Index

_

__del__() (molecular_simulations.simulate.reporters.RCReporter method) __init__() (molecular_simulations.analysis.autocluster.AutoKMeans method) (molecular_simulations.analysis.autocluster.DataloaderProtocol method) (molecular_simulations.analysis.autocluster.Decomposition method) (molecular_simulations.analysis.autocluster.GenericDataloader method) (molecular_simulations.analysis.autocluster.PeriodicDataloader method) (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) (molecular_simulations.analysis.constant_pH_analysis.UWHAMSolver method) (molecular_simulations.analysis.cov_ppi.PPInteractions method) (molecular_simulations.analysis.fingerprinter.Fingerprinter method) (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy method) (molecular_simulations.analysis.interaction_energy.InteractionEnergy method) (molecular_simulations.analysis.interaction_energy.InteractionEnergyFrame method) (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy method) (molecular_simulations.analysis.ipSAE.ipSAE method) (molecular_simulations.analysis.ipSAE.ModelParser method) (molecular_simulations.analysis.ipSAE.ScoreCalculator method) (molecular_simulations.analysis.sasa.RelativeSASA method) (molecular_simulations.analysis.sasa.SASA method) (molecular_simulations.analysis.utils.EmbedData method) (molecular_simulations.analysis.utils.EmbedEnergyData method) (molecular_simulations.build.build_amber.ExplicitSolvent method) (molecular_simulations.build.build_amber.ImplicitSolvent method) (molecular_simulations.build.build_interface.InterfaceBuilder method) (molecular_simulations.build.build_ligand.ComplexBuilder method) (molecular_simulations.build.build_ligand.LigandBuilder method) (molecular_simulations.build.build_ligand.LigandError method) (molecular_simulations.build.build_ligand.PLINDERBuilder method) (molecular_simulations.simulate.constantph.constantph.ConstantPH method) (molecular_simulations.simulate.constantph.constantph.ResidueState method) (molecular_simulations.simulate.constantph.constantph.ResidueTitration method) (molecular_simulations.simulate.constantph.logging.JsonFormatter method) (molecular_simulations.simulate.constantph.reference_energy.ReferenceEnergyFinder method) (molecular_simulations.simulate.free_energy.ConvergenceResult method) (molecular_simulations.simulate.free_energy.EquilibrationResult method) (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalysisResult method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) (molecular_simulations.simulate.free_energy.EVBCalculation method) (molecular_simulations.simulate.free_energy.OverlapResult method) (molecular_simulations.simulate.free_energy.PMFResult method) (molecular_simulations.simulate.mmpbsa.FileHandler method) (molecular_simulations.simulate.mmpbsa.MMPBSA method) (molecular_simulations.simulate.mmpbsa.MMPBSASettings method) (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) (molecular_simulations.simulate.omm_simulator.CustomForcesSimulator method) (molecular_simulations.simulate.omm_simulator.ImplicitSimulator method) (molecular_simulations.simulate.omm_simulator.Minimizer method) (molecular_simulations.simulate.omm_simulator.Simulator method) (molecular_simulations.simulate.reporters.RCReporter method)

A

account (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute) add_backbone_posres() (molecular_simulations.simulate.omm_simulator.Simulator static method) add_chains() (in module molecular_simulations.build) add_forces() (molecular_simulations.simulate.omm_simulator.CustomForcesSimulator method) add_ion_to_pdb() (molecular_simulations.build.build_ligand.ComplexBuilder method) ag (molecular_simulations.analysis.sasa.SASA attribute) analyze_cph() (in module molecular_simulations.analysis.constant_pH_analysis) analyze_hbond() (molecular_simulations.analysis.cov_ppi.PPInteractions method) analyze_hydrophobic() (molecular_simulations.analysis.cov_ppi.PPInteractions method) analyze_overlap() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) analyze_saltbridge() (molecular_simulations.analysis.cov_ppi.PPInteractions method) analyzer (molecular_simulations.simulate.mmpbsa.MMPBSA attribute) anion_list (molecular_simulations.build.build_ligand.PLINDERBuilder property)

assemble_system() (molecular_simulations.build.build_amber.ExplicitSolvent method) (molecular_simulations.build.build_ligand.ComplexBuilder method) (molecular_simulations.build.build_ligand.PLINDERBuilder method) assign_chainids() (in module molecular_simulations.utils.amber_utils) assign_nonbonded_params() (molecular_simulations.analysis.fingerprinter.Fingerprinter method) assign_residue_mapping() (molecular_simulations.analysis.fingerprinter.Fingerprinter method) attach_reporters() (molecular_simulations.simulate.omm_simulator.Simulator method) attemptMCStep() (molecular_simulations.simulate.constantph.constantph.ConstantPH method) AuroraSettings (class in molecular_simulations.utils.parsl_settings) AutoKMeans (class in molecular_simulations.analysis.autocluster) available_accelerators (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) (molecular_simulations.utils.parsl_settings.LocalSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute)

B

BaseComputeSettings (class in molecular_simulations.utils.parsl_settings) BaseSettings (class in molecular_simulations.utils.parsl_settings) bin_centers (molecular_simulations.simulate.free_energy.PMFResult attribute), [1] binder (molecular_simulations.build.build_interface.InterfaceBuilder attribute) binder_fingerprint (molecular_simulations.analysis.fingerprinter.Fingerprinter attribute) binder_selection (molecular_simulations.analysis.fingerprinter.Fingerprinter attribute) block_means (molecular_simulations.simulate.free_energy.ConvergenceResult attribute), [1] build() (molecular_simulations.build.build_amber.ExplicitSolvent method) (molecular_simulations.build.build_amber.ImplicitSolvent method) (molecular_simulations.build.build_ligand.ComplexBuilder method) (molecular_simulations.build.build_ligand.PLINDERBuilder method)

build_all() (molecular_simulations.build.build_interface.InterfaceBuilder method) build_dir (molecular_simulations.build.build_ligand.ComplexBuilder attribute) (molecular_simulations.build.build_ligand.PLINDERBuilder attribute) build_protein_token_indices() (molecular_simulations.analysis.ipSAE.ModelParser method) build_system() (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy method)

C

calculate_energy() (molecular_simulations.simulate.mmpbsa.MMPBSA method) calculate_fingerprints() (molecular_simulations.analysis.fingerprinter.Fingerprinter method) calculate_sasa() (molecular_simulations.simulate.mmpbsa.MMPBSA method) canonical_resname (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve property) cation_list (molecular_simulations.build.build_ligand.PLINDERBuilder property) centers (molecular_simulations.analysis.autocluster.AutoKMeans attribute) chain (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy attribute) chain_pair_type (molecular_simulations.analysis.ipSAE.ScoreCalculator attribute) chain_types (molecular_simulations.analysis.ipSAE.ModelParser attribute) chains (molecular_simulations.analysis.ipSAE.ModelParser attribute) (molecular_simulations.analysis.ipSAE.ScoreCalculator attribute) check_bonded_terms() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) check_convergence() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) check_ligand() (molecular_simulations.build.build_ligand.PLINDERBuilder method) check_num_steps_left() (molecular_simulations.simulate.omm_simulator.Simulator method) check_ptms() (molecular_simulations.build.build_ligand.PLINDERBuilder method) check_run_status() (molecular_simulations.simulate.free_energy.EVBAnalyzer method) check_sqm() (molecular_simulations.build.build_ligand.LigandBuilder method) classify_chains() (molecular_simulations.analysis.ipSAE.ModelParser method) clean_up_directory() (molecular_simulations.build.build_amber.ExplicitSolvent method) cluster_centers (molecular_simulations.analysis.autocluster.AutoKMeans attribute) com (molecular_simulations.build.build_interface.InterfaceBuilder attribute) compare_methods() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) ComplexBuilder (class in molecular_simulations.build.build_ligand) compute() (molecular_simulations.analysis.interaction_energy.InteractionEnergy method) (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy method) compute_d0() (molecular_simulations.analysis.ipSAE.ScoreCalculator static method) compute_d0_array() (molecular_simulations.analysis.ipSAE.ScoreCalculator static method) compute_dG() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) compute_energies() (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy method) compute_expectation_at_pH() (molecular_simulations.analysis.constant_pH_analysis.UWHAMSolver method) compute_interactions() (molecular_simulations.analysis.cov_ppi.PPInteractions method)

compute_ipTM_ipSAE() (molecular_simulations.analysis.ipSAE.ScoreCalculator method) compute_LIS() (molecular_simulations.analysis.ipSAE.ScoreCalculator method) compute_log_weights() (molecular_simulations.analysis.constant_pH_analysis.UWHAMSolver method) compute_pDockQ_scores() (molecular_simulations.analysis.ipSAE.ScoreCalculator method) compute_pmf() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) compute_pTM() (molecular_simulations.analysis.ipSAE.ScoreCalculator static method) compute_scores() (molecular_simulations.analysis.ipSAE.ScoreCalculator method) compute_titrations() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) compute_titrations_bootstrap() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) compute_titrations_curvefit() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) compute_titrations_weighted() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) config_factory() (molecular_simulations.utils.parsl_settings.AuroraSettings method) (molecular_simulations.utils.parsl_settings.BaseComputeSettings method) (molecular_simulations.utils.parsl_settings.HeterogeneousSettings method) (molecular_simulations.utils.parsl_settings.LocalCPUSettings method) (molecular_simulations.utils.parsl_settings.LocalSettings method) (molecular_simulations.utils.parsl_settings.PolarisSettings method) configure_logging() (in module molecular_simulations.logging_config) ConstantPH (class in molecular_simulations.simulate.constantph.constantph) construct_rc() (molecular_simulations.simulate.free_energy.EVB method) convergence (molecular_simulations.simulate.free_energy.EVBAnalysisResult attribute), [1] ConvergenceResult (class in molecular_simulations.simulate.free_energy) convert_cif_with_biopython() (in module molecular_simulations.build) convert_cif_with_gemmi() (in module molecular_simulations.build) convert_to_mol2() (molecular_simulations.build.build_ligand.LigandBuilder method) coor_file (molecular_simulations.simulate.omm_simulator.Simulator attribute) coordinates (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy attribute) cores_per_worker (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) coulomb (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy attribute) cpus_per_node (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute) CustomForcesSimulator (class in molecular_simulations.simulate.omm_simulator)

D

data (molecular_simulations.analysis.autocluster.AutoKMeans attribute) (molecular_simulations.analysis.autocluster.DataloaderProtocol property) (molecular_simulations.analysis.autocluster.GenericDataloader property) data_array (molecular_simulations.analysis.autocluster.GenericDataloader attribute), [1] dataloader (molecular_simulations.analysis.autocluster.AutoKMeans attribute) DataloaderProtocol (class in molecular_simulations.analysis.autocluster) dcd (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] debug_tleap() (molecular_simulations.build.build_amber.ImplicitSolvent method) decomposer (molecular_simulations.analysis.autocluster.Decomposition attribute)

Decomposition (class in molecular_simulations.analysis.autocluster) describeNextReport() (molecular_simulations.simulate.reporters.RCReporter method) detect_equilibration() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) diagnose() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) diagnose_residue() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) dist_mat() (in module molecular_simulations.analysis.fingerprinter) dump_yaml() (molecular_simulations.utils.parsl_settings.BaseSettings method) DynamicInteractionEnergy (class in molecular_simulations.analysis.interaction_energy)

E

electrostatic() (in module molecular_simulations.analysis.fingerprinter) electrostatic_sum() (in module molecular_simulations.analysis.fingerprinter) embed() (molecular_simulations.analysis.utils.EmbedData method) embed_selection() (molecular_simulations.analysis.utils.EmbedData method) EmbedData (class in molecular_simulations.analysis.utils) embeddings (molecular_simulations.analysis.utils.EmbedData attribute) EmbedEnergyData (class in molecular_simulations.analysis.utils) energies (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy attribute) energy() (molecular_simulations.analysis.interaction_energy.InteractionEnergy method) (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy static method)

equilibrate() (molecular_simulations.simulate.omm_simulator.ImplicitSimulator method) (molecular_simulations.simulate.omm_simulator.Simulator method) equilibration (molecular_simulations.simulate.free_energy.EVBAnalysisResult attribute), [1] EquilibrationResult (class in molecular_simulations.simulate.free_energy) evaluate_hbond() (molecular_simulations.analysis.cov_ppi.PPInteractions method) EVB (class in molecular_simulations.simulate.free_energy) EVBAnalysisResult (class in molecular_simulations.simulate.free_energy) EVBAnalyzer (class in molecular_simulations.simulate.free_energy) EVBCalculation (class in molecular_simulations.simulate.free_energy) ExplicitSolvent (class in molecular_simulations.build.build_amber) export_protonation_states() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method)

F

ffs (molecular_simulations.build.build_amber.ImplicitSolvent attribute) fh (molecular_simulations.simulate.mmpbsa.MMPBSA attribute) FileHandler (class in molecular_simulations.simulate.mmpbsa) files (molecular_simulations.analysis.autocluster.DataloaderProtocol attribute) (molecular_simulations.analysis.autocluster.GenericDataloader attribute) (molecular_simulations.simulate.mmpbsa.FileHandler property) files_chunked (molecular_simulations.simulate.mmpbsa.FileHandler property) findReferenceEnergies() (molecular_simulations.simulate.constantph.reference_energy.ReferenceEnergyFinder method) Fingerprinter (class in molecular_simulations.analysis.fingerprinter) fingerprints() (in module molecular_simulations.analysis.fingerprinter) first_frame (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] fit() (molecular_simulations.analysis.autocluster.Decomposition method)

fit_transform() (molecular_simulations.analysis.autocluster.Decomposition method) fix_pdb() (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy method) format() (molecular_simulations.simulate.constantph.logging.JsonFormatter method) format_for_cpptraj() (molecular_simulations.simulate.mmpbsa.MMPBSA static method) fraction_discarded (molecular_simulations.simulate.free_energy.EquilibrationResult attribute), [1] free_energies (molecular_simulations.simulate.free_energy.PMFResult attribute), [1] free_energy (molecular_simulations.simulate.mmpbsa.MMPBSA attribute) (molecular_simulations.simulate.mmpbsa.OutputAnalyzer attribute) free_energy_uncertainty (molecular_simulations.simulate.free_energy.PMFResult attribute), [1] from_evb_instance() (molecular_simulations.simulate.free_energy.EVBAnalyzer class method) from_metadata() (molecular_simulations.simulate.free_energy.EVBAnalyzer class method) from_yaml() (molecular_simulations.utils.parsl_settings.BaseSettings class method)

G

g (molecular_simulations.simulate.free_energy.EquilibrationResult attribute), [1] gb (molecular_simulations.simulate.mmpbsa.OutputAnalyzer attribute) gb_surfoff (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] gb_surften (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] generate_summary() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) GenericDataloader (class in molecular_simulations.analysis.autocluster) get_analyzer() (molecular_simulations.simulate.free_energy.EVB method) get_available_windows() (molecular_simulations.simulate.free_energy.EVBAnalyzer method) get_covariance() (molecular_simulations.analysis.cov_ppi.PPInteractions method) get_ion_numbers() (molecular_simulations.build.build_amber.ExplicitSolvent static method) get_max_values() (molecular_simulations.analysis.ipSAE.ScoreCalculator method)

get_occupancy_for_resid() (molecular_simulations.analysis.constant_pH_analysis.UWHAMSolver method) get_pdb_extent() (molecular_simulations.build.build_amber.ExplicitSolvent method) get_protonation_string() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) get_ref_energies() (in module molecular_simulations.data.constant_ph_reference_energies) get_restraint_indices() (molecular_simulations.simulate.omm_simulator.Simulator method) get_results() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) get_selection() (molecular_simulations.analysis.interaction_energy.InteractionEnergy method) (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy method) get_selections() (molecular_simulations.simulate.mmpbsa.MMPBSA method) get_sphere() (molecular_simulations.analysis.sasa.SASA method) get_system() (molecular_simulations.analysis.interaction_energy.InteractionEnergyFrame method) (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy method)

H

HeterogeneousSettings (class in molecular_simulations.utils.parsl_settings)

hill_equation() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve static method)

I

identify_interaction_type() (molecular_simulations.analysis.cov_ppi.PPInteractions method) IE (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy attribute) ImplicitSimulator (class in molecular_simulations.simulate.omm_simulator) ImplicitSolvent (class in molecular_simulations.build.build_amber) initialize() (molecular_simulations.simulate.free_energy.EVB method) inject_fasta() (molecular_simulations.build.build_ligand.PLINDERBuilder method) InteractionEnergy (class in molecular_simulations.analysis.interaction_energy) InteractionEnergyFrame (class in molecular_simulations.analysis.interaction_energy)

interactions (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy property) InterfaceBuilder (class in molecular_simulations.build.build_interface) interfaces (molecular_simulations.build.build_interface.InterfaceBuilder attribute) interpret_covariance() (molecular_simulations.analysis.cov_ppi.PPInteractions method) ION_ELEMENTS (molecular_simulations.simulate.constantph.constantph.ConstantPH attribute) ions (molecular_simulations.build.build_ligand.PLINDERBuilder attribute) ipSAE (class in molecular_simulations.analysis.ipSAE) is_converged (molecular_simulations.simulate.free_energy.ConvergenceResult attribute), [1] iterate_frames() (molecular_simulations.analysis.fingerprinter.Fingerprinter method)

J

JsonFormatter (class in molecular_simulations.simulate.constantph.logging)

K

k_umbrella (molecular_simulations.simulate.free_energy.EVBAnalysisResult attribute), [1]

L

label (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) (molecular_simulations.utils.parsl_settings.LocalSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute) labels (molecular_simulations.analysis.autocluster.AutoKMeans attribute) last_frame (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] lennard_jones() (in module molecular_simulations.analysis.fingerprinter) lennard_jones_sum() (in module molecular_simulations.analysis.fingerprinter) lig (molecular_simulations.build.build_ligand.ComplexBuilder attribute) (molecular_simulations.build.build_ligand.LigandBuilder attribute) lig_param_prefix (molecular_simulations.build.build_ligand.ComplexBuilder attribute) ligand_handler() (molecular_simulations.build.build_ligand.PLINDERBuilder method) LigandBuilder (class in molecular_simulations.build.build_ligand) LigandError ligs (molecular_simulations.build.build_ligand.PLINDERBuilder attribute) lj (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy attribute) ln (molecular_simulations.build.build_ligand.LigandBuilder attribute) load_amber() (molecular_simulations.simulate.omm_simulator.Minimizer method) load_amber_files() (molecular_simulations.simulate.omm_simulator.CustomForcesSimulator method) (molecular_simulations.simulate.omm_simulator.ImplicitSimulator method) (molecular_simulations.simulate.omm_simulator.Simulator method)

load_charmm_files() (molecular_simulations.simulate.omm_simulator.Simulator method) load_checkpoint() (molecular_simulations.simulate.omm_simulator.Simulator method) load_data() (molecular_simulations.analysis.autocluster.GenericDataloader method) (molecular_simulations.analysis.autocluster.PeriodicDataloader method) (molecular_simulations.analysis.constant_pH_analysis.UWHAMSolver method) load_files() (molecular_simulations.simulate.omm_simulator.Minimizer method) load_gromacs() (molecular_simulations.simulate.omm_simulator.Minimizer method) load_PAE_file() (molecular_simulations.analysis.ipSAE.ipSAE method) load_pdb() (molecular_simulations.analysis.fingerprinter.Fingerprinter method) (molecular_simulations.simulate.omm_simulator.Minimizer method) load_pLDDT_file() (molecular_simulations.analysis.ipSAE.ipSAE method) load_rc_data() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) load_system() (molecular_simulations.simulate.omm_simulator.Simulator method) load_traj() (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy method) LocalCPUSettings (class in molecular_simulations.utils.parsl_settings) LocalSettings (class in molecular_simulations.utils.parsl_settings)

M

make_plot() (molecular_simulations.analysis.cov_ppi.PPInteractions method) map_centers_to_frames() (molecular_simulations.analysis.autocluster.AutoKMeans method) mapping (molecular_simulations.analysis.cov_ppi.PPInteractions attribute) max_radii (molecular_simulations.analysis.sasa.SASA attribute) max_workers_per_node (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) mean_rc (molecular_simulations.simulate.free_energy.ConvergenceResult attribute), [1] measure_sasa() (molecular_simulations.analysis.sasa.SASA method) merge_proteins() (molecular_simulations.build.build_interface.InterfaceBuilder method) migrate_files() (molecular_simulations.build.build_ligand.PLINDERBuilder method) min_overlap (molecular_simulations.simulate.free_energy.OverlapResult attribute), [1] minimize() (molecular_simulations.simulate.omm_simulator.Minimizer method) Minimizer (class in molecular_simulations.simulate.omm_simulator) MMPBSA (class in molecular_simulations.simulate.mmpbsa) MMPBSASettings (class in molecular_simulations.simulate.mmpbsa) model_config (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.BaseComputeSettings attribute) (molecular_simulations.utils.parsl_settings.BaseSettings attribute) (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) (molecular_simulations.utils.parsl_settings.LocalSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute) ModelParser (class in molecular_simulations.analysis.ipSAE) module molecular_simulations molecular_simulations.analysis molecular_simulations.analysis.autocluster molecular_simulations.analysis.constant_pH_analysis molecular_simulations.analysis.cov_ppi molecular_simulations.analysis.fingerprinter molecular_simulations.analysis.interaction_energy molecular_simulations.analysis.ipSAE molecular_simulations.analysis.sasa molecular_simulations.analysis.utils molecular_simulations.build molecular_simulations.build.build_amber molecular_simulations.build.build_interface molecular_simulations.build.build_ligand molecular_simulations.data molecular_simulations.data.constant_ph_reference_energies molecular_simulations.logging_config molecular_simulations.simulate molecular_simulations.simulate.constantph molecular_simulations.simulate.constantph.constantph molecular_simulations.simulate.constantph.logging molecular_simulations.simulate.constantph.reference_energy molecular_simulations.simulate.free_energy molecular_simulations.simulate.mmpbsa molecular_simulations.simulate.omm_simulator molecular_simulations.simulate.reporters molecular_simulations.utils molecular_simulations.utils.amber_utils molecular_simulations.utils.mda_utils molecular_simulations.utils.parsl_settings molecular_simulations module molecular_simulations.analysis module

molecular_simulations.analysis.autocluster module molecular_simulations.analysis.constant_pH_analysis module molecular_simulations.analysis.cov_ppi module molecular_simulations.analysis.fingerprinter module molecular_simulations.analysis.interaction_energy module molecular_simulations.analysis.ipSAE module molecular_simulations.analysis.sasa module molecular_simulations.analysis.utils module molecular_simulations.build module molecular_simulations.build.build_amber module molecular_simulations.build.build_interface module molecular_simulations.build.build_ligand module molecular_simulations.data module molecular_simulations.data.constant_ph_reference_energies module molecular_simulations.logging_config module molecular_simulations.simulate module molecular_simulations.simulate.constantph module molecular_simulations.simulate.constantph.constantph module molecular_simulations.simulate.constantph.logging module molecular_simulations.simulate.constantph.reference_energy module molecular_simulations.simulate.free_energy module molecular_simulations.simulate.mmpbsa module molecular_simulations.simulate.omm_simulator module molecular_simulations.simulate.reporters module molecular_simulations.utils module molecular_simulations.utils.amber_utils module molecular_simulations.utils.mda_utils module molecular_simulations.utils.parsl_settings module morse_bond (molecular_simulations.simulate.free_energy.EVB property) morse_bond_force() (molecular_simulations.simulate.free_energy.EVBCalculation static method) move_antechamber_outputs() (molecular_simulations.build.build_ligand.LigandBuilder method)

N

n_blocks (molecular_simulations.simulate.free_energy.ConvergenceResult attribute), [1] n_cpus (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] n_effective (molecular_simulations.simulate.free_energy.EquilibrationResult attribute), [1] n_frames (molecular_simulations.analysis.cov_ppi.PPInteractions attribute) n_points (molecular_simulations.analysis.sasa.SASA attribute) n_res (molecular_simulations.analysis.ipSAE.ScoreCalculator attribute)

nodes (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) (molecular_simulations.utils.parsl_settings.LocalSettings attribute) NUCLEIC_ACIDS (molecular_simulations.analysis.ipSAE.ModelParser attribute) num_nodes (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute)

O

offset (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] (molecular_simulations.simulate.mmpbsa.OutputAnalyzer attribute) out (molecular_simulations.analysis.cov_ppi.PPInteractions attribute) (molecular_simulations.analysis.fingerprinter.Fingerprinter attribute) (molecular_simulations.analysis.utils.EmbedData attribute) (molecular_simulations.build.build_amber.ImplicitSolvent attribute) (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1]

out_lig (molecular_simulations.build.build_ligand.LigandBuilder attribute) OutputAnalyzer (class in molecular_simulations.simulate.mmpbsa) overlap (molecular_simulations.simulate.free_energy.EVBAnalysisResult attribute), [1] overlap_matrix (molecular_simulations.simulate.free_energy.OverlapResult attribute), [1] OverlapResult (class in molecular_simulations.simulate.free_energy)

P

package_line() (molecular_simulations.analysis.ipSAE.ModelParser static method) pad (molecular_simulations.build.build_amber.ExplicitSolvent attribute) pae_file (molecular_simulations.analysis.ipSAE.ipSAE attribute) parameterize_ligand() (molecular_simulations.build.build_ligand.LigandBuilder method) parse_cif_line() (molecular_simulations.analysis.ipSAE.ModelParser static method) parse_energy_file() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) parse_interface() (molecular_simulations.build.build_interface.InterfaceBuilder method) parse_line() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer static method) parse_log() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve static method) parse_outputs() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) parse_pdb_line() (molecular_simulations.analysis.ipSAE.ModelParser static method) parse_results() (molecular_simulations.analysis.cov_ppi.PPInteractions method) parse_structure_file() (molecular_simulations.analysis.ipSAE.ipSAE method) (molecular_simulations.analysis.ipSAE.ModelParser method) parser (molecular_simulations.analysis.ipSAE.ipSAE attribute) path (molecular_simulations.analysis.ipSAE.ipSAE attribute) (molecular_simulations.build.build_amber.ImplicitSolvent attribute) (molecular_simulations.build.build_ligand.LigandBuilder attribute) (molecular_simulations.simulate.mmpbsa.FileHandler attribute) (molecular_simulations.simulate.mmpbsa.MMPBSA attribute) (molecular_simulations.simulate.mmpbsa.OutputAnalyzer attribute) (molecular_simulations.simulate.omm_simulator.Simulator attribute) path_restraint() (molecular_simulations.simulate.free_energy.EVBCalculation static method) pb (molecular_simulations.simulate.mmpbsa.OutputAnalyzer attribute) pdb (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy attribute) (molecular_simulations.analysis.utils.EmbedData attribute) (molecular_simulations.build.build_amber.ImplicitSolvent attribute) pdb4amber (molecular_simulations.build.build_amber.ImplicitSolvent attribute) pdbs (molecular_simulations.simulate.mmpbsa.FileHandler attribute) pDockQ2_score() (molecular_simulations.analysis.ipSAE.ScoreCalculator static method) pDockQ_score() (molecular_simulations.analysis.ipSAE.ScoreCalculator static method) PeriodicDataloader (class in molecular_simulations.analysis.autocluster) permute_chains() (molecular_simulations.analysis.ipSAE.ScoreCalculator method) permuted (molecular_simulations.analysis.ipSAE.ScoreCalculator attribute) place_binder() (molecular_simulations.build.build_interface.InterfaceBuilder method) place_ions() (molecular_simulations.build.build_ligand.PLINDERBuilder method) platform (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy attribute)

plddt_file (molecular_simulations.analysis.ipSAE.ipSAE attribute) PLINDERBuilder (class in molecular_simulations.build.build_ligand) plot() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) plot_all() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) plot_protonation_summary() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) plot_residue() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) plot_results() (molecular_simulations.analysis.cov_ppi.PPInteractions method) plot_summary() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) pmf (molecular_simulations.simulate.free_energy.EVBAnalysisResult attribute), [1] (molecular_simulations.simulate.free_energy.PMFResult attribute), [1] pmf_uncertainty (molecular_simulations.simulate.free_energy.PMFResult attribute), [1] PMFResult (class in molecular_simulations.simulate.free_energy) PolarisSettings (class in molecular_simulations.utils.parsl_settings) postprocess() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) PPInteractions (class in molecular_simulations.analysis.cov_ppi) prep_pdb() (molecular_simulations.build.build_amber.ExplicitSolvent method) prep_protein() (molecular_simulations.build.build_ligand.PLINDERBuilder method) prepare() (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve method) (molecular_simulations.simulate.free_energy.EVBCalculation method) prepare_inputs() (molecular_simulations.simulate.free_energy.EVB method) prepare_scorer() (molecular_simulations.analysis.ipSAE.ipSAE method) prepare_topologies() (molecular_simulations.simulate.mmpbsa.FileHandler method) prepare_trajectories() (molecular_simulations.simulate.mmpbsa.FileHandler method) preprocess() (molecular_simulations.analysis.utils.EmbedEnergyData method) pretty_print() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) printTitrationState() (molecular_simulations.simulate.constantph.constantph.ConstantPH method) probe_radius (molecular_simulations.analysis.sasa.SASA attribute) problem_pairs (molecular_simulations.simulate.free_energy.OverlapResult attribute), [1] process_evb_run() (molecular_simulations.simulate.free_energy.EVB method) process_ligand() (molecular_simulations.build.build_ligand.ComplexBuilder method) process_pdb() (molecular_simulations.build.build_ligand.LigandBuilder method) process_sdf() (molecular_simulations.build.build_ligand.LigandBuilder method) production() (molecular_simulations.simulate.omm_simulator.ImplicitSimulator method) (molecular_simulations.simulate.omm_simulator.Simulator method) PROTEIN_RESIDUES (molecular_simulations.simulate.constantph.constantph.ConstantPH attribute) protein_token_indices (molecular_simulations.analysis.ipSAE.ModelParser attribute) protonation_mapping (molecular_simulations.analysis.constant_pH_analysis.TitrationCurve property)

Q

queue (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute)

R

radii (molecular_simulations.analysis.sasa.SASA attribute) rc_data (molecular_simulations.simulate.free_energy.EVBAnalysisResult attribute), [1] RCReporter (class in molecular_simulations.simulate.reporters) read_GB() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) read_PB() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) read_sasa() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) recommend_protonation() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) reduce_dimensionality() (molecular_simulations.analysis.autocluster.AutoKMeans method) reduced (molecular_simulations.analysis.autocluster.AutoKMeans attribute) ReferenceEnergyFinder (class in molecular_simulations.simulate.constantph.reference_energy) relative_area (molecular_simulations.analysis.sasa.RelativeSASA.results attribute) RelativeSASA (class in molecular_simulations.analysis.sasa) remove_harmonic_bond() (molecular_simulations.simulate.free_energy.EVBCalculation static method) remove_periodicity() (molecular_simulations.analysis.autocluster.PeriodicDataloader method) report() (molecular_simulations.simulate.reporters.RCReporter method) res_map() (molecular_simulations.analysis.cov_ppi.PPInteractions method) residues (molecular_simulations.analysis.ipSAE.ModelParser attribute)

ResidueState (class in molecular_simulations.simulate.constantph.constantph) ResidueTitration (class in molecular_simulations.simulate.constantph.constantph) retries (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) (molecular_simulations.utils.parsl_settings.LocalSettings attribute) root (molecular_simulations.build.build_interface.InterfaceBuilder attribute) run() (molecular_simulations.analysis.autocluster.AutoKMeans method) (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) (molecular_simulations.analysis.cov_ppi.PPInteractions method) (molecular_simulations.analysis.fingerprinter.Fingerprinter method) (molecular_simulations.analysis.ipSAE.ipSAE method) (molecular_simulations.simulate.free_energy.EVBCalculation method) (molecular_simulations.simulate.mmpbsa.MMPBSA method) (molecular_simulations.simulate.omm_simulator.Simulator method) run_evb() (molecular_simulations.simulate.free_energy.EVB method) run_full_analysis() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method)

S

sanitize_data() (molecular_simulations.analysis.utils.EmbedEnergyData static method) SASA (class in molecular_simulations.analysis.sasa) sasa (molecular_simulations.analysis.sasa.RelativeSASA.results attribute) (molecular_simulations.analysis.sasa.SASA.results attribute) save() (molecular_simulations.analysis.cov_ppi.PPInteractions method) (molecular_simulations.analysis.fingerprinter.Fingerprinter method) save_analysis_results() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) save_centers() (molecular_simulations.analysis.autocluster.AutoKMeans method) save_labels() (molecular_simulations.analysis.autocluster.AutoKMeans method) save_metadata() (molecular_simulations.simulate.free_energy.EVB method) (molecular_simulations.simulate.free_energy.EVBAnalyzer method) save_results() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) save_scores() (molecular_simulations.analysis.ipSAE.ipSAE method) scheduler_options (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute) ScoreCalculator (class in molecular_simulations.analysis.ipSAE) scores (molecular_simulations.analysis.ipSAE.ipSAE attribute) (molecular_simulations.analysis.ipSAE.ScoreCalculator attribute) selection (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy attribute) selections (molecular_simulations.simulate.mmpbsa.FileHandler attribute) (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] sem (molecular_simulations.simulate.free_energy.ConvergenceResult attribute), [1] setPH() (molecular_simulations.simulate.constantph.constantph.ConstantPH method) setResidueState() (molecular_simulations.simulate.constantph.constantph.ConstantPH method)

setup_barostat() (molecular_simulations.simulate.omm_simulator.Simulator method) setup_pbar() (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy method) setup_sim() (molecular_simulations.simulate.omm_simulator.Simulator method) setup_task_logger() (in module molecular_simulations.simulate.constantph.logging) shape (molecular_simulations.analysis.autocluster.AutoKMeans attribute) (molecular_simulations.analysis.autocluster.DataloaderProtocol property) (molecular_simulations.analysis.autocluster.GenericDataloader property) shapes (molecular_simulations.analysis.autocluster.GenericDataloader attribute), [1] shutdown() (molecular_simulations.simulate.free_energy.EVB method) simulation (molecular_simulations.simulate.omm_simulator.Simulator attribute) Simulator (class in molecular_simulations.simulate.omm_simulator) solve() (molecular_simulations.analysis.constant_pH_analysis.UWHAMSolver method) solvent_probe (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] STANDARD_RESIDUES (molecular_simulations.analysis.ipSAE.ModelParser attribute) StaticInteractionEnergy (class in molecular_simulations.analysis.interaction_energy) strategy (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute) stride (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy attribute) (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] structure (molecular_simulations.analysis.ipSAE.ModelParser attribute) summary() (molecular_simulations.analysis.constant_pH_analysis.TitrationAnalyzer method) surften (molecular_simulations.simulate.mmpbsa.OutputAnalyzer attribute) survey_donors_acceptors() (molecular_simulations.analysis.cov_ppi.PPInteractions method) sweep_n_clusters() (molecular_simulations.analysis.autocluster.AutoKMeans method) system (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy attribute) system_id (molecular_simulations.build.build_ligand.PLINDERBuilder attribute)

T

t0 (molecular_simulations.simulate.free_energy.EquilibrationResult attribute), [1] target (molecular_simulations.build.build_interface.InterfaceBuilder attribute) target_fingerprint (molecular_simulations.analysis.fingerprinter.Fingerprinter attribute) target_selection (molecular_simulations.analysis.fingerprinter.Fingerprinter attribute) temp_tleap() (molecular_simulations.build.build_amber.ImplicitSolvent method) temperature (molecular_simulations.simulate.free_energy.EVBAnalysisResult attribute), [1] (molecular_simulations.simulate.omm_simulator.Simulator attribute) TITRATION_H_DIFF (molecular_simulations.simulate.constantph.constantph.ConstantPH attribute) TitrationAnalyzer (class in molecular_simulations.analysis.constant_pH_analysis) TitrationCurve (class in molecular_simulations.analysis.constant_pH_analysis) tleap (molecular_simulations.build.build_amber.ImplicitSolvent attribute) tleap_it() (molecular_simulations.build.build_amber.ImplicitSolvent method)

top (molecular_simulations.simulate.mmpbsa.FileHandler attribute) (molecular_simulations.simulate.mmpbsa.MMPBSASettings attribute), [1] top_file (molecular_simulations.simulate.omm_simulator.Simulator attribute) topologies (molecular_simulations.simulate.mmpbsa.FileHandler attribute) topology (molecular_simulations.analysis.fingerprinter.Fingerprinter attribute) traj (molecular_simulations.simulate.mmpbsa.FileHandler attribute) trajectories (molecular_simulations.simulate.mmpbsa.FileHandler attribute) trajectory (molecular_simulations.analysis.fingerprinter.Fingerprinter attribute) trajectory_chunks (molecular_simulations.simulate.mmpbsa.FileHandler attribute) transform() (molecular_simulations.analysis.autocluster.Decomposition method) triage_pdb() (molecular_simulations.build.build_ligand.PLINDERBuilder method) trim_trajectory() (in module molecular_simulations.utils.mda_utils)

U

u (molecular_simulations.analysis.cov_ppi.PPInteractions attribute) (molecular_simulations.analysis.utils.EmbedData attribute) umbrella (molecular_simulations.simulate.free_energy.EVB property)

umbrella_force() (molecular_simulations.simulate.free_energy.EVBCalculation static method) unique_chains (molecular_simulations.analysis.ipSAE.ScoreCalculator attribute) unravel_index() (in module molecular_simulations.analysis.fingerprinter) UWHAMSolver (class in molecular_simulations.analysis.constant_pH_analysis)

V

validateStates() (molecular_simulations.simulate.constantph.constantph.ConstantPH method)

W

walltime (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute) water_box (molecular_simulations.build.build_amber.ExplicitSolvent attribute) WATER_ION_NAMES (molecular_simulations.simulate.constantph.constantph.ConstantPH attribute) weights (molecular_simulations.simulate.constantph.constantph.ConstantPH property) window_idx (molecular_simulations.simulate.free_energy.ConvergenceResult attribute), [1] (molecular_simulations.simulate.free_energy.EquilibrationResult attribute), [1] worker_init (molecular_simulations.utils.parsl_settings.AuroraSettings attribute) (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) (molecular_simulations.utils.parsl_settings.LocalSettings attribute) (molecular_simulations.utils.parsl_settings.PolarisSettings attribute)

worker_port_range (molecular_simulations.utils.parsl_settings.HeterogeneousSettings attribute) (molecular_simulations.utils.parsl_settings.LocalCPUSettings attribute) (molecular_simulations.utils.parsl_settings.LocalSettings attribute) write_cvae_yaml() (molecular_simulations.build.build_interface.InterfaceBuilder method) write_ddmd_yaml() (molecular_simulations.build.build_interface.InterfaceBuilder method) write_file() (molecular_simulations.simulate.mmpbsa.FileHandler static method) write_leap() (molecular_simulations.build.build_ligand.LigandBuilder method) write_mdins() (molecular_simulations.simulate.mmpbsa.MMPBSA method) write_new_pdb() (molecular_simulations.analysis.utils.EmbedData method)