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/Adaptive/__init__.py
pele_platform/Adaptive/main.py
pele_platform/Adaptive/simulation.py
pele_platform/Analysis/__init__.py
pele_platform/Analysis/pdf_report.py
pele_platform/Analysis/plots.py
pele_platform/Analysis/to_mae.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/analysis/input.yaml
pele_platform/Examples/analysis/input_flags.yaml
pele_platform/Examples/analysis/input_flags0.yaml
pele_platform/Examples/analysis/input_mae.yaml
pele_platform/Examples/bias/complex.pdb
pele_platform/Examples/bias/input.yaml
pele_platform/Examples/bias/input_defaults.yaml
pele_platform/Examples/exit/input.yaml
pele_platform/Examples/exit/input_defaults.yaml
pele_platform/Examples/exit_soft/input.yaml
pele_platform/Examples/exit_soft/input_defaults.yaml
pele_platform/Examples/flags/input.yaml
pele_platform/Examples/frag/core.pdb
pele_platform/Examples/frag/input_ai.yaml
pele_platform/Examples/global/input.yaml
pele_platform/Examples/global/input_defaults.yaml
pele_platform/Examples/induced_fit/input_exhaustive.yaml
pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml
pele_platform/Examples/induced_fit/input_external_constraints.yaml
pele_platform/Examples/induced_fit/input_fast.yaml
pele_platform/Examples/induced_fit/input_fast_defaults.yaml
pele_platform/Examples/induced_fit/input_mae.yaml
pele_platform/Examples/inputs/input.yaml
pele_platform/Examples/inputs/mn4.sl
pele_platform/Examples/inputs/nord3.sge
pele_platform/Examples/out_in/1_3ZON_complex.pdb
pele_platform/Examples/out_in/input.yaml
pele_platform/Examples/pca/1.pdb
pele_platform/Examples/pca/2.pdb
pele_platform/Examples/pca/3.pdb
pele_platform/Examples/pca/input.yaml
pele_platform/Examples/production/input.sl
pele_platform/Examples/production/input_mae.yaml
pele_platform/Examples/rescoring/input.yaml
pele_platform/Examples/rescoring/input_defaults.yaml
pele_platform/Examples/restart/input.yaml
pele_platform/Examples/water/input_all.yaml
pele_platform/Examples/water/input_bs.yaml
pele_platform/Examples/water/input_bs_defaults.yaml
pele_platform/Examples/water/input_lig.yaml
pele_platform/Examples/water/input_lig_defaults.yaml
pele_platform/Examples/water/water_processed.pdb
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/calculatePCA4PELE.py
pele_platform/Utilities/Helpers/center_of_mass.py
pele_platform/Utilities/Helpers/check_env_var.py
pele_platform/Utilities/Helpers/conda_deployment.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/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/PCA/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.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
tests/data/L01.log
tests/data/MG.rot.assign
tests/data/STR.log
tests/data/STR.rot.assign
tests/data/adaptive.conf
tests/data/input.yaml
tests/data/input_flags.yaml
tests/data/input_flags0.yaml
tests/data/input_mae.yaml
tests/data/mgz
tests/data/pele.conf
tests/data/strz
tests/data/summary_results.pdf
tests/data/output/originalControlFile.conf
tests/data/output/summary.csv
tests/data/output/0/report_1
tests/data/output/0/topologyMapping.txt
tests/data/output/0/trajectory_1.pdb
tests/data/output/0/clustering/object.pkl
tests/data/output/0/clustering/summary.txt
tests/data/output/synchronization/syncFile.lock
tests/data/output/topologies/topologies.pkl
tests/data/output/topologies/topology_0.pdb
tests/data/results/BestStructs/epoch0_trajectory_1.0_BindingEnergy1.26468.mae
tests/data/results/BestStructs/epoch0_trajectory_2.0_BindingEnergy0.644256.mae
tests/data/results/BestStructs/epoch0_trajectory_2.1_BindingEnergy1.84474.mae
tests/data/results/Plots/Binding_Energy.1_Binding_Energy_plot.png
tests/data/results/Plots/currentEnergy_Binding_Energy_Binding_Energy.1_plot.png
tests/data/results/Plots/currentEnergy_Binding_Energy_sasaLig_plot.png
tests/data/results/Plots/sasaLig_Binding_Energy_plot.png
tests/data/results/clusters/clusters_Binding Energy_boxplot.png
tests/data/xtc/summary.csv
tests/data/xtc/0/report_1
tests/data/xtc/0/report_2
tests/data/xtc/0/trajectory_1.xtc
tests/data/xtc/0/trajectory_2.xtc
tests/data/xtc/topologies/topology_0.pdb