MANIFEST.in
README.rst
setup.py
AdaptivePELE/__init__.py
AdaptivePELE/adaptiveSampling.py
AdaptivePELE/automateRoundsAdaptive.py
AdaptivePELE/makeRelease.py
AdaptivePELE/runAllTests.py
AdaptivePELE.egg-info/PKG-INFO
AdaptivePELE.egg-info/SOURCES.txt
AdaptivePELE.egg-info/dependency_links.txt
AdaptivePELE.egg-info/requires.txt
AdaptivePELE.egg-info/top_level.txt
AdaptivePELE/analysis/__init__.py
AdaptivePELE/analysis/addRejectedSteps.py
AdaptivePELE/analysis/analyse.py
AdaptivePELE/analysis/analyseClustering.py
AdaptivePELE/analysis/analysis_utils.py
AdaptivePELE/analysis/autoCorrelation.py
AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py
AdaptivePELE/analysis/bestStructs.py
AdaptivePELE/analysis/calculateDistances.py
AdaptivePELE/analysis/calculateSASAvalues.py
AdaptivePELE/analysis/cluster.py
AdaptivePELE/analysis/clusterAdaptiveRun.py
AdaptivePELE/analysis/clusters_lagtime_grid.py
AdaptivePELE/analysis/compareClustering.py
AdaptivePELE/analysis/convertTrajectory.py
AdaptivePELE/analysis/correctRMSD.py
AdaptivePELE/analysis/count_clusters.py
AdaptivePELE/analysis/crossValidationClustering.py
AdaptivePELE/analysis/dehidratate_and_align.py
AdaptivePELE/analysis/extract_ligand_traj.py
AdaptivePELE/analysis/filter_by_radius.py
AdaptivePELE/analysis/findfirstbindingevent.py
AdaptivePELE/analysis/foldersFirstBindingEvent.py
AdaptivePELE/analysis/generateBox.py
AdaptivePELE/analysis/histCM.py
AdaptivePELE/analysis/identifyClusterSnapshot.py
AdaptivePELE/analysis/interactivePlot.py
AdaptivePELE/analysis/makePNGs.py
AdaptivePELE/analysis/networkCM.py
AdaptivePELE/analysis/numberOfClusters.py
AdaptivePELE/analysis/pathwayRMSD.py
AdaptivePELE/analysis/plot3DNetwork.py
AdaptivePELE/analysis/plotAdaptive.py
AdaptivePELE/analysis/plotRMSF.py
AdaptivePELE/analysis/plotSpawningClusters.py
AdaptivePELE/analysis/reportSimulation.py
AdaptivePELE/analysis/selectOnPlot.py
AdaptivePELE/analysis/simple_postprocessing.py
AdaptivePELE/analysis/simulationToCsv.py
AdaptivePELE/analysis/splitTrajectory.py
AdaptivePELE/analysis/standarize_MD_energies.py
AdaptivePELE/analysis/trajectory_processing.py
AdaptivePELE/analysis/unbinding.py
AdaptivePELE/analysis/writeClusteringStructures.py
AdaptivePELE/analysis/writeNetworkFiles.py
AdaptivePELE/analysis/writeTrajToSnapshot.py
AdaptivePELE/atomset/RMSDCalculator.c
AdaptivePELE/atomset/RMSDCalculator.cpython-36m-x86_64-linux-gnu.so
AdaptivePELE/atomset/RMSDCalculator.cpython-37m-x86_64-linux-gnu.so
AdaptivePELE/atomset/RMSDCalculator.pxd
AdaptivePELE/atomset/RMSDCalculator.pyx
AdaptivePELE/atomset/SymmetryContactMapEvaluator.c
AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-36m-x86_64-linux-gnu.so
AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-37m-x86_64-linux-gnu.so
AdaptivePELE/atomset/SymmetryContactMapEvaluator.pxd
AdaptivePELE/atomset/SymmetryContactMapEvaluator.pyx
AdaptivePELE/atomset/__init__.py
AdaptivePELE/atomset/atomset.c
AdaptivePELE/atomset/atomset.cpython-36m-x86_64-linux-gnu.so
AdaptivePELE/atomset/atomset.cpython-37m-x86_64-linux-gnu.so
AdaptivePELE/atomset/atomset.pxd
AdaptivePELE/atomset/atomset.pyx
AdaptivePELE/atomset/setup.py
AdaptivePELE/atomset/__pycache__/__init__.cpython-36.pyc
AdaptivePELE/atomset/__pycache__/__init__.cpython-37.pyc
AdaptivePELE/atomset/__pycache__/__init__.cpython-38.pyc
AdaptivePELE/clustering/__init__.py
AdaptivePELE/clustering/clustering.py
AdaptivePELE/clustering/clusteringTypes.py
AdaptivePELE/clustering/thresholdcalculator.py
AdaptivePELE/clustering/thresholdcalculatortypes.py
AdaptivePELE/constants/__init__.py
AdaptivePELE/constants/blockNames.py
AdaptivePELE/constants/buildEnvironments.py
AdaptivePELE/constants/constants.py
AdaptivePELE/constants/symmetries.py
AdaptivePELE/freeEnergies/__init__.py
AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py
AdaptivePELE/freeEnergies/calculateDGiterations.py
AdaptivePELE/freeEnergies/checkDetailedBalance.py
AdaptivePELE/freeEnergies/cluster.py
AdaptivePELE/freeEnergies/computeDGGrid.py
AdaptivePELE/freeEnergies/computeDeltaG.py
AdaptivePELE/freeEnergies/estimate.py
AdaptivePELE/freeEnergies/estimateDG.py
AdaptivePELE/freeEnergies/estimateDGAdaptive.py
AdaptivePELE/freeEnergies/extendTrajectories.py
AdaptivePELE/freeEnergies/extractCoords.py
AdaptivePELE/freeEnergies/getRepresentativeStructures.py
AdaptivePELE/freeEnergies/ownBuildMSM.py
AdaptivePELE/freeEnergies/prepareMSMFolders.py
AdaptivePELE/freeEnergies/runMarkovChainModel.py
AdaptivePELE/freeEnergies/utilitiesFreeEnergies.py
AdaptivePELE/freeEnergies/utils.c
AdaptivePELE/freeEnergies/utils.cpython-36m-x86_64-linux-gnu.so
AdaptivePELE/freeEnergies/utils.cpython-37m-x86_64-linux-gnu.so
AdaptivePELE/freeEnergies/utils.pyx
AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py
AdaptivePELE/simulation/__init__.py
AdaptivePELE/simulation/openmm_simulations.py
AdaptivePELE/simulation/simulationTypes.py
AdaptivePELE/simulation/simulationrunner.py
AdaptivePELE/spawning/__init__.py
AdaptivePELE/spawning/densitycalculator.py
AdaptivePELE/spawning/densitycalculatortypes.py
AdaptivePELE/spawning/spawning.py
AdaptivePELE/spawning/spawningTypes.py
AdaptivePELE/tests/__init__.py
AdaptivePELE/tests/testAdaptiveSampling.py
AdaptivePELE/tests/testAtomset.py
AdaptivePELE/tests/testClustering.py
AdaptivePELE/tests/testDensityCalculator.py
AdaptivePELE/tests/testMD.py
AdaptivePELE/tests/testMD_CUDA.py
AdaptivePELE/tests/testReporter.py
AdaptivePELE/tests/testSpawning.py
AdaptivePELE/tests/testThresholdcalculator.py
AdaptivePELE/utilities/PDBLoader.py
AdaptivePELE/utilities/__init__.py
AdaptivePELE/utilities/clusteringUtilities.py
AdaptivePELE/utilities/conda_deployment.py
AdaptivePELE/utilities/generate_topology_object.py
AdaptivePELE/utilities/synchronization.py
AdaptivePELE/utilities/utilities.py
AdaptivePELE/validator/__init__.py
AdaptivePELE/validator/controlFileValidator.py
AdaptivePELE/validator/validatorBlockNames.py