Index _ | A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | W _ __init__() (topo.core.system method) _append_topology() (in module topo.csp.ribosome) _bead_type() (in module topo.csp.ribosome) _constructHeaders() (topo.reporter.topo_reporter.topoReporter method) _constructReportValues() (topo.reporter.topo_reporter.topoReporter method) _dump_topology_psf() (in module topo.csp.core) _finalize_nascent() (in module topo.csp.core) _format_header() (topo.reporter.topo_reporter.topoReporter method) _format_row() (topo.reporter.topo_reporter.topoReporter method) _is_csp_layout() (in module topo.csp.movie) _make_cfg() (in module topo.csp.core) _module_version() (in module topo.utils.runinfo) _norm_chain() (in module topo.utils.nonbonded) _optimize_loop() (in module topo.optimize.optimize) _pick_traj() (in module topo.csp.movie) _ptc_bead_index() (in module topo.csp.core) _residue_chain() (in module topo.utils.nonbonded) _safe_platform_property() (in module topo.utils.runinfo) _setParameters() (topo.core.system static method) _split_cli() (in module topo.utils.multichain) _value_to_str() (topo.reporter.topo_reporter.topoReporter method) _vprint() (in module topo.csp.core) _write_pdb() (in module topo.csp.core) _write_tcl() (in module topo.csp.movie) A add_cterm_restraint() (in module topo.csp.core) add_trna_tether() (in module topo.csp.ribosome) add_tunnel_cylinder() (in module topo.csp.cylinder) add_tunnel_wall() (in module topo.csp.ribosome) addCustomNonBondedForce() (topo.core.system method) addGaussianAngleForces() (topo.core.system method) addHarmonicBondForces() (topo.core.system method) addParticles() (topo.core.system method) addPeriodicTorsionForce() (topo.core.system method) addSystemForces() (topo.core.system method) addYukawaForces() (topo.core.system method) anchor_coord() (in module topo.csp.ribosome) anneal (topo.utils.config.SimulationConfig attribute) anneal_ramp (topo.utils.config.SimulationConfig attribute) anneal_ramp_increments (topo.utils.config.SimulationConfig attribute) anneal_ramp_steps (topo.utils.config.SimulationConfig attribute) anneal_steps (topo.utils.config.SimulationConfig attribute) append_ribosome() (in module topo.csp.ribosome) attach_reporters() (in module topo.engine) B bead_system_index() (in module topo.csp.ribosome) bond() (topo.core.geometry.geometry static method) box_dimension (topo.utils.config.SimulationConfig attribute) build_codon_time_lists() (in module topo.csp.kinetics) build_hb_contact_matrix() (in module topo.utils.nonbonded) build_kwargs() (topo.utils.config.SimulationConfig method) build_length_model() (in module topo.csp.core) build_native_contacts() (in module topo.analysis) (in module topo.analysis.native_contacts) build_nonbonded_interaction() (in module topo.utils.nonbonded) build_system() (in module topo.engine) buildCoarseGrainModel() (topo.core.models.models static method) BuiltSystem (class in topo.engine) C calculate_rmin_2_values() (in module topo.utils.nonbonded) cgModel (topo.engine.BuiltSystem attribute) charges (topo.csp.ribosome.Ribosome attribute) checkBondDistances() (topo.core.system method) checkLargeForces() (topo.core.system method) checkpoint (topo.engine.RunContext attribute) (topo.utils.config.SimulationConfig attribute) checkpoint_path() (topo.utils.config.SimulationConfig method) codon_time_list() (in module topo.csp.kinetics) codon_time_table_path (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) cold_start_positions() (in module topo.csp.core) collect_cuda_metadata() (in module topo.utils.runinfo) config_file (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) (topo.utils.config.SimulationConfig attribute) constraint_tolerance (topo.utils.config.SimulationConfig attribute) constraints (topo.csp.core.RunParams attribute) (topo.utils.config.SimulationConfig attribute) coords_nm (topo.csp.ribosome.Ribosome attribute) copy_shift (topo.utils.config.SimulationConfig attribute) createSystemObject() (topo.core.system method) csp() (in module topo.csp.protocol) CSPConfig (class in topo.csp.protocol) cylinder() (in module topo.csp.cylinder) CylinderConfig (class in topo.csp.cylinder) CylinderParams (class in topo.csp.cylinder) D describe_schedule() (in module topo.mdrun.protocol) describeNextReport() (topo.csp.core.NascentDCDReporter method) device (topo.csp.core.RunParams attribute) (topo.utils.config.SimulationConfig attribute) dissociation_steps (topo.csp.core.RunParams attribute) domain_def (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) (topo.utils.config.SimulationConfig attribute) done_steps (topo.engine.RunContext attribute) dt (topo.utils.config.SimulationConfig attribute) dt_ps (topo.csp.core.RunParams attribute) dumpForceFieldData() (topo.core.system method) dumpStructure() (topo.core.system method) dumpTopology() (topo.core.system method) E ejection_steps (topo.csp.core.RunParams attribute) F finalize_simulation() (in module topo.engine) find_lengths() (in module topo.csp.movie) find_post() (in module topo.csp.movie) find_stage_segments() (in module topo.csp.movie) folded_fraction() (topo.optimize.optimize.Scorer static method) fraction_native_contacts() (in module topo.analysis) (in module topo.analysis.native_contacts) frequency_p (topo.utils.config.SimulationConfig attribute) G geometry (class in topo.core.geometry) get_bs_contact_matrix() (in module topo.utils.nonbonded) get_hb_contact_matrix() (in module topo.utils.nonbonded) get_residue_mapping() (in module topo.utils.nonbonded) get_scaling_ss_matrix() (in module topo.utils.nonbonded) get_ss_contact_matrix() (in module topo.utils.nonbonded) get_ss_interaction_energy() (in module topo.utils.nonbonded) getAngles() (topo.core.system method) getAtoms() (topo.core.system method) getBonds() (topo.core.system method) getCAlphaOnly() (topo.core.system method) getTorsions() (topo.core.system method) I init_position (topo.utils.config.SimulationConfig attribute) initiation_rate (topo.csp.core.RunParams attribute) L L0 (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) L_max (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) label() (topo.optimize.optimize.Scorer static method) load_bt_potential() (in module topo.utils.nonbonded) load_dihedral_parameters() (in module topo.utils.read_parms) load_dihedral_params() (in module topo.parameters.dihedral) load_domains() (in module topo.analysis) (in module topo.analysis.native_contacts) load_ribosome() (in module topo.csp.ribosome) load_universe() (in module topo.analysis.native_contacts) loadForcefieldFromFile() (topo.core.system method) log_precision (topo.utils.config.SimulationConfig attribute) log_width (topo.utils.config.SimulationConfig attribute) M main() (in module topo.analysis.native_contacts) (in module topo.csp.movie) make_noninteracting_copies() (in module topo.utils.multichain) make_platform() (topo.utils.config.SimulationConfig method) max_steps_per_stage (topo.csp.core.RunParams attribute) md_steps (topo.utils.config.SimulationConfig attribute) mdrun() (in module topo.mdrun.mdrun) min_steps_per_stage (topo.csp.core.RunParams attribute) minimize (topo.csp.core.RunParams attribute) (topo.utils.config.SimulationConfig attribute) model (topo.utils.config.SimulationConfig attribute) models (class in topo.core.models) module topo.analysis topo.analysis.native_contacts topo.core.geometry topo.csp.core topo.csp.cylinder topo.csp.kinetics topo.csp.movie topo.csp.protocol topo.csp.ribosome topo.engine topo.mdrun.mdrun topo.mdrun.protocol topo.optimize.optimize topo.parameters.model_parameters topo.reporter topo.reporter.topo_reporter topo.utils topo.utils.config topo.utils.multichain topo.utils.nonbonded topo.utils.read_parms topo.utils.runinfo mrna (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) N n (topo.csp.ribosome.Ribosome property) n_contacts() (topo.optimize.optimize.Scorer method) n_copies (topo.utils.config.SimulationConfig attribute) n_steps (topo.csp.core.RunParams attribute) names (topo.csp.ribosome.Ribosome attribute) nascent_ev_radii (topo.csp.core.RunParams attribute) NascentDCDReporter (class in topo.csp.core) normalize_class() (in module topo.optimize.optimize) nscale_for() (in module topo.optimize.optimize) nstchk (topo.utils.config.SimulationConfig attribute) nstcomm (topo.utils.config.SimulationConfig attribute) nstlog (topo.utils.config.SimulationConfig attribute) nstout (topo.csp.core.RunParams attribute) nstxout (topo.utils.config.SimulationConfig attribute) O optimal_ptc_targets() (in module topo.csp.core) optimize() (in module topo.optimize.optimize) outdir (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) outname (topo.utils.config.SimulationConfig attribute) output_dir (topo.utils.config.SimulationConfig attribute) output_path() (topo.utils.config.SimulationConfig method) P params (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) parse_args() (in module topo.analysis.native_contacts) (in module topo.optimize.optimize) parse_codon_times() (in module topo.csp.kinetics) parse_hydrogen_bonds() (in module topo.utils.nonbonded) parse_residue_list() (in module topo.utils.nonbonded) pbc (topo.utils.config.SimulationConfig attribute) pcoupl (topo.utils.config.SimulationConfig attribute) pdb_file (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) (topo.utils.config.SimulationConfig attribute) position2Array() (topo.core.geometry.geometry static method) positions (topo.engine.BuiltSystem attribute) ppn (topo.csp.core.RunParams attribute) (topo.utils.config.SimulationConfig attribute) precompute_contacts() (in module topo.csp.core) prepare_output_dir() (topo.utils.config.SimulationConfig method) print_pairs_with_multiple_hb() (in module topo.utils.nonbonded) production_schedule() (in module topo.mdrun.protocol) Q q_per_frame() (topo.optimize.optimize.Scorer method) quench_schedule() (in module topo.mdrun.protocol) quench_steps() (topo.utils.config.SimulationConfig method) quiet (topo.utils.config.SimulationConfig attribute) R random_seed (topo.csp.core.RunParams attribute) read_anchor() (in module topo.csp.core) read_codon_time_table() (in module topo.csp.kinetics) read_csp_config() (in module topo.csp.protocol) read_cylinder_config() (in module topo.csp.cylinder) read_mrna() (in module topo.csp.kinetics) read_optimize_config() (in module topo.optimize.optimize) read_simulation_config() (in module topo.utils.config) read_yaml_config() (in module topo.utils.nonbonded) readOpenMMReporterFile() (in module topo.reporter.topo_reporter) ref_p (topo.utils.config.SimulationConfig attribute) ref_t (topo.csp.core.RunParams attribute) (topo.utils.config.SimulationConfig attribute) reference_residue_geometry() (in module topo.analysis) (in module topo.analysis.native_contacts) replicate_positions() (in module topo.utils.multichain) replicate_system_intra_only() (in module topo.utils.multichain) replicate_topology() (in module topo.utils.multichain) report() (topo.csp.core.NascentDCDReporter method) (topo.reporter.topo_reporter.topoReporter method) resids (topo.csp.ribosome.Ribosome attribute) resnames (topo.csp.ribosome.Ribosome attribute) restart (topo.utils.config.SimulationConfig attribute) restart_active (topo.engine.RunContext attribute) restraint_k (topo.csp.core.RunParams attribute) Ribosome (class in topo.csp.ribosome) ribosome (topo.csp.protocol.CSPConfig attribute) ribosome_traffic (topo.csp.core.RunParams attribute) ribosome_traffic_times() (in module topo.csp.kinetics) Rmin_2_nm (topo.csp.ribosome.Ribosome attribute) run_continuous_synthesis() (in module topo.csp.protocol) run_cylinder_synthesis() (in module topo.csp.cylinder) run_length() (in module topo.csp.core) (in module topo.csp.cylinder) run_md() (in module topo.optimize.optimize) run_optimizer() (in module topo.optimize.optimize) run_protocol() (in module topo.mdrun.protocol) run_subprocess() (in module topo.optimize.optimize) RunContext (class in topo.engine) runinfo_path (topo.engine.RunContext attribute) RunParams (class in topo.csp.core) S sample_fpt() (in module topo.csp.kinetics) scale_factor (topo.csp.core.RunParams attribute) Scorer (class in topo.optimize.optimize) seconds_to_steps() (in module topo.csp.kinetics) seed_positions() (in module topo.csp.core) segids (topo.csp.ribosome.Ribosome attribute) setBondForceConstants() (topo.core.system method) setCAChargePerResidueType() (topo.core.system method) setCAMassPerResidueType() (topo.core.system method) setCARadiusPerResidueType() (topo.core.system method) setParticlesCharge() (topo.core.system method) setParticlesMass() (topo.core.system method) setParticlesRadii() (topo.core.system method) setup_simulation() (in module topo.engine) simulation (topo.engine.RunContext attribute) SimulationConfig (class in topo.utils.config) split_chains() (in module topo.utils.multichain) split_indices() (in module topo.utils.multichain) stage_dwell_times() (in module topo.csp.kinetics) stage_steps() (in module topo.csp.kinetics) stitch_length_movie() (in module topo.csp.movie) stitch_movie() (in module topo.csp.movie) stitch_segments() (in module topo.csp.movie) stride_output_file (topo.csp.cylinder.CylinderConfig attribute) (topo.csp.protocol.CSPConfig attribute) (topo.utils.config.SimulationConfig attribute) strtobool() (in module topo.utils.config) system (class in topo.core) (topo.engine.BuiltSystem attribute) T t_high (topo.utils.config.SimulationConfig attribute) tau_t (topo.csp.core.RunParams attribute) (topo.utils.config.SimulationConfig attribute) tcoupl (topo.utils.config.SimulationConfig attribute) time_stage_1 (topo.csp.core.RunParams attribute) time_stage_2 (topo.csp.core.RunParams attribute) topo.analysis module topo.analysis.native_contacts module topo.core.geometry module topo.csp.core module topo.csp.cylinder module topo.csp.kinetics module topo.csp.movie module topo.csp.protocol module topo.csp.ribosome module topo.engine module topo.mdrun.mdrun module topo.mdrun.protocol module topo.optimize.optimize module topo.parameters.model_parameters module topo.reporter module topo.reporter.topo_reporter module topo.utils module topo.utils.config module topo.utils.multichain module topo.utils.nonbonded module topo.utils.read_parms module topo.utils.runinfo module topology (topo.engine.BuiltSystem attribute) topoReporter (class in topo.reporter.topo_reporter) total_steps() (topo.utils.config.SimulationConfig method) trna_tether (topo.csp.core.RunParams attribute) tunnel_center_nm (topo.csp.cylinder.CylinderParams attribute) tunnel_k (topo.csp.cylinder.CylinderParams attribute) tunnel_length_nm (topo.csp.cylinder.CylinderParams attribute) tunnel_mouth_round_nm (topo.csp.cylinder.CylinderParams attribute) tunnel_radius_nm (topo.csp.cylinder.CylinderParams attribute) tunnel_wall (topo.csp.core.RunParams attribute) tunnel_wall_k (topo.csp.core.RunParams attribute) tunnel_wall_x0_nm (topo.csp.core.RunParams attribute) tunnel_x_lo_nm (topo.csp.cylinder.CylinderParams attribute) U uniform_codon_time (topo.csp.core.RunParams attribute) uniform_codon_time_list() (in module topo.csp.kinetics) unit_keys() (topo.optimize.optimize.Scorer method) W write_domain_yaml() (in module topo.optimize.optimize) write_round_ini() (in module topo.optimize.optimize) write_run_end() (in module topo.utils.runinfo) write_run_start() (in module topo.utils.runinfo) write_section() (in module topo.utils.runinfo) write_subset_structure() (in module topo.csp.core)