MANIFEST.in
README.rst
setup.cfg
setup.py
versioneer.py
pele_platform/__init__.py
pele_platform/_version.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/box.py
pele_platform/Adaptive/ligand_parametrization.py
pele_platform/Adaptive/metrics.py
pele_platform/Adaptive/pca.py
pele_platform/Adaptive/simulation.py
pele_platform/Adaptive/solvent.py
pele_platform/Allosteric/__init__.py
pele_platform/Allosteric/cluster.py
pele_platform/Allosteric/main.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/Checker/__init__.py
pele_platform/Checker/environment_variables.py
pele_platform/Checker/executable.py
pele_platform/Checker/main.py
pele_platform/Checker/python_version.py
pele_platform/Checker/valid_flags.py
pele_platform/Errors/__init__.py
pele_platform/Errors/custom_errors.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/Allosteric/complex.pdb
pele_platform/Examples/Allosteric/input_folder.yaml
pele_platform/Examples/Allosteric/input_global.yaml
pele_platform/Examples/Allosteric/input_global_xtc.yaml
pele_platform/Examples/Allosteric/input_restart.yaml
pele_platform/Examples/Allosteric/input_skipref.yaml
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_1A28_xray_-_minimized_processed.pdb
pele_platform/Examples/Msm/PR_AS4.pdb
pele_platform/Examples/Msm/input.yaml
pele_platform/Examples/PPI/1f47_ligand.pdb
pele_platform/Examples/PPI/1f47_prep.pdb
pele_platform/Examples/PPI/1tnf_ligand.pdb
pele_platform/Examples/PPI/1tnf_prep.pdb
pele_platform/Examples/PPI/input.yaml
pele_platform/Examples/PPI/input_folder.yaml
pele_platform/Examples/PPI/input_skipref.yaml
pele_platform/Examples/RNA/2l94.yaml
pele_platform/Examples/RNA/5C45_prep.pdb
pele_platform/Examples/RNA/5C45_prep_proc.pdb
pele_platform/Examples/RNA/input.yaml
pele_platform/Examples/RNA/input_induced.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/analysis/data/MG.rot.assign
pele_platform/Examples/analysis/data/STR.rot.assign
pele_platform/Examples/analysis/data/adaptive.conf
pele_platform/Examples/analysis/data/input.yaml
pele_platform/Examples/analysis/data/input_flags.yaml
pele_platform/Examples/analysis/data/input_flags0.yaml
pele_platform/Examples/analysis/data/input_mae.yaml
pele_platform/Examples/analysis/data/mgz
pele_platform/Examples/analysis/data/pele.conf
pele_platform/Examples/analysis/data/strz
pele_platform/Examples/analysis/data/inputs/input1.pdb
pele_platform/Examples/analysis/data/inputs/input2.pdb
pele_platform/Examples/analysis/data/inputs/input3.pdb
pele_platform/Examples/analysis/data/output/originalControlFile.conf
pele_platform/Examples/analysis/data/output/0/report_1
pele_platform/Examples/analysis/data/output/0/topologyMapping.txt
pele_platform/Examples/analysis/data/output/0/trajectory_1.pdb
pele_platform/Examples/analysis/data/output/0/clustering/object.pkl
pele_platform/Examples/analysis/data/output/0/clustering/summary.txt
pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock
pele_platform/Examples/analysis/data/output/topologies/topologies.pkl
pele_platform/Examples/analysis/data/output/topologies/topology_0.pdb
pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_1.0_BindingEnergy1.26468.pdb
pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_2.0_BindingEnergy0.644256.pdb
pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_2.1_BindingEnergy1.84474.pdb
pele_platform/Examples/analysis/data/results/Plots/Binding_Energy.1_Binding_Energy_plot.png
pele_platform/Examples/analysis/data/results/Plots/currentEnergy_Binding_Energy_Binding_Energy.1_plot.png
pele_platform/Examples/analysis/data/results/Plots/currentEnergy_Binding_Energy_sasaLig_plot.png
pele_platform/Examples/analysis/data/results/Plots/sasaLig_Binding_Energy_plot.png
pele_platform/Examples/analysis/data/results/clusters/clusters_Binding Energy_boxplot.png
pele_platform/Examples/analysis/data/xtc/summary.csv
pele_platform/Examples/analysis/data/xtc/0/report_1
pele_platform/Examples/analysis/data/xtc/0/report_2
pele_platform/Examples/analysis/data/xtc/0/trajectory_1.xtc
pele_platform/Examples/analysis/data/xtc/0/trajectory_2.xtc
pele_platform/Examples/analysis/data/xtc/topologies/topology_0.pdb
pele_platform/Examples/bias/complex.pdb
pele_platform/Examples/bias/input_defaults.yaml
pele_platform/Examples/box/input.yaml
pele_platform/Examples/checker/complex.pdb
pele_platform/Examples/checker/input.yaml
pele_platform/Examples/checker/input_atom_string.yaml
pele_platform/Examples/checker/input_env.yaml
pele_platform/Examples/checker/input_pele_exec.yaml
pele_platform/Examples/checker/input_rotamer.yaml
pele_platform/Examples/checker/input_template.yaml
pele_platform/Examples/constraints/1zop.pdb
pele_platform/Examples/constraints/4l3a_prep.pdb
pele_platform/Examples/constraints/4qnr_prep.pdb
pele_platform/Examples/constraints/4w4o_prep.pdb
pele_platform/Examples/constraints/4w5i_prep.pdb
pele_platform/Examples/constraints/4zu9_prep.pdb
pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml
pele_platform/Examples/constraints/input_all_metal_constraints.yaml
pele_platform/Examples/constraints/input_external_constraints.yaml
pele_platform/Examples/constraints/input_ignore.yaml
pele_platform/Examples/constraints/input_k.yaml
pele_platform/Examples/constraints/input_metals.yaml
pele_platform/Examples/constraints/input_no_metal_constraints.yaml
pele_platform/Examples/constraints/input_permissive_exception.yaml
pele_platform/Examples/constraints/input_ppp.pdb
pele_platform/Examples/constraints/input_ppp.yaml
pele_platform/Examples/constraints/input_square_planar.yaml
pele_platform/Examples/constraints/input_square_planar_polarisation.yaml
pele_platform/Examples/constraints/input_tetrahedral.yaml
pele_platform/Examples/constraints/pass_input_permissive_constraints.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/1w7h_preparation_structure_2w.pdb
pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb
pele_platform/Examples/frag/amino.pdb
pele_platform/Examples/frag/core.pdb
pele_platform/Examples/frag/flags.conf
pele_platform/Examples/frag/input_ai.yaml
pele_platform/Examples/frag/input_core.yaml
pele_platform/Examples/frag/input_core_sdf.yaml
pele_platform/Examples/frag/input_flags.yaml
pele_platform/Examples/frag/input_sim.yaml
pele_platform/Examples/frag/ligands.sdf
pele_platform/Examples/frag/sequential.conf
pele_platform/Examples/frag/checker/4RFM_proc.pdb
pele_platform/Examples/frag/checker/4RFM_series.sdf
pele_platform/Examples/frag/checker/receptor.sdf
pele_platform/Examples/frag/sdf_joiner/13_serie.sdf
pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb
pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb
pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf
pele_platform/Examples/frag/sdf_joiner/core2.pdb
pele_platform/Examples/frag/sdf_joiner/core3.pdb
pele_platform/Examples/frag/sdf_joiner/frag.sdf
pele_platform/Examples/frag/sdf_joiner/frag.yml
pele_platform/Examples/frag/sdf_joiner/frag2.sdf
pele_platform/Examples/frag/sdf_joiner/frag2.yml
pele_platform/Examples/frag/sdf_joiner/frag3.sdf
pele_platform/Examples/frag/sdf_joiner/frag3.yml
pele_platform/Examples/frag/sdf_joiner/frag31.sdf
pele_platform/Examples/frag/sdf_joiner/frag4.yml
pele_platform/Examples/frag/sdf_joiner/frag5.yml
pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb
pele_platform/Examples/global/input.yaml
pele_platform/Examples/global/input_defaults.yaml
pele_platform/Examples/global/input_inputs.yaml
pele_platform/Examples/global/input_inputs_asterisc.yaml
pele_platform/Examples/gpcr/complex.pdb
pele_platform/Examples/gpcr/complex_processed.pdb
pele_platform/Examples/gpcr/input.yaml
pele_platform/Examples/gpcr/input_atom_error.yaml
pele_platform/Examples/gpcr/input_defaults.yaml
pele_platform/Examples/gpcr/input_defaults2.yaml
pele_platform/Examples/induced_fit/input_exhaustive.yaml
pele_platform/Examples/induced_fit/input_exhaustive_defaults.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/out_in/input_default.yaml
pele_platform/Examples/out_in/input_flag_error.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/pca/input_str.yaml
pele_platform/Examples/preparation/6qmk_correct.pdb
pele_platform/Examples/preparation/6qmk_repeated.pdb
pele_platform/Examples/preparation/complex.pdb
pele_platform/Examples/preparation/complex_2.pdb
pele_platform/Examples/preparation/input.yaml
pele_platform/Examples/preparation/input_nonstandard.yaml
pele_platform/Examples/preparation/input_space.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/tutorials/gpcr/complex.pdb
pele_platform/Examples/tutorials/gpcr/input.yaml
pele_platform/Examples/tutorials/induced_fit/docking.pdb
pele_platform/Examples/tutorials/induced_fit/input.yaml
pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb
pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb
pele_platform/Examples/tutorials/ppi/input.yaml
pele_platform/Examples/water/complex_induced.pdb
pele_platform/Examples/water/complex_ref_LESSH2O.pdb
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_induced.yaml
pele_platform/Examples/water/input_lig.yaml
pele_platform/Examples/water/input_lig_defaults.yaml
pele_platform/Examples/water/input_nwaters.yaml
pele_platform/Examples/water/input_previous_water.yaml
pele_platform/Examples/water/water_processed.pdb
pele_platform/Frag/__init__.py
pele_platform/Frag/atoms.py
pele_platform/Frag/checker.py
pele_platform/Frag/fragments.py
pele_platform/Frag/generative_model.py
pele_platform/Frag/helpers.py
pele_platform/Frag/simulation.py
pele_platform/Frag/parameters/__init__.py
pele_platform/Frag/parameters/files.py
pele_platform/Frag/parameters/main.py
pele_platform/Frag/parameters/metrics.py
pele_platform/Frag/parameters/opcionals.py
pele_platform/Frag/parameters/simulation.py
pele_platform/Frag/parameters/water.py
pele_platform/PPI/__init__.py
pele_platform/PPI/main.py
pele_platform/PPI/preparation.py
pele_platform/PPI/simulation_launcher.py
pele_platform/RNA/__init__.py
pele_platform/RNA/prep.py
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/bestStructs.py
pele_platform/Utilities/Helpers/calculatePCA4PELE.py
pele_platform/Utilities/Helpers/center_of_mass.py
pele_platform/Utilities/Helpers/conda_deployment.py
pele_platform/Utilities/Helpers/constraints.py
pele_platform/Utilities/Helpers/helpers.py
pele_platform/Utilities/Helpers/launcher.py
pele_platform/Utilities/Helpers/missing_residues.py
pele_platform/Utilities/Helpers/plop_launcher.py
pele_platform/Utilities/Helpers/protein_wizard.py
pele_platform/Utilities/Helpers/randomize.py
pele_platform/Utilities/Helpers/simulation.py
pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py
pele_platform/Utilities/Helpers/system_prep.py
pele_platform/Utilities/Helpers/template_builder.py
pele_platform/Utilities/Helpers/water.py
pele_platform/Utilities/Helpers/yaml_parser.py
pele_platform/Utilities/Helpers/Metals/__init__.py
pele_platform/Utilities/Helpers/Metals/metal_constraints.py
pele_platform/Utilities/Helpers/Metals/metal_polarisation.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/SimulationParams/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py
pele_platform/Utilities/Parameters/SimulationParams/Allosteric/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/Allosteric/allosteric.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/PPI/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py
pele_platform/constants/__init__.py
pele_platform/constants/constants.py
pele_platform/constants/pele_params.py
pele_platform/features/__init__.py
pele_platform/features/adaptive.py
pele_platform/features/frag.py
pele_platform/gpcr/__init__.py
pele_platform/gpcr/main.py
pele_platform/out_in/__init__.py
pele_platform/out_in/main.py