Index

A

account (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.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) analyze_hbond() (molecular_simulations.analysis.cov_ppi.PPInteractions method) analyze_hydrophobic() (molecular_simulations.analysis.cov_ppi.PPInteractions method) analyze_saltbridge() (molecular_simulations.analysis.cov_ppi.PPInteractions method) 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_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) AuroraSettings (class in molecular_simulations.simulate.parsl_settings) AutoKMeans (class in molecular_simulations.analysis.autocluster) available_accelerators (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.LocalSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute)

B

BaseComputeSettings (class in molecular_simulations.simulate.parsl_settings) BaseSettings (class in molecular_simulations.simulate.parsl_settings) 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_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) cation_list (molecular_simulations.build.build_ligand.PLINDERBuilder property) check_bonded_terms() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer 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_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) 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_dG() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method)

compute_energies() (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy 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_pDockQ_scores() (molecular_simulations.analysis.ipSAE.ScoreCalculator method) compute_pTM (molecular_simulations.analysis.ipSAE.ScoreCalculator attribute) compute_scores() (molecular_simulations.analysis.ipSAE.ScoreCalculator method) config_factory() (molecular_simulations.simulate.parsl_settings.AuroraSettings method) (molecular_simulations.simulate.parsl_settings.BaseComputeSettings method) (molecular_simulations.simulate.parsl_settings.LocalSettings method) (molecular_simulations.simulate.parsl_settings.PolarisSettings method) 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) cpus_per_node (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute) CustomForcesSimulator (class in molecular_simulations.simulate.omm_simulator)

D

data (molecular_simulations.analysis.autocluster.GenericDataloader property) dcd (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) Decomposition (class in molecular_simulations.analysis.autocluster)

dist_mat() (in module molecular_simulations.analysis.fingerprinter) dump_yaml() (molecular_simulations.simulate.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) EmbedEnergyData (class in molecular_simulations.analysis.utils)

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) evaluate_hbond() (molecular_simulations.analysis.cov_ppi.PPInteractions method) ExplicitSolvent (class in molecular_simulations.build.build_amber)

F

FileHandler (class in molecular_simulations.simulate.mmpbsa) files (molecular_simulations.simulate.mmpbsa.FileHandler property) Fingerprinter (class in molecular_simulations.analysis.fingerprinter) fingerprints() (in module molecular_simulations.analysis.fingerprinter)

first_frame (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) fit() (molecular_simulations.analysis.autocluster.Decomposition method) fit_transform() (molecular_simulations.analysis.autocluster.Decomposition method) fix_pdb() (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy method) from_yaml() (molecular_simulations.simulate.parsl_settings.BaseSettings class method)

G

gb_surfoff (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) gb_surften (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) generate_summary() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) GenericDataloader (class in molecular_simulations.analysis.autocluster) 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_pdb_extent() (molecular_simulations.build.build_amber.ExplicitSolvent method) get_restraint_indices() (molecular_simulations.simulate.omm_simulator.Simulator method) get_selection() (molecular_simulations.analysis.interaction_energy.InteractionEnergy method) (molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy 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)

I

identify_interaction_type() (molecular_simulations.analysis.cov_ppi.PPInteractions method) ImplicitSimulator (class in molecular_simulations.simulate.omm_simulator) ImplicitSolvent (class in molecular_simulations.build.build_amber) 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) interpret_covariance() (molecular_simulations.analysis.cov_ppi.PPInteractions method) ipSAE (class in molecular_simulations.analysis.ipSAE) iterate_frames() (molecular_simulations.analysis.fingerprinter.Fingerprinter method)

L

label (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.LocalSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute) last_frame (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) lennard_jones() (in module molecular_simulations.analysis.fingerprinter) lennard_jones_sum() (in module molecular_simulations.analysis.fingerprinter) ligand_handler() (molecular_simulations.build.build_ligand.PLINDERBuilder method) LigandBuilder (class in molecular_simulations.build.build_ligand) LigandError 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_checkpoint() (molecular_simulations.simulate.omm_simulator.Simulator method) load_data() (molecular_simulations.analysis.autocluster.GenericDataloader method) (molecular_simulations.analysis.autocluster.PeriodicDataloader 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_traj() (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy method) LocalSettings (class in molecular_simulations.simulate.parsl_settings)

M

make_plot() (molecular_simulations.analysis.cov_ppi.PPInteractions method) map_centers_to_frames() (molecular_simulations.analysis.autocluster.AutoKMeans method) 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) minimize() (molecular_simulations.simulate.omm_simulator.Minimizer method) Minimizer (class in molecular_simulations.simulate.omm_simulator) MMPBSA (class in molecular_simulations.simulate.mmpbsa) MMPBSA_settings (class in molecular_simulations.simulate.mmpbsa) model_config (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.BaseComputeSettings attribute) (molecular_simulations.simulate.parsl_settings.BaseSettings attribute) (molecular_simulations.simulate.parsl_settings.LocalSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute) ModelParser (class in molecular_simulations.analysis.ipSAE) module molecular_simulations molecular_simulations.analysis molecular_simulations.analysis.autocluster 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.simulate molecular_simulations.simulate.mmpbsa molecular_simulations.simulate.omm_simulator molecular_simulations.simulate.parsl_settings molecular_simulations module

molecular_simulations.analysis module molecular_simulations.analysis.autocluster 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.simulate module molecular_simulations.simulate.mmpbsa module molecular_simulations.simulate.omm_simulator module molecular_simulations.simulate.parsl_settings module move_antechamber_outputs() (molecular_simulations.build.build_ligand.LigandBuilder method)

N

n_cpus (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) nucleic_acids (molecular_simulations.analysis.ipSAE.ModelParser property)

num_nodes (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute)

O

offset (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute)

out (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) OutputAnalyzer (class in molecular_simulations.simulate.mmpbsa)

P

package_line() (molecular_simulations.analysis.ipSAE.ModelParser static method) 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_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) pdbfix_it() (molecular_simulations.build.build_amber.ImplicitSolvent method) 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)

place_binder() (molecular_simulations.build.build_interface.InterfaceBuilder method) place_ions() (molecular_simulations.build.build_ligand.PLINDERBuilder method) PLINDERBuilder (class in molecular_simulations.build.build_ligand) plot_results() (molecular_simulations.analysis.cov_ppi.PPInteractions method) PolarisSettings (class in molecular_simulations.simulate.parsl_settings) 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_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) 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.Simulator method)

Q

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

R

read_GB() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) read_PB() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) read_sasa() (molecular_simulations.simulate.mmpbsa.OutputAnalyzer method) reduce_dimensionality() (molecular_simulations.analysis.autocluster.AutoKMeans method) RelativeSASA (class in molecular_simulations.analysis.sasa) remove_periodicity() (molecular_simulations.analysis.autocluster.PeriodicDataloader method) res_map() (molecular_simulations.analysis.cov_ppi.PPInteractions method)

retries (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.LocalSettings attribute) run() (molecular_simulations.analysis.autocluster.AutoKMeans method) (molecular_simulations.analysis.cov_ppi.PPInteractions method) (molecular_simulations.analysis.fingerprinter.Fingerprinter method) (molecular_simulations.analysis.ipSAE.ipSAE method) (molecular_simulations.simulate.mmpbsa.MMPBSA method) (molecular_simulations.simulate.omm_simulator.Simulator method)

S

sanitize_data() (molecular_simulations.analysis.utils.EmbedEnergyData static method) SASA (class in molecular_simulations.analysis.sasa) save() (molecular_simulations.analysis.cov_ppi.PPInteractions method) (molecular_simulations.analysis.fingerprinter.Fingerprinter method) save_centers() (molecular_simulations.analysis.autocluster.AutoKMeans method) save_labels() (molecular_simulations.analysis.autocluster.AutoKMeans method) save_scores() (molecular_simulations.analysis.ipSAE.ipSAE method) scheduler_options (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute) ScoreCalculator (class in molecular_simulations.analysis.ipSAE) selections (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute)

setup_pbar() (molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy method) setup_sim() (molecular_simulations.simulate.omm_simulator.Simulator method) shape (molecular_simulations.analysis.autocluster.GenericDataloader property) Simulator (class in molecular_simulations.simulate.omm_simulator) solvent_probe (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) StaticInteractionEnergy (class in molecular_simulations.analysis.interaction_energy) strategy (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute) stride (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) survey_donors_acceptors() (molecular_simulations.analysis.cov_ppi.PPInteractions method) sweep_n_clusters() (molecular_simulations.analysis.autocluster.AutoKMeans method)

T

temp_tleap() (molecular_simulations.build.build_amber.ImplicitSolvent method) tleap_it() (molecular_simulations.build.build_amber.ImplicitSolvent method)

top (molecular_simulations.simulate.mmpbsa.MMPBSA_settings attribute) transform() (molecular_simulations.analysis.autocluster.Decomposition method) triage_pdb() (molecular_simulations.build.build_ligand.PLINDERBuilder method)

U

unravel_index() (in module molecular_simulations.analysis.fingerprinter)

W

walltime (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute) worker_init (molecular_simulations.simulate.parsl_settings.AuroraSettings attribute) (molecular_simulations.simulate.parsl_settings.PolarisSettings attribute) worker_port_range (molecular_simulations.simulate.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_amber.ImplicitSolvent method) (molecular_simulations.build.build_ligand.LigandBuilder method) write_mdins() (molecular_simulations.simulate.mmpbsa.MMPBSA method) write_new_pdb() (molecular_simulations.analysis.utils.EmbedData method)