Index

A

add_anneal_NVT() (iphasimulator.openmmscript_builder.OpenMMScriptBuilder method) add_basic_NPT() (iphasimulator.openmmscript_builder.OpenMMScriptBuilder method) add_basic_NVT() (iphasimulator.openmmscript_builder.OpenMMScriptBuilder method) add_minimization() (iphasimulator.openmmscript_builder.OpenMMScriptBuilder method) add_thermal_ramp() (iphasimulator.openmmscript_builder.OpenMMScriptBuilder method) ADDED_RESIDUES_PATTERN (in module iphasimulator.amber_solvation) amb_coordinates (iphasimulator.sw_openmm.AmberSimulation attribute) amb_topology (iphasimulator.sw_openmm.AmberSimulation attribute) AmberSimulation (class in iphasimulator.sw_openmm) AmberSolvationSettings (class in iphasimulator.amber_solvation) AmberSystemOutputs (class in iphasimulator.amber_solvation) ambertools_available() (in module iphasimulator.parameterization_gaff2) AmberToolsError analysis_trajectory_path (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs property) anion (iphasimulator.amber_solvation.AmberSolvationSettings attribute) anion_count (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation attribute)

anion_itp_path (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) ANION_MOLECULE_NAMES (in module iphasimulator.simulation_gromacs_runner) anneal_help() (iphasimulator.sw_openmm.BuildSimulation class method) anneal_NVT() (iphasimulator.sw_openmm.BuildSimulation method) anneal_parameters (iphasimulator.sw_openmm.BuildSimulation attribute) annotate_slurm_stage_lengths() (in module iphasimulator.charmmgui_import) antechamber_log (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) antechamber_seconds (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) atom (iphasimulator.charmmgui_import.SignedVolume attribute) atom_name (iphasimulator.charmmgui_import.GroAtom attribute) atom_rows (iphasimulator.analysis_contacts.AtomSelections attribute) atoms (iphasimulator.charmmgui_import.ItpMolecule attribute) (iphasimulator.docking_inputs.PolymerPdbExport attribute) (iphasimulator.docking_inputs.PolymerWholeCheck attribute) AtomSelections (class in iphasimulator.analysis_contacts) AVOGADRO (in module iphasimulator.build_single_PHA_systems) AVOGADRO_CONSTANT (in module iphasimulator.system_builder_packmol)

B

BACKBONE_ATOMS (in module iphasimulator.data.amber_openmm.run_openmm_md) BACKBONE_NAMES (in module iphasimulator.analysis_contacts) backbone_restraint (iphasimulator.amber_solvation.OpenMMProtocol attribute) barostat_frequency (iphasimulator.amber_solvation.OpenMMProtocol attribute) basic_NPT() (iphasimulator.sw_openmm.BuildSimulation method) basic_NPT_help() (iphasimulator.sw_openmm.BuildSimulation class method) basic_NVT() (iphasimulator.sw_openmm.BuildSimulation method) BenchmarkTarget (class in iphasimulator.workflows.md_benchmark) bonds (iphasimulator.charmmgui_import.ItpMolecule attribute) box_shape (iphasimulator.amber_solvation.AmberSolvationSettings attribute) box_size_nm (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) box_vectors_nm (iphasimulator.simulation_gromacs_runner.GromacsBoxValidation attribute) boxes_A_degrees (iphasimulator.analysis_contacts.ContactResult attribute) broken_bonds (iphasimulator.docking_inputs.PolymerWholeCheck attribute)

build_argument_parser() (in module iphasimulator.trajectory_gromacs_merge) build_custom_pha() (in module iphasimulator.build) build_dry_PHA() (in module iphasimulator.build_single_PHA_systems) build_packmol_solvated_system() (in module iphasimulator.system_builder_packmol) build_pha_by_sidechain() (in module iphasimulator.build) build_pha_chain() (in module iphasimulator.build) build_PHA_copolymer() (iphasimulator.build_pha.PHAPolymerBuilder method) build_PHA_polymer() (iphasimulator.build_pha.PHAPolymerBuilder method) build_solvated_amber_system() (in module iphasimulator.amber_solvation) build_solvated_PHA() (in module iphasimulator.build_single_PHA_systems) build_solvated_PHA_ions() (in module iphasimulator.build_single_PHA_systems) build_validation_molecules() (in module iphasimulator.workflows.validation) BuildSimulation (class in iphasimulator.sw_openmm) built_PHAs_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute)

C

calculate_distances() (in module iphasimulator.analysis_contacts) calculate_ion_pairs_from_rst7() (in module iphasimulator.build_single_PHA_systems) can_compare (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation property) canonical_monomer_code() (in module iphasimulator.naming) cation (iphasimulator.amber_solvation.AmberSolvationSettings attribute) cation_count (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation attribute) cation_itp_path (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) CATION_MOLECULE_NAMES (in module iphasimulator.simulation_gromacs_runner) center (iphasimulator.trajectory_processing.ProcessingConfig attribute) center_and_compact_wrap() (in module iphasimulator.trajectory_gromacs_trjconv) center_group (iphasimulator.trajectory_centering.CenterIndexResult attribute) (iphasimulator.trajectory_processing.ProcessingConfig attribute) center_index (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) center_result (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) centered_trajectory_path (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) CenterIndexResult (class in iphasimulator.trajectory_centering) CGENFF_TYPE_PATTERN (in module iphasimulator.charmmgui_import) CGenFFPenaltyReport (class in iphasimulator.charmmgui_import) charge (iphasimulator.charmmgui_import.ItpAtom attribute) (iphasimulator.charmmgui_import.ItpMolecule property) CHARGE_METHODS (in module iphasimulator.workflows.md_benchmark) charge_penalties (iphasimulator.charmmgui_import.CGenFFPenaltyReport attribute) CHARMM_DEFAULTS (in module iphasimulator.charmmgui_import) CHARMM_GROMACS_MDP_FILES (in module iphasimulator.charmmgui_import) CHARMM_GROMACS_TEMPLATE_DIR (in module iphasimulator.charmmgui_import) CHARMM_GUI_INDEX_GROUPS (in module iphasimulator.charmmgui_import) charmm_gui_membrane_dir (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) charmm_gui_membrane_hpc_script_path (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) CHARMM_POLYMER_TEMPLATE_DIR (in module iphasimulator.charmmgui_import) CHARMM_TO_AMBER_HISTIDINE (in module iphasimulator.amber_complex) CharmmPolymerWaterFolder (class in iphasimulator.charmmgui_import) check (iphasimulator.docking_inputs.PolymerPdbExport attribute) check_atom_counts() (in module iphasimulator.charmmgui_import) check_cgenff_penalties() (in module iphasimulator.charmmgui_import) check_cgenff_types() (in module iphasimulator.charmmgui_import) check_charmm_defaults() (in module iphasimulator.charmmgui_import) check_gromacs_minimization_inputs() (in module iphasimulator.simulation_gromacs_runner) check_gromacs_run_files() (in module iphasimulator.charmmgui_import) check_includes() (in module iphasimulator.charmmgui_import) check_ligand_atom_order() (in module iphasimulator.charmmgui_import) check_ligand_charges_match_rtf() (in module iphasimulator.charmmgui_import) check_ligand_signed_volumes() (in module iphasimulator.charmmgui_import) check_ligand_stereocentres() (in module iphasimulator.charmmgui_import) check_molecule_counts() (in module iphasimulator.charmmgui_import) check_net_charge() (in module iphasimulator.charmmgui_import) check_output_safety() (in module iphasimulator.trajectory_processing) check_polymer_whole() (in module iphasimulator.docking_inputs) check_required_files() (in module iphasimulator.build_single_PHA_systems)

CheckResult (class in iphasimulator.charmmgui_import) chiral_smiles (iphasimulator.monomers.Monomer attribute) chloride_count (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation property) (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) CHLORIDE_PDB (in module iphasimulator.system_builder_packmol) choose_frames() (in module iphasimulator.analysis_contacts) code (iphasimulator.monomers.Monomer attribute) combine_itps() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) command (iphasimulator.simulation_gromacs_runner.GromacsGromppValidation attribute) (iphasimulator.simulation_gromacs_runner.GromacsLocalMinimizationCheck attribute) (iphasimulator.trajectory_gromacs_merge.GromacsCheckResult attribute) (iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult attribute) (iphasimulator.trajectory_gromacs_trjconv.TrjconvResult attribute) command_plan() (in module iphasimulator.trajectory_processing) command_text (iphasimulator.simulation_gromacs_runner.GromacsLocalMinimizationCheck property) common_name (iphasimulator.workflows.design.PolymerDesign attribute) compact_wrap() (in module iphasimulator.trajectory_gromacs_trjconv) constraint_tolerance (iphasimulator.amber_solvation.OpenMMProtocol attribute) contact_occupancy() (in module iphasimulator.analysis_contacts) ContactConfig (class in iphasimulator.analysis_contacts) ContactResult (class in iphasimulator.analysis_contacts) CONTINUATION_PREFIX (in module iphasimulator.trajectory_gromacs_merge) convert_amber_to_gromacs() (in module iphasimulator.conversion_amber_to_gromacs) coordinate_atom_count (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation attribute) coordinates_file (iphasimulator.sw_openmm.AmberSimulation attribute) (iphasimulator.sw_openmm.GromacsSimulation attribute) copied_polymer_paths (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) count_gro_atoms() (in module iphasimulator.simulation_gromacs_runner) COUNT_INPUT (in module iphasimulator.amber_solvation) COUNT_LOG (in module iphasimulator.amber_solvation) counts (iphasimulator.analysis_contacts.AtomSelections attribute) create_built_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) create_dry_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) create_gromacs_simulation_box() (in module iphasimulator.simulation_gromacs_runner) create_named_PHA_melt_simulation_run_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) create_openmm_simulation() (iphasimulator.sw_openmm.BuildSimulation method) create_openmm_system() (iphasimulator.sw_openmm.BuildSimulation method) create_PHA_melt_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) create_PHA_melt_simulation_run_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) create_PHA_type_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) create_solvated_ions_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) create_solvated_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) created (iphasimulator.trajectory_centering.CenterIndexResult attribute) csv_path (iphasimulator.pha_filepath_manager.PHAResidueCodeManager attribute) cubic (iphasimulator.amber_solvation.AmberSolvationSettings attribute) custom_groups (iphasimulator.trajectory_processing.ProcessingConfig attribute) custom_monomer_smiles (iphasimulator.workflows.design.PolymerDesign attribute) cutoff_nm (iphasimulator.amber_solvation.OpenMMProtocol attribute) cutoffs_A (iphasimulator.analysis_contacts.ContactConfig property) cutoffs_nm (iphasimulator.simulation_gromacs_runner.GromacsBoxValidation attribute)

D

DataWriter (class in iphasimulator.sw_openmm) dcdReporter (iphasimulator.sw_openmm.DcdWriter attribute) DcdWriter (class in iphasimulator.sw_openmm) DEFAULT_CENTER_GROUP (in module iphasimulator.trajectory_centering) DEFAULT_REPO_ROOT (in module iphasimulator.workflows.md_benchmark) DEFAULT_VALIDATION_TARGETS (in module iphasimulator.workflows.validation) DEFAULT_WORKFLOW_CONFIG (in module iphasimulator.workflows.hpc) degree (iphasimulator.workflows.design.PolymerDesign attribute) (iphasimulator.workflows.validation.ValidationTarget attribute) density_g_per_ml() (in module iphasimulator.amber_solvation) describe_molecules() (in module iphasimulator.workflows.validation) describe_run_folder_protocol() (in module iphasimulator.charmmgui_import) design_polymer() (in module iphasimulator.workflows.design) discover_gromacs_outputs() (in module iphasimulator.trajectory_gromacs_merge) discover_targets() (in module iphasimulator.workflows.md_benchmark)

discovered (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) DiscoveredGromacsOutputs (class in iphasimulator.trajectory_gromacs_merge) display_start_time() (iphasimulator.sw_openmm.BuildSimulation class method) distance_block_size (iphasimulator.analysis_contacts.ContactConfig attribute) distances_A (iphasimulator.analysis_contacts.ContactResult attribute) DRY_COORDINATES (in module iphasimulator.charmmgui_import) DRY_DEFFNM (in module iphasimulator.charmmgui_import) dry_dir (iphasimulator.charmmgui_import.CharmmPolymerWaterFolder attribute) DRY_MDP (in module iphasimulator.charmmgui_import) DRY_MINIMIZATION_MDP (in module iphasimulator.charmmgui_import) dry_PHAs_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute) dry_polymer_dir (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) dry_run (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) (iphasimulator.trajectory_processing.ProcessingConfig attribute) dt_ps (iphasimulator.charmmgui_import.MdpStage attribute)

E

edit_acpype_topology_for_polyply() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) edr_files (iphasimulator.trajectory_gromacs_merge.DiscoveredGromacsOutputs attribute) ELEMENT_BY_MASS (in module iphasimulator.charmmgui_import) end_ns (iphasimulator.analysis_contacts.ContactConfig attribute) end_time_ps (iphasimulator.trajectory_gromacs_merge.GromacsCheckResult attribute) energy_merge (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) energy_output (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) energy_output_filename() (in module iphasimulator.trajectory_gromacs_merge) energy_skipped_reason (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) ensure_built_polymer_exists() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) ensure_center_index() (in module iphasimulator.trajectory_centering) ensure_gromacs_polymer_exists() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) ENZYME_POLYMER_IN_WATER_PROTOCOL (in module iphasimulator.amber_solvation) ENZYME_SOLVATION_SETTINGS (in module iphasimulator.amber_solvation)

equilibration_frame_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) errors (iphasimulator.amber_solvation.TleapLogSummary attribute) ESTER_BOND (in module iphasimulator.build) estimate_ion_pairs() (in module iphasimulator.system_builder_packmol) estimate_tip3p_water_count() (in module iphasimulator.system_builder_packmol) evidence (iphasimulator.charmmgui_import.CheckResult attribute) ewald_error_tolerance (iphasimulator.amber_solvation.OpenMMProtocol attribute) expected_atom_count (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation attribute) expected_stereochemistry (iphasimulator.monomers.Monomer attribute) export_molecules() (in module iphasimulator.workflows.validation) export_polymer_pdb() (in module iphasimulator.docking_inputs) extra_cutoffs_A (iphasimulator.analysis_contacts.ContactConfig attribute) extract_first_frame() (in module iphasimulator.trajectory_frame_extraction) extract_frame() (in module iphasimulator.trajectory_frame_extraction)

F

filename (iphasimulator.sw_openmm.AmberSimulation attribute) (iphasimulator.sw_openmm.BuildSimulation attribute) (iphasimulator.sw_openmm.GromacsSimulation attribute) files_read (iphasimulator.charmmgui_import.CGenFFPenaltyReport attribute) FILES_VERSION_PATTERN (in module iphasimulator.charmmgui_import) final_pdb_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) find_file() (iphasimulator.pha_filepath_manager.PHAFileManager method) find_files() (iphasimulator.pha_filepath_manager.PHAFileManager method) find_lig_topology() (in module iphasimulator.charmmgui_import) fit (iphasimulator.trajectory_processing.ProcessingConfig attribute) fit_group (iphasimulator.trajectory_processing.ProcessingConfig attribute) fit_result (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute)

fit_trajectory() (in module iphasimulator.trajectory_gromacs_trjconv) fitted_trajectory_path (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) forbidden_codes (iphasimulator.pha_filepath_manager.PHAResidueCodeManager attribute) format_cgenff_penalty_report() (in module iphasimulator.charmmgui_import) format_checks() (in module iphasimulator.charmmgui_import) format_concentration_label() (iphasimulator.pha_filepath_manager.PHAFileManager method) format_ion_label() (iphasimulator.pha_filepath_manager.PHAFileManager method) frame_indices (iphasimulator.analysis_contacts.ContactResult attribute) frame_result (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) frcmod_path (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) friction_coeff (iphasimulator.sw_openmm.BuildSimulation attribute) friction_per_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute)

G

gaff2_dir (iphasimulator.workflows.md_benchmark.BenchmarkTarget property) Gaff2Outputs (class in iphasimulator.parameterization_gaff2) generate_polymer_melt() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) generate_polymer_prepins() (iphasimulator.build_pha.PHAPolymerBuilder method) generate_polymer_smiles_from_sequence() (iphasimulator.build_pha.PHAPolymerBuilder method) generate_unique_codes() (iphasimulator.pha_filepath_manager.PHAResidueCodeManager method) get_built_PHA_amber_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_built_PHA_amber_files() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_built_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_built_PHA_gromacs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_built_PHA_leap_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_built_PHA_name() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_code() (iphasimulator.pha_filepath_manager.PHAResidueCodeManager method) get_dry_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_dry_PHA_inputs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_dry_PHA_simulations_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_dry_PHA_system_name() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_dry_PHAs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_melt_name() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) get_monomer() (in module iphasimulator.monomers) get_monomer_smiles() (iphasimulator.build_pha.PHAPolymerBuilder method) get_PHA_input_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_leap_template_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_melt_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_melt_inputs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_melt_name() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_melt_simulations_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_monomer_unit_files() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_monomer_units_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_trimer_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_PHA_type_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_platform() (iphasimulator.sw_openmm.BuildSimulation method) get_polymer_smiles_csv() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_residue_codes_csv() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_root_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_ions_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_ions_PHA_inputs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_ions_PHA_simulations_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_ions_PHA_system_name() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_ions_PHAs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_PHA_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_PHA_inputs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method)

get_solvated_PHA_simulations_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_PHA_system_name() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_solvated_PHAs_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_temp_dir() (iphasimulator.pha_filepath_manager.PHAFileManager method) get_used_codes() (iphasimulator.pha_filepath_manager.PHAResidueCodeManager method) gmx (iphasimulator.trajectory_processing.ProcessingConfig attribute) graph_state_data() (iphasimulator.sw_openmm.BuildSimulation static method) graph_state_data_help() (iphasimulator.sw_openmm.BuildSimulation class method) gro_coordinates (iphasimulator.sw_openmm.GromacsSimulation attribute) gro_path (iphasimulator.conversion_amber_to_gromacs.GromacsConversionOutputs attribute) (iphasimulator.simulation_gromacs_runner.GromacsBoxValidation attribute) (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation attribute) gro_topology (iphasimulator.sw_openmm.GromacsSimulation attribute) GroAtom (class in iphasimulator.charmmgui_import) GROMACS_ALL_MDP_TEMPLATE_NAMES (in module iphasimulator.simulation_gromacs_runner) GROMACS_CHARMM_GUI_MEMBRANE_MDP_TEMPLATE_NAMES (in module iphasimulator.simulation_gromacs_runner) gromacs_dir (iphasimulator.workflows.md_benchmark.BenchmarkTarget property) GROMACS_MDP_TEMPLATE_NAMES (in module iphasimulator.simulation_gromacs_runner) GROMACS_POLYMER_MDP_TEMPLATE_NAMES (in module iphasimulator.simulation_gromacs_runner) GROMACS_SOLVATION_TEMPLATE_DIR (in module iphasimulator.simulation_gromacs_runner) GROMACS_SOLVATION_TEMPLATE_NAMES (in module iphasimulator.simulation_gromacs_runner) GROMACS_SOLVATION_TOPOLOGY_INCLUDE_NAMES (in module iphasimulator.simulation_gromacs_runner) GROMACS_WORKFLOW_HPC_STEPS (in module iphasimulator.simulation_gromacs_runner) GROMACS_WORKFLOW_MDP_TEMPLATE_NAMES (in module iphasimulator.simulation_gromacs_runner) GromacsBoxValidation (class in iphasimulator.simulation_gromacs_runner) GromacsCheckResult (class in iphasimulator.trajectory_gromacs_merge) GromacsConversionOutputs (class in iphasimulator.conversion_amber_to_gromacs) GromacsCoordinateTopologyValidation (class in iphasimulator.simulation_gromacs_runner) GromacsGromppValidation (class in iphasimulator.simulation_gromacs_runner) GromacsIndex (class in iphasimulator.trajectory_centering) GromacsLocalMinimizationCheck (class in iphasimulator.simulation_gromacs_runner) GromacsMergeCommandResult (class in iphasimulator.trajectory_gromacs_merge) GromacsMergeOutputsResult (class in iphasimulator.trajectory_gromacs_merge) GromacsPreparedRunFolder (class in iphasimulator.simulation_gromacs_runner) GromacsRunFiles (class in iphasimulator.simulation_gromacs_runner) GromacsSimulation (class in iphasimulator.sw_openmm) GromacsSolvatedTopologyValidation (class in iphasimulator.simulation_gromacs_runner) GromacsSolvationFiles (class in iphasimulator.simulation_gromacs_runner) GromacsTopologyValidation (class in iphasimulator.simulation_gromacs_runner) group() (iphasimulator.trajectory_centering.GromacsIndex method) GROUP_HEADER_PATTERN (in module iphasimulator.trajectory_centering) groups (iphasimulator.trajectory_centering.GromacsIndex attribute)

H

has_group() (iphasimulator.trajectory_centering.GromacsIndex method) has_ions (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation property) has_water (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation property) head_residue_code (iphasimulator.monomers.Monomer property) header (iphasimulator.pha_filepath_manager.PHAResidueCodeManager attribute) heavy (iphasimulator.analysis_contacts.AtomSelections attribute) heavy_atom_mask() (in module iphasimulator.analysis_contacts) heavy_atoms (iphasimulator.amber_complex.PoseTransferResult attribute) heavy_bonds (iphasimulator.docking_inputs.PolymerWholeCheck attribute) HISTIDINE_NAMES (in module iphasimulator.amber_complex)

histidines (iphasimulator.amber_complex.ProteinPdbSummary attribute) HPC_SCRIPT (in module iphasimulator.amber_solvation) (in module iphasimulator.charmmgui_import) hpc_script_path (iphasimulator.charmmgui_import.CharmmPolymerWaterFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) HPC_SCRIPT_TEMPLATE (in module iphasimulator.amber_solvation) (in module iphasimulator.charmmgui_import) HYDROGEN_MAX_MASS (in module iphasimulator.docking_inputs) hydrogens_placed (iphasimulator.amber_complex.PoseTransferResult attribute)

I

INCLUDE_PATTERN (in module iphasimulator.simulation_gromacs_runner) included_files (iphasimulator.simulation_gromacs_runner.GromacsTopologyValidation attribute) index (iphasimulator.trajectory_processing.ProcessingConfig attribute) index_ndx_path (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) index_path (iphasimulator.trajectory_centering.CenterIndexResult attribute) INITIAL_PREFIX (in module iphasimulator.trajectory_gromacs_merge) inpcrd_path (iphasimulator.amber_solvation.AmberSystemOutputs attribute) (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) (iphasimulator.workflows.md_benchmark.BenchmarkTarget property) input_checks (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) input_files (iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult attribute) input_signature() (in module iphasimulator.data.amber_openmm.run_openmm_md) input_trajectory (iphasimulator.trajectory_processing.ProcessingConfig attribute) inspect_trajectory() (in module iphasimulator.analysis_contacts) instruction_file (iphasimulator.trajectory_processing.ProcessingConfig attribute) integrator (iphasimulator.charmmgui_import.MdpStage attribute) ION_MOLECULES (in module iphasimulator.charmmgui_import) ion_parameter_files (iphasimulator.amber_solvation.AmberSystemOutputs attribute) (iphasimulator.amber_solvation.TleapLogSummary attribute) ION_PARAMETERS_PATTERN (in module iphasimulator.amber_solvation) ions_mdp_path (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) iphasimulator module iphasimulator.amber_complex module iphasimulator.amber_solvation module iphasimulator.analysis_contacts module iphasimulator.build module iphasimulator.build_pha module iphasimulator.build_single_PHA_systems module iphasimulator.charmmgui_import module iphasimulator.conversion_amber_to_gromacs module iphasimulator.data.amber_openmm.run_openmm_md module iphasimulator.docking_inputs module iphasimulator.exceptions module iphasimulator.export module iphasimulator.monomers module

iphasimulator.naming module iphasimulator.openmmscript_builder module iphasimulator.parameterization_gaff2 module iphasimulator.pha_filepath_manager module iphasimulator.pha_melt_builder module iphasimulator.simulation_gromacs_runner module iphasimulator.simulation_openmm_amber_runner module iphasimulator.stereochemistry module iphasimulator.sw_openmm module iphasimulator.system_builder_packmol module iphasimulator.trajectory_centering module iphasimulator.trajectory_frame_extraction module iphasimulator.trajectory_gromacs_merge module iphasimulator.trajectory_gromacs_trjconv module iphasimulator.trajectory_preprocessing module iphasimulator.trajectory_processing module iphasimulator.visualisation.visualiser module iphasimulator.workflows module iphasimulator.workflows.design module iphasimulator.workflows.hpc module iphasimulator.workflows.md_benchmark module iphasimulator.workflows.validation module is_standalone (iphasimulator.simulation_gromacs_runner.GromacsTopologyValidation attribute) is_whole (iphasimulator.docking_inputs.PolymerWholeCheck property) ItpAtom (class in iphasimulator.charmmgui_import) ItpMolecule (class in iphasimulator.charmmgui_import)

K

kind (iphasimulator.trajectory_gromacs_merge.GromacsCheckResult attribute) (iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult attribute)

L

label (iphasimulator.analysis_contacts.ContactConfig attribute) (iphasimulator.charmmgui_import.PenaltyEntry attribute) (iphasimulator.charmmgui_import.SignedVolume attribute) LARGE_VALIDATION_TARGETS (in module iphasimulator.workflows.validation) LEAP_ERRORS_PATTERN (in module iphasimulator.amber_solvation) LEGACY_MONOMER_ALIASES (in module iphasimulator.naming) length_ps (iphasimulator.charmmgui_import.MdpStage property) length_text() (iphasimulator.charmmgui_import.MdpStage method) lig_dir (iphasimulator.charmmgui_import.CGenFFPenaltyReport attribute) ligand_signed_volumes() (in module iphasimulator.charmmgui_import) ligand_stereocentres() (in module iphasimulator.charmmgui_import) LITERS_PER_NM3 (in module iphasimulator.system_builder_packmol) load_available_PHA_monomers() (in module iphasimulator.visualisation.visualiser) load_config() (in module iphasimulator.analysis_contacts) (in module iphasimulator.trajectory_processing)

load_distances() (in module iphasimulator.analysis_contacts) load_openmm_runner() (in module iphasimulator.amber_solvation) load_polymer_smiles() (in module iphasimulator.visualisation.visualiser) load_protocol() (in module iphasimulator.data.amber_openmm.run_openmm_md) load_rows() (iphasimulator.pha_filepath_manager.PHAResidueCodeManager method) load_workflow_config() (in module iphasimulator.workflows.hpc) LOCAL_MINIMIZATION_REQUIRED_FILENAMES (in module iphasimulator.simulation_gromacs_runner) LOCAL_SCRIPT (in module iphasimulator.amber_solvation) (in module iphasimulator.charmmgui_import) local_script_path (iphasimulator.charmmgui_import.CharmmPolymerWaterFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) LOCAL_SCRIPT_TEXT (in module iphasimulator.amber_solvation) log_path (iphasimulator.charmmgui_import.MinimizationResult attribute) (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) longest_bond (iphasimulator.docking_inputs.PolymerWholeCheck attribute)

M

main() (in module iphasimulator.analysis_contacts) (in module iphasimulator.data.amber_openmm.run_openmm_md) (in module iphasimulator.trajectory_gromacs_merge) (in module iphasimulator.trajectory_processing) (in module iphasimulator.workflows.md_benchmark) main_residue_code (iphasimulator.monomers.Monomer property) manager (iphasimulator.sw_openmm.AmberSimulation attribute) (iphasimulator.sw_openmm.BuildSimulation attribute) (iphasimulator.sw_openmm.GromacsSimulation attribute) mass (iphasimulator.charmmgui_import.ItpAtom attribute) MAX_BOND_NM (in module iphasimulator.docking_inputs) max_bond_nm (iphasimulator.docking_inputs.PolymerWholeCheck attribute) max_charge_penalty (iphasimulator.charmmgui_import.CGenFFPenaltyReport property) max_cutoff_nm (iphasimulator.simulation_gromacs_runner.GromacsBoxValidation property) max_parameter_penalty (iphasimulator.charmmgui_import.CGenFFPenaltyReport property) maximum_energy_part() (in module iphasimulator.trajectory_gromacs_merge) maximum_force (iphasimulator.charmmgui_import.MinimizationResult attribute) MAXIMUM_FORCE_PATTERN (in module iphasimulator.charmmgui_import) maximum_trajectory_part() (in module iphasimulator.trajectory_gromacs_merge) MDP_CUTOFF_KEYS (in module iphasimulator.simulation_gromacs_runner) mdp_path (iphasimulator.simulation_gromacs_runner.GromacsBoxValidation attribute) mdp_paths (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) MdpStage (class in iphasimulator.charmmgui_import) merge_simulation_outputs() (in module iphasimulator.trajectory_gromacs_merge) merged_group_atoms() (in module iphasimulator.trajectory_centering) min_temp (iphasimulator.sw_openmm.BuildSimulation attribute) MINIM_MDP (in module iphasimulator.simulation_gromacs_runner) minim_mdp_path (iphasimulator.simulation_gromacs_runner.GromacsRunFiles attribute) minimization_max_iterations (iphasimulator.amber_solvation.OpenMMProtocol attribute) minimization_seconds (iphasimulator.simulation_openmm_amber_runner.OpenMMStageTimings attribute) minimization_tolerance (iphasimulator.amber_solvation.OpenMMProtocol attribute) MinimizationResult (class in iphasimulator.charmmgui_import) minimize_energy() (iphasimulator.sw_openmm.BuildSimulation method) minimize_energy_help() (iphasimulator.sw_openmm.BuildSimulation class method) minimized_only (iphasimulator.sw_openmm.BuildSimulation attribute) minimized_pdb_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) minimum_atom_distances() (in module iphasimulator.analysis_contacts) missing_files (iphasimulator.simulation_gromacs_runner.GromacsLocalMinimizationCheck attribute) (iphasimulator.simulation_gromacs_runner.GromacsTopologyValidation attribute) mode_masks (iphasimulator.analysis_contacts.AtomSelections attribute) MODES (in module iphasimulator.analysis_contacts) modes (iphasimulator.analysis_contacts.ContactConfig attribute) module iphasimulator iphasimulator.amber_complex iphasimulator.amber_solvation iphasimulator.analysis_contacts iphasimulator.build iphasimulator.build_pha iphasimulator.build_single_PHA_systems iphasimulator.charmmgui_import iphasimulator.conversion_amber_to_gromacs iphasimulator.data.amber_openmm.run_openmm_md iphasimulator.docking_inputs iphasimulator.exceptions iphasimulator.export iphasimulator.monomers iphasimulator.naming iphasimulator.openmmscript_builder iphasimulator.parameterization_gaff2 iphasimulator.pha_filepath_manager iphasimulator.pha_melt_builder iphasimulator.simulation_gromacs_runner iphasimulator.simulation_openmm_amber_runner iphasimulator.stereochemistry iphasimulator.sw_openmm iphasimulator.system_builder_packmol iphasimulator.trajectory_centering iphasimulator.trajectory_frame_extraction iphasimulator.trajectory_gromacs_merge iphasimulator.trajectory_gromacs_trjconv iphasimulator.trajectory_preprocessing iphasimulator.trajectory_processing iphasimulator.visualisation.visualiser iphasimulator.workflows iphasimulator.workflows.design iphasimulator.workflows.hpc iphasimulator.workflows.md_benchmark iphasimulator.workflows.validation

mol2_path (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) molecule_atom_counts (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation attribute) molecule_counts (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation attribute) Monomer (class in iphasimulator.monomers) monomer (iphasimulator.workflows.validation.ValidationTarget attribute) MONOMER_TO_POLYMER (in module iphasimulator.naming) monomer_to_polymer_code() (in module iphasimulator.naming) MONOMERS (in module iphasimulator.monomers) multi_chain_system_name() (in module iphasimulator.naming)

N

name (iphasimulator.amber_solvation.OpenMMProtocol attribute) (iphasimulator.charmmgui_import.CheckResult attribute) (iphasimulator.charmmgui_import.ItpAtom attribute) (iphasimulator.charmmgui_import.ItpMolecule attribute) (iphasimulator.charmmgui_import.MdpStage attribute) (iphasimulator.workflows.design.PolymerDesign attribute) (iphasimulator.workflows.md_benchmark.BenchmarkTarget attribute) (iphasimulator.workflows.validation.ValidationTarget property) names (iphasimulator.trajectory_centering.GromacsIndex property) neighbours (iphasimulator.charmmgui_import.SignedVolume attribute) nonbondedcutoff (iphasimulator.sw_openmm.BuildSimulation attribute) npt_frame_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) npt_log_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) NPT_MDP (in module iphasimulator.simulation_gromacs_runner) npt_mdp_path (iphasimulator.simulation_gromacs_runner.GromacsRunFiles attribute)

npt_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) npt_report_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) npt_seconds (iphasimulator.simulation_openmm_amber_runner.OpenMMStageTimings attribute) npt_timestep_fs (iphasimulator.amber_solvation.OpenMMProtocol attribute) npt_trajectory_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) nsteps (iphasimulator.charmmgui_import.MdpStage attribute) number_of_polymers (iphasimulator.openmmscript_builder.OpenMMScriptBuilder attribute) nvt_log_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) NVT_MDP (in module iphasimulator.simulation_gromacs_runner) nvt_mdp_path (iphasimulator.simulation_gromacs_runner.GromacsRunFiles attribute) nvt_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) nvt_report_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) nvt_seconds (iphasimulator.simulation_openmm_amber_runner.OpenMMStageTimings attribute) nvt_timestep_fs (iphasimulator.amber_solvation.OpenMMProtocol attribute) nvt_trajectory_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute)

O

ok (iphasimulator.simulation_gromacs_runner.GromacsGromppValidation property) (iphasimulator.trajectory_gromacs_trjconv.TrjconvResult property) oligomer_name() (in module iphasimulator.naming) open_universe() (in module iphasimulator.analysis_contacts) openmm_available() (in module iphasimulator.simulation_openmm_amber_runner) openmm_dir (iphasimulator.workflows.md_benchmark.BenchmarkTarget property) OpenMMOutputs (class in iphasimulator.simulation_openmm_amber_runner) OpenMMProtocol (class in iphasimulator.amber_solvation) OpenMMRunnerError OpenMMScriptBuilder (class in iphasimulator.openmmscript_builder) OpenMMStageTimings (class in iphasimulator.simulation_openmm_amber_runner) output_checks (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) output_dir (iphasimulator.amber_solvation.AmberSystemOutputs attribute) (iphasimulator.conversion_amber_to_gromacs.GromacsConversionOutputs attribute) (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) (iphasimulator.simulation_gromacs_runner.GromacsLocalMinimizationCheck attribute) (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsRunFiles attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) (iphasimulator.trajectory_processing.ProcessingConfig attribute) (iphasimulator.workflows.md_benchmark.BenchmarkTarget attribute)

output_group (iphasimulator.trajectory_processing.ProcessingConfig attribute) output_mol2 (iphasimulator.amber_complex.PoseTransferResult attribute) output_path (iphasimulator.amber_complex.ProteinPdbSummary attribute) (iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult attribute) (iphasimulator.trajectory_gromacs_trjconv.TrjconvResult attribute) output_root (iphasimulator.analysis_contacts.ContactConfig attribute) OutputKind (in module iphasimulator.trajectory_gromacs_merge) overwrite (iphasimulator.trajectory_processing.ProcessingConfig attribute)

P

packmol_input_path (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) packmol_log_path (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) PackmolBuildResult (class in iphasimulator.system_builder_packmol) padding_nm (iphasimulator.amber_solvation.AmberSolvationSettings attribute) PARAMETER_FILE (in module iphasimulator.charmmgui_import) parameter_files_version (iphasimulator.charmmgui_import.CGenFFPenaltyReport attribute) parameter_penalties (iphasimulator.charmmgui_import.CGenFFPenaltyReport attribute) PARAMETER_PENALTY_PATTERN (in module iphasimulator.charmmgui_import) parameterise_trimer() (iphasimulator.build_pha.PHAPolymerBuilder method) parameterize_gaff2() (in module iphasimulator.parameterization_gaff2) parmchk2_log (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) parmchk2_seconds (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) parse_args() (in module iphasimulator.workflows.md_benchmark) parse_built_PHA_name() (iphasimulator.pha_filepath_manager.PHAFileManager method) parse_polymer_name() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) parse_tleap_log() (in module iphasimulator.amber_solvation) passed (iphasimulator.charmmgui_import.CheckResult property) path (iphasimulator.trajectory_gromacs_merge.GromacsCheckResult attribute) paths (iphasimulator.build_pha.PHAPolymerBuilder attribute) (iphasimulator.pha_filepath_manager.PHAResidueCodeManager attribute) (iphasimulator.pha_melt_builder.PHAMeltBuilder attribute) pbc (iphasimulator.trajectory_processing.ProcessingConfig attribute) pdb_path (iphasimulator.amber_solvation.AmberSystemOutputs attribute) (iphasimulator.docking_inputs.PolymerPdbExport attribute) (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) penalty (iphasimulator.charmmgui_import.PenaltyEntry attribute) penalty_category() (in module iphasimulator.charmmgui_import) penalty_grade() (in module iphasimulator.charmmgui_import) PENALTY_GRADE_RULES (in module iphasimulator.charmmgui_import) PenaltyEntry (class in iphasimulator.charmmgui_import) pha (iphasimulator.analysis_contacts.AtomSelections attribute) PHA_melts_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute) pha_selection (iphasimulator.analysis_contacts.ContactConfig attribute) PHA_type_exists() (iphasimulator.pha_filepath_manager.PHAResidueCodeManager method) PHA_types_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute) PHAFileManager (class in iphasimulator.pha_filepath_manager) PHAMeltBuilder (class in iphasimulator.pha_melt_builder) PHAPolymerBuilder (class in iphasimulator.build_pha) PHAResidueCodeManager (class in iphasimulator.pha_filepath_manager) plot_available_PHA_monomers() (in module iphasimulator.visualisation.visualiser) plot_available_PHA_polymers() (in module iphasimulator.visualisation.visualiser) plot_contacts() (in module iphasimulator.analysis_contacts) polymer_builder (iphasimulator.pha_melt_builder.PHAMeltBuilder attribute) polymer_counts (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) POLYMER_IN_WATER_PROTOCOL (in module iphasimulator.amber_solvation) polymer_name (iphasimulator.monomers.Monomer attribute) polymer_names (iphasimulator.openmmscript_builder.OpenMMScriptBuilder attribute) polymer_smiles_csv (iphasimulator.pha_filepath_manager.PHAFileManager attribute)

POLYMER_TO_MONOMER (in module iphasimulator.naming) PolymerDesign (class in iphasimulator.workflows.design) PolymerPdbExport (class in iphasimulator.docking_inputs) PolymerWholeCheck (class in iphasimulator.docking_inputs) pose_polymer_mol2() (in module iphasimulator.amber_complex) PoseTransferResult (class in iphasimulator.amber_complex) position (iphasimulator.charmmgui_import.GroAtom attribute) position_restraints (iphasimulator.charmmgui_import.MdpStage attribute) potential_energy (iphasimulator.charmmgui_import.MinimizationResult attribute) POTENTIAL_ENERGY_PATTERN (in module iphasimulator.charmmgui_import) preflight() (in module iphasimulator.trajectory_processing) prepare_charmm_dry_polymer_folder() (in module iphasimulator.charmmgui_import) prepare_charmm_gui_run_folder() (in module iphasimulator.charmmgui_import) prepare_charmm_polymer_water_folder() (in module iphasimulator.charmmgui_import) prepare_dry_ligand_folder() (in module iphasimulator.charmmgui_import) prepare_gromacs_run_folder() (in module iphasimulator.simulation_gromacs_runner) prepare_molecule_3d() (in module iphasimulator.export) prepare_polyply_inputs() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) prepare_single_system_inputs() (in module iphasimulator.build_single_PHA_systems) prepare_vmd (iphasimulator.trajectory_processing.ProcessingConfig attribute) preprocess_gromacs_trajectory() (in module iphasimulator.trajectory_preprocessing) pressure (iphasimulator.sw_openmm.BuildSimulation attribute) pressure_bar (iphasimulator.amber_solvation.OpenMMProtocol attribute) pressure_coupling (iphasimulator.charmmgui_import.MdpStage attribute) preview_frames (iphasimulator.analysis_contacts.ContactConfig attribute) PREVIOUS_STAGE (in module iphasimulator.data.amber_openmm.run_openmm_md) primary_cutoff_A (iphasimulator.analysis_contacts.ContactConfig attribute) prmtop_path (iphasimulator.amber_solvation.AmberSystemOutputs attribute) (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) (iphasimulator.workflows.md_benchmark.BenchmarkTarget property) process_trajectory() (in module iphasimulator.trajectory_processing) ProcessingConfig (class in iphasimulator.trajectory_processing) production_frame_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) production_log_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) PRODUCTION_MDP (in module iphasimulator.simulation_gromacs_runner) production_mdp_path (iphasimulator.simulation_gromacs_runner.GromacsRunFiles attribute) production_ns (iphasimulator.amber_solvation.OpenMMProtocol attribute) production_seconds (iphasimulator.simulation_openmm_amber_runner.OpenMMStageTimings attribute) production_timestep_fs (iphasimulator.amber_solvation.OpenMMProtocol attribute) production_trajectory_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) program_version (iphasimulator.charmmgui_import.CGenFFPenaltyReport attribute) PROGRAM_VERSION_PATTERN (in module iphasimulator.charmmgui_import) protein (iphasimulator.analysis_contacts.AtomSelections attribute) PROTEIN_RESIDUES (in module iphasimulator.data.amber_openmm.run_openmm_md) protein_selection (iphasimulator.analysis_contacts.ContactConfig attribute) ProteinPdbSummary (class in iphasimulator.amber_complex) PROTOCOL_FILE (in module iphasimulator.amber_solvation) provenance (iphasimulator.analysis_contacts.ContactResult attribute)

R

raw_antechamber_log (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) raw_trajectory_path (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) read_cgenff_penalties() (in module iphasimulator.charmmgui_import) read_cgenff_version() (in module iphasimulator.charmmgui_import) read_charmm_histidine_states() (in module iphasimulator.amber_complex) read_gro() (in module iphasimulator.charmmgui_import) read_index() (in module iphasimulator.trajectory_centering) read_mdp_stage() (in module iphasimulator.charmmgui_import) read_minimization_result() (in module iphasimulator.charmmgui_import) read_rtf_charges() (in module iphasimulator.charmmgui_import) read_topology_defaults() (in module iphasimulator.charmmgui_import) read_topology_molecule_counts() (in module iphasimulator.charmmgui_import) read_topology_molecules() (in module iphasimulator.charmmgui_import) ready (iphasimulator.simulation_gromacs_runner.GromacsLocalMinimizationCheck property) reconstruct_molecules() (in module iphasimulator.trajectory_gromacs_trjconv) register_PHA_type() (iphasimulator.pha_filepath_manager.PHAResidueCodeManager method) removed_hydrogens (iphasimulator.amber_complex.ProteinPdbSummary attribute) render_slurm_script() (in module iphasimulator.workflows.hpc) replace_pdb_residue_name() (iphasimulator.build_pha.PHAPolymerBuilder method) report_ps (iphasimulator.amber_solvation.OpenMMProtocol attribute) reporter_freq (iphasimulator.sw_openmm.BuildSimulation attribute) representative_frame_path (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) require_ambertools() (in module iphasimulator.parameterization_gaff2) required_files (iphasimulator.simulation_gromacs_runner.GromacsLocalMinimizationCheck attribute) resi_penalties (iphasimulator.charmmgui_import.CGenFFPenaltyReport attribute) RESI_PENALTY_PATTERN (in module iphasimulator.charmmgui_import) residue_code (iphasimulator.monomers.Monomer attribute) residue_codes (iphasimulator.build_pha.PHAPolymerBuilder attribute) residue_codes_csv (iphasimulator.pha_filepath_manager.PHAFileManager attribute) residue_metadata() (in module iphasimulator.analysis_contacts) residue_minima() (in module iphasimulator.analysis_contacts) residue_name (iphasimulator.charmmgui_import.GroAtom attribute) (iphasimulator.docking_inputs.PolymerWholeCheck attribute) residue_number (iphasimulator.charmmgui_import.GroAtom attribute) RESIDUE_ROLE_SUFFIXES (in module iphasimulator.naming) residue_variant_name() (in module iphasimulator.naming) residue_variant_names() (in module iphasimulator.naming)

ResidueRole (in module iphasimulator.naming) residues (iphasimulator.amber_complex.ProteinPdbSummary attribute) (iphasimulator.analysis_contacts.AtomSelections attribute) (iphasimulator.analysis_contacts.ContactResult attribute) resolve_center_source_groups() (in module iphasimulator.trajectory_centering) resolved_settings() (in module iphasimulator.trajectory_processing) restrain_heavy_atoms() (iphasimulator.sw_openmm.BuildSimulation method) restrain_heavys (iphasimulator.sw_openmm.BuildSimulation attribute) restraint_groups() (in module iphasimulator.data.amber_openmm.run_openmm_md) returncode (iphasimulator.simulation_gromacs_runner.GromacsGromppValidation attribute) (iphasimulator.trajectory_gromacs_trjconv.TrjconvResult attribute) reused_existing_center (iphasimulator.trajectory_centering.CenterIndexResult attribute) root_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute) run_acpype() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) run_benchmark() (in module iphasimulator.workflows.md_benchmark) run_charmm_polymer_solvation() (in module iphasimulator.charmmgui_import) run_command() (iphasimulator.build_pha.PHAPolymerBuilder method) (iphasimulator.pha_melt_builder.PHAMeltBuilder method) run_contacts() (in module iphasimulator.analysis_contacts) run_dir (iphasimulator.charmmgui_import.CharmmPolymerWaterFolder attribute) run_dry_minimization() (in module iphasimulator.charmmgui_import) run_gmx_check() (in module iphasimulator.trajectory_gromacs_merge) run_gromacs_local_minimization() (in module iphasimulator.simulation_gromacs_runner) run_name (iphasimulator.openmmscript_builder.OpenMMScriptBuilder attribute) (iphasimulator.sw_openmm.BuildSimulation attribute) run_openmm_short_test() (in module iphasimulator.amber_solvation) run_openmm_stages() (in module iphasimulator.amber_solvation) run_openmm_with_amber_topology() (in module iphasimulator.simulation_openmm_amber_runner) run_polyply() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) RUN_SCRIPT (in module iphasimulator.amber_solvation) run_script_path (iphasimulator.simulation_gromacs_runner.GromacsRunFiles attribute) RUN_SCRIPT_SOURCE (in module iphasimulator.amber_solvation) run_short_test() (in module iphasimulator.data.amber_openmm.run_openmm_md) run_stage() (in module iphasimulator.data.amber_openmm.run_openmm_md) run_tleap() (in module iphasimulator.build_single_PHA_systems) run_trjconv() (in module iphasimulator.trajectory_gromacs_trjconv) Runner (in module iphasimulator.trajectory_gromacs_merge) (in module iphasimulator.trajectory_gromacs_trjconv)

S

salt_ion_pairs (iphasimulator.amber_solvation.AmberSystemOutputs attribute) salt_ion_pairs() (in module iphasimulator.amber_solvation) salt_molar (iphasimulator.amber_solvation.AmberSolvationSettings attribute) sample_interval_ns (iphasimulator.analysis_contacts.ContactConfig attribute) save_distances() (in module iphasimulator.analysis_contacts) save_polymer_smiles() (iphasimulator.build_pha.PHAPolymerBuilder method) save_rst() (iphasimulator.sw_openmm.BuildSimulation method) savepdb_traj (iphasimulator.sw_openmm.BuildSimulation attribute) savepdb_trajectories() (iphasimulator.sw_openmm.BuildSimulation class method) schema_version (iphasimulator.trajectory_processing.ProcessingConfig attribute) sdf_label (iphasimulator.charmmgui_import.SignedVolume attribute) sdf_path (iphasimulator.workflows.md_benchmark.BenchmarkTarget attribute) select_atoms() (in module iphasimulator.analysis_contacts) selected_atom_counts (iphasimulator.analysis_contacts.ContactResult attribute) selected_system_names() (in module iphasimulator.workflows.md_benchmark) selections (iphasimulator.trajectory_gromacs_trjconv.TrjconvResult attribute) set_anneal_parameters() (iphasimulator.sw_openmm.BuildSimulation class method) set_anneal_parameters_help() (iphasimulator.sw_openmm.BuildSimulation class method) set_friction_coeff() (iphasimulator.sw_openmm.BuildSimulation class method) set_nonbondedcutoff() (iphasimulator.sw_openmm.BuildSimulation class method) set_pressure() (iphasimulator.sw_openmm.BuildSimulation class method) set_reporter_freq() (iphasimulator.sw_openmm.BuildSimulation class method) set_temperature() (iphasimulator.sw_openmm.BuildSimulation class method) set_timestep() (iphasimulator.sw_openmm.BuildSimulation class method) set_total_steps() (iphasimulator.sw_openmm.BuildSimulation class method) SHORT_TEST_MINIMIZATION_ITERATIONS (in module iphasimulator.data.amber_openmm.run_openmm_md) SHORT_TEST_PS (in module iphasimulator.data.amber_openmm.run_openmm_md) shortest_box_vector_nm (iphasimulator.simulation_gromacs_runner.GromacsBoxValidation attribute) show_available_PHA_monomers() (in module iphasimulator.visualisation.visualiser) show_available_PHA_polymers() (in module iphasimulator.visualisation.visualiser) show_PHA_monomer() (in module iphasimulator.visualisation.visualiser) show_PHA_polymer() (in module iphasimulator.visualisation.visualiser) side_chain (iphasimulator.monomers.Monomer property) side_chain_carbons (iphasimulator.workflows.design.PolymerDesign attribute) side_chain_length (iphasimulator.monomers.Monomer attribute) sidechain_restraint (iphasimulator.amber_solvation.OpenMMProtocol attribute) SignedVolume (class in iphasimulator.charmmgui_import) simulation_dir (iphasimulator.trajectory_gromacs_merge.DiscoveredGromacsOutputs attribute) SLURM_STAGES (in module iphasimulator.charmmgui_import) smiles_to_mol() (in module iphasimulator.visualisation.visualiser) smiles_to_pdb() (iphasimulator.build_pha.PHAPolymerBuilder method) sodium_count (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation property) (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) SODIUM_PDB (in module iphasimulator.system_builder_packmol) SOLVATE_SCRIPT (in module iphasimulator.charmmgui_import)

solvate_script_path (iphasimulator.charmmgui_import.CharmmPolymerWaterFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) solvated_dir (iphasimulator.charmmgui_import.CharmmPolymerWaterFolder attribute) solvated_ions_PHAs_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute) solvated_pdb_path (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) solvated_PHAs_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute) solvated_polymer_dir (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) solvation_itp_paths (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) SOLVENT_AND_IONS (in module iphasimulator.amber_complex) solvent_itp_path (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles attribute) source (iphasimulator.charmmgui_import.PenaltyEntry attribute) source_groups (iphasimulator.trajectory_centering.CenterIndexResult attribute) sqm_log (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) stage_intervals() (in module iphasimulator.data.amber_openmm.run_openmm_md) stage_steps() (in module iphasimulator.data.amber_openmm.run_openmm_md) STAGES (in module iphasimulator.data.amber_openmm.run_openmm_md) start_ns (iphasimulator.analysis_contacts.ContactConfig attribute) start_time_ps (iphasimulator.trajectory_gromacs_merge.GromacsCheckResult attribute) state_xml_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) stateDataReporter (iphasimulator.sw_openmm.DataWriter attribute) status (iphasimulator.charmmgui_import.CheckResult attribute) stderr (iphasimulator.simulation_gromacs_runner.GromacsGromppValidation attribute) (iphasimulator.trajectory_gromacs_merge.GromacsCheckResult attribute) (iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult attribute) (iphasimulator.trajectory_gromacs_trjconv.TrjconvResult attribute) stdout (iphasimulator.simulation_gromacs_runner.GromacsGromppValidation attribute) (iphasimulator.trajectory_gromacs_merge.GromacsCheckResult attribute) (iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult attribute) (iphasimulator.trajectory_gromacs_trjconv.TrjconvResult attribute) step5_input_gro_path (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) steps (iphasimulator.openmmscript_builder.OpenMMScriptBuilder attribute) stereocentres (iphasimulator.amber_complex.PoseTransferResult attribute) stereochemistry (iphasimulator.workflows.design.PolymerDesign attribute) (iphasimulator.workflows.validation.ValidationTarget attribute) stride (iphasimulator.trajectory_processing.ProcessingConfig attribute) structure (iphasimulator.trajectory_processing.ProcessingConfig attribute) structure_path (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) summarise() (in module iphasimulator.analysis_contacts) summary_log_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) support_structure_paths (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) supported_polymer_table() (in module iphasimulator.workflows.design) system_dir (iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs attribute) SYSTEM_INPCRD (in module iphasimulator.amber_solvation) SYSTEM_PDB (in module iphasimulator.amber_solvation) SYSTEM_PRMTOP (in module iphasimulator.amber_solvation) SYSTEMS (in module iphasimulator.workflows.md_benchmark)

T

tail_residue_code (iphasimulator.monomers.Monomer property) target_stage_name() (in module iphasimulator.workflows.hpc) targets_from_config() (in module iphasimulator.workflows.hpc) temp (iphasimulator.sw_openmm.BuildSimulation attribute) temp_dir (iphasimulator.pha_filepath_manager.PHAFileManager attribute) temperature (iphasimulator.charmmgui_import.MdpStage attribute) temperature_kelvin (iphasimulator.amber_solvation.OpenMMProtocol attribute) test_polymer_melt_simulation() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) thermal_ramp() (iphasimulator.sw_openmm.BuildSimulation method) TIME_ATOL_NS (in module iphasimulator.analysis_contacts) times_ns (iphasimulator.analysis_contacts.ContactResult attribute) timestamp (iphasimulator.sw_openmm.BuildSimulation attribute) timestep (iphasimulator.sw_openmm.BuildSimulation attribute) timing_log (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) tip3p_ions_itp_path (iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles property) TIP3P_WATER_DENSITY_PER_NM3 (in module iphasimulator.system_builder_packmol) TIP3P_WATER_PDB (in module iphasimulator.system_builder_packmol) TLEAP_INPUT (in module iphasimulator.amber_solvation) tleap_input_path (iphasimulator.amber_solvation.AmberSystemOutputs attribute) (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) TLEAP_LOG (in module iphasimulator.amber_solvation) tleap_log (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) tleap_log_path (iphasimulator.amber_solvation.AmberSystemOutputs attribute) tleap_seconds (iphasimulator.parameterization_gaff2.Gaff2Outputs attribute) TleapLogSummary (class in iphasimulator.amber_solvation)

to_pdb() (in module iphasimulator.export) to_script() (iphasimulator.openmmscript_builder.OpenMMScriptBuilder method) to_sdf() (in module iphasimulator.export) top_charge_penalties() (iphasimulator.charmmgui_import.CGenFFPenaltyReport method) top_parameter_penalties() (iphasimulator.charmmgui_import.CGenFFPenaltyReport method) top_path (iphasimulator.conversion_amber_to_gromacs.GromacsConversionOutputs attribute) topol_top_path (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation attribute) (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation attribute) (iphasimulator.simulation_gromacs_runner.GromacsTopologyValidation attribute) topology (iphasimulator.analysis_contacts.ContactConfig attribute) topology_file (iphasimulator.sw_openmm.AmberSimulation attribute) (iphasimulator.sw_openmm.GromacsSimulation attribute) TOPOLOGY_FILES (in module iphasimulator.charmmgui_import) total_steps (iphasimulator.sw_openmm.BuildSimulation attribute) trajectory (iphasimulator.analysis_contacts.ContactConfig attribute) trajectory_merge (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) trajectory_output (iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult attribute) trajectory_output_filename() (in module iphasimulator.trajectory_gromacs_merge) TRAJECTORY_OUTPUT_PREFIX (in module iphasimulator.trajectory_gromacs_merge) trajectory_path (iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs attribute) TrajectoryPreprocessingOutputs (class in iphasimulator.trajectory_preprocessing) TrjconvResult (class in iphasimulator.trajectory_gromacs_trjconv) type (iphasimulator.charmmgui_import.ItpAtom attribute) type_of_simulation() (iphasimulator.sw_openmm.BuildSimulation method)

V

valid (iphasimulator.simulation_gromacs_runner.GromacsBoxValidation property) (iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation property) (iphasimulator.simulation_gromacs_runner.GromacsTopologyValidation property) valid_box() (in module iphasimulator.analysis_contacts) validate() (iphasimulator.analysis_contacts.ContactConfig method) validate_charmm_gui_run_folder() (in module iphasimulator.charmmgui_import) validate_charmm_polymer_water_folder() (in module iphasimulator.charmmgui_import) validate_chiral_centres() (in module iphasimulator.stereochemistry) validate_dry_ligand_folder() (in module iphasimulator.charmmgui_import) validate_gromacs_box_against_mdp() (in module iphasimulator.simulation_gromacs_runner) validate_gromacs_coordinate_topology_counts() (in module iphasimulator.simulation_gromacs_runner) validate_gromacs_run_folder() (in module iphasimulator.simulation_gromacs_runner) validate_gromacs_solvated_topology() (in module iphasimulator.simulation_gromacs_runner)

validate_gromacs_solvation_grompp() (in module iphasimulator.simulation_gromacs_runner) validate_inputs() (in module iphasimulator.data.amber_openmm.run_openmm_md) validate_melt_inputs() (iphasimulator.pha_melt_builder.PHAMeltBuilder method) validate_monomer_code() (in module iphasimulator.naming) validate_oligomer_name() (in module iphasimulator.naming) validate_pha_chain() (in module iphasimulator.build) validate_pha_name() (in module iphasimulator.naming) validate_polymer_code() (in module iphasimulator.naming) validate_r_chiral_centres() (in module iphasimulator.stereochemistry) validate_stereochemistry_option() (in module iphasimulator.stereochemistry) validate_system_name() (in module iphasimulator.naming) ValidationTarget (class in iphasimulator.workflows.validation) volume_md (iphasimulator.charmmgui_import.SignedVolume attribute) volume_sdf (iphasimulator.charmmgui_import.SignedVolume attribute)

W

water_count (iphasimulator.amber_solvation.AmberSystemOutputs attribute) (iphasimulator.amber_solvation.TleapLogSummary attribute) (iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation attribute) (iphasimulator.system_builder_packmol.PackmolBuildResult attribute) WATER_ION_ATOMTYPES_INCLUDE (in module iphasimulator.charmmgui_import) WATER_ION_MOLECULE_INCLUDES (in module iphasimulator.charmmgui_import) WATER_MOLARITY (in module iphasimulator.amber_solvation) WATER_MOLECULE_NAMES (in module iphasimulator.simulation_gromacs_runner) WATER_MOLECULES (in module iphasimulator.charmmgui_import) WHOLE_MOLECULE_ADVICE (in module iphasimulator.docking_inputs) WORKFLOW (in module iphasimulator.trajectory_processing)

WORKFLOW_CENTER_SOURCES (in module iphasimulator.trajectory_centering) workflow_plan() (in module iphasimulator.workflows.hpc) workflow_type (iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder attribute) write_charmm_polymer_solvation_files() (in module iphasimulator.charmmgui_import) write_gromacs_run_files() (in module iphasimulator.simulation_gromacs_runner) write_gromacs_solvation_files() (in module iphasimulator.simulation_gromacs_runner) write_index() (in module iphasimulator.trajectory_centering) write_openmm_run_files() (in module iphasimulator.amber_solvation) write_protein_pdb() (in module iphasimulator.amber_complex) write_script() (iphasimulator.openmmscript_builder.OpenMMScriptBuilder method) write_tleap_file() (in module iphasimulator.build_single_PHA_systems) write_tleap_input() (in module iphasimulator.amber_solvation)

X

xtc_files (iphasimulator.trajectory_gromacs_merge.DiscoveredGromacsOutputs attribute)