MANIFEST.in
README.rst
setup.py
pele_platform/__init__.py
pele_platform/features.py
pele_platform/main.py
pele_platform.egg-info/PKG-INFO
pele_platform.egg-info/SOURCES.txt
pele_platform.egg-info/dependency_links.txt
pele_platform.egg-info/requires.txt
pele_platform.egg-info/top_level.txt
pele_platform/AdaptivePELE/__init__.py
pele_platform/AdaptivePELE/adaptiveSampling.py
pele_platform/AdaptivePELE/automateRoundsAdaptive.py
pele_platform/AdaptivePELE/makeRelease.py
pele_platform/AdaptivePELE/runAllTests.py
pele_platform/AdaptivePELE/analysis/__init__.py
pele_platform/AdaptivePELE/analysis/addRejectedSteps.py
pele_platform/AdaptivePELE/analysis/analyse.py
pele_platform/AdaptivePELE/analysis/analyseClustering.py
pele_platform/AdaptivePELE/analysis/analysis_utils.py
pele_platform/AdaptivePELE/analysis/autoCorrelation.py
pele_platform/AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py
pele_platform/AdaptivePELE/analysis/bestStructs.py
pele_platform/AdaptivePELE/analysis/calculateSASAvalues.py
pele_platform/AdaptivePELE/analysis/cluster.py
pele_platform/AdaptivePELE/analysis/clusterAdaptiveRun.py
pele_platform/AdaptivePELE/analysis/clusters_lagtime_grid.py
pele_platform/AdaptivePELE/analysis/compareClustering.py
pele_platform/AdaptivePELE/analysis/convertTrajectory.py
pele_platform/AdaptivePELE/analysis/correctRMSD.py
pele_platform/AdaptivePELE/analysis/count_clusters.py
pele_platform/AdaptivePELE/analysis/crossValidationClustering.py
pele_platform/AdaptivePELE/analysis/dehidratate_and_align.py
pele_platform/AdaptivePELE/analysis/extract_ligand_traj.py
pele_platform/AdaptivePELE/analysis/filter_by_radius.py
pele_platform/AdaptivePELE/analysis/findfirstbindingevent.py
pele_platform/AdaptivePELE/analysis/foldersFirstBindingEvent.py
pele_platform/AdaptivePELE/analysis/generateBox.py
pele_platform/AdaptivePELE/analysis/histCM.py
pele_platform/AdaptivePELE/analysis/identifyClusterSnapshot.py
pele_platform/AdaptivePELE/analysis/interactivePlot.py
pele_platform/AdaptivePELE/analysis/makePNGs.py
pele_platform/AdaptivePELE/analysis/networkCM.py
pele_platform/AdaptivePELE/analysis/numberOfClusters.py
pele_platform/AdaptivePELE/analysis/pathwayRMSD.py
pele_platform/AdaptivePELE/analysis/plot3DNetwork.py
pele_platform/AdaptivePELE/analysis/plotAdaptive.py
pele_platform/AdaptivePELE/analysis/plotRMSF.py
pele_platform/AdaptivePELE/analysis/plotSpawningClusters.py
pele_platform/AdaptivePELE/analysis/reportSimulation.py
pele_platform/AdaptivePELE/analysis/selectOnPlot.py
pele_platform/AdaptivePELE/analysis/simple_postprocessing.py
pele_platform/AdaptivePELE/analysis/simulationToCsv.py
pele_platform/AdaptivePELE/analysis/splitTrajectory.py
pele_platform/AdaptivePELE/analysis/standarize_MD_energies.py
pele_platform/AdaptivePELE/analysis/trajectory_processing.py
pele_platform/AdaptivePELE/analysis/unbinding.py
pele_platform/AdaptivePELE/analysis/writeClusteringStructures.py
pele_platform/AdaptivePELE/analysis/writeNetworkFiles.py
pele_platform/AdaptivePELE/analysis/writeTrajToSnapshot.py
pele_platform/AdaptivePELE/atomset/RMSDCalculator.c
pele_platform/AdaptivePELE/atomset/RMSDCalculator.pxd
pele_platform/AdaptivePELE/atomset/RMSDCalculator.pyx
pele_platform/AdaptivePELE/atomset/SymmetryContactMapEvaluator.c
pele_platform/AdaptivePELE/atomset/SymmetryContactMapEvaluator.pxd
pele_platform/AdaptivePELE/atomset/SymmetryContactMapEvaluator.pyx
pele_platform/AdaptivePELE/atomset/__init__.py
pele_platform/AdaptivePELE/atomset/atomset.c
pele_platform/AdaptivePELE/atomset/atomset.pxd
pele_platform/AdaptivePELE/atomset/atomset.pyx
pele_platform/AdaptivePELE/atomset/setup.py
pele_platform/AdaptivePELE/clustering/__init__.py
pele_platform/AdaptivePELE/clustering/clustering.py
pele_platform/AdaptivePELE/clustering/clusteringTypes.py
pele_platform/AdaptivePELE/clustering/thresholdcalculator.py
pele_platform/AdaptivePELE/clustering/thresholdcalculatortypes.py
pele_platform/AdaptivePELE/constants/__init__.py
pele_platform/AdaptivePELE/constants/blockNames.py
pele_platform/AdaptivePELE/constants/constants.py
pele_platform/AdaptivePELE/constants/symmetries.py
pele_platform/AdaptivePELE/freeEnergies/__init__.py
pele_platform/AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py
pele_platform/AdaptivePELE/freeEnergies/calculateDGiterations.py
pele_platform/AdaptivePELE/freeEnergies/checkDetailedBalance.py
pele_platform/AdaptivePELE/freeEnergies/cluster.py
pele_platform/AdaptivePELE/freeEnergies/computeDGGrid.py
pele_platform/AdaptivePELE/freeEnergies/computeDeltaG.py
pele_platform/AdaptivePELE/freeEnergies/estimate.py
pele_platform/AdaptivePELE/freeEnergies/estimateDG.py
pele_platform/AdaptivePELE/freeEnergies/estimateDGAdaptive.py
pele_platform/AdaptivePELE/freeEnergies/extendTrajectories.py
pele_platform/AdaptivePELE/freeEnergies/extractCoords.py
pele_platform/AdaptivePELE/freeEnergies/getRepresentativeStructures.py
pele_platform/AdaptivePELE/freeEnergies/ownBuildMSM.py
pele_platform/AdaptivePELE/freeEnergies/plotResults.gpl
pele_platform/AdaptivePELE/freeEnergies/prepareMSMFolders.py
pele_platform/AdaptivePELE/freeEnergies/runMarkovChainModel.py
pele_platform/AdaptivePELE/freeEnergies/summary.txt
pele_platform/AdaptivePELE/freeEnergies/utils.c
pele_platform/AdaptivePELE/freeEnergies/utils.pyx
pele_platform/AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py
pele_platform/AdaptivePELE/simulation/__init__.py
pele_platform/AdaptivePELE/simulation/openmm_simulations.py
pele_platform/AdaptivePELE/simulation/simulationTypes.py
pele_platform/AdaptivePELE/simulation/simulationrunner.py
pele_platform/AdaptivePELE/spawning/__init__.py
pele_platform/AdaptivePELE/spawning/densitycalculator.py
pele_platform/AdaptivePELE/spawning/densitycalculatortypes.py
pele_platform/AdaptivePELE/spawning/spawning.py
pele_platform/AdaptivePELE/spawning/spawningTypes.py
pele_platform/AdaptivePELE/utilities/PDBLoader.py
pele_platform/AdaptivePELE/utilities/__init__.py
pele_platform/AdaptivePELE/utilities/clusteringUtilities.py
pele_platform/AdaptivePELE/utilities/generate_topology_object.py
pele_platform/AdaptivePELE/utilities/synchronization.py
pele_platform/AdaptivePELE/utilities/utilities.py
pele_platform/AdaptivePELE/validator/__init__.py
pele_platform/AdaptivePELE/validator/controlFileValidator.py
pele_platform/AdaptivePELE/validator/validatorBlockNames.py
pele_platform/Examples/test.sl
pele_platform/Examples/Adaptive/STR.rot.assign
pele_platform/Examples/Adaptive/adaptive.conf
pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf
pele_platform/Examples/Adaptive/strz
pele_platform/Examples/Adaptive/test.sl
pele_platform/Examples/Frag/181l_prepared.pdb
pele_platform/Examples/Frag/methyl.pdb
pele_platform/Examples/Msm/AS4_INIT.mae
pele_platform/Examples/Msm/PR_1A28_protein.pdb
pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb
pele_platform/Examples/Msm/PR_AS4.pdb
pele_platform/Examples/Msm/input.yaml
pele_platform/Examples/bias/complex.pdb
pele_platform/Examples/bias/input.yaml
pele_platform/Examples/exit/input.yaml
pele_platform/Examples/exit_soft/input.yaml
pele_platform/Examples/flags/input.yaml
pele_platform/Examples/global/input.yaml
pele_platform/Examples/induced_fit/input.yaml
pele_platform/Examples/induced_fit/input_mae.yaml
pele_platform/Examples/out_in/1_3ZON_complex.pdb
pele_platform/Examples/out_in/input.yaml
pele_platform/Examples/production/input.sl
pele_platform/Examples/production/input_mae.yaml
pele_platform/Examples/restart/input.yaml
pele_platform/Examples/water/hit1_complex_processed.pdb
pele_platform/Examples/water/input_bs.yaml
pele_platform/Examples/water/input_lig.yaml
pele_platform/Examples/water/water_processed.pdb
pele_platform/Ligand_growing/__init__.py
pele_platform/Ligand_growing/complex_to_smile.py
pele_platform/Ligand_growing/constants.py
pele_platform/Ligand_growing/grow_for_pele.py
pele_platform/Ligand_growing/variables.py
pele_platform/Ligand_growing/Growing/__init__.py
pele_platform/Ligand_growing/Growing/add_fragment_from_pdbs.py
pele_platform/Ligand_growing/Growing/bestStructs.py
pele_platform/Ligand_growing/Growing/simulations_linker.py
pele_platform/Ligand_growing/Growing/template_fragmenter.py
pele_platform/Ligand_growing/Growing/template_handler.py
pele_platform/Ligand_growing/Growing/template_selector.py
pele_platform/Ligand_growing/Growing/AddingFragHelpers/__init__.py
pele_platform/Ligand_growing/Growing/AddingFragHelpers/complex_to_prody.py
pele_platform/Ligand_growing/Growing/AddingFragHelpers/pdb_joiner.py
pele_platform/Ligand_growing/Growing/AddingFragHelpers/smile_to_pdb.py
pele_platform/Ligand_growing/Growing/AddingFragHelpers/smiles_joiner.py
pele_platform/Ligand_growing/Helpers/__init__.py
pele_platform/Ligand_growing/Helpers/clusterizer.py
pele_platform/Ligand_growing/Helpers/templatize.py
pele_platform/Rescore/__init__.py
pele_platform/Rescore/main.py
pele_platform/Rescore/simulation.py
pele_platform/Templates/adaptive_exit.conf
pele_platform/Templates/adaptive_exit_test.conf
pele_platform/Templates/adaptive_long.conf
pele_platform/Templates/adaptive_long_test.conf
pele_platform/Templates/box.pdb
pele_platform/Templates/conf.sl
pele_platform/Templates/glide.in
pele_platform/Templates/pele_SP.conf
pele_platform/Templates/pele_XP.conf
pele_platform/Templates/pele_exit.conf
pele_platform/Templates/pele_template.conf
pele_platform/Templates/solventParamsHCTOBC.txt
pele_platform/Templates/template_adaptive.conf
pele_platform/Utilities/__init__.py
pele_platform/Utilities/Helpers/__init__.py
pele_platform/Utilities/Helpers/best_structs.py
pele_platform/Utilities/Helpers/center_of_mass.py
pele_platform/Utilities/Helpers/check_env_var.py
pele_platform/Utilities/Helpers/constraints.py
pele_platform/Utilities/Helpers/external_files.py
pele_platform/Utilities/Helpers/helpers.py
pele_platform/Utilities/Helpers/metrics.py
pele_platform/Utilities/Helpers/missing_residues.py
pele_platform/Utilities/Helpers/prepwizard.py
pele_platform/Utilities/Helpers/randomize.py
pele_platform/Utilities/Helpers/simulation.py
pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py
pele_platform/Utilities/Helpers/split_trajectories.py
pele_platform/Utilities/Helpers/system_prep.py
pele_platform/Utilities/Helpers/template_builder.py
pele_platform/Utilities/Helpers/tica.py
pele_platform/Utilities/PPP/__init__.py
pele_platform/Utilities/PPP/adjustments_module.py
pele_platform/Utilities/PPP/checks_module.py
pele_platform/Utilities/PPP/coordinates_module.py
pele_platform/Utilities/PPP/global_processes.py
pele_platform/Utilities/PPP/global_variables.py
pele_platform/Utilities/PPP/hydrogens_addition.py
pele_platform/Utilities/PPP/main.py
pele_platform/Utilities/PPP/mutate_PELE.py
pele_platform/Utilities/PPP/mutational_module.py
pele_platform/Utilities/PPP/parameters_help.py
pele_platform/Utilities/PPP/program_own_classes.py
pele_platform/Utilities/PPP/read_force_field_parameters.py
pele_platform/Utilities/PPP/Data/RotamerLibs/ARG.side
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pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TRPTHR.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TRPTRP.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TRPTYR.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TRPVAL.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRALA.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRARG.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRASN.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRASP.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRCYS.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRGLN.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRGLU.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRGLY.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRHIS.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRILE.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRLEU.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRLYS.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRMET.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRPHE.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRPRO.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRSER.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRTHR.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRTRP.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRTYR.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/TYRVAL.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALALA.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALARG.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALASN.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALASP.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALCYS.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALGLN.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALGLU.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALGLY.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALHIS.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALILE.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALLEU.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALLYS.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALMET.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALPHE.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALPRO.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALSER.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALTHR.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALTRP.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALTYR.back
pele_platform/Utilities/PPP/Data/RotamerLibs/dipep/VALVAL.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H02.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H03.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H04.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H05.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H06.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H07.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H08.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H09.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H10.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H11.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H12.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H13.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H14.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H15.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H16.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H17.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H18.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H19.back
pele_platform/Utilities/PPP/Data/RotamerLibs/helix/H20.back
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/caz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/caz_OBCParams.txt
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/clz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/cuz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/hohz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/mgz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/naz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/HeteroAtoms/znz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/aba
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ace
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/aceb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ala
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/alab
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/alae
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/alaz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/arg
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/argb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/arge
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/argz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/arn
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/arnb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/arne
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/as1
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ash
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ashb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ashe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/asn
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/asnb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/asne
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/asnz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/asp
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/aspb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/aspe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/aspz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/bmt
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cea
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ch6
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cro
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/css
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cys
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cysb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cyse
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cysz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cyt
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cyx
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cyxb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cyxe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/cyxz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/dal
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/disulphide_bonds
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/dle
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/dpr
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/gl1
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glh
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glhb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glhe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/gln
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glnb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glne
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glnz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glu
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glub
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glue
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/gluz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/gly
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glyb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glye
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/glyz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hid
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hidb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hide
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hidz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hie
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hieb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hiee
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hiez
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hip
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hipb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hipe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hipz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/hoh
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ile
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ileb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ilee
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ilez
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/inter_residue_bonds
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/leu
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/leub
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/leue
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/leuz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/lyn
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/lynb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/lyne
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/lys
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/lysb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/lyse
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/lysz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/mdl
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/met
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pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/mete
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/metz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/mis
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/mle
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/mse
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/mseb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/msee
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/msez
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/mva
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/nal
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/nh2
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/nma
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/nmae
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/nmy
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/pca
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/phe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/pheb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/phee
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/phez
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/pro
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/prob
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/proe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/proz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ptr
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ptrb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ptre
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/rad
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/sar
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/sep
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/sepb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/sepe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/ser
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/serb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/sere
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/serz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tho
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/thr
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/thrb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/thre
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/thrz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tpo
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tpob
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tpoe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/trp
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/trpb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/trpe
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/trpz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tyo
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tyr
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tyrb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tyre
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/tyrz
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/val
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/valb
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/vale
pele_platform/Utilities/PPP/Data/Templates/OPLS2005/Protein/valz
pele_platform/Utilities/Parameters/__init__.py
pele_platform/Utilities/Parameters/pele_env.py
pele_platform/Utilities/Parameters/SimulationFolders/__init__.py
pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py
pele_platform/Utilities/Parameters/SimulationFolders/GlideFolders/__init__.py
pele_platform/Utilities/Parameters/SimulationFolders/GlideFolders/glide_folders.py
pele_platform/Utilities/Parameters/SimulationFolders/MSMFolders/__init__.py
pele_platform/Utilities/Parameters/SimulationFolders/MSMFolders/msm_folders.py
pele_platform/Utilities/Parameters/SimulationParams/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py
pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py
pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py
pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py
pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py
pele_platform/Utilities/Parameters/SimulationParams/WaterExp/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/WaterExp/waterexp_params.py
pele_platform/Utilities/PlopRotTemp/PlopRotTemp.py
pele_platform/Utilities/PlopRotTemp/__init__.py
pele_platform/Utilities/PlopRotTemp/launcher.py
pele_platform/Utilities/PlopRotTemp/main.py
pele_platform/Utilities/PlopRotTemp/Utilities/__init__.py
pele_platform/Utilities/PlopRotTemp/Utilities/non_standard_res.py
pele_platform/Utilities/PlopRotTemp/param/f14_sgbnp.param
pele_platform/Utilities/PlopRotTemp/param/params.cov
pele_platform/Utilities/PlopRotTemp/param/params.nb
pele_platform/Utilities/PlopRotTemp/param/sgbnp.param
pele_platform/Utilities/PlopRotTemp/param/similarity.param
pele_platform/Utilities/PlopRotTemp/template/__init__.py
pele_platform/Utilities/PlopRotTemp/template/chargeHandler.py
pele_platform/Utilities/PlopRotTemp/template/templateBuilder.py
pele_platform/Utilities/PlopRotTemp/template/tmp_helpers.py
pele_platform/constants/__init__.py
pele_platform/constants/constants.py
pele_platform/constants/pele_params.py
pele_platform/msm_pele/__init__.py
pele_platform/msm_pele/constants.py
pele_platform/msm_pele/main.py
pele_platform/msm_pele/Analysis/MSM_report.py
pele_platform/msm_pele/Analysis/__init__.py
pele_platform/msm_pele/Analysis/accepted_ratio.py
pele_platform/msm_pele/Analysis/extract_cluster_representative.py
pele_platform/msm_pele/Analysis/msm_analysis.py
pele_platform/msm_pele/Analysis/plotMSMAdvancedInfo.py
pele_platform/msm_pele/Box/__init__.py
pele_platform/msm_pele/Box/box.py
pele_platform/msm_pele/Box/box_helpers.py
pele_platform/msm_pele/Box/fixed_box.py
pele_platform/msm_pele/Box/multiple_box.py
pele_platform/msm_pele/Helpers/__init__.py
pele_platform/msm_pele/Helpers/best_structs.py
pele_platform/msm_pele/Helpers/center_of_mass.py
pele_platform/msm_pele/Helpers/check_env_var.py
pele_platform/msm_pele/Helpers/clusterAdaptiveRun.py
pele_platform/msm_pele/Helpers/constraints.py
pele_platform/msm_pele/Helpers/helpers.py
pele_platform/msm_pele/Helpers/missing_residues.py
pele_platform/msm_pele/Helpers/pele_env.py
pele_platform/msm_pele/Helpers/simulation.py
pele_platform/msm_pele/Helpers/solventOBCParamsGenerator.py
pele_platform/msm_pele/Helpers/system_prep.py
pele_platform/msm_pele/Helpers/template_builder.py
pele_platform/msm_pele/Helpers/tica.py
pele_platform/msm_pele/PPP/__init__.py
pele_platform/msm_pele/PPP/adjustments_module.py
pele_platform/msm_pele/PPP/checks_module.py
pele_platform/msm_pele/PPP/coordinates_module.py
pele_platform/msm_pele/PPP/enviroment_parameters.py
pele_platform/msm_pele/PPP/global_processes.py
pele_platform/msm_pele/PPP/global_variables.py
pele_platform/msm_pele/PPP/hydrogens_addition.py
pele_platform/msm_pele/PPP/mut_prep4pele.py
pele_platform/msm_pele/PPP/mutational_module.py
pele_platform/msm_pele/PPP/mutations_maps_generation.py
pele_platform/msm_pele/PPP/parameters_help.py
pele_platform/msm_pele/PPP/program_own_classes.py
pele_platform/msm_pele/PPP/read_force_field_parameters.py
pele_platform/msm_pele/PlopRotTemp/PlopRotTemp.py
pele_platform/msm_pele/PlopRotTemp/__init__.py
pele_platform/msm_pele/PlopRotTemp/launcher.py
pele_platform/msm_pele/PlopRotTemp/main.py
pele_platform/msm_pele/PlopRotTemp/template/__init__.py
pele_platform/msm_pele/PlopRotTemp/template/chargeHandler.py
pele_platform/msm_pele/PlopRotTemp/template/templateBuilder.py
pele_platform/msm_pele/PlopRotTemp/template/tmp_helpers.py
tests/data/LIG.rot.assign
tests/data/MG.rot.assign
tests/data/ligz
tests/data/mgz