Index

_

__call__() (htmd.membranebuilder.globalminimization.RandomDisplacementBounds method) (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) acecloud (module) acecloud.client (module) acecloud.cloud (module) acecloud.exception (module) acecloud.instancetypes (module) acecloud.job (module) acecloud.joblist (module) acecloud.requesttype (module) acecloud.status (module) AceCloudQueue (class in htmd.queues.acecloudqueue) Acemd (class in htmd.apps.acemd) (class in htmd.apps.acemd_v2) Acemd3 (class in htmd.apps.acemd3) 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.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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm 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) addInstance() (acecloud.instancetypes.InstanceTypes method) addPoint() (htmd.pathplanning.Tree method) addTypeEqualityFunc() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) aggregateTime (htmd.metricdata.MetricData attribute) align() (htmd.molecule.molecule.Molecule method) alignBySequence() (htmd.molecule.molecule.Molecule method) AMBER (htmd.parameterization.fftype.FFTypeMethod 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) args (acecloud.exception.CloudError attribute) (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.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) array_cache (htmd.smallmol.smallmol.SmallMol attribute) assert_() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertAlmostEquals() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertCountEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertDictContainsSubset() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertDictEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertEquals() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertFalse() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertGreater() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertGreaterEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertIn() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertIs() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertIsInstance() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertIsNone() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertIsNot() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertIsNotNone() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertLess() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method)

assertLessEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertListEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertLogs() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertMultiLineEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotAlmostEquals() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotEquals() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotIn() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotIsInstance() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertNotRegexpMatches() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertRaises() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertRaisesRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertRaisesRegexp() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertRegexpMatches() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertSameAsReferenceDir() (in module htmd.util) assertSequenceEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertSetEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertTrue() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertTupleEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertWarns() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) assertWarnsRegex() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) atominfo (htmd.molecule.readers.Topology attribute) AtomRestraint (class in htmd.apps.acemd3) 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.fake.FakeQM attribute) (htmd.qm.fake.FakeQM2 attribute) (htmd.qm.gaussian.Gaussian attribute) (htmd.qm.psi4.Psi4 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) BooleanValidator (class in htmd.protocols.oldprotocolinterface) bootstrap() (htmd.metricdata.MetricData method) boundingBox() (in module htmd.molecule.util) box (htmd.molecule.molecule.Molecule attribute) build() (in module htmd.builder.amber) (in module htmd.builder.charmm) BuildError buildMembrane() (in module htmd.membranebuilder.build_membrane) byInstanceType() (acecloud.instancetypes.InstanceTypes method)

C

calculate() (htmd.ffevaluation.ffevaluate.FFEvaluate method) (htmd.mutualinformation.MutualInformation method) calculateEnergies() (htmd.ffevaluation.ffevaluate.FFEvaluate method) calculateSets() (in module htmd.ffevaluation.ffevaluate) canonicalize() (htmd.smallmol.tautomers.TautomerCanonicalizer method) canonicalizeAtomNames() (in module htmd.parameterization.util) 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) CGenFF_2b6 (htmd.parameterization.fftype.FFTypeMethod attribute) charge (htmd.molecule.molecule.Molecule attribute) (htmd.qm.QMResult attribute) (htmd.qm.base.QMResult attribute) CHARGEMAP (htmd.smallmol.molvstautomer.TautomerTransform attribute) CHARMM (htmd.parameterization.fftype.FFTypeMethod 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) Cloud (class in acecloud.cloud) CloudError cluster (htmd.metricdata.Trajectory attribute) cluster() (htmd.metricdata.MetricData method) 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 (acecloud.status.Status attribute) 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) 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) coords (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute)

copy() (acecloud.instancetypes.InstanceType method) (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.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.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.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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm 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) currentResult (htmd.builder.amber.TestAmberBuild attribute)

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) DCDReporter (class in htmd.membranebuilder.dcdreporter) debug() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm 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.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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) defaultTopo() (in module htmd.builder.amber) (in module htmd.builder.charmm) DefinitionContainer (class in htmd.molecule.pdbx.reader.PdbxContainers) delete() (acecloud.job.Job method) (acecloud.joblist.JobList method) (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) DELETED (acecloud.status.Status attribute) depict_tautomers() (htmd.smallmol.tautomers.TautomerCanonicalizer method) describeNextReport() (htmd.membranebuilder.dcdreporter.DCDReporter method) (htmd.membranebuilder.pdbreporter.PDBReporter method) (htmd.membranebuilder.pdbreporter.PDBxReporter method)

detectDisulfideBonds() (in module htmd.builder.builder) detectEquivalentAtoms() (in module htmd.parameterization.detect) detectParameterizableCores() (in module htmd.parameterization.detect) detectParameterizableDihedrals() (in module htmd.parameterization.detect) 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.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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm 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) drawForce() (in module htmd.ffevaluation.test_ffevaluate) 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

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)

EquilibrationAcemd3 (class in htmd.protocols.equilibration_v2) ERROR (acecloud.status.Status attribute) errored (htmd.qm.base.QMResult attribute) (htmd.qm.QMResult attribute) ESP (class in htmd.parameterization.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

factory (htmd.smallmol.smallmol.SmallMol attribute) fail() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) failIf() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) failIfAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) failIfEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) failUnless() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) failUnlessAlmostEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method)

failUnlessEqual() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) failUnlessRaises() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) failureException (htmd.builder.amber.TestAmberBuild attribute) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils attribute) (htmd.parameterization.dihedral.TestDihedralFitting attribute) (htmd.parameterization.esp.TestESP attribute) (htmd.parameterization.parameterset.Test attribute) (htmd.parameterization.test.TestParameterize attribute) (htmd.projections.metriccoordinate.TestMetricCoordinate attribute) (htmd.qm.test.TestGaussian attribute) (htmd.qm.test.TestPsi4AceCloud attribute) (htmd.qm.test.TestPsi4Local attribute) (htmd.qm.test.TestPsi4Slurm attribute) FakeQM (class in htmd.qm) (class in htmd.qm.fake) FakeQM2 (class in htmd.qm) (class in htmd.qm.fake) fdefName (htmd.smallmol.smallmol.SmallMol attribute) FFEvaluate (class in htmd.ffevaluation.ffevaluate) fftype() (in module htmd.parameterization.fftype) FFTypeMethod (class in htmd.parameterization.fftype) fileloc (htmd.molecule.molecule.Molecule attribute) FileValidator (class in htmd.protocols.oldprotocolinterface) filter() (acecloud.joblist.JobList method) (htmd.molecule.molecule.Molecule method) filter_tautomers() (htmd.smallmol.tautomers.TautomerCanonicalizer static method) findHbonds() (htmd.builder.preparationdata.PreparationData method) 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) fitCharges() (in module htmd.parameterization.util) fitDihedrals() (in module htmd.parameterization.util) fixed (htmd.parameterization.esp.ESP attribute) fixParameters() (in module htmd.ffevaluation.test_ffevaluate) format() (htmd.apps.acemd3.AtomRestraint method) (htmd.apps.acemd3.GroupRestraint method) formatEnergies() (htmd.ffevaluation.ffevaluate.FFEvaluate static method) FormatError 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) GAFF (htmd.parameterization.fftype.FFTypeMethod attribute) GAFF2 (htmd.parameterization.fftype.FFTypeMethod attribute) Gaussian (class in htmd.qm) (class in htmd.qm.gaussian) generate_conformers() (htmd.smallmol.smallmol.SmallMol method) generate_points() (htmd.parameterization.esp.ESP static 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) get_bonds() (htmd.smallmol.smallmol.SmallMol method) get_center() (htmd.smallmol.smallmol.SmallMol method) get_charges() (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_coords() (htmd.smallmol.smallmol.SmallMol method) get_depiction_atoms() (htmd.smallmol.tautomers.MolFragmenter method) get_elements() (htmd.smallmol.smallmol.SmallMol method) get_fragment() (htmd.smallmol.tautomers.MolFragmenter method) get_graphs() (htmd.smallmol.tautomers.MolFragmenter method) get_invalid_indexes() (htmd.smallmol.smallmol.SmallMolStack method) get_longest_path() (htmd.smallmol.tautomers.MolFragmenter method) get_name() (htmd.smallmol.smallmol.SmallMol method) get_natoms() (htmd.smallmol.smallmol.SmallMol 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) get_voxels() (htmd.smallmol.smallmol.SmallMol method) getAllNeighbours() (in module htmd.membranebuilder.ringpenetration) getArgumentParser() (in module htmd.parameterization.cli) 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) getConcurrentAvailability() (acecloud.cloud.Cloud 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) getEquivalentsAndDihedrals() (in module htmd.parameterization.util) 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) getImproperParameter() (in module htmd.parameterization.parameterset) getIndex() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getItemNameList() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) getJobs() (acecloud.cloud.Cloud 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)

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) getPlatform() (in module htmd.membranebuilder.simulate_openmm) getPointDescriptors() (in module htmd.molecule.voxeldescriptors) getProfile() (in module htmd.molecule.hhblitsprofile) getRates() (htmd.kinetics.Kinetics method) (htmd.kineticshmm.KineticsHMM method) 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) getSortedAndUniqueTypes() (in module htmd.parameterization.writers) getSpotPrice() (acecloud.cloud.Cloud method) getSSHCredentials() (acecloud.cloud.Cloud method) 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) getUniqueID() (acecloud.job.Job 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) getVerifySslConfig() (acecloud.cloud.Cloud method) getVMDpath() (in module htmd.vmdviewer) getVoxelDescriptors() (in module htmd.molecule.voxeldescriptors) GJFread() (in module htmd.molecule.readers) graphs (htmd.smallmol.tautomers.Fragment attribute) GROTOPread() (in module htmd.molecule.readers) GroupRestraint (class in htmd.apps.acemd3) GROwrite() (in module htmd.molecule.writers) guessAnglesAndDihedrals() (in module htmd.molecule.util) guessbonds() (in module htmd.molecule.vmdparser) guessElementFromName() (in module htmd.parameterization.util) GWPCA (class in htmd.projections.gwpca)

H

halton_sequence() (in module htmd.membranebuilder.ljfluid) hasAttribute() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) hasEmphemeralStorage() (acecloud.instancetypes.InstanceType 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.acemd3 (module) htmd.apps.acemd_v2 (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.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.dcdreporter (module) htmd.membranebuilder.globalminimization (module) htmd.membranebuilder.ljfluid (module) htmd.membranebuilder.pdbreporter (module) htmd.membranebuilder.ringpenetration (module) htmd.membranebuilder.simulate_openmm (module) htmd.membranebuilder.wrappingdist (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.esp (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.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.molvstautomer (module) htmd.smallmol.smallmol (module) htmd.smallmol.tautomers (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.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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) images() (acecloud.instancetypes.InstanceTypes method) 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) InstanceType (class in acecloud.instancetypes) InstanceTypes (class in acecloud.instancetypes) inventAtomTypes() (in module htmd.parameterization.parameterset) 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) isValidInstanceType() (acecloud.cloud.Cloud method)

J

Job (class in acecloud.job)

JobList (class in acecloud.joblist)

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) listFiles() (in module htmd.builder.amber) (in module htmd.builder.charmm) listLipids() (in module htmd.membranebuilder.build_membrane) ListListValidator (class in htmd.protocols.oldprotocolinterface) ListValidator (class in htmd.protocols.oldprotocolinterface) load() (htmd.apps.acemd.Acemd method) (htmd.apps.acemd3.Acemd3 method) (htmd.apps.acemd_v2.Acemd method) (htmd.apps.pmemd.Pmemd method) (htmd.metricdata.MetricData method) (htmd.model.Model method) load_tests() (in module htmd.parameterization.esp) loadMI() (htmd.mutualinformation.MutualInformation method) loadMol() (htmd.vmdviewer.VMD method) LocalCPUQueue (class in htmd.queues.localqueue)

LocalGPUQueue (class in htmd.queues.localqueue) longMessage (htmd.builder.amber.TestAmberBuild attribute) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils attribute) (htmd.parameterization.dihedral.TestDihedralFitting attribute) (htmd.parameterization.esp.TestESP attribute) (htmd.parameterization.parameterset.Test attribute) (htmd.parameterization.test.TestParameterize attribute) (htmd.projections.metriccoordinate.TestMetricCoordinate attribute) (htmd.qm.test.TestGaussian attribute) (htmd.qm.test.TestPsi4AceCloud attribute) (htmd.qm.test.TestPsi4Local attribute) (htmd.qm.test.TestPsi4Slurm 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_acecloud() (in module acecloud.client) main_parameterize() (in module htmd.parameterization.cli) make_script() (acecloud.job.Job method) 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) match() (acecloud.instancetypes.InstanceType method) (acecloud.instancetypes.InstanceTypes method) 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.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.util.TestUtils attribute) (htmd.parameterization.dihedral.TestDihedralFitting attribute) (htmd.parameterization.esp.TestESP attribute) (htmd.parameterization.parameterset.Test attribute) (htmd.parameterization.test.TestParameterize attribute) (htmd.projections.metriccoordinate.TestMetricCoordinate attribute) (htmd.qm.test.TestGaussian attribute) (htmd.qm.test.TestPsi4AceCloud attribute) (htmd.qm.test.TestPsi4Local attribute) (htmd.qm.test.TestPsi4Slurm 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() (in module htmd.membranebuilder.globalminimization) (in module htmd.parameterization.util) 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.parameterization.dihedral.DihedralFitting attribute) (htmd.parameterization.esp.ESP attribute) (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) 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.smallmol.tautomers.Fragment attribute) name() (acecloud.instancetypes.InstanceType method) 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.parameterization.esp.ESP attribute)

NONE (htmd.parameterization.fftype.FFTypeMethod 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) 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) numResidues (htmd.molecule.molecule.Molecule attribute) numTrajectories (htmd.metricdata.MetricData attribute)

O

ObjectValidator (class in htmd.protocols.oldprotocolinterface) omega() (htmd.projections.metricdihedral.Dihedral static method) (htmd.projections.metricdihedral.MetricDihedral static method) ONDEMAND (acecloud.requesttype.RequestType attribute)

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() (acecloud.job.Job method) 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) 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) 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) PENDING (acecloud.status.Status attribute) 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)

PREEMPTED (acecloud.status.Status attribute) PreparationData (class in htmd.builder.preparationdata) pretty_print_status() (in module acecloud.client) prettyPrintResidue() (in module htmd.builder.preparationdata) printConfig() (acecloud.cloud.Cloud method) printEnergies() (in module htmd.membranebuilder.simulate_openmm) (in module htmd.parameterization.cli) 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) printReport() (in module htmd.parameterization.cli) 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) ProductionAcemd3 (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.parameterization.dihedral.DihedralFitting attribute) (htmd.parameterization.esp.ESP 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) rand() (in module htmd.parameterization.esp) RandomDisplacementBounds (class in htmd.membranebuilder.globalminimization) 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) readCharmmParameters() (in module htmd.membranebuilder.simulate_openmm) 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) 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) remove_invalid_indexes() (htmd.smallmol.smallmol.SmallMolStack method) removeAtomsInHull() (in module htmd.builder.builder) removeHET() (in module htmd.builder.builder) removeLipidsInProtein() (in module htmd.builder.builder) 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.dcdreporter.DCDReporter method) (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) RequestType (class in acecloud.requesttype) ResidueInsertionError resolveRingPenetrations() (in module htmd.membranebuilder.ringpenetration) restrained_dihedrals (htmd.qm.Psi4 attribute) (htmd.qm.psi4.Psi4 attribute) result_directory (htmd.parameterization.dihedral.DihedralFitting attribute) retrieve() (acecloud.job.Job method) (acecloud.joblist.JobList method) (htmd.qm.FakeQM method) (htmd.qm.FakeQM2 method) (htmd.qm.Gaussian method) (htmd.qm.Psi4 method) (htmd.qm.base.QMBase 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.ffevaluation.ffevaluate.FFEvaluate 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.util.TestUtils method) (htmd.parameterization.dihedral.DihedralFitting method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.ESP method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.FakeQM method) (htmd.qm.FakeQM2 method) (htmd.qm.Gaussian method) (htmd.qm.Psi4 method) (htmd.qm.base.QMBase 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) run_job() (htmd.queues.localqueue.LocalCPUQueue method) (htmd.queues.localqueue.LocalGPUQueue method) RUNNING (acecloud.status.Status attribute)

S

sampleClusters() (htmd.metricdata.MetricData method) sampleRegion() (htmd.metricdata.MetricData method) sampleStates() (htmd.model.Model method) save() (htmd.apps.acemd.Acemd method) (htmd.apps.acemd3.Acemd3 method) (htmd.apps.acemd_v2.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) 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) 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) 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) 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.acemd3.Acemd3 method) (htmd.apps.acemd_v2.Acemd method) (htmd.apps.pmemd.Pmemd method) setUp() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate 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.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) setup() (in module acecloud.client) setUpClass() (htmd.builder.amber.TestAmberBuild class method) (htmd.builder.charmm.TestCharmmBuild class method) (htmd.molecule.molecule.TestMolecule class method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests class method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests class method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests class method) (htmd.molecule.util.TestUtils class method) (htmd.parameterization.dihedral.TestDihedralFitting class method) (htmd.parameterization.esp.TestESP class method) (htmd.parameterization.parameterset.Test class method) (htmd.parameterization.test.TestParameterize class method) (htmd.projections.metriccoordinate.TestMetricCoordinate class method) (htmd.qm.test.TestGaussian class method) (htmd.qm.test.TestPsi4AceCloud class method) (htmd.qm.test.TestPsi4Local class method) (htmd.qm.test.TestPsi4Slurm class method) setValue() (htmd.molecule.pdbx.reader.PdbxContainers.DataCategory method) shortDescription() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method)

show() (htmd.apps.acemd.Acemd method) (htmd.apps.acemd3.Acemd3 method) (htmd.apps.acemd_v2.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.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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) SlurmQueue (class in htmd.queues.slurmqueue) SmallMol (class in htmd.smallmol.smallmol) SmallMolStack (class in 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.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) SPOT (acecloud.requesttype.RequestType attribute) St (htmd.metricdata.MetricData attribute), [1] Status (class in acecloud.status) status() (acecloud.job.Job method) (acecloud.joblist.JobList method) 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) STOPPED (acecloud.status.Status attribute) string_to_tempfile() (in module htmd.molecule.support) StringValidator (class in htmd.protocols.oldprotocolinterface) submit() (acecloud.cloud.Cloud method) (htmd.qm.FakeQM method) (htmd.qm.FakeQM2 method) (htmd.qm.Gaussian method) (htmd.qm.Psi4 method) (htmd.qm.base.QMBase 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 subrandom_particle_positions() (in module htmd.membranebuilder.ljfluid) subTest() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) suite() (in module htmd.molecule.pdbx.tests.PdbxWriterTests) syntax() (in module acecloud.client) SyntaxError, [1]

T

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.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.util.TestUtils method) (htmd.parameterization.dihedral.TestDihedralFitting method) (htmd.parameterization.esp.TestESP method) (htmd.parameterization.parameterset.Test method) (htmd.parameterization.test.TestParameterize method) (htmd.projections.metriccoordinate.TestMetricCoordinate method) (htmd.qm.test.TestGaussian method) (htmd.qm.test.TestPsi4AceCloud method) (htmd.qm.test.TestPsi4Local method) (htmd.qm.test.TestPsi4Slurm method) tearDownClass() (htmd.builder.amber.TestAmberBuild class method) (htmd.builder.charmm.TestCharmmBuild class method) (htmd.molecule.molecule.TestMolecule class method) (htmd.molecule.pdbx.tests.PdbxReadWriteTests.PdbxReadWriteTests class method) (htmd.molecule.pdbx.tests.PdbxReaderTests.PdbxReaderTests class method) (htmd.molecule.pdbx.tests.PdbxWriterTests.PdbxWriterTests class method) (htmd.molecule.util.TestUtils class method) (htmd.parameterization.dihedral.TestDihedralFitting class method) (htmd.parameterization.esp.TestESP class method) (htmd.parameterization.parameterset.Test class method) (htmd.parameterization.test.TestParameterize class method) (htmd.projections.metriccoordinate.TestMetricCoordinate class method) (htmd.qm.test.TestGaussian class method) (htmd.qm.test.TestPsi4AceCloud class method) (htmd.qm.test.TestPsi4Local class method) (htmd.qm.test.TestPsi4Slurm class method) tempname() (in module htmd.util) Test (class in htmd.parameterization.parameterset) 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_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_rtf_prm() (htmd.parameterization.test.TestParameterize method) test_build() (htmd.builder.charmm.TestCharmmBuild method) test_compute_objective() (htmd.parameterization.esp.TestESP method) test_constraint_function() (htmd.parameterization.esp.TestESP 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_customDisulfideBonds() (htmd.builder.amber.TestAmberBuild method) (htmd.builder.charmm.TestCharmmBuild 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_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.parameterization.esp.TestESP method) test_getBounds() (htmd.parameterization.dihedral.TestDihedralFitting method) test_getEquivalentDihedrals() (htmd.parameterization.parameterset.Test method) test_getValidQMResults() (htmd.parameterization.dihedral.TestDihedralFitting 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_select_1_restart() (htmd.parameterization.test.TestParameterize method) test_glycol_dihed_select_2_restart() (htmd.parameterization.test.TestParameterize 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_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_inventAtomTypes() (htmd.parameterization.parameterset.Test method) test_mapping() (htmd.parameterization.esp.TestESP method) test_mdtrajWriter() (htmd.molecule.molecule.TestMolecule 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.parameterization.esp.TestESP method) test_numDihedrals() (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_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_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_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_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_tmscore() (htmd.molecule.util.TestUtils 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) 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.parameterization.esp) TestGaussian (class in htmd.qm.test) TestMetricCoordinate (class in htmd.projections.metriccoordinate) 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) 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) 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.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) to_molecule() (htmd.smallmol.smallmol.SmallMol method) Topology (class in htmd.molecule.readers) TopologyInconsistencyError totalContacts() (in module htmd.membranebuilder.globalminimization) tq() (htmd.vmdgraphics.VMDBox static method) (htmd.vmdgraphics.VMDConvexHull static method) (htmd.vmdgraphics.VMDGraphicObject static method) (htmd.vmdgraphics.VMDIsosurface static method) (htmd.vmdgraphics.VMDLabels static method) (htmd.vmdgraphics.VMDSphere static method) (htmd.vmdgraphics.VMDText static 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)

UNKNOWN (acecloud.status.Status attribute) 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.test_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) vox_fun() (htmd.smallmol.smallmol.SmallMolStack method) voxel_generator() (htmd.smallmol.smallmol.SmallMolStack 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() (acecloud.exception.CloudError method) (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.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_numba() (in module htmd.membranebuilder.wrappingdist) wrapping_dist_python() (in module htmd.membranebuilder.wrappingdist) 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.equilibration_v2.EquilibrationAcemd3 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_v5.ProductionAcemd3 method) (htmd.protocols.production_v6.Production method) (htmd.protocols.production_v6.ProductionAcemd3 method) writeConf() (htmd.apps.acemd.Acemd method) (htmd.apps.acemd3.Acemd3 method) (htmd.apps.acemd_v2.Acemd method) (htmd.apps.pmemd.Pmemd method) writeConfig() (acecloud.cloud.Cloud 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) writeVoxels() (in module htmd.molecule.util)

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)