LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
versioneer.py
pele_platform/__init__.py
pele_platform/_version.py
pele_platform/converter.py
pele_platform/main.py
pele_platform/pathway_extractor.py
pele_platform/plotter.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/interaction_restrictions.py
pele_platform/Adaptive/metrics.py
pele_platform/Adaptive/parametrizer.py
pele_platform/Adaptive/pca.py
pele_platform/Adaptive/plop_ligand_parametrization.py
pele_platform/Adaptive/plop_solvent.py
pele_platform/Adaptive/preequilibrator.py
pele_platform/Adaptive/simulation.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/pdb_checker.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/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_xtc.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/empty_reports_output/0/report_1
pele_platform/Examples/analysis/data/empty_reports_output/0/report_2
pele_platform/Examples/analysis/data/empty_reports_output/0/topologyMapping.txt
pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_1.pdb
pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_2.pdb
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/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/capped.pdb
pele_platform/Examples/checker/capped_no_connects.pdb
pele_platform/Examples/checker/complex.pdb
pele_platform/Examples/checker/complex2.pdb
pele_platform/Examples/checker/complex_unk.yaml
pele_platform/Examples/checker/incompatible_flags.yaml
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_map_atom_num.yaml
pele_platform/Examples/checker/input_map_atom_str.yaml
pele_platform/Examples/checker/input_pele_exec.yaml
pele_platform/Examples/checker/input_rotamer.yaml
pele_platform/Examples/checker/input_space.yaml
pele_platform/Examples/checker/input_tab.yaml
pele_platform/Examples/checker/input_template.yaml
pele_platform/Examples/checker/input_underscore.yaml
pele_platform/Examples/checker/input_unk.yaml
pele_platform/Examples/checker/ligand2.pdb
pele_platform/Examples/checker/mapping_complex.pdb
pele_platform/Examples/checker/multiple_simulations.yaml
pele_platform/Examples/checker/negative_residues.pdb
pele_platform/Examples/clustering/summary.csv
pele_platform/Examples/clustering/0/report_1
pele_platform/Examples/clustering/0/report_2
pele_platform/Examples/clustering/0/report_3
pele_platform/Examples/clustering/0/report_4
pele_platform/Examples/clustering/0/topologyMapping.txt
pele_platform/Examples/clustering/0/trajectory_1.pdb
pele_platform/Examples/clustering/0/trajectory_2.pdb
pele_platform/Examples/clustering/0/trajectory_3.pdb
pele_platform/Examples/clustering/0/trajectory_4.pdb
pele_platform/Examples/clustering/0/clustering/object.pkl
pele_platform/Examples/clustering/0/clustering/summary.txt
pele_platform/Examples/clustering_xtc/water_clustering.yaml
pele_platform/Examples/clustering_xtc/0/report_1
pele_platform/Examples/clustering_xtc/0/report_2
pele_platform/Examples/clustering_xtc/0/report_3
pele_platform/Examples/clustering_xtc/0/report_4
pele_platform/Examples/clustering_xtc/0/topology.pdb
pele_platform/Examples/clustering_xtc/0/trajectory_1.xtc
pele_platform/Examples/clustering_xtc/0/trajectory_2.xtc
pele_platform/Examples/clustering_xtc/0/trajectory_3.xtc
pele_platform/Examples/clustering_xtc/0/trajectory_4.xtc
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/ca_constraints.pdb
pele_platform/Examples/constraints/complex_smiles_error.pdb
pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml
pele_platform/Examples/constraints/input_all_metal_constraints.yaml
pele_platform/Examples/constraints/input_ca_noppp.yaml
pele_platform/Examples/constraints/input_ca_ppp.yaml
pele_platform/Examples/constraints/input_constrain_smarts.yaml
pele_platform/Examples/constraints/input_constrain_smiles.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_smiles_error.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/no_connects.pdb
pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml
pele_platform/Examples/covalent_docking/5XXD_prepared.pdb
pele_platform/Examples/covalent_docking/6M06_prepared.pdb
pele_platform/Examples/covalent_docking/6P0M_prepared.pdb
pele_platform/Examples/covalent_docking/input1.yaml
pele_platform/Examples/covalent_docking/input2.yaml
pele_platform/Examples/covalent_docking/input3.yaml
pele_platform/Examples/covalent_docking/input_defaults.yaml
pele_platform/Examples/covalent_docking/input_defaults_refinement.yaml
pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml
pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml
pele_platform/Examples/enzyme_engineering/wrong_cpus.yaml
pele_platform/Examples/enzyme_engineering/directory_to_restart/completed_mutations.log
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/ANL.mae
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/adaptive.conf
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/pele.conf
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/restart_saturated_mutagenesis.yaml
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs/ANL.rot.assign
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms/anlz
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A_processed.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D_processed.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/ligand.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/receptor.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/originalControlFile.conf
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/topologyMapping.txt
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/object.pkl
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/summary.txt
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_1
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_3
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_1.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_3.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_2
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_4
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_2.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_4.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization/syncFile.lock
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topologies.pkl
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_0.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_1.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/controlFile0.conf
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_0.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_1.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/ANL.mae
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/adaptive.conf
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/pele.conf
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/restart_saturated_mutagenesis.yaml
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E_processed.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/ligand.pdb
pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/receptor.pdb
pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb
pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb
pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb
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/1dyi_no_waters.pdb
pele_platform/Examples/frag/1dyi_waters.pdb
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/analysis.conf
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_frag_waters.yaml
pele_platform/Examples/frag/input_fragment_atom.yaml
pele_platform/Examples/frag/input_lib_pdb.yaml
pele_platform/Examples/frag/input_lib_sdf.yaml
pele_platform/Examples/frag/input_point_analysis.yaml
pele_platform/Examples/frag/input_sim.yaml
pele_platform/Examples/frag/input_sim_xtc.yaml
pele_platform/Examples/frag/input_symmetry.yaml
pele_platform/Examples/frag/ligands.sdf
pele_platform/Examples/frag/ligands_water.sdf
pele_platform/Examples/frag/sequential.conf
pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_1
pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_2
pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_1.pdb
pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_2.pdb
pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_1.1_BindingEnergy-23.4636.pdb
pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_2.1_BindingEnergy-25.1634.pdb
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/pdb_test_lib/mol1.pdb
pele_platform/Examples/frag/pdb_test_lib/mol2.pdb
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/frag/sdf_test_lib/test_library.sdf
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_auto_clustering.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/interaction_restrictions/complex.pdb
pele_platform/Examples/interaction_restrictions/input.yaml
pele_platform/Examples/interaction_restrictions/input_error.yaml
pele_platform/Examples/interaction_restrictions/input_error_2.yaml
pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt
pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt
pele_platform/Examples/ligand_conformations/1.pdb
pele_platform/Examples/ligand_conformations/2.pdb
pele_platform/Examples/ligand_conformations/3.pdb
pele_platform/Examples/ligand_conformations/input.yaml
pele_platform/Examples/minimum_steps/complex.pdb
pele_platform/Examples/minimum_steps/input.yaml
pele_platform/Examples/out_in/1_3ZON_complex.pdb
pele_platform/Examples/out_in/input.yaml
pele_platform/Examples/out_in/input_auto_clustering.yaml
pele_platform/Examples/out_in/input_box_center.yaml
pele_platform/Examples/out_in/input_default.yaml
pele_platform/Examples/out_in/input_flag_error.yaml
pele_platform/Examples/out_in/input_metrics.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/preparation/parametrization_flags.yaml
pele_platform/Examples/production/input.sl
pele_platform/Examples/production/input_mae.yaml
pele_platform/Examples/randomize/ligand1.pdb
pele_platform/Examples/randomize/ligand2.pdb
pele_platform/Examples/randomize/ligand3.pdb
pele_platform/Examples/randomize/receptor.pdb
pele_platform/Examples/randomize/ref_ligand.pdb
pele_platform/Examples/rescoring/input.yaml
pele_platform/Examples/rescoring/input_defaults.yaml
pele_platform/Examples/restart/restart.yaml
pele_platform/Examples/singularity/input_adaptive.yaml
pele_platform/Examples/singularity/input_adaptive_mpi_params.yaml
pele_platform/Examples/singularity/input_frag.yaml
pele_platform/Examples/site_finder/complex.pdb
pele_platform/Examples/site_finder/global.yaml
pele_platform/Examples/site_finder/input_custom_box.yaml
pele_platform/Examples/site_finder/input_folder.yaml
pele_platform/Examples/site_finder/input_global.yaml
pele_platform/Examples/site_finder/input_global_xtc.yaml
pele_platform/Examples/site_finder/input_restart.yaml
pele_platform/Examples/site_finder/input_skipref.yaml
pele_platform/Examples/site_finder/local.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/water2_pele.conf
pele_platform/Examples/water/water_pele.conf
pele_platform/Examples/water/water_processed.pdb
pele_platform/Frag/__init__.py
pele_platform/Frag/analysis.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/libraries.py
pele_platform/Frag/simulation.py
pele_platform/Frag/parameters/__init__.py
pele_platform/Frag/parameters/files.py
pele_platform/Frag/parameters/metrics.py
pele_platform/Frag/parameters/optional.py
pele_platform/Frag/parameters/simulation.py
pele_platform/Frag/parameters/water.py
pele_platform/PPI/__init__.py
pele_platform/PPI/cluster.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/helpers.py
pele_platform/Utilities/Helpers/interaction_constraints.py
pele_platform/Utilities/Helpers/launcher.py
pele_platform/Utilities/Helpers/ligand_conformations.py
pele_platform/Utilities/Helpers/map_atoms.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/Helpers/constraints/__init__.py
pele_platform/Utilities/Helpers/constraints/alpha_constraints.py
pele_platform/Utilities/Helpers/constraints/smiles_constraints.py
pele_platform/Utilities/Parameters/__init__.py
pele_platform/Utilities/Parameters/parameters.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/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/Utilities/Parameters/SimulationParams/site_finder/__init__.py
pele_platform/Utilities/Parameters/SimulationParams/site_finder/site_finder.py
pele_platform/analysis/__init__.py
pele_platform/analysis/analysis.py
pele_platform/analysis/clustering.py
pele_platform/analysis/data.py
pele_platform/analysis/interactive_plot.py
pele_platform/analysis/pdf_report.py
pele_platform/analysis/plot.py
pele_platform/constants/__init__.py
pele_platform/constants/constants.py
pele_platform/constants/pele_params.py
pele_platform/covalent_docking/__init__.py
pele_platform/covalent_docking/main.py
pele_platform/enzyme_engineering/__init__.py
pele_platform/enzyme_engineering/saturated_mutagenesis.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
pele_platform/site_finder/__init__.py
pele_platform/site_finder/main.py