Index

A

AdaptivePELE.__init__ module AdaptivePELE.adaptiveSampling module AdaptivePELE.analysis.backtrackAdaptiveTrajectory module AdaptivePELE.analysis.correctRMSD module AdaptivePELE.analysis.foldersFirstBindingEvent module AdaptivePELE.analysis.makePNGs module AdaptivePELE.analysis.numberOfClusters module AdaptivePELE.analysis.plotAdaptive module AdaptivePELE.analysis.writeClusteringStructures module AdaptivePELE.atomset.atomset module AdaptivePELE.atomset.RMSDCalculator module AdaptivePELE.atomset.SymmetryContactMapEvaluator module AdaptivePELE.automateRoundsAdaptive module AdaptivePELE.clustering.clustering module AdaptivePELE.clustering.clusteringTypes module AdaptivePELE.clustering.thresholdcalculator module AdaptivePELE.clustering.thresholdcalculatortypes module

AdaptivePELE.simulation.simulationrunner module AdaptivePELE.simulation.simulationTypes module AdaptivePELE.spawning.densitycalculator module AdaptivePELE.spawning.densitycalculatortypes module AdaptivePELE.spawning.spawning module AdaptivePELE.spawning.spawningTypes module AdaptivePELE.utilities.clusteringUtilities module AdaptivePELE.utilities.utilities module AdaptivePELE.validator.controlFileValidator module add_edge() (AdaptivePELE.clustering.clustering.ConformationNetwork method) add_node() (AdaptivePELE.clustering.clustering.ConformationNetwork method) addCluster() (AdaptivePELE.clustering.clustering.Clusters method) addElement() (AdaptivePELE.clustering.clustering.Cluster method) addLine() (in module AdaptivePELE.analysis.plotAdaptive) addSnapshotToCluster() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.SequentialLastSnapshotClustering method) addStructure() (AdaptivePELE.clustering.clustering.AltStructures method) altSpawnSelection() (AdaptivePELE.clustering.clustering.AltStructures method) AltStructures (class in AdaptivePELE.clustering.clustering) assertSymmetriesDict() (in module AdaptivePELE.utilities.utilities) Atom (class in AdaptivePELE.atomset.atomset) ATOM_LINE_TEMPLATE (AdaptivePELE.atomset.atomset.PDB attribute) atomList (AdaptivePELE.atomset.atomset.PDB attribute) atoms (AdaptivePELE.atomset.atomset.PDB attribute) atomSerial (AdaptivePELE.atomset.atomset.Atom attribute) automateSimulation() (in module AdaptivePELE.automateRoundsAdaptive)

B

build() (AdaptivePELE.clustering.clustering.similarityEvaluatorBuilder method) (AdaptivePELE.clustering.thresholdcalculator.ThresholdCalculatorBuilder method) (AdaptivePELE.simulation.simulationrunner.ExitConditionBuilder method) (AdaptivePELE.simulation.simulationrunner.RunnerBuilder method) (AdaptivePELE.spawning.densitycalculator.DensityCalculatorBuilder method) (AdaptivePELE.spawning.spawning.SpawningAlgorithmBuilder method) buildClustering() (AdaptivePELE.clustering.clustering.ClusteringBuilder method)

buildClustersPerValue() (in module AdaptivePELE.analysis.numberOfClusters) buildContactMap() (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator method) buildContactMapWithRowMap() (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator method) buildNewClusteringAndWriteInitialStructuresInNewSimulation() (in module AdaptivePELE.adaptiveSampling) buildNewClusteringAndWriteInitialStructuresInRestart() (in module AdaptivePELE.adaptiveSampling) buildOptimalPermutationContactMap() (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator method) buildSpawningCalculator() (AdaptivePELE.spawning.spawning.SpawningBuilder method) buildSpawningParameters() (AdaptivePELE.spawning.spawning.SpawningParams method)

C

calculate() (AdaptivePELE.clustering.thresholdcalculator.ThresholdCalculator method) (AdaptivePELE.clustering.thresholdcalculator.ThresholdCalculatorConstant method) (AdaptivePELE.clustering.thresholdcalculator.ThresholdCalculatorHeaviside method) (AdaptivePELE.spawning.densitycalculator.ContinuousDensityCalculator method) (AdaptivePELE.spawning.densitycalculator.DensityCalculator method) (AdaptivePELE.spawning.densitycalculator.DensityCalculatorHeaviside method) (AdaptivePELE.spawning.densitycalculator.ExitContinousDensityCalculator method) (AdaptivePELE.spawning.densitycalculator.NullDensityCalculator method) (AdaptivePELE.spawning.spawning.EpsilonDegeneracyCalculator method) (AdaptivePELE.spawning.spawning.FASTDegeneracyCalculator method) (AdaptivePELE.spawning.spawning.IndependentMSMCalculator method) (AdaptivePELE.spawning.spawning.InverselyProportionalToPopulationCalculator method) (AdaptivePELE.spawning.spawning.MetastabilityMSMCalculator method) (AdaptivePELE.spawning.spawning.NullSpawningCalculator method) (AdaptivePELE.spawning.spawning.ProbabilityMSMCalculator method) (AdaptivePELE.spawning.spawning.REAPCalculator method) (AdaptivePELE.spawning.spawning.SameWeightDegeneracyCalculator method) (AdaptivePELE.spawning.spawning.SimulatedAnnealingCalculator method) (AdaptivePELE.spawning.spawning.SpawningCalculator method) (AdaptivePELE.spawning.spawning.UCBCalculator method) (AdaptivePELE.spawning.spawning.UncertaintyMSMCalculator method) (AdaptivePELE.spawning.spawning.VariableEpsilonDegeneracyCalculator method) calculate_q() (AdaptivePELE.spawning.spawning.UncertaintyMSMCalculator method) calculate_rmsd_traj() (in module AdaptivePELE.analysis.correctRMSD) calculateContactMapEigen() (in module AdaptivePELE.utilities.utilities) calculateContactsVar() (in module AdaptivePELE.spawning.spawning) calculateCorrelationContactMaps() (in module AdaptivePELE.atomset.SymmetryContactMapEvaluator) calculateDensities() (AdaptivePELE.spawning.spawning.DensitySpawningCalculator method) calculatedG() (AdaptivePELE.spawning.spawning.MSMCalculator method) calculateEpsilonValue() (AdaptivePELE.spawning.spawning.VariableEpsilonDegeneracyCalculator method) calculateEquilibrationLength() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) calculateNormalisedMetrics() (AdaptivePELE.spawning.spawning.FASTDegeneracyCalculator method) calculateNormalisedSizes() (AdaptivePELE.spawning.spawning.FASTDegeneracyCalculator method) centroid (AdaptivePELE.atomset.atomset.PDB attribute) check_types() (in module AdaptivePELE.validator.controlFileValidator) checkAmbertools() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) checkAttributes() (AdaptivePELE.clustering.clustering.CMClusteringEvaluator method) (AdaptivePELE.clustering.clustering.ContactsClusteringEvaluator method) (AdaptivePELE.clustering.clustering.RMSDOnlyClusteringEvaluator method) checkExitCondition() (AdaptivePELE.simulation.simulationrunner.ClusteringExitCondition method) (AdaptivePELE.simulation.simulationrunner.MetricExitCondition method) (AdaptivePELE.simulation.simulationrunner.MetricMultipleTrajsExitCondition method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) checkIntegrityClusteringObject() (in module AdaptivePELE.adaptiveSampling) checkMetricExitConditionMultipleTrajsinRestart() (in module AdaptivePELE.adaptiveSampling) checkSimulationInterrupted() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) checkSymmetryDict() (in module AdaptivePELE.adaptiveSampling) cleanCheckpointFiles() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) cleanContactMap() (AdaptivePELE.clustering.clustering.ClusteringEvaluator method) cleanPQ() (AdaptivePELE.clustering.clustering.AltStructures method) cleanPreviousSimulation() (in module AdaptivePELE.adaptiveSampling) cleanProcessesFiles() (in module AdaptivePELE.adaptiveSampling)

cleanTopologies() (AdaptivePELE.utilities.utilities.Topology method) cleanup() (in module AdaptivePELE.utilities.utilities) Cluster (class in AdaptivePELE.clustering.clustering) cluster() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.MSMClustering method) (AdaptivePELE.clustering.clustering.NullClustering method) (AdaptivePELE.clustering.clustering.SequentialLastSnapshotClustering method) clusterEpochTrajs() (in module AdaptivePELE.adaptiveSampling) clusterEquilibrationStructures() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) CLUSTERING (AdaptivePELE.simulation.simulationTypes.EXITCONDITION_TYPE attribute) Clustering (class in AdaptivePELE.clustering.clustering) CLUSTERING_TYPES (class in AdaptivePELE.clustering.clusteringTypes) ClusteringBuilder (class in AdaptivePELE.clustering.clustering) ClusteringEvaluator (class in AdaptivePELE.clustering.clustering) ClusteringExitCondition (class in AdaptivePELE.simulation.simulationrunner) clusterIterator() (AdaptivePELE.clustering.clustering.Clustering method) clusterPreviousEpochs() (in module AdaptivePELE.adaptiveSampling) Clusters (class in AdaptivePELE.clustering.clustering) CMAtoms (AdaptivePELE.atomset.atomset.PDB attribute) CMClusteringEvaluator (class in AdaptivePELE.clustering.clustering) CMSimilarityEvaluator (class in AdaptivePELE.clustering.clustering) com (AdaptivePELE.atomset.atomset.PDB attribute) computeCOMDifference() (in module AdaptivePELE.atomset.atomset) computeCOMSquaredDifference() (in module AdaptivePELE.atomset.atomset) computeNonSymmAtoms() (AdaptivePELE.atomset.RMSDCalculator.RMSDCalculator method) computeRMSD() (AdaptivePELE.atomset.RMSDCalculator.RMSDCalculator method) computeRMSD2() (AdaptivePELE.atomset.RMSDCalculator.RMSDCalculator method) computeSquaredCentroidDifference() (in module AdaptivePELE.atomset.atomset) computeTemperature() (AdaptivePELE.spawning.spawning.SimulatedAnnealingCalculator method) computeTotalMass() (AdaptivePELE.atomset.atomset.PDB method) ConformationNetwork (class in AdaptivePELE.clustering.clustering) constant (AdaptivePELE.clustering.thresholdcalculatortypes.THRESHOLD_CALCULATOR_TYPES attribute) contactMap (AdaptivePELE.clustering.clusteringTypes.CLUSTERING_TYPES attribute) ContactMapAccumulativeClustering (class in AdaptivePELE.clustering.clustering) ContactsClustering (class in AdaptivePELE.clustering.clustering) ContactsClusteringEvaluator (class in AdaptivePELE.clustering.clustering) contactsVariation (AdaptivePELE.spawning.spawningTypes.EPSILON_VARIATION_TYPES attribute) contactsVariation() (AdaptivePELE.spawning.spawning.VariableEpsilonDegeneracyCalculator method) continousDensity() (in module AdaptivePELE.spawning.densitycalculator) continuous (AdaptivePELE.spawning.densitycalculatortypes.DENSITY_CALCULATOR_TYPES attribute) ContinuousDensityCalculator (class in AdaptivePELE.spawning.densitycalculator) convert_trajectory_to_pdb() (in module AdaptivePELE.utilities.utilities) copyInitialStructures() (in module AdaptivePELE.adaptiveSampling) correlation (AdaptivePELE.clustering.clusteringTypes.SIMILARITY_TYPES attribute) countContacts() (AdaptivePELE.atomset.atomset.PDB method) createContactMap() (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator method) createMappingForFirstEpoch() (in module AdaptivePELE.adaptiveSampling) createMultipleComplexesFilenames() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) createPathwayToCluster() (AdaptivePELE.clustering.clustering.ConformationNetwork method) createPlot() (in module AdaptivePELE.analysis.plotAdaptive) createPlots() (AdaptivePELE.spawning.spawning.MSMCalculator method) (AdaptivePELE.spawning.spawning.SpawningCalculator method) createSymbolicLinks() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method)

D

DENSITY_CALCULATOR_TYPES (class in AdaptivePELE.spawning.densitycalculatortypes) DensityCalculator (class in AdaptivePELE.spawning.densitycalculator) DensityCalculatorBuilder (class in AdaptivePELE.spawning.densitycalculator) DensityCalculatorHeaviside (class in AdaptivePELE.spawning.densitycalculator) DensitySpawningCalculator (class in AdaptivePELE.spawning.spawning)

differenceDistance (AdaptivePELE.clustering.clusteringTypes.SIMILARITY_TYPES attribute) distanceCOM() (in module AdaptivePELE.utilities.utilities) divideInverselyProportionalToArray() (AdaptivePELE.spawning.spawning.SpawningCalculator method) divideProcessorsMetricProportional() (AdaptivePELE.spawning.spawning.EpsilonDegeneracyCalculator method) divideProportionalToArray() (AdaptivePELE.spawning.spawning.SpawningCalculator method) divideTrajAccordingToWeights() (AdaptivePELE.spawning.spawning.SpawningCalculator method)

E

emptyClustering() (AdaptivePELE.clustering.clustering.Clustering method) ensure_connectivity_msm() (in module AdaptivePELE.utilities.utilities) epsilon (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) EPSILON_VARIATION_TYPES (class in AdaptivePELE.spawning.spawningTypes) EpsilonDegeneracyCalculator (class in AdaptivePELE.spawning.spawning) equilibrate() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) equivalentResname() (AdaptivePELE.atomset.atomset.Atom method) estimateMSM() (AdaptivePELE.spawning.spawning.MSMCalculator method) evaluateCorrelation() (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator method)

evaluateDifferenceDistance() (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator method) evaluateJaccard() (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator method) EXITCONDITION_TYPE (class in AdaptivePELE.simulation.simulationTypes) ExitConditionBuilder (class in AdaptivePELE.simulation.simulationrunner) exitContinous (AdaptivePELE.spawning.densitycalculatortypes.DENSITY_CALCULATOR_TYPES attribute) ExitContinousDensityCalculator (class in AdaptivePELE.spawning.densitycalculator) expandInitialStructuresWildcard() (in module AdaptivePELE.adaptiveSampling) extractCentroid() (AdaptivePELE.atomset.atomset.PDB method) extractCOM() (AdaptivePELE.atomset.atomset.PDB method) extractLigand() (AdaptivePELE.simulation.simulationrunner.MDSimulation method)

F

FAST (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) FASTDegeneracyCalculator (class in AdaptivePELE.spawning.spawning) filterClustersAccordingToBox() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.MSMClustering method) filterClustersAccordingToMetric() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.MSMClustering method)

filterRepeatedReports() (in module AdaptivePELE.clustering.clustering) findDifferentClustersForAllEpochs() (in module AdaptivePELE.analysis.numberOfClusters) findDifferentClustersInEpoch() (in module AdaptivePELE.analysis.numberOfClusters) findFirstRun() (in module AdaptivePELE.adaptiveSampling) fixReportsSymmetry() (in module AdaptivePELE.adaptiveSampling)

G

gen_atom_name() (in module AdaptivePELE.utilities.utilities) generatePELECommand() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) generatePlot() (in module AdaptivePELE.analysis.plotAdaptive) generateRotationMatrixAroundAxis() (in module AdaptivePELE.utilities.utilities) generateTrajectorySelectionString() (in module AdaptivePELE.adaptiveSampling) get_available_backend() (in module AdaptivePELE.utilities.utilities) get_epoch_folders() (in module AdaptivePELE.utilities.utilities) get_file_extension() (in module AdaptivePELE.utilities.utilities) get_file_name() (in module AdaptivePELE.utilities.utilities) get_file_name_extension() (in module AdaptivePELE.utilities.utilities) get_mdtraj_object_PDBstring() (in module AdaptivePELE.utilities.utilities) get_pdb_string() (AdaptivePELE.atomset.atomset.PDB method) get_string_from_array() (in module AdaptivePELE.utilities.utilities) get_workers_output() (in module AdaptivePELE.utilities.utilities) getAllDifferentValues() (in module AdaptivePELE.analysis.numberOfClusters) getAllTrajectories() (in module AdaptivePELE.clustering.clustering) getAtom() (AdaptivePELE.atomset.atomset.PDB method) getAtomCoords() (AdaptivePELE.atomset.atomset.Atom method) getAtomNames() (in module AdaptivePELE.utilities.utilities) getCentroid() (AdaptivePELE.atomset.atomset.PDB method) getCluster() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.Clusters method) getClusteringInfo() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) getClusteringLigandInfo() (in module AdaptivePELE.adaptiveSampling) getClusteringSummaryContent() (in module AdaptivePELE.analysis.numberOfClusters) getClusterListForSpawning() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.MSMClustering method) getCOM() (AdaptivePELE.atomset.atomset.PDB method) getContacts() (AdaptivePELE.clustering.clustering.Cluster method) getCpuCount() (in module AdaptivePELE.utilities.utilities) getEquilibrationControlFile() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) getFileExtension() (in module AdaptivePELE.utilities.utilities) getFileSuffix() (in module AdaptivePELE.utilities.utilities) getInnerLimit() (AdaptivePELE.clustering.clustering.CMClusteringEvaluator method) (AdaptivePELE.clustering.clustering.ContactsClusteringEvaluator method) getMaxThreshold() (AdaptivePELE.clustering.thresholdcalculator.ThresholdCalculatorConstant method) (AdaptivePELE.clustering.thresholdcalculator.ThresholdCalculatorHeaviside method) getMetric() (AdaptivePELE.clustering.clustering.Cluster method) getMetricColumns() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) getMetricFromColumn() (AdaptivePELE.clustering.clustering.Cluster method)

getMetrics() (AdaptivePELE.spawning.spawning.SpawningCalculator method) getMetricsFromColumn() (AdaptivePELE.clustering.clustering.Clustering method) getMetricsFromReportsInEpoch() (in module AdaptivePELE.utilities.utilities) getNextIterationBox() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) getNumberClusters() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.Clusters method) getNumberOfAtoms() (AdaptivePELE.atomset.atomset.PDB method) getNumberOfClustersPerEpochForGivenColumn() (in module AdaptivePELE.analysis.numberOfClusters) getNumReplicas() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) getOptimalMetric() (AdaptivePELE.clustering.clustering.Clustering method) getPELEControlFileDict() (in module AdaptivePELE.utilities.utilities) getPrmtopNum() (in module AdaptivePELE.utilities.utilities) getReportAndTrajectoryWildcard() (in module AdaptivePELE.utilities.utilities) getReportList() (in module AdaptivePELE.utilities.utilities) getReportNum() (in module AdaptivePELE.utilities.utilities) getResname() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) getRMSD() (in module AdaptivePELE.utilities.utilities) getSASAcolumnFromControlFile() (in module AdaptivePELE.utilities.utilities) getSASAvalues() (AdaptivePELE.spawning.spawning.MSMCalculator method) getSizes() (in module AdaptivePELE.spawning.spawning) getSnapshots() (in module AdaptivePELE.utilities.utilities) getSortedEigen() (in module AdaptivePELE.utilities.utilities) getStationaryDistr() (in module AdaptivePELE.utilities.utilities) getTopology() (AdaptivePELE.utilities.utilities.Topology method) (AdaptivePELE.utilities.utilities.TopologyCompat method) getTopologyFile() (AdaptivePELE.utilities.utilities.Topology method) (AdaptivePELE.utilities.utilities.TopologyCompat method) (in module AdaptivePELE.utilities.utilities) getTopologyFromIndex() (AdaptivePELE.utilities.utilities.Topology method) getTopologyIndex() (AdaptivePELE.utilities.utilities.Topology method) (AdaptivePELE.utilities.utilities.TopologyCompat method) getTopologyObject() (in module AdaptivePELE.utilities.utilities) getTotalNumberOfClustersPerEpoch() (in module AdaptivePELE.analysis.numberOfClusters) getTrajNum() (in module AdaptivePELE.utilities.utilities) getWorkingClusteringObjectAndReclusterIfNecessary() (in module AdaptivePELE.adaptiveSampling) getWorkingProcessors() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) (AdaptivePELE.simulation.simulationrunner.TestSimulation method) glob_sorted() (in module AdaptivePELE.utilities.utilities)

H

hasExitCondition() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method)

heaviside (AdaptivePELE.clustering.thresholdcalculatortypes.THRESHOLD_CALCULATOR_TYPES attribute) (AdaptivePELE.spawning.densitycalculatortypes.DENSITY_CALCULATOR_TYPES attribute)

I

id (AdaptivePELE.atomset.atomset.Atom attribute) independent (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) independentMetric (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) IndependentMetricCalculator (class in AdaptivePELE.spawning.spawning) IndependentMSMCalculator (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) (class in AdaptivePELE.spawning.spawning) IndependentRunsCalculator (class in AdaptivePELE.spawning.spawning) initialise() (AdaptivePELE.atomset.atomset.PDB method) insertCluster() (AdaptivePELE.clustering.clustering.Clusters method) inverselyProportional (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute)

InverselyProportionalToPopulationCalculator (class in AdaptivePELE.spawning.spawning) isElement() (AdaptivePELE.clustering.clustering.CMClusteringEvaluator method) (AdaptivePELE.clustering.clustering.ContactsClusteringEvaluator method) isfromPDBFile() (AdaptivePELE.atomset.atomset.PDB method) isHeavyAtom() (AdaptivePELE.atomset.atomset.Atom method) isHeteroAtom() (AdaptivePELE.atomset.atomset.Atom method) ispdb (AdaptivePELE.atomset.atomset.PDB attribute) isProtein() (AdaptivePELE.atomset.atomset.Atom method) isReport() (in module AdaptivePELE.utilities.utilities) isSimilarCluster() (AdaptivePELE.clustering.clustering.CMSimilarityEvaluator method)

J

Jaccard (AdaptivePELE.clustering.clusteringTypes.SIMILARITY_TYPES attribute)

join_coordinates_prob() (in module AdaptivePELE.utilities.utilities) join_PDB_lines() (AdaptivePELE.atomset.atomset.PDB method)

L

lastSnapshot (AdaptivePELE.clustering.clusteringTypes.CLUSTERING_TYPES attribute) ligandList (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator attribute) limitMax (AdaptivePELE.clustering.clustering.CMClusteringEvaluator attribute) limitSlope (AdaptivePELE.clustering.clustering.CMClusteringEvaluator attribute) linearVariation (AdaptivePELE.spawning.spawningTypes.EPSILON_VARIATION_TYPES attribute) linearVariation() (AdaptivePELE.spawning.spawning.VariableEpsilonDegeneracyCalculator method) loadParams() (in module AdaptivePELE.adaptiveSampling) loadReportFile() (in module AdaptivePELE.clustering.clustering) loadtxtfile() (in module AdaptivePELE.utilities.utilities)

log() (AdaptivePELE.spawning.spawning.EpsilonDegeneracyCalculator method) (AdaptivePELE.spawning.spawning.FASTDegeneracyCalculator method) (AdaptivePELE.spawning.spawning.InverselyProportionalToPopulationCalculator method) (AdaptivePELE.spawning.spawning.REAPCalculator method) (AdaptivePELE.spawning.spawning.SameWeightDegeneracyCalculator method) (AdaptivePELE.spawning.spawning.SimulatedAnnealingCalculator method) (AdaptivePELE.spawning.spawning.SpawningCalculator method) (AdaptivePELE.spawning.spawning.UCBCalculator method) logVariableEpsilon() (AdaptivePELE.spawning.spawning.VariableEpsilonDegeneracyCalculator method)

M

main() (in module AdaptivePELE.adaptiveSampling) (in module AdaptivePELE.analysis.backtrackAdaptiveTrajectory) (in module AdaptivePELE.analysis.correctRMSD) (in module AdaptivePELE.analysis.foldersFirstBindingEvent) (in module AdaptivePELE.analysis.numberOfClusters) (in module AdaptivePELE.analysis.writeClusteringStructures) (in module AdaptivePELE.automateRoundsAdaptive) makeFolder() (in module AdaptivePELE.utilities.utilities) makeWorkingControlFile() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) (AdaptivePELE.simulation.simulationrunner.TestSimulation method) mapEpochTopologies() (AdaptivePELE.utilities.utilities.Topology method) mass (AdaptivePELE.atomset.atomset.Atom attribute) MD (AdaptivePELE.simulation.simulationTypes.SIMULATION_TYPE attribute) MDSimulation (class in AdaptivePELE.simulation.simulationrunner) mergeFilteredClustersAccordingToBox() (in module AdaptivePELE.adaptiveSampling) MetastabilityMSMCalculator (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) (class in AdaptivePELE.spawning.spawning) METRIC (AdaptivePELE.simulation.simulationTypes.EXITCONDITION_TYPE attribute) MetricExitCondition (class in AdaptivePELE.simulation.simulationrunner) METRICMULTIPLETRAJS (AdaptivePELE.simulation.simulationTypes.EXITCONDITION_TYPE attribute) MetricMultipleTrajsExitCondition (class in AdaptivePELE.simulation.simulationrunner) module AdaptivePELE.__init__ AdaptivePELE.adaptiveSampling AdaptivePELE.analysis.backtrackAdaptiveTrajectory AdaptivePELE.analysis.correctRMSD AdaptivePELE.analysis.foldersFirstBindingEvent AdaptivePELE.analysis.makePNGs AdaptivePELE.analysis.numberOfClusters AdaptivePELE.analysis.plotAdaptive AdaptivePELE.analysis.writeClusteringStructures AdaptivePELE.atomset.atomset AdaptivePELE.atomset.RMSDCalculator AdaptivePELE.atomset.SymmetryContactMapEvaluator AdaptivePELE.automateRoundsAdaptive AdaptivePELE.clustering.clustering AdaptivePELE.clustering.clusteringTypes AdaptivePELE.clustering.thresholdcalculator AdaptivePELE.clustering.thresholdcalculatortypes AdaptivePELE.simulation.simulationrunner AdaptivePELE.simulation.simulationTypes AdaptivePELE.spawning.densitycalculator AdaptivePELE.spawning.densitycalculatortypes AdaptivePELE.spawning.spawning AdaptivePELE.spawning.spawningTypes AdaptivePELE.utilities.clusteringUtilities AdaptivePELE.utilities.utilities AdaptivePELE.validator.controlFileValidator

MSMCalculator (class in AdaptivePELE.spawning.spawning) MSMClustering (AdaptivePELE.clustering.clusteringTypes.CLUSTERING_TYPES attribute) (class in AdaptivePELE.clustering.clustering)

N

name (AdaptivePELE.atomset.atomset.Atom attribute) needToRecluster() (in module AdaptivePELE.adaptiveSampling) nonSymmetricalAtomsSet (AdaptivePELE.atomset.RMSDCalculator.RMSDCalculator attribute) normaliseArray() (AdaptivePELE.spawning.spawning.FASTDegeneracyCalculator method) null (AdaptivePELE.clustering.clusteringTypes.CLUSTERING_TYPES attribute) (AdaptivePELE.spawning.densitycalculatortypes.DENSITY_CALCULATOR_TYPES attribute) (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute)

NullClustering (class in AdaptivePELE.clustering.clustering) NullDensityCalculator (class in AdaptivePELE.spawning.densitycalculator) NullSpawningCalculator (class in AdaptivePELE.spawning.spawning)

P

parseArgs() (in module AdaptivePELE.adaptiveSampling) (in module AdaptivePELE.analysis.writeClusteringStructures) parseArguments() (in module AdaptivePELE.analysis.backtrackAdaptiveTrajectory) (in module AdaptivePELE.analysis.correctRMSD) (in module AdaptivePELE.analysis.foldersFirstBindingEvent) (in module AdaptivePELE.analysis.makePNGs) (in module AdaptivePELE.analysis.plotAdaptive) (in module AdaptivePELE.automateRoundsAdaptive) pdb (AdaptivePELE.atomset.atomset.PDB attribute) PDB (class in AdaptivePELE.atomset.atomset) PELE (AdaptivePELE.simulation.simulationTypes.SIMULATION_TYPE attribute) PeleSimulation (class in AdaptivePELE.simulation.simulationrunner) plotClustersPerValue() (in module AdaptivePELE.analysis.numberOfClusters) plotContactsHistogram() (in module AdaptivePELE.analysis.numberOfClusters) prepareControlFile() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) prepareLigand() (AdaptivePELE.simulation.simulationrunner.MDSimulation method)

print_unbuffered() (in module AdaptivePELE.utilities.utilities) printAtom() (AdaptivePELE.atomset.atomset.Atom method) printAtoms() (AdaptivePELE.atomset.atomset.PDB method) printCluster() (AdaptivePELE.clustering.clustering.Cluster method) printClusters() (AdaptivePELE.clustering.clustering.Clusters method) printHelp() (in module AdaptivePELE.analysis.numberOfClusters) printRunInfo() (in module AdaptivePELE.adaptiveSampling) ProbabilityMSMCalculator (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) (class in AdaptivePELE.spawning.spawning) processTraj() (in module AdaptivePELE.simulation.simulationrunner) processTraj_mdanalysis() (in module AdaptivePELE.simulation.simulationrunner) processTraj_mdtraj() (in module AdaptivePELE.simulation.simulationrunner) processTrajectories() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) protein (AdaptivePELE.atomset.atomset.Atom attribute) proteinList (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator attribute)

R

readClusteringObject() (in module AdaptivePELE.utilities.utilities) readConstraints() (in module AdaptivePELE.utilities.utilities) readControlFile() (in module AdaptivePELE.analysis.correctRMSD) readMappingFromDisk() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) (AdaptivePELE.utilities.utilities.Topology method) readPDB() (in module AdaptivePELE.atomset.atomset) readProcessorMappingFromDisk() (in module AdaptivePELE.utilities.utilities) REAP (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) REAPCalculator (class in AdaptivePELE.spawning.spawning) resChain (AdaptivePELE.atomset.atomset.Atom attribute) resname (AdaptivePELE.atomset.atomset.Atom attribute) resnum (AdaptivePELE.atomset.atomset.Atom attribute)

return_sign() (in module AdaptivePELE.spawning.spawning) reward() (in module AdaptivePELE.spawning.spawning) rmsd (AdaptivePELE.clustering.clusteringTypes.CLUSTERING_TYPES attribute) RMSDCalculator (class in AdaptivePELE.atomset.RMSDCalculator) RMSDOnlyClusteringEvaluator (class in AdaptivePELE.clustering.clustering) runEquilibrationPELE() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) RunnerBuilder (class in AdaptivePELE.simulation.simulationrunner) runSimulation() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) (AdaptivePELE.simulation.simulationrunner.TestSimulation method) runTleap() (AdaptivePELE.simulation.simulationrunner.MDSimulation method)

S

sameWeight (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) SameWeightDegeneracyCalculator (class in AdaptivePELE.spawning.spawning) saveInitialControlFile() (in module AdaptivePELE.adaptiveSampling) selectEquilibratedStructure() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) selectEquilibrationLastSnapshot() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) selectInitialBoxCenter() (AdaptivePELE.simulation.simulationrunner.PeleSimulation method) SequentialLastSnapshotClustering (class in AdaptivePELE.clustering.clustering) set_properties() (AdaptivePELE.atomset.atomset.Atom method) setCol() (AdaptivePELE.clustering.clustering.Clustering method) setProcessors() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.MSMClustering method) setTopologies() (AdaptivePELE.utilities.utilities.Topology method) setZeroMapping() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) shouldWriteStructures() (AdaptivePELE.spawning.spawning.NullSpawningCalculator method) (AdaptivePELE.spawning.spawning.SpawningCalculator method) sign() (in module AdaptivePELE.utilities.utilities) SIMILARITY_TYPES (class in AdaptivePELE.clustering.clusteringTypes)

similarityEvaluatorBuilder (class in AdaptivePELE.clustering.clustering) simulatedAnnealing (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) SimulatedAnnealingCalculator (class in AdaptivePELE.spawning.spawning) SIMULATION_TYPE (class in AdaptivePELE.simulation.simulationTypes) SimulationParameters (class in AdaptivePELE.simulation.simulationrunner) SimulationRunner (class in AdaptivePELE.simulation.simulationrunner) sizePQ() (AdaptivePELE.clustering.clustering.AltStructures method) SPAWNING_TYPES (class in AdaptivePELE.spawning.spawningTypes) SpawningAlgorithmBuilder (class in AdaptivePELE.spawning.spawning) SpawningBuilder (class in AdaptivePELE.spawning.spawning) SpawningCalculator (class in AdaptivePELE.spawning.spawning) SpawningParams (class in AdaptivePELE.spawning.spawning) squaredDistance() (AdaptivePELE.atomset.atomset.Atom method) symmetricAtoms (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator attribute) symmetries (AdaptivePELE.atomset.RMSDCalculator.RMSDCalculator attribute) (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator attribute) SymmetryContactMapEvaluator (class in AdaptivePELE.atomset.SymmetryContactMapEvaluator) symToRowMap (AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator attribute)

T

TEST (AdaptivePELE.simulation.simulationTypes.SIMULATION_TYPE attribute) TestSimulation (class in AdaptivePELE.simulation.simulationrunner) THRESHOLD_CALCULATOR_TYPES (class in AdaptivePELE.clustering.thresholdcalculatortypes) ThresholdCalculator (class in AdaptivePELE.clustering.thresholdcalculator) ThresholdCalculatorBuilder (class in AdaptivePELE.clustering.thresholdcalculator) ThresholdCalculatorConstant (class in AdaptivePELE.clustering.thresholdcalculator)

ThresholdCalculatorHeaviside (class in AdaptivePELE.clustering.thresholdcalculator) Topology (class in AdaptivePELE.utilities.utilities) TopologyCompat (class in AdaptivePELE.utilities.utilities) topologyFilesIterator() (AdaptivePELE.utilities.utilities.Topology method) (AdaptivePELE.utilities.utilities.TopologyCompat method) totalMass (AdaptivePELE.atomset.atomset.PDB attribute) type (AdaptivePELE.atomset.atomset.Atom attribute)

U

UCB (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) UCBCalculator (class in AdaptivePELE.spawning.spawning) UncertaintyMSMCalculator (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) (class in AdaptivePELE.spawning.spawning) unifyReportNames() (AdaptivePELE.simulation.simulationrunner.MDSimulation method) (AdaptivePELE.simulation.simulationrunner.SimulationRunner method)

updateConstraints() (in module AdaptivePELE.simulation.simulationrunner) updateCoords() (AdaptivePELE.atomset.atomset.PDB method) updateIndex() (AdaptivePELE.clustering.clustering.AltStructures method) updateMappingProcessors() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) updateRepeatParameters() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.MSMClustering method)

V

validate() (in module AdaptivePELE.validator.controlFileValidator) validateBlock() (in module AdaptivePELE.validator.controlFileValidator)

validateGeneralBlock() (in module AdaptivePELE.validator.controlFileValidator) variableEpsilon (AdaptivePELE.spawning.spawningTypes.SPAWNING_TYPES attribute) VariableEpsilonDegeneracyCalculator (class in AdaptivePELE.spawning.spawning)

W

write_mdtraj_object_PDB() (in module AdaptivePELE.utilities.utilities) write_PDB_clusters() (in module AdaptivePELE.utilities.utilities) write_xtc_to_pdb() (in module AdaptivePELE.utilities.utilities) writeClusterMetric() (AdaptivePELE.clustering.clustering.Clustering method) writeConformationNetwork() (AdaptivePELE.clustering.clustering.ConformationNetwork method) writeConformationNodePopulation() (AdaptivePELE.clustering.clustering.Clustering method) writeFDT() (AdaptivePELE.clustering.clustering.ConformationNetwork method) writeMappingToDisk() (AdaptivePELE.simulation.simulationrunner.SimulationRunner method) (AdaptivePELE.utilities.utilities.Topology method) writeNewConstraints() (in module AdaptivePELE.utilities.utilities) writeObject() (in module AdaptivePELE.utilities.utilities) writeOutput() (AdaptivePELE.clustering.clustering.Clustering method) (AdaptivePELE.clustering.clustering.MSMClustering method) (AdaptivePELE.clustering.clustering.NullClustering method)

writePathwayOptimalCluster() (AdaptivePELE.clustering.clustering.Clustering method) writePathwayTrajectory() (AdaptivePELE.clustering.clustering.Clustering method) writePDB() (AdaptivePELE.atomset.atomset.PDB method) (AdaptivePELE.clustering.clustering.Cluster method) writeProcessorMappingToDisk() (in module AdaptivePELE.utilities.utilities) writeSpawningInitialStructures() (AdaptivePELE.spawning.spawning.IndependentMetricCalculator method) (AdaptivePELE.spawning.spawning.IndependentMSMCalculator method) (AdaptivePELE.spawning.spawning.IndependentRunsCalculator method) (AdaptivePELE.spawning.spawning.SpawningCalculator method) writeSpawningStructure() (AdaptivePELE.clustering.clustering.Cluster method) writeStructures() (in module AdaptivePELE.utilities.clusteringUtilities) writeTopologyFiles() (in module AdaptivePELE.adaptiveSampling) writeTopologyObject() (AdaptivePELE.utilities.utilities.Topology method)

X

x (AdaptivePELE.atomset.atomset.Atom attribute)

Y

y (AdaptivePELE.atomset.atomset.Atom attribute)

Z

z (AdaptivePELE.atomset.atomset.Atom attribute)