsecondarystructure.MetricSecondaryStructure method) (htmd.projections.metricshell.MetricShell method) (htmd.projections.metricsphericalcoordinate.MetricSphericalCoordinate method) (htmd.projections.metrictmscore.MetricTMscore method) (htmd.projections.projection.Projection method) (htmd.simlist.Sim method) (htmd.smallmol.smallmol.SmallMol method) (htmd.smallmol.smallmol.SmallMolLib method) (htmd.vmdviewer.VMD method)

correction (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) CORRECTIONS (htmd.qm.base.QMBase attribute) (htmd.qm.FakeQM attribute) (htmd.qm.FakeQM2 attribute) (htmd.qm.Gaussian attribute) (htmd.qm.Psi4 attribute) (htmd.qm.custom.CustomQM attribute) (htmd.qm.fake.FakeQM attribute) (htmd.qm.fake.FakeQM2 attribute) (htmd.qm.gaussian.Gaussian attribute) (htmd.qm.psi4.Psi4 attribute) count (htmd.vmdgraphics.VMDLabels attribute) counter (htmd.vmdgraphics.VMDBox attribute) (htmd.vmdgraphics.VMDConvexHull attribute) (htmd.vmdgraphics.VMDGraphicObject attribute) (htmd.vmdgraphics.VMDIsosurface attribute) (htmd.vmdgraphics.VMDLabels attribute) (htmd.vmdgraphics.VMDSphere attribute) (htmd.vmdgraphics.VMDText attribute) countTestCases() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) CRDCARDread() (in module htmd.molecule.readers) CRDread() (in module htmd.molecule.readers) createCoreSetModel() (htmd.model.Model method) createMultitermDihedralTypes() (in module htmd.parameterization.parameterset) createProductGraph() (in module htmd.molecule.graphalignment) createState() (htmd.model.Model method) cross (in module htmd.numbautil) crystalinfo (htmd.molecule.molecule.Molecule attribute) currentResult (htmd.builder.amber.TestAmberBuild attribute) CustomEnergyBasedMinimizer (class in htmd.qm.custom) CustomQM (class in htmd.qm.custom)

D

dat (htmd.metricdata.MetricData attribute), [1] data (htmd.builder.preparationdata.PreparationData attribute) DataCategory (class in htmd.molecule.pdbx.reader.PdbxContainers) DataCategoryBase (class in htmd.molecule.pdbx.reader.PdbxContainers) DataContainer (class in htmd.molecule.pdbx.reader.PdbxContainers) debug() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) deconcatenate() (htmd.metricdata.MetricData method) defaultFf() (in module htmd.builder.amber) defaultParam() (in module htmd.builder.amber) (in module htmd.builder.charmm) defaultStream() (in module htmd.builder.charmm) defaultTestResult() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) defaultTopo() (in module htmd.builder.amber) (in module htmd.builder.charmm) DefinitionContainer (class in htmd.molecule.pdbx.reader.PdbxContainers) delete() (htmd.vmdgraphics.VMDBox method) (htmd.vmdgraphics.VMDConvexHull method) (htmd.vmdgraphics.VMDGraphicObject method) (htmd.vmdgraphics.VMDIsosurface method) (htmd.vmdgraphics.VMDLabels method) (htmd.vmdgraphics.VMDSphere method) (htmd.vmdgraphics.VMDText method) deleteBonds() (htmd.molecule.molecule.Molecule method) depict() (htmd.smallmol.smallmol.SmallMol method) (htmd.smallmol.smallmol.SmallMolLib method) depict_tautomers() (htmd.smallmol.tautomers.TautomerCanonicalizer method)

depictMultipleMols() (in module htmd.smallmol.util) describeNextReport() (htmd.membranebuilder.pdbreporter.PDBReporter method) (htmd.membranebuilder.pdbreporter.PDBxReporter method) detectChiralCenters() (in module htmd.parameterization.util) detectDisulfideBonds() (in module htmd.builder.builder) detectEquivalentAtoms() (in module htmd.parameterization.detect) detectImproperCenter() (in module htmd.ffevaluation.ffevaluate) detectParameterizableCores() (in module htmd.parameterization.detect) detectParameterizableDihedrals() (in module htmd.parameterization.detect) DiceDistances() (in module htmd.smallmol.tools.clustering) DictionaryValidator (class in htmd.protocols.oldprotocolinterface) diffMolecules() (in module htmd.util) Dihedral (class in htmd.projections.metricdihedral) dihedralAngle() (in module htmd.numbautil) dihedralAngleFrames (in module htmd.numbautil) dihedralAngleFull (in module htmd.numbautil) DihedralFitting (class in htmd.parameterization.dihedral) dihedrals (htmd.molecule.molecule.Molecule attribute) (htmd.parameterization.dihedral.DihedralFitting attribute) dihedralsToIndexes() (htmd.projections.metricdihedral.Dihedral static method) dipole (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute) directory (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) disableDispersionCorrection() (in module htmd.ffevaluation.test_ffevaluate) distance (htmd.clustering.kcenters.KCenter attribute) distributeLipids() (in module htmd.membranebuilder.ljfluid) DisulfideBridge (class in htmd.builder.builder) dock() (in module htmd.dock) doCleanups() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) docString() (htmd.protocols.oldprotocolinterface.BinaryValidator method) (htmd.protocols.oldprotocolinterface.BooleanValidator method) (htmd.protocols.oldprotocolinterface.ClassValidator method) (htmd.protocols.oldprotocolinterface.DictionaryValidator method) (htmd.protocols.oldprotocolinterface.FileValidator method) (htmd.protocols.oldprotocolinterface.FunctionValidator method) (htmd.protocols.oldprotocolinterface.ListListValidator method) (htmd.protocols.oldprotocolinterface.ListValidator method) (htmd.protocols.oldprotocolinterface.ObjectValidator method) (htmd.protocols.oldprotocolinterface.StringValidator method) (htmd.protocols.oldprotocolinterface.TimestepValidator method) (htmd.protocols.oldprotocolinterface.Validator method) (htmd.protocols.oldprotocolinterface.ValueValidator method) dot (in module htmd.numbautil) drawIsoSurface() (in module htmd.smallmol.util) dropDimensions() (htmd.metricdata.MetricData method) dropFrames() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) (htmd.molecule.molecule.Molecule method) dropTraj() (htmd.metricdata.MetricData method) dumpIt() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method)

E

element (htmd.molecule.molecule.Molecule attribute) embed() (in module htmd.builder.builder) empty() (htmd.molecule.molecule.Molecule method) energy (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute) ensurelist() (in module htmd.util) enumerate() (htmd.smallmol.molvstautomer.TautomerEnumerator method) epochSimIndexes() (in module htmd.adaptive.adaptive) eqDistribution() (htmd.model.Model method) (htmd.modelhmm.ModelHMM method) equilibrateSystem() (in module htmd.membranebuilder.simulate_openmm) Equilibration (class in htmd.protocols.equilibration_v1) (class in htmd.protocols.equilibration_v2) (class in htmd.protocols.pmemdequilibration)

errored (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute) ESP (class in htmd.charge.esp) esp_points (htmd.qm.base.QMResult attribute) (htmd.qm.Psi4 attribute) (htmd.qm.QMResult attribute) (htmd.qm.psi4.Psi4 attribute) esp_values (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute) exists() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method)

F

fail() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) failIf() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) failIfAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) failIfEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) failUnless() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) failUnlessAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method)

failUnlessEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) failUnlessRaises() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) failureException (htmd.builder.amber.TestAmberBuild attribute) (htmd.builder.charmm.TestCharmmBuild attribute) (htmd.charge.compare.ChargeComparison attribute) (htmd.charge.esp.TestESP attribute) (htmd.molecule.graphalignment.TestGraphAlignment attribute) (htmd.molecule.molecule.TestMolecule attribute) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests attribute) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests attribute) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests attribute) (htmd.molecule.readers.TestReaders attribute) (htmd.molecule.util.TestUtils attribute) (htmd.parameterization.dihedral.TestDihedralFitting attribute) (htmd.parameterization.fftype.TestFftypeCGenFF attribute) (htmd.parameterization.fftype.TestFftypeGAFF attribute) (htmd.parameterization.parameterset.Test attribute) (htmd.parameterization.test.TestParameterize attribute) (htmd.projections.metriccoordinate.TestMetricCoordinate attribute) (htmd.projections.metricdistance.TestMetricDistance attribute) (htmd.qm.test.TestGaussian attribute) (htmd.qm.test.TestPsi4AceCloud attribute) (htmd.qm.test.TestPsi4Local attribute) (htmd.qm.test.TestPsi4Slurm attribute) (htmd.smallmol.test_chemlab.TestSmallMol attribute) (htmd.smallmol.test_smallmol.TestSmallMol attribute) (htmd.smallmol.test_smallmollib.TestSmallMol attribute) (htmd.smallmol.test_tools.TestSmallMol attribute) FakeQM (class in htmd.qm) (class in htmd.qm.fake) FakeQM2 (class in htmd.qm) (class in htmd.qm.fake) FFEvaluate (class in htmd.ffevaluation.ffevaluate) fftype() (in module htmd.parameterization.fftype) fileloc (htmd.molecule.molecule.Molecule attribute) FileValidator (class in htmd.protocols.oldprotocolinterface) filter() (htmd.molecule.molecule.Molecule method) filter_tautomers() (htmd.smallmol.tautomers.TautomerCanonicalizer static method) filterQMResults() (in module htmd.parameterization.util) findDihedralType() (in module htmd.parameterization.parameterset) findHbonds() (htmd.builder.preparationdata.PreparationData method) findImproperType() (in module htmd.parameterization.parameterset) fit() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) fit_predict() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) fit_transform() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) fitChargesWithAntechamber() (in module htmd.charge.charge) fitESPCharges() (in module htmd.charge.charge) fitGasteigerCharges() (in module htmd.charge.charge) fixed (htmd.charge.esp.ESP attribute) fixParameters() (in module htmd.ffevaluation.test_ffevaluate) formatEnergies() (htmd.ffevaluation.ffevaluate.FFEvaluate static method) FormatError foundBondBetween() (htmd.smallmol.smallmol.SmallMol method) Fragment (class in htmd.smallmol.tautomers) fragment() (htmd.smallmol.tautomers.MolFragmenter method) fragments (htmd.smallmol.tautomers.MolFragmenter attribute) Frame (class in htmd.simlist) frame (htmd.molecule.molecule.Molecule attribute), [1] (htmd.simlist.Frame attribute) fromMolecule() (htmd.molecule.molecule.UniqueAtomID static method) (htmd.molecule.molecule.UniqueResidueID static method) (htmd.molecule.readers.Topology method) fstep (htmd.metricdata.MetricData attribute) (htmd.molecule.molecule.Molecule attribute) ftype (htmd.smallmol.tautomers.Fragment attribute) FunctionValidator (class in htmd.protocols.oldprotocolinterface)

G

g0eq (htmd.kinetics.Rates attribute) Gaussian (class in htmd.qm) (class in htmd.qm.gaussian) generateConformers() (htmd.smallmol.smallmol.SmallMol method) genTemplate() (htmd.projections.metricplumed2.PlumedCV method) (in module htmd.projections.metricplumed2) get() (htmd.molecule.molecule.Molecule method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategoryBase method) (htmd.smallmol.smallmol.SmallMol method) get_conjugate() (htmd.smallmol.tautomers.TautomerCanonicalizer method) get_conjugate_length() (htmd.smallmol.tautomers.MolFragmenter method) get_connection() (htmd.smallmol.tautomers.Fragment method) get_depiction_atoms() (htmd.smallmol.tautomers.MolFragmenter method) get_fragment() (htmd.smallmol.tautomers.MolFragmenter method) get_graphs() (htmd.smallmol.tautomers.MolFragmenter method) get_longest_path() (htmd.smallmol.tautomers.MolFragmenter method) get_num_fragments() (htmd.smallmol.tautomers.MolFragmenter method) get_params() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) get_rotationMatrix() (in module htmd.smallmol.util) getAllNeighbours() (in module htmd.membranebuilder.ringpenetration) getArgumentParser() (in module htmd.parameterization.cli) getAtom() (htmd.smallmol.chemlab.periodictable.PeriodicTable method) getAtoms() (htmd.smallmol.smallmol.SmallMol method) getAtomTypeMapping() (in module htmd.parameterization.writers) getAttributeCount() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getAttributeIndex() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getAttributeLengthMaximumList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getAttributeList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getAttributeListWithOrder() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getAttributeValueMaxLengthList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getBondRadius() (htmd.smallmol.chemlab.periodictable.PeriodicTable method) getBonds() (htmd.smallmol.smallmol.SmallMol method) getBondType() (htmd.smallmol.chemlab.periodictable.PeriodicTable method) getCenter() (htmd.smallmol.smallmol.SmallMol method) getChemblLigandByDrugName() (in module htmd.smallmol.util) getChemblSimilarLigandsBySmile() (in module htmd.smallmol.util) getConformers() (htmd.smallmol.smallmol.SmallMol method) getCoords() (htmd.smallmol.smallmol.SmallMol method) getCurrentAttribute() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getCurrentViewer() (in module htmd.vmdviewer) getDihedral() (htmd.molecule.molecule.Molecule method) getDipole() (in module htmd.parameterization.util) getEpochFromName() (in module htmd.adaptive.adaptive) getFixedChargeAtomIndices() (in module htmd.parameterization.util) getFormatTypeList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getFormatTypeListX() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getFullRow() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getGlobal() (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) getHybridization() (htmd.smallmol.chemlab.periodictable.PeriodicTable method) getImproperParameter() (in module htmd.ffevaluation.ffevaluate) getIndex() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getItemNameList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getMapping() (htmd.projections.metric.Metric method) (htmd.projections.metriccoordinate.MetricCoordinate method) (htmd.projections.metricdihedral.MetricDihedral method) (htmd.projections.metricdistance.MetricDistance method) (htmd.projections.metricdistance.MetricSelfDistance method) (htmd.projections.metricfluctuation.MetricFluctuation method) (htmd.projections.metricnull.MetricNull method) (htmd.projections.metricplumed2.MetricPlumed2 method) (htmd.projections.metricrmsd.MetricRmsd method) (htmd.projections.metricsasa.MetricSasa method) (htmd.projections.metricsecondarystructure.MetricSecondaryStructure method) (htmd.projections.metricshell.MetricShell method) (htmd.projections.metricsphericalcoordinate.MetricSphericalCoordinate method) (htmd.projections.metrictmscore.MetricTMscore method) (htmd.projections.projection.Projection method)

getMaximumCommonSubstructure() (in module htmd.smallmol.tools.clustering) getMissingValence() (htmd.smallmol.chemlab.periodictable.PeriodicTable method) getMols() (htmd.smallmol.smallmol.SmallMolLib method) getName() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) getObj() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) getObjNameList() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) getParameter() (in module htmd.parameterization.parameterset) getPdbStrings() (in module htmd.util) getPointDescriptors() (in module htmd.molecule.voxeldescriptors) getPoints() (htmd.charge.esp.MoleculeGrid method) getProfile() (in module htmd.molecule.hhblitsprofile) getProp() (htmd.smallmol.smallmol.SmallMol method) getRates() (htmd.kinetics.Kinetics method) (htmd.kineticshmm.KineticsHMM method) getRCSBLigandByLigname() (in module htmd.smallmol.util) getRow() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getRowCount() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getRowIndex() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getRowList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getSmallMol() (htmd.smallmol.chemlab.builder.Builder method) getSortedAndUniqueTypes() (in module htmd.parameterization.writers) getStates() (htmd.model.Model method) getStateStatistic() (in module htmd.model) getTerminiBuriedness() (htmd.builder.preparationdata.PreparationData method) getTerminiHbonds() (htmd.builder.preparationdata.PreparationData method) getType() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) getValue() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getValueFormatted() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getValueFormattedByIndex() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getVMDpath() (in module htmd.vmdviewer) getVoxelDescriptors() (in module htmd.molecule.voxeldescriptors) getVoxels() (htmd.smallmol.smallmol.SmallMol method) GJFread() (in module htmd.molecule.readers) graphs (htmd.smallmol.tautomers.Fragment attribute) GROTOPread() (in module htmd.molecule.readers) GROwrite() (in module htmd.molecule.writers) guessAnglesAndDihedrals() (in module htmd.molecule.util) guessbonds() (in module htmd.molecule.vmdparser) guessBondType() (in module htmd.parameterization.util) guessElements() (in module htmd.parameterization.util) GWPCA (class in htmd.projections.gwpca)

H

hasAttribute() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) header (htmd.builder.preparationdata.PreparationData attribute) home() (in module htmd.home) htmd (module) htmd.adaptive (module) htmd.adaptive.adaptive (module) htmd.adaptive.adaptivegoal (module) htmd.adaptive.adaptivegoaleg (module) htmd.adaptive.adaptiverun (module) htmd.apps (module) htmd.apps.acemd (module) htmd.apps.pmemd (module) htmd.builder (module) htmd.builder.amber (module) htmd.builder.builder (module) htmd.builder.charmm (module) htmd.builder.ionize (module) htmd.builder.loopmodeler (module) htmd.builder.preparation (module) htmd.builder.preparationdata (module) htmd.builder.solvate (module) htmd.charge (module) htmd.charge.charge (module) htmd.charge.compare (module) htmd.charge.esp (module) htmd.clustering (module) htmd.clustering.kcenters (module) htmd.clustering.regular (module) htmd.config (module) htmd.decorators (module) htmd.dock (module) htmd.ffevaluation (module) htmd.ffevaluation.ffevaluate (module) htmd.ffevaluation.test_ffevaluate (module) htmd.home (module) htmd.kinetics (module) htmd.kineticshmm (module) htmd.latest (module) htmd.membranebuilder (module) htmd.membranebuilder.build_membrane (module) htmd.membranebuilder.globalminimization (module) htmd.membranebuilder.ljfluid (module) htmd.membranebuilder.pdbreporter (module) htmd.membranebuilder.ringpenetration (module) htmd.membranebuilder.simulate_openmm (module) htmd.metricdata (module) htmd.model (module) htmd.modelhmm (module) htmd.molecule (module) htmd.molecule.crystalpacking (module) htmd.molecule.graphalignment (module) htmd.molecule.hhblitsprofile (module) htmd.molecule.molecule (module) htmd.molecule.pdbx (module) htmd.molecule.pdbx.reader (module) htmd.molecule.pdbx.reader.PdbxContainers (module) htmd.molecule.pdbx.reader.PdbxParser (module) htmd.molecule.pdbx.reader.PdbxReader (module) htmd.molecule.pdbx.tests (module) htmd.molecule.pdbx.tests.PdbxReaderTests (module) htmd.molecule.pdbx.tests.PdbxReadWriteTests (module) htmd.molecule.pdbx.tests.PdbxWriterTests (module) htmd.molecule.pdbx.writer (module) htmd.molecule.pdbx.writer.PdbxWriter (module) htmd.molecule.pka (module) htmd.molecule.readers (module) htmd.molecule.support (module) htmd.molecule.util (module) htmd.molecule.vdw (module) htmd.molecule.vmdparser (module) htmd.molecule.voxeldescriptors (module) htmd.molecule.wrap (module) htmd.molecule.writers (module) htmd.mutualinformation (module) htmd.numbautil (module) htmd.parallelprogress (module) htmd.parameterization (module) htmd.parameterization.cli (module)

htmd.parameterization.detect (module) htmd.parameterization.dihedral (module) htmd.parameterization.fftype (module) htmd.parameterization.parameterset (module) htmd.parameterization.readers (module) htmd.parameterization.test (module) htmd.parameterization.util (module) htmd.parameterization.writers (module) htmd.pathplanning (module) htmd.projections (module) 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.metricnull (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.projection (module) htmd.projections.tica (module) htmd.projections.util (module) htmd.protocols (module) htmd.protocols.equilibration_v1 (module) htmd.protocols.equilibration_v2 (module) htmd.protocols.oldprotocolinterface (module) htmd.protocols.pmemdequilibration (module) htmd.protocols.pmemdproduction (module) htmd.protocols.production_v1 (module) htmd.protocols.production_v2 (module) htmd.protocols.production_v3 (module) htmd.protocols.production_v4 (module) htmd.protocols.production_v5 (module) htmd.protocols.production_v6 (module) htmd.qm (module) htmd.qm.base (module) htmd.qm.custom (module) htmd.qm.fake (module) htmd.qm.gaussian (module) htmd.qm.psi4 (module) htmd.qm.test (module) htmd.queues (module) htmd.queues.acecloudqueue (module) htmd.queues.localqueue (module) htmd.queues.lsfqueue (module) htmd.queues.pbsqueue (module) htmd.queues.simqueue (module) htmd.queues.slurmqueue (module) htmd.rotationmatrix (module) htmd.session (module) htmd.simlist (module) htmd.smallmol (module) htmd.smallmol.chemlab (module) htmd.smallmol.chemlab.builder (module) htmd.smallmol.chemlab.periodictable (module) htmd.smallmol.molvstautomer (module) htmd.smallmol.smallmol (module) htmd.smallmol.tautomers (module) htmd.smallmol.test_chemlab (module) htmd.smallmol.test_smallmol (module) htmd.smallmol.test_smallmollib (module) htmd.smallmol.test_tools (module) htmd.smallmol.tools (module) htmd.smallmol.tools.clustering (module) htmd.smallmol.util (module) htmd.ui (module) htmd.units (module) htmd.util (module) htmd.version (module) htmd.vmdgraphics (module) htmd.vmdviewer (module) htmdload() (in module htmd.session) htmdsave() (in module htmd.session)

I

id() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method)

improperGraph() (in module htmd.ffevaluation.ffevaluate) impropers (htmd.molecule.molecule.Molecule attribute) init() (in module htmd.ffevaluation.ffevaluate) inprogress() (htmd.queues.acecloudqueue.AceCloudQueue method) (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method) (htmd.queues.lsfqueue.LsfQueue method) (htmd.queues.pbsqueue.PBSQueue method) (htmd.queues.simqueue.SimQueue method) (htmd.queues.slurmqueue.SlurmQueue method) InProgressError input (htmd.simlist.Sim attribute) insert() (htmd.molecule.molecule.Molecule method) insertion (htmd.molecule.molecule.Molecule attribute) inventAtomTypes() (in module htmd.parameterization.parameterset) invertChirality() (htmd.smallmol.smallmol.SmallMol method) invokeAttributeMethod() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) invokeCategoryMethod() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) invokeDataBlockMethod() (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) ionize() (in module htmd.builder.ionize) ionizePlace() (in module htmd.builder.ionize) isAttribute() (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) isCategory() (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) isChiral() (htmd.smallmol.smallmol.SmallMol method)

K

K (htmd.metricdata.MetricData attribute) KCenter (class in htmd.clustering.kcenters) kdeq (htmd.kinetics.Rates attribute) keepForces() (in module htmd.ffevaluation.test_ffevaluate) keepForcesAmber() (in module htmd.ffevaluation.test_ffevaluate)

Kinetics (class in htmd.kinetics) KineticsHMM (class in htmd.kineticshmm) KMeansTri (class in htmd.projections.kmeanstri) koff (htmd.kinetics.Rates attribute) kon (htmd.kinetics.Rates attribute)

L

labels_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) least_square_fit_plane() (in module htmd.membranebuilder.ringpenetration) list() (htmd.molecule.molecule.Representations method) listBondTypes() (htmd.smallmol.chemlab.periodictable.PeriodicTable method) listFiles() (in module htmd.builder.amber) (in module htmd.builder.charmm) listHybridizations() (htmd.smallmol.chemlab.periodictable.PeriodicTable method) listLipids() (in module htmd.membranebuilder.build_membrane) ListListValidator (class in htmd.protocols.oldprotocolinterface) listProps (htmd.smallmol.smallmol.SmallMol attribute) listPropsAtoms (htmd.smallmol.smallmol.SmallMol attribute) ListValidator (class in htmd.protocols.oldprotocolinterface) load() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) (htmd.metricdata.MetricData method) (htmd.model.Model method) load_tests() (in module htmd.charge.esp) loadMI() (htmd.mutualinformation.MutualInformation method) loadMol() (htmd.smallmol.chemlab.builder.Builder method) (htmd.vmdviewer.VMD method) loadParameters() (in module htmd.ffevaluation.ffevaluate) LocalCPUQueue (class in htmd.queues.localqueue) LocalGPUQueue (class in htmd.queues.localqueue) longMessage (htmd.builder.amber.TestAmberBuild attribute) (htmd.builder.charmm.TestCharmmBuild attribute) (htmd.charge.compare.ChargeComparison attribute) (htmd.charge.esp.TestESP attribute) (htmd.molecule.graphalignment.TestGraphAlignment attribute) (htmd.molecule.molecule.TestMolecule attribute) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests attribute) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests attribute) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests attribute) (htmd.molecule.readers.TestReaders attribute) (htmd.molecule.util.TestUtils attribute) (htmd.parameterization.dihedral.TestDihedralFitting attribute) (htmd.parameterization.fftype.TestFftypeCGenFF attribute) (htmd.parameterization.fftype.TestFftypeGAFF attribute) (htmd.parameterization.parameterset.Test attribute) (htmd.parameterization.test.TestParameterize attribute) (htmd.projections.metriccoordinate.TestMetricCoordinate attribute) (htmd.projections.metricdistance.TestMetricDistance attribute) (htmd.qm.test.TestGaussian attribute) (htmd.qm.test.TestPsi4AceCloud attribute) (htmd.qm.test.TestPsi4Local attribute) (htmd.qm.test.TestPsi4Slurm attribute) (htmd.smallmol.test_chemlab.TestSmallMol attribute) (htmd.smallmol.test_smallmol.TestSmallMol attribute) (htmd.smallmol.test_smallmollib.TestSmallMol attribute) (htmd.smallmol.test_tools.TestSmallMol attribute)

loopModeller() (in module htmd.builder.loopmodeler) LsfQueue (class in htmd.queues.lsfqueue)

M

macro_ofcluster (htmd.model.Model attribute) macro_ofmicro (htmd.model.Model attribute) macroAccumulate() (in module htmd.model) macronum (htmd.model.Model attribute) (htmd.modelhmm.ModelHMM attribute) MAEread() (in module htmd.molecule.readers) main_parameterize() (in module htmd.parameterization.cli) makeAtomNamesUnique() (in module htmd.parameterization.util) makeMolGraph() (in module htmd.molecule.graphalignment) manual() (in module htmd.projections.metricplumed2) map (htmd.metricdata.MetricData attribute), [1] mapAtomTypesParameterSet() (in module htmd.parameterization.writers) markovModel() (htmd.model.Model method) (htmd.modelhmm.ModelHMM method) massByElement() (in module htmd.molecule.vdw) masses (htmd.molecule.molecule.Molecule attribute) MAX_DIHEDRAL_MULTIPLICITY (htmd.parameterization.dihedral.DihedralFitting attribute) MAX_TAUTOMERS (in module htmd.smallmol.molvstautomer) maxConnectedLag() (htmd.model.Model method) maxDiff (htmd.builder.amber.TestAmberBuild attribute) (htmd.builder.charmm.TestCharmmBuild attribute) (htmd.charge.compare.ChargeComparison attribute) (htmd.charge.esp.TestESP attribute) (htmd.molecule.graphalignment.TestGraphAlignment attribute) (htmd.molecule.molecule.TestMolecule attribute) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests attribute) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests attribute) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests attribute) (htmd.molecule.readers.TestReaders attribute) (htmd.molecule.util.TestUtils attribute) (htmd.parameterization.dihedral.TestDihedralFitting attribute) (htmd.parameterization.fftype.TestFftypeCGenFF attribute) (htmd.parameterization.fftype.TestFftypeGAFF attribute) (htmd.parameterization.parameterset.Test attribute) (htmd.parameterization.test.TestParameterize attribute) (htmd.projections.metriccoordinate.TestMetricCoordinate attribute) (htmd.projections.metricdistance.TestMetricDistance attribute) (htmd.qm.test.TestGaussian attribute) (htmd.qm.test.TestPsi4AceCloud attribute) (htmd.qm.test.TestPsi4Local attribute) (htmd.qm.test.TestPsi4Slurm attribute) (htmd.smallmol.test_chemlab.TestSmallMol attribute) (htmd.smallmol.test_smallmol.TestSmallMol attribute) (htmd.smallmol.test_smallmollib.TestSmallMol attribute) (htmd.smallmol.test_tools.TestSmallMol attribute) maxDistance() (in module htmd.molecule.util) maximalSubstructureAlignment() (in module htmd.molecule.graphalignment) MDTRAJread() (in module htmd.molecule.readers) MDTRAJTOPOread() (in module htmd.molecule.readers) MDTRAJwrite() (in module htmd.molecule.writers) memoized_property() (in module htmd.smallmol.molvstautomer) memory (htmd.queues.acecloudqueue.AceCloudQueue attribute) (htmd.queues.localqueue.LocalCPUQueue attribute) (htmd.queues.localqueue.LocalGPUQueue attribute) (htmd.queues.lsfqueue.LsfQueue attribute) (htmd.queues.pbsqueue.PBSQueue attribute) (htmd.queues.simqueue.SimQueue attribute) (htmd.queues.slurmqueue.SlurmQueue attribute)

Metric (class in htmd.projections.metric) MetricCoordinate (class in htmd.projections.metriccoordinate) MetricData (class in htmd.metricdata) MetricDihedral (class in htmd.projections.metricdihedral) MetricDistance (class in htmd.projections.metricdistance) MetricFluctuation (class in htmd.projections.metricfluctuation) MetricNull (class in htmd.projections.metricnull) MetricPlumed2 (class in htmd.projections.metricplumed2) MetricRmsd (class in htmd.projections.metricrmsd) MetricSasa (class in htmd.projections.metricsasa) MetricSecondaryStructure (class in htmd.projections.metricsecondarystructure) MetricSelfDistance (class in htmd.projections.metricdistance) MetricShell (class in htmd.projections.metricshell) MetricSphericalCoordinate (class in htmd.projections.metricsphericalcoordinate) MetricTMscore (class in htmd.projections.metrictmscore) mfptGraph() (htmd.kinetics.Kinetics method) mfptoff (htmd.kinetics.Rates attribute) mfpton (htmd.kinetics.Rates attribute) micro_ofcluster (htmd.model.Model attribute) micronum (htmd.model.Model attribute) minimalRotation() (in module htmd.builder.builder) minimize() (htmd.qm.custom.CustomEnergyBasedMinimizer method) (htmd.qm.custom.Minimizer method) (htmd.qm.custom.OMMMinimizer method) (in module htmd.membranebuilder.globalminimization) (in module htmd.parameterization.util) Minimizer (class in htmd.qm.custom) missedLigands (htmd.builder.preparationdata.PreparationData attribute) MissingAngleError MissingAtomTypeError MissingBondError MissingParameterError MissingTorsionError MixedSegmentError Model (class in htmd.model) ModelHMM (class in htmd.modelhmm) mol (htmd.smallmol.tautomers.MolFragmenter attribute) MOL2read() (in module htmd.molecule.readers) MOL2write() (in module htmd.molecule.writers) mol_equal() (in module htmd.molecule.molecule) Molecule (class in htmd.molecule.molecule) molecule (htmd.charge.esp.ESP attribute) (htmd.parameterization.dihedral.DihedralFitting attribute) (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) MoleculeGrid (class in htmd.charge.esp) MolFactory (class in htmd.molecule.readers) molfile (htmd.simlist.Sim attribute) MolFragmenter (class in htmd.smallmol.tautomers) molRMSD() (in module htmd.molecule.util) molTMscore() (in module htmd.molecule.util) moveBy() (htmd.molecule.molecule.Molecule method) moveLipidToPos() (in module htmd.membranebuilder.ringpenetration) mulliken (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute) multiplity (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) mutateResidue() (htmd.molecule.molecule.Molecule method) MutualInformation (class in htmd.mutualinformation)

N

N (htmd.metricdata.MetricData attribute) name (htmd.molecule.molecule.Molecule attribute) (htmd.smallmol.tautomers.Fragment attribute) ncpu (htmd.queues.acecloudqueue.AceCloudQueue attribute) (htmd.queues.localqueue.LocalCPUQueue attribute) (htmd.queues.localqueue.LocalGPUQueue attribute) (htmd.queues.lsfqueue.LsfQueue attribute) (htmd.queues.pbsqueue.PBSQueue attribute) (htmd.queues.simqueue.SimQueue attribute) (htmd.queues.slurmqueue.SlurmQueue attribute) nestedListToArray() (in module htmd.ffevaluation.ffevaluate) ngpu (htmd.queues.acecloudqueue.AceCloudQueue attribute) (htmd.queues.localqueue.LocalCPUQueue attribute) (htmd.queues.localqueue.LocalGPUQueue attribute) (htmd.queues.lsfqueue.LsfQueue attribute) (htmd.queues.pbsqueue.PBSQueue attribute) (htmd.queues.simqueue.SimQueue attribute) (htmd.queues.slurmqueue.SlurmQueue attribute) ngroups (htmd.charge.esp.ESP attribute) norm (in module htmd.numbautil)

notcompleted() (htmd.queues.acecloudqueue.AceCloudQueue method) (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method) (htmd.queues.lsfqueue.LsfQueue method) (htmd.queues.pbsqueue.PBSQueue method) (htmd.queues.simqueue.SimQueue method) (htmd.queues.slurmqueue.SlurmQueue method) numAtoms (htmd.molecule.molecule.Molecule attribute) (htmd.smallmol.smallmol.SmallMol attribute) numConformers (htmd.smallmol.smallmol.SmallMol attribute) numDihedrals (htmd.parameterization.dihedral.DihedralFitting attribute) numDimensions (htmd.metricdata.MetricData attribute) (htmd.metricdata.Trajectory attribute) numFrames (htmd.metricdata.MetricData attribute) (htmd.metricdata.Trajectory attribute) (htmd.molecule.molecule.Molecule attribute) (htmd.molecule.readers.Trajectory attribute) numframes (htmd.simlist.Sim attribute) numMols (htmd.smallmol.smallmol.SmallMolLib attribute), [1] numResidues (htmd.molecule.molecule.Molecule attribute) numTrajectories (htmd.metricdata.MetricData attribute)

O

ObjectValidator (class in htmd.protocols.oldprotocolinterface) occupancy (htmd.molecule.molecule.Molecule attribute) omega() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) OMMMinimizer (class in htmd.qm.custom)

openbabelConvert() (in module htmd.smallmol.util) openmm_energy() (in module htmd.ffevaluation.test_ffevaluate) opm() (in module htmd.util) optimize (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) orient() (in module htmd.molecule.util)

P

P (htmd.model.Model attribute) pack_double_buffer() (in module htmd.molecule.support) pack_int_buffer() (in module htmd.molecule.support) pack_string_buffer() (in module htmd.molecule.support) pack_ulong_buffer() (in module htmd.molecule.support) pairwise() (in module htmd.smallmol.molvstautomer) pairwiseRMSD (in module htmd.numbautil) ParallelExecutor() (in module htmd.parallelprogress) parallelfunc() (in module htmd.pathplanning) parent (htmd.metricdata.MetricData attribute) (htmd.simlist.Sim attribute) paths (htmd.smallmol.tautomers.MolFragmenter attribute) PBSQueue (class in htmd.queues.pbsqueue) pdbGuessElementByName() (in module htmd.molecule.readers) PDBQTread() (in module htmd.molecule.readers) PDBread() (in module htmd.molecule.readers) PDBReporter (class in htmd.membranebuilder.pdbreporter) PDBwrite() (in module htmd.molecule.writers) PdbxError, [1], [2] PDBXMMCIFread() (in module htmd.molecule.readers) PdbxReader (class in htmd.molecule.pdbx.reader.PdbxParser) (class in htmd.molecule.pdbx.reader.PdbxReader) PdbxReaderTests (class in htmd.molecule.pdbx.tests.PdbxReaderTests) PdbxReadWriteTests (class in htmd.molecule.pdbx.tests.PdbxReadWriteTests) PDBxReporter (class in htmd.membranebuilder.pdbreporter) PdbxWriter (class in htmd.molecule.pdbx.reader.PdbxParser) (class in htmd.molecule.pdbx.writer.PdbxWriter) PdbxWriterTests (class in htmd.molecule.pdbx.tests.PdbxWriterTests) PeriodicTable (class in htmd.smallmol.chemlab.periodictable) phi() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) piece (htmd.simlist.Frame attribute) pka() (in module htmd.molecule.pka) plotClusters() (htmd.metricdata.MetricData method) plotConformerEnergies() (htmd.parameterization.dihedral.DihedralFitting method) plotCounts() (htmd.metricdata.MetricData method) plotDihedralEnergies() (htmd.parameterization.dihedral.DihedralFitting method) plotFES() (htmd.model.Model method) plotFluxPathways() (htmd.kinetics.Kinetics method) plotRates() (htmd.kinetics.Kinetics method) plotTimescales() (htmd.model.Model method) (htmd.modelhmm.ModelHMM method) plotTrajSizes() (htmd.metricdata.MetricData method) PlumedCOM (class in htmd.projections.metricplumed2) PlumedCV (class in htmd.projections.metricplumed2) PlumedGenericGroup (class in htmd.projections.metricplumed2) PlumedGroup (class in htmd.projections.metricplumed2) PlumedMolinfo (class in htmd.projections.metricplumed2) PlumedStatement (class in htmd.projections.metricplumed2)

PlumedVerbatim (class in htmd.projections.metricplumed2) Pmemd (class in htmd.apps.pmemd) pp_calcDistances() (in module htmd.projections.util) pp_calcMinDistances() (in module htmd.projections.util) PreparationData (class in htmd.builder.preparationdata) prettyPrintResidue() (in module htmd.builder.preparationdata) printIt() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) PRMTOPread() (in module htmd.molecule.readers) Production (class in htmd.protocols.pmemdproduction) (class in htmd.protocols.production_v1) (class in htmd.protocols.production_v2) (class in htmd.protocols.production_v3) (class in htmd.protocols.production_v4) (class in htmd.protocols.production_v5) (class in htmd.protocols.production_v6) project() (htmd.projections.gwpca.GWPCA method) (htmd.projections.kmeanstri.KMeansTri method) (htmd.projections.metric.Metric method) (htmd.projections.metriccoordinate.MetricCoordinate method) (htmd.projections.metricdihedral.MetricDihedral method) (htmd.projections.metricdistance.MetricDistance method) (htmd.projections.metricdistance.MetricSelfDistance method) (htmd.projections.metricfluctuation.MetricFluctuation method) (htmd.projections.metricnull.MetricNull method) (htmd.projections.metricplumed2.MetricPlumed2 method) (htmd.projections.metricrmsd.MetricRmsd method) (htmd.projections.metricsasa.MetricSasa method) (htmd.projections.metricsecondarystructure.MetricSecondaryStructure method) (htmd.projections.metricshell.MetricShell method) (htmd.projections.metricsphericalcoordinate.MetricSphericalCoordinate method) (htmd.projections.metrictmscore.MetricTMscore method) (htmd.projections.projection.Projection method) (htmd.projections.tica.TICA method) Projection (class in htmd.projections.projection) projection (htmd.metricdata.Trajectory attribute) ProjectNotExistError propkaContainer (htmd.builder.preparationdata.PreparationData attribute) proteinDihedrals() (htmd.projections.metricdihedral.Dihedral static method) proteinPrepare() (in module htmd.builder.preparation) ProtocolInterface (class in htmd.protocols.oldprotocolinterface) PSFread() (in module htmd.molecule.readers) PSFwrite() (in module htmd.molecule.writers) psi() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) Psi4 (class in htmd.qm) (class in htmd.qm.psi4)

Q

qm_results (htmd.charge.esp.ESP attribute) (htmd.parameterization.dihedral.DihedralFitting attribute) QMBase (class in htmd.qm.base) QMResult (class in htmd.qm) (class in htmd.qm.base)

quadrupole (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute) queue (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute)

R

radiusByElement() (in module htmd.molecule.vdw) randomPointsOnSphere() (in module htmd.charge.esp) Rates (class in htmd.kinetics) raytracing() (in module htmd.pathplanning) rcsbFindLigands() (in module htmd.molecule.util) rcsbFindMutatedResidues() (in module htmd.molecule.util) read() (htmd.molecule.molecule.Molecule method) (htmd.molecule.pdbx.reader.PdbxParser.PdbxReader method) (htmd.molecule.pdbx.reader.PdbxReader.PdbxReader method) readFRCMOD() (in module htmd.parameterization.readers) readPREPI() (in module htmd.parameterization.readers) readRTF() (in module htmd.parameterization.readers) readSimlistIndices() (in module htmd.projections.util) reconstructAdaptiveTraj() (in module htmd.adaptive.adaptive) reconstructContactMap() (in module htmd.projections.metricdistance) record (htmd.molecule.molecule.Molecule attribute) recreateParameters() (in module htmd.parameterization.parameterset) ref (htmd.metricdata.MetricData attribute), [1] reference (htmd.metricdata.Trajectory attribute) RegCluster (class in htmd.clustering.regular) rel2sim() (htmd.metricdata.MetricData method) remove() (htmd.molecule.molecule.Molecule method) (htmd.molecule.molecule.Representations method) (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) removeAtomsInHull() (in module htmd.builder.builder) removeConformers() (htmd.smallmol.smallmol.SmallMol method) removeHET() (in module htmd.builder.builder) removeHydrogens() (htmd.smallmol.chemlab.builder.Builder method) removeLipidsInProtein() (in module htmd.builder.builder) removeMols() (htmd.smallmol.smallmol.SmallMolLib method) removeRow() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) rename() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) renameAttribute() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) render() (htmd.vmdviewer.VMD method) renumberResidues() (htmd.molecule.molecule.Molecule method) rep() (htmd.vmdviewer.VMD method) replace() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) replaceSubstring() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) replaceValue() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) report() (htmd.membranebuilder.pdbreporter.PDBReporter method) (htmd.membranebuilder.pdbreporter.PDBxReporter method) reprepare() (htmd.builder.preparationdata.PreparationData method) Representations (class in htmd.molecule.molecule) reps (htmd.molecule.molecule.Molecule attribute) resid (htmd.molecule.molecule.Molecule attribute) ResidueInsertionError resname (htmd.molecule.molecule.Molecule attribute) resolveRingPenetrations() (in module htmd.membranebuilder.ringpenetration) restrained_dihedrals (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) restraint_factor (htmd.charge.esp.ESP attribute) result_directory (htmd.parameterization.dihedral.DihedralFitting attribute) retrieve() (htmd.qm.base.QMBase method) (htmd.qm.FakeQM method) (htmd.qm.FakeQM2 method) (htmd.qm.Gaussian method) (htmd.qm.Psi4 method) (htmd.qm.custom.CustomQM method) (htmd.qm.fake.FakeQM method) (htmd.qm.fake.FakeQM2 method) (htmd.qm.gaussian.Gaussian method) (htmd.qm.psi4.Psi4 method) (htmd.queues.acecloudqueue.AceCloudQueue method) (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method) (htmd.queues.lsfqueue.LsfQueue method) (htmd.queues.pbsqueue.PBSQueue method) (htmd.queues.simqueue.SimQueue method) (htmd.queues.slurmqueue.SlurmQueue method)

RetrieveError rotate() (in module htmd.smallmol.util) rotateBy() (htmd.molecule.molecule.Molecule method) rotationMatrix() (in module htmd.rotationmatrix) rrt() (in module htmd.pathplanning) rrtstarsmart() (in module htmd.pathplanning) run() (htmd.adaptive.adaptive.AdaptiveBase method) (htmd.adaptive.adaptivegoal.AdaptiveGoal method) (htmd.adaptive.adaptivegoaleg.AdaptiveGoalEG method) (htmd.adaptive.adaptiverun.AdaptiveMD method) (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.ESP method) (htmd.charge.esp.TestESP method) (htmd.ffevaluation.ffevaluate.FFEvaluate method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.DihedralFitting method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.FakeQM method) (htmd.qm.FakeQM2 method) (htmd.qm.Gaussian method) (htmd.qm.Psi4 method) (htmd.qm.base.QMBase method) (htmd.qm.custom.CustomQM method) (htmd.qm.fake.FakeQM method) (htmd.qm.fake.FakeQM2 method) (htmd.qm.gaussian.Gaussian method) (htmd.qm.psi4.Psi4 method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) run_job() (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method)

S

sampleClusters() (htmd.metricdata.MetricData method) sampleRegion() (htmd.metricdata.MetricData method) sampleStates() (htmd.model.Model method) save() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) (htmd.metricdata.MetricData method) (htmd.model.Model method) save_graphml() (htmd.mutualinformation.MutualInformation method) saveMI() (htmd.mutualinformation.MutualInformation method) scanDihedrals() (in module htmd.parameterization.util) SCORE_dict (htmd.smallmol.tautomers.MolFragmenter attribute) SDFwrite() (in module htmd.molecule.writers) search() (in module htmd.builder.charmm) search_fragment_by_atom() (htmd.smallmol.tautomers.MolFragmenter method) segid (htmd.molecule.molecule.Molecule attribute) selectAtom() (htmd.molecule.molecule.UniqueAtomID method) selectAtoms() (htmd.molecule.molecule.UniqueResidueID method) send() (htmd.vmdviewer.VMD method) sequence() (htmd.molecule.molecule.Molecule method) sequenceID() (in module htmd.molecule.util) sequenceStructureAlignment() (in module htmd.molecule.util) serial (htmd.molecule.molecule.Molecule attribute) set() (htmd.molecule.molecule.Molecule method) (htmd.projections.metric.Metric method) set_params() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) setAttributeNameList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategoryBase method) setDihedral() (htmd.molecule.molecule.Molecule method) setGlobal() (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) setName() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategoryBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) setProp() (htmd.smallmol.smallmol.SmallMol method) setPropsAtoms() (htmd.smallmol.smallmol.SmallMol method) setRowList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) (htmd.molecule.pdbx.reader.PdbxContainers.DataCategoryBase method) setRowPartition() (htmd.molecule.pdbx.writer.PdbxWriter.PdbxWriter method) setType() (htmd.molecule.pdbx.reader.PdbxContainers.ContainerBase method) (htmd.molecule.pdbx.reader.PdbxContainers.DataContainer method) (htmd.molecule.pdbx.reader.PdbxContainers.DefinitionContainer method) setup() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) setUp() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) setup() (htmd.qm.base.QMBase method) (htmd.qm.FakeQM method) (htmd.qm.FakeQM2 method) (htmd.qm.Gaussian method) (htmd.qm.Psi4 method) (htmd.qm.custom.CustomQM method) (htmd.qm.fake.FakeQM method) (htmd.qm.fake.FakeQM2 method) (htmd.qm.gaussian.Gaussian method) (htmd.qm.psi4.Psi4 method) setUp() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) setUpClass() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule class method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance class method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) setValue() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) shortDescription() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method)

show() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) Sim (class in htmd.simlist) sim (htmd.simlist.Frame attribute) simfilter() (in module htmd.simlist) simid (htmd.simlist.Sim attribute) simlist (htmd.metricdata.MetricData attribute), [1] simlist() (in module htmd.simlist) simmerge() (in module htmd.simlist) simpleSuite() (in module htmd.molecule.pdbx.tests.PdbxReaderTests) (in module htmd.molecule.pdbx.tests.PdbxReadWriteTests) SimQueue (class in htmd.queues.simqueue) skipTest() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) SlurmQueue (class in htmd.queues.slurmqueue) SmallMol (class in htmd.smallmol.smallmol) SmallMolLib (class in htmd.smallmol.smallmol) SmallMolStack (in module htmd.smallmol.smallmol) smarts (htmd.smallmol.molvstautomer.TautomerScore attribute) solvate() (in module htmd.builder.solvate) solvent (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) SOLVENTS (htmd.qm.base.QMBase attribute) (htmd.qm.FakeQM attribute) (htmd.qm.FakeQM2 attribute) (htmd.qm.Gaussian attribute) (htmd.qm.Psi4 attribute) (htmd.qm.custom.CustomQM attribute) (htmd.qm.fake.FakeQM attribute) (htmd.qm.fake.FakeQM2 attribute) (htmd.qm.gaussian.Gaussian attribute) (htmd.qm.psi4.Psi4 attribute) split() (in module htmd.builder.charmm) splitCols() (htmd.metricdata.MetricData method) St (htmd.metricdata.MetricData attribute), [1] step (htmd.molecule.molecule.Molecule attribute) stop() (htmd.queues.acecloudqueue.AceCloudQueue method) (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method) (htmd.queues.lsfqueue.LsfQueue method) (htmd.queues.pbsqueue.PBSQueue method) (htmd.queues.simqueue.SimQueue method) (htmd.queues.slurmqueue.SlurmQueue method) string_to_tempfile() (in module htmd.molecule.support) StringValidator (class in htmd.protocols.oldprotocolinterface) submit() (htmd.qm.base.QMBase method) (htmd.qm.FakeQM method) (htmd.qm.FakeQM2 method) (htmd.qm.Gaussian method) (htmd.qm.Psi4 method) (htmd.qm.custom.CustomQM method) (htmd.qm.fake.FakeQM method) (htmd.qm.fake.FakeQM2 method) (htmd.qm.gaussian.Gaussian method) (htmd.qm.psi4.Psi4 method) (htmd.queues.acecloudqueue.AceCloudQueue method) (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method) (htmd.queues.lsfqueue.LsfQueue method) (htmd.queues.pbsqueue.PBSQueue method) (htmd.queues.simqueue.SimQueue method) (htmd.queues.slurmqueue.SlurmQueue method) SubmitError subTest() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) suite() (in module htmd.molecule.pdbx.tests.PdbxWriterTests) symmetrizeCharges() (in module htmd.charge.charge) SyntaxError, [1]

T

TanimotoDistances() (in module htmd.smallmol.tools.clustering) tautomer (htmd.smallmol.molvstautomer.TautomerTransform attribute) TAUTOMER_SCORES (in module htmd.smallmol.molvstautomer) TAUTOMER_TRANSFORMS (in module htmd.smallmol.molvstautomer) TautomerCanonicalizer (class in htmd.smallmol.tautomers) TautomerEnumerator (class in htmd.smallmol.molvstautomer) TautomerScore (class in htmd.smallmol.molvstautomer) TautomerTransform (class in htmd.smallmol.molvstautomer) tearDown() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) tearDownClass() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) (htmd.charge.compare.ChargeComparison method) (htmd.charge.esp.TestESP method) (htmd.molecule.graphalignment.TestGraphAlignment method) (htmd.molecule.molecule.TestMolecule method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) (htmd.molecule.readers.TestReaders method) (htmd.molecule.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.fftype.TestFftypeCGenFF method) (htmd.parameterization.fftype.TestFftypeGAFF method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.projections.metricdistance.TestMetricDistance method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) (htmd.smallmol.test_chemlab.TestSmallMol method) (htmd.smallmol.test_smallmol.TestSmallMol method) (htmd.smallmol.test_smallmollib.TestSmallMol method) (htmd.smallmol.test_tools.TestSmallMol method) tempname() (in module htmd.util) Test (class in htmd.parameterization.parameterset) test_00_getCommonStructure() (htmd.smallmol.test_tools.TestSmallMol method) test_00_methanol() (htmd.charge.compare.ChargeComparison method) test_01_cluster_maccs() (htmd.smallmol.test_tools.TestSmallMol method) test_01_getBondRadius() (htmd.smallmol.test_chemlab.TestSmallMol method) test_01_hydroxylamine() (htmd.charge.compare.ChargeComparison method) test_01_loadMol2file() (htmd.smallmol.test_smallmol.TestSmallMol method) test_01_loaSdffile() (htmd.smallmol.test_smallmollib.TestSmallMol method) test_02_cluster_pathFingerprints() (htmd.smallmol.test_tools.TestSmallMol method) test_02_getMissingValence() (htmd.smallmol.test_chemlab.TestSmallMol method) test_02_loadPdbfile() (htmd.smallmol.test_smallmol.TestSmallMol method) test_02_urea() (htmd.charge.compare.ChargeComparison method) test_02_writeSdf() (htmd.smallmol.test_smallmollib.TestSmallMol method) test_03_appendSmallMolLib() (htmd.smallmol.test_smallmollib.TestSmallMol method) test_03_cluster_atomsFingerprints() (htmd.smallmol.test_tools.TestSmallMol method) test_03_getAtomInfo() (htmd.smallmol.test_chemlab.TestSmallMol method) test_03_isobutanol() (htmd.charge.compare.ChargeComparison method) test_03_loadSmile() (htmd.smallmol.test_smallmol.TestSmallMol method) test_04_appendSmallMol() (htmd.smallmol.test_smallmollib.TestSmallMol method) test_04_Builder() (htmd.smallmol.test_chemlab.TestSmallMol method) test_04_cluster_torsionsFingerprints() (htmd.smallmol.test_tools.TestSmallMol method) test_04_loadSdffile() (htmd.smallmol.test_smallmol.TestSmallMol method) test_04_methylaldoxime() (htmd.charge.compare.ChargeComparison method) test_05_Builder_load() (htmd.smallmol.test_chemlab.TestSmallMol method) test_05_cluster_circularFingerprints() (htmd.smallmol.test_tools.TestSmallMol method) test_05_dimethylsulphonamide() (htmd.charge.compare.ChargeComparison method) test_05_getAtoms() (htmd.smallmol.test_smallmol.TestSmallMol method) test_05_removeMols() (htmd.smallmol.test_smallmollib.TestSmallMol method) test_06_cluster_shape() (htmd.smallmol.test_tools.TestSmallMol method) test_06_convertToDataFrame() (htmd.smallmol.test_smallmollib.TestSmallMol method) test_06_getSmallMol() (htmd.smallmol.test_chemlab.TestSmallMol method) test_06_isChiral() (htmd.smallmol.test_smallmol.TestSmallMol method) test_06_trisulphate() (htmd.charge.compare.ChargeComparison method) test_07_addHydrogens() (htmd.smallmol.test_chemlab.TestSmallMol method) test_07_cluster_mcs() (htmd.smallmol.test_tools.TestSmallMol method) test_07_depict() (htmd.smallmol.test_smallmollib.TestSmallMol method) test_07_foundBond() (htmd.smallmol.test_smallmol.TestSmallMol method) test_07_phenyldiphosphate() (htmd.charge.compare.ChargeComparison method) test_08_generateConformers() (htmd.smallmol.test_smallmol.TestSmallMol method) test_08_removeHydrogens() (htmd.smallmol.test_chemlab.TestSmallMol method) test_09_anglesMETHANE() (htmd.smallmol.test_chemlab.TestSmallMol method) test_09_writeGenerateAndWriteConformers() (htmd.smallmol.test_smallmol.TestSmallMol method) test_10_angleETHENE() (htmd.smallmol.test_chemlab.TestSmallMol method) test_10_removeGenerateConformer() (htmd.smallmol.test_smallmol.TestSmallMol method) test_11_angleETHINE() (htmd.smallmol.test_chemlab.TestSmallMol method) test_11_invertChirality() (htmd.smallmol.test_smallmol.TestSmallMol method) test_12_convertToRdkit() (htmd.smallmol.test_smallmol.TestSmallMol method) test_13_convertToMolecule() (htmd.smallmol.test_smallmol.TestSmallMol method) test_14_getBonds() (htmd.smallmol.test_smallmol.TestSmallMol method) test_15_depict() (htmd.smallmol.test_smallmol.TestSmallMol method) test_alignToReference() (htmd.molecule.molecule.TestMolecule method) test_alignToReferenceMatchingFrames() (htmd.molecule.molecule.TestMolecule method) test_alignToReferenceSpecificFrames() (htmd.molecule.molecule.TestMolecule method) test_append_trajectories() (htmd.molecule.readers.TestReaders method) test_appendingBondsBondtypes() (htmd.molecule.molecule.TestMolecule method) test_basis_sets() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_benzamidine_am1_bcc() (htmd.parameterization.test.TestParameterize method) test_benzamidine_cgenff() (htmd.parameterization.test.TestParameterize method) test_benzamidine_dihed_select_restart() (htmd.parameterization.test.TestParameterize method) test_benzamidine_esp_freeze_restart() (htmd.parameterization.test.TestParameterize method) test_benzamidine_full() (htmd.parameterization.test.TestParameterize method) test_benzamidine_full_restart() (htmd.parameterization.test.TestParameterize method) test_benzamidine_gaff() (htmd.parameterization.test.TestParameterize method) test_benzamidine_gaff2() (htmd.parameterization.test.TestParameterize method) test_benzamidine_gasteiger() (htmd.parameterization.test.TestParameterize method) test_benzamidine_rtf_prm() (htmd.parameterization.test.TestParameterize method) test_broken_atomname() (htmd.parameterization.fftype.TestFftypeGAFF method) test_build() (htmd.builder.charmm.TestCharmmBuild method) test_combine_topo_traj() (htmd.molecule.readers.TestReaders method) test_constraint() (htmd.charge.esp.TestESP method) test_contacts() (htmd.projections.metricdistance.TestMetricDistance method) test_corrections() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_crd() (htmd.molecule.readers.TestReaders method) test_customDisulfideBonds() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild method) test_dcd() (htmd.molecule.readers.TestReaders method) test_dcd_frames() (htmd.molecule.readers.TestReaders method) test_dcd_into_prmtop() (htmd.molecule.readers.TestReaders method) test_defaults() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_directory() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_distances() (htmd.projections.metricdistance.TestMetricDistance method) test_disulfideWithInsertion() (htmd.builder.charmm.TestCharmmBuild method) test_ethanolamine_dihed_fix() (htmd.parameterization.test.TestParameterize method) test_ethanolamine_dihed_fix_restart() (htmd.parameterization.test.TestParameterize method) test_ethene_dihed_fix() (htmd.parameterization.test.TestParameterize method) test_ethene_dihed_fix_restart() (htmd.parameterization.test.TestParameterize method) test_get_bounds() (htmd.charge.esp.TestESP method) test_getBounds() (htmd.parameterization.dihedral.TestDihedralFitting method) test_getEquivalentDihedrals() (htmd.parameterization.parameterset.Test method) test_glycol_dihed_fix() (htmd.parameterization.test.TestParameterize method) test_glycol_dihed_fix_restart() (htmd.parameterization.test.TestParameterize method) test_glycol_dihed_fix_restart_2() (htmd.parameterization.test.TestParameterize method) test_glycol_dihed_opt_mm_fake() (htmd.parameterization.test.TestParameterize method) test_glycol_dihed_select_1_restart() (htmd.parameterization.test.TestParameterize method) test_glycol_dihed_select_2_restart() (htmd.parameterization.test.TestParameterize method) test_glycol_min_mm_fake() (htmd.parameterization.test.TestParameterize method) test_gromacs_top() (htmd.molecule.readers.TestReaders method) test_guessAnglesDihedrals() (htmd.molecule.util.TestUtils method) test_guessBonds() (htmd.molecule.molecule.TestMolecule method) test_h2o2_dihed_fix() (htmd.parameterization.test.TestParameterize method) test_h2o2_dihed_fix_restart() (htmd.parameterization.test.TestParameterize method) test_h2o2_dihed_opt() (htmd.parameterization.test.TestParameterize method)

test_h2o2_dihed_opt_mm_fake() (htmd.parameterization.test.TestParameterize method) test_h2o2_dihed_opt_restart() (htmd.parameterization.test.TestParameterize method) test_h2o2_esp() (htmd.parameterization.test.TestParameterize method) test_h2o2_esp_restart() (htmd.parameterization.test.TestParameterize method) test_h2o2_full_fake() (htmd.parameterization.test.TestParameterize method) test_h2o2_full_fake_restart() (htmd.parameterization.test.TestParameterize method) test_h2o2_gaff2() (htmd.parameterization.test.TestParameterize method) test_h2o2_list() (htmd.parameterization.test.TestParameterize method) test_h2o2_min() (htmd.parameterization.test.TestParameterize method) test_h2o2_min_restart() (htmd.parameterization.test.TestParameterize method) test_h2o2_outdir() (htmd.parameterization.test.TestParameterize method) test_h2o2_zero_searches_restart() (htmd.parameterization.test.TestParameterize method) test_integer_resnames() (htmd.molecule.readers.TestReaders method) test_inventAtomTypes() (htmd.parameterization.parameterset.Test method) test_load_time() (htmd.parameterization.test.TestParameterize method) test_mae() (htmd.molecule.readers.TestReaders method) test_mapping() (htmd.charge.esp.TestESP method) test_maximalSubstructureAlignment() (htmd.molecule.graphalignment.TestGraphAlignment method) test_mdtrajWriter() (htmd.molecule.molecule.TestMolecule method) test_mindistances() (htmd.projections.metricdistance.TestMetricDistance method) test_mindistances_skip() (htmd.projections.metricdistance.TestMetricDistance method) test_missing_crystal_info() (htmd.molecule.readers.TestReaders method) test_missing_occu_beta() (htmd.molecule.readers.TestReaders method) test_mmcif_multi_frame() (htmd.molecule.readers.TestReaders method) test_mmcif_single_frame() (htmd.molecule.readers.TestReaders method) test_mol() (htmd.parameterization.fftype.TestFftypeGAFF method) test_mol2() (htmd.molecule.readers.TestReaders method) test_multiple_file_fileloc() (htmd.molecule.readers.TestReaders method) test_multiplicity() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_multistructure() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_ngroups() (htmd.charge.esp.TestESP method) test_numDihedrals() (htmd.parameterization.dihedral.TestDihedralFitting method) test_objective() (htmd.charge.esp.TestESP method) (htmd.parameterization.dihedral.TestDihedralFitting method) test_optimization() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_paramsToVector() (htmd.parameterization.dihedral.TestDihedralFitting method) test_pdb() (htmd.molecule.readers.TestReaders method) test_pdb_charges() (htmd.molecule.readers.TestReaders method) test_pdb_element_guessing() (htmd.molecule.readers.TestReaders method) test_prmtop() (htmd.molecule.readers.TestReaders method) test_project() (htmd.projections.metriccoordinate.TestMetricCoordinate method) test_project_align() (htmd.projections.metriccoordinate.TestMetricCoordinate method) test_properties() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_psf() (htmd.molecule.readers.TestReaders method) test_queue() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_restrained_dihedrals() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_rtf_prm() (htmd.parameterization.fftype.TestFftypeCGenFF method) test_selfalign() (htmd.molecule.molecule.TestMolecule method) test_selfmindistance_auto() (htmd.projections.metricdistance.TestMetricDistance method) test_selfmindistance_manual() (htmd.projections.metricdistance.TestMetricDistance method) test_setDihedral() (htmd.molecule.molecule.TestMolecule method) test_solvents() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_star_indexes() (htmd.molecule.readers.TestReaders method) test_theories() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_tmp_files() (htmd.parameterization.fftype.TestFftypeCGenFF method) test_tmscore() (htmd.molecule.util.TestUtils method) test_topo_overwriting() (htmd.molecule.readers.TestReaders method) test_trajReadingAppending() (htmd.molecule.molecule.TestMolecule method) test_type() (htmd.qm.test.TestBase method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) test_uniqueAtomID() (htmd.molecule.molecule.TestMolecule method) test_uniqueResidueID() (htmd.molecule.molecule.TestMolecule method) test_updateBondsAnglesDihedrals() (htmd.molecule.molecule.TestMolecule method) test_vectorToParams() (htmd.parameterization.dihedral.TestDihedralFitting method) test_water_full() (htmd.parameterization.test.TestParameterize method) test_water_min_mm_charge_bcc() (htmd.parameterization.test.TestParameterize method) test_water_min_mm_charge_none() (htmd.parameterization.test.TestParameterize method) test_xtc() (htmd.molecule.readers.TestReaders method) test_xtc_frames() (htmd.molecule.readers.TestReaders method) TestAmberBuild (class in htmd.builder.amber) TestBase (class in htmd.qm.test) TestCharmmBuild (class in htmd.builder.charmm) testDHFR() (in module htmd.util) TestDihedralFitting (class in htmd.parameterization.dihedral) TestESP (class in htmd.charge.esp) TestFftypeCGenFF (class in htmd.parameterization.fftype) TestFftypeGAFF (class in htmd.parameterization.fftype) testfolder() (htmd.molecule.readers.TestReaders method) TestGaussian (class in htmd.qm.test) TestGraphAlignment (class in htmd.molecule.graphalignment) TestMetricCoordinate (class in htmd.projections.metriccoordinate) TestMetricDistance (class in htmd.projections.metricdistance) TestMolecule (class in htmd.molecule.molecule) TestParameterize (class in htmd.parameterization.test) testProteinLigand() (htmd.builder.amber.TestAmberBuild method) TestPsi4AceCloud (class in htmd.qm.test) TestPsi4Local (class in htmd.qm.test) TestPsi4Slurm (class in htmd.qm.test) testReadBigDataFile() (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) testReadDataFile() (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) TestReaders (class in htmd.molecule.readers) testReadSFDataFile() (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) testReadSmallDataFile() (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests method) testReadWriteDataFile() (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) testSimpleInitialization() (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) TestSmallMol (class in htmd.smallmol.test_chemlab) (class in htmd.smallmol.test_smallmol) (class in htmd.smallmol.test_smallmollib) (class in htmd.smallmol.test_tools) testUpdateDataFile() (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) TestUtils (class in htmd.molecule.util) testWithoutProteinPrepare() (htmd.builder.amber.TestAmberBuild method) testWithProteinPrepare() (htmd.builder.amber.TestAmberBuild method) testWriteDataFile() (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests method) THEORIES (htmd.qm.base.QMBase attribute) (htmd.qm.FakeQM attribute) (htmd.qm.FakeQM2 attribute) (htmd.qm.Gaussian attribute) (htmd.qm.Psi4 attribute) (htmd.qm.custom.CustomQM attribute) (htmd.qm.fake.FakeQM attribute) (htmd.qm.fake.FakeQM2 attribute) (htmd.qm.gaussian.Gaussian attribute) (htmd.qm.psi4.Psi4 attribute) theory (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) TICA (class in htmd.projections.tica) tileMembrane() (in module htmd.builder.builder) time (htmd.molecule.molecule.Molecule attribute) TimestepValidator (class in htmd.protocols.oldprotocolinterface) toDataFrame() (htmd.smallmol.smallmol.SmallMolLib method) toMol2() (htmd.smallmol.smallmol.SmallMol method) toMolecule() (htmd.smallmol.smallmol.SmallMol method) Topology (class in htmd.molecule.readers) TopologyInconsistencyError, [1] toRdkitMol() (htmd.smallmol.smallmol.SmallMol method) toSmarts() (htmd.smallmol.smallmol.SmallMol method) toSmile() (htmd.smallmol.smallmol.SmallMol method) totalcharge (htmd.smallmol.smallmol.SmallMol attribute) tq() (htmd.vmdgraphics.VMDBox method) (htmd.vmdgraphics.VMDConvexHull method) (htmd.vmdgraphics.VMDGraphicObject static method) (htmd.vmdgraphics.VMDIsosurface method) (htmd.vmdgraphics.VMDLabels method) (htmd.vmdgraphics.VMDSphere method) (htmd.vmdgraphics.VMDText method) Trajectory (class in htmd.metricdata) (class in htmd.molecule.readers) trajectory (htmd.simlist.Sim attribute) trajLengths (htmd.metricdata.MetricData attribute) Tree (class in htmd.pathplanning)

U

uniformRandomRotation() (in module htmd.molecule.util) UniqueAtomID (class in htmd.molecule.molecule)

UniqueResidueID (class in htmd.molecule.molecule) UnknownResidueError unwrap_self() (in module htmd.smallmol.smallmol)

V

validate() (htmd.protocols.oldprotocolinterface.BinaryValidator method) (htmd.protocols.oldprotocolinterface.BooleanValidator method) (htmd.protocols.oldprotocolinterface.ClassValidator method) (htmd.protocols.oldprotocolinterface.DictionaryValidator method) (htmd.protocols.oldprotocolinterface.FileValidator method) (htmd.protocols.oldprotocolinterface.FunctionValidator method) (htmd.protocols.oldprotocolinterface.ListListValidator method) (htmd.protocols.oldprotocolinterface.ListValidator method) (htmd.protocols.oldprotocolinterface.ObjectValidator method) (htmd.protocols.oldprotocolinterface.StringValidator method) (htmd.protocols.oldprotocolinterface.TimestepValidator method) (htmd.protocols.oldprotocolinterface.ValueValidator method) Validator (class in htmd.protocols.oldprotocolinterface) ValueValidator (class in htmd.protocols.oldprotocolinterface) version() (in module htmd.version) view() (htmd.molecule.molecule.Molecule method) viewCrystalPacking() (htmd.molecule.molecule.Molecule method) (in module htmd.molecule.crystalpacking)

viewer() (in module htmd.vmdviewer) viewForces() (in module htmd.ffevaluation.ffevaluate) viewname (htmd.molecule.molecule.Molecule attribute) viewStates() (htmd.model.Model method) (htmd.modelhmm.ModelHMM method) VMD (class in htmd.vmdviewer) VMDBox (class in htmd.vmdgraphics) VMDConvexHull (class in htmd.vmdgraphics) VMDGraphicObject (class in htmd.vmdgraphics) VMDIsosurface (class in htmd.vmdgraphics) VMDLabels (class in htmd.vmdgraphics) vmdselection() (in module htmd.molecule.vmdparser) VMDSphere (class in htmd.vmdgraphics) VMDText (class in htmd.vmdgraphics) voxel_generator() (htmd.smallmol.smallmol.SmallMolLib method) voxFun() (htmd.smallmol.smallmol.SmallMolLib method)

W

wait() (htmd.queues.acecloudqueue.AceCloudQueue method) (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method) (htmd.queues.lsfqueue.LsfQueue method) (htmd.queues.pbsqueue.PBSQueue method) (htmd.queues.simqueue.SimQueue method) (htmd.queues.slurmqueue.SlurmQueue method) warnIfTerminiSuspect() (htmd.builder.preparationdata.PreparationData method) weightGraph() (htmd.mutualinformation.MutualInformation method) with_traceback() (htmd.builder.builder.BuildError method) (htmd.builder.builder.MissingAngleError method) (htmd.builder.builder.MissingAtomTypeError method) (htmd.builder.builder.MissingBondError method) (htmd.builder.builder.MissingParameterError method) (htmd.builder.builder.MissingTorsionError method) (htmd.builder.builder.MixedSegmentError method) (htmd.builder.builder.ResidueInsertionError method) (htmd.builder.builder.UnknownResidueError method) (htmd.molecule.molecule.TopologyInconsistencyError method) (htmd.molecule.pdbx.reader.PdbxParser.PdbxError method) (htmd.molecule.pdbx.reader.PdbxParser.SyntaxError method) (htmd.molecule.pdbx.reader.PdbxReader.PdbxError method) (htmd.molecule.pdbx.reader.PdbxReader.SyntaxError method) (htmd.molecule.pdbx.writer.PdbxWriter.PdbxError method) (htmd.molecule.readers.FormatError method) (htmd.molecule.readers.TopologyInconsistencyError method) (htmd.queues.simqueue.InProgressError method) (htmd.queues.simqueue.ProjectNotExistError method) (htmd.queues.simqueue.RetrieveError method) (htmd.queues.simqueue.SubmitError method) wrap() (htmd.molecule.molecule.Molecule method) (in module htmd.membranebuilder.ringpenetration) (in module htmd.molecule.wrap)

wrapBondedDistance (in module htmd.numbautil) wrapDistance (in module htmd.numbautil) wrapping_dist_python() (in module htmd.membranebuilder.build_membrane) write() (htmd.molecule.molecule.Molecule method) (htmd.molecule.pdbx.reader.PdbxParser.PdbxWriter method) (htmd.molecule.pdbx.writer.PdbxWriter.PdbxWriter method) (htmd.protocols.equilibration_v1.Equilibration method) (htmd.protocols.equilibration_v2.Equilibration method) (htmd.protocols.pmemdequilibration.Equilibration method) (htmd.protocols.pmemdproduction.Production method) (htmd.protocols.production_v1.Production method) (htmd.protocols.production_v2.Production method) (htmd.protocols.production_v3.Production method) (htmd.protocols.production_v4.Production method) (htmd.protocols.production_v5.Production method) (htmd.protocols.production_v6.Production method) writeConf() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) writeConformers() (htmd.smallmol.smallmol.SmallMol method) writeContainer() (htmd.molecule.pdbx.reader.PdbxParser.PdbxWriter method) (htmd.molecule.pdbx.writer.PdbxWriter.PdbxWriter method) writeFRCMOD() (in module htmd.parameterization.writers) writeParameters() (in module htmd.parameterization.writers) writePRM() (in module htmd.parameterization.writers) writeRTF() (in module htmd.parameterization.writers) writeSdf() (htmd.smallmol.smallmol.SmallMolLib method) writeSmiles() (htmd.smallmol.smallmol.SmallMolLib method) writeVoxels() (in module htmd.molecule.util) writeXYZ() (htmd.charge.esp.MoleculeGrid method)

X

x (htmd.molecule.molecule.Molecule attribute) xtc_lib() (in module htmd.molecule.support) XTCread() (in module htmd.molecule.readers)

XTCwrite() (in module htmd.molecule.writers) XYZread() (in module htmd.molecule.readers) XYZwrite() (in module htmd.molecule.writers)

Y

y (htmd.molecule.molecule.Molecule attribute)

Z

z (htmd.molecule.molecule.Molecule attribute)

zerod_parameters (htmd.parameterization.dihedral.DihedralFitting attribute)