Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W A all_atoms (batter.config.simulation.SimulationConfig attribute) allow_run_id_mismatch (batter.config.run.RunSection attribute) analysis_start_step (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) anchor_atoms (batter.config.run.CreateArgs attribute) anion (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) B backend (batter.config.run.RunConfig attribute) barostat (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) batch_gpus (batter.config.run.RunSection attribute) batch_gpus_per_task (batter.config.run.RunSection attribute) batch_ligand_process() (in module batter.param.ligand) batch_mode (batter.config.run.RunSection attribute) batch_srun_extra (batter.config.run.RunSection attribute) batter.param.ligand module blocks (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) buffer_x (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) buffer_y (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) buffer_z (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) C cation (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) clean_failures (batter.config.run.RunSection attribute) component_lambdas (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) component_windows (batter.config.simulation.SimulationConfig attribute) components (batter.config.simulation.SimulationConfig attribute) create (batter.config.run.RunConfig attribute) create_ligand() (batter.param.ligand.LigandFactory method) cut (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) D dec_int (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) dec_method (batter.config.simulation.SimulationConfig attribute) dic_n_steps (batter.config.simulation.SimulationConfig attribute) dry_run (batter.config.run.RunSection attribute) dt (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) dump_run_config() (in module batter.config) dump_simulation_config() (in module batter.config) E email_on_completion (batter.config.run.RunSection attribute) email_sender (batter.config.run.RunSection attribute) enable_mcwat (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) eq_steps (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) extra_conformation_restraints (batter.config.run.CreateArgs attribute) extra_restraint_fc (batter.config.run.CreateArgs attribute) extra_restraints (batter.config.run.CreateArgs attribute) F fe_sim (batter.config.run.RunConfig attribute) fe_type (batter.config.simulation.SimulationConfig attribute) fetch_from_existing_db() (batter.param.ligand.LigandProcessing method) G gamma_ln (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) H hmr (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) I infe (batter.config.simulation.SimulationConfig attribute) ion_conc (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) ion_def (batter.config.simulation.SimulationConfig attribute) L l1_range (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) l1_x (batter.config.simulation.SimulationConfig attribute) l1_y (batter.config.simulation.SimulationConfig attribute) l1_z (batter.config.simulation.SimulationConfig attribute) lambdas (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) lig_angle_force (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) lig_buffer (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) lig_com_force (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) lig_dihcf_force (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) lig_distance_force (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) ligand_dict (batter.config.simulation.SimulationConfig attribute) ligand_ff (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) ligand_input (batter.config.run.CreateArgs attribute) ligand_paths (batter.config.run.CreateArgs attribute) ligand_sdf_path (batter.param.ligand.LigandProcessing property) LigandFactory (class in batter.param.ligand) LigandProcessing (class in batter.param.ligand) lipid_ff (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) lipid_mol (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) load_run_config() (in module batter.config) load_simulation_config() (in module batter.config) M max_active_jobs (batter.config.run.RunSection attribute) max_adis (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) max_workers (batter.config.run.RunSection attribute) membrane_simulation (batter.config.simulation.SimulationConfig attribute) min_adis (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) module batter.param.ligand MOL2_LigandProcessing (class in batter.param.ligand) N n_bootstraps (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) n_steps (batter.config.run.FESimArgs attribute) n_steps_dict (batter.config.simulation.SimulationConfig attribute) name (batter.param.ligand.LigandProcessing property) neut (batter.config.simulation.SimulationConfig attribute) neutralize_only (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) ntpr (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) ntwe (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) ntwr (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) ntwx (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) O on_failure (batter.config.run.RunSection attribute) only_fe_preparation (batter.config.run.RunSection attribute) other_mol (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) output_folder (batter.config.run.RunSection attribute) overwrite (batter.config.run.CreateArgs attribute) P p1 (batter.config.simulation.SimulationConfig attribute) p2 (batter.config.simulation.SimulationConfig attribute) p3 (batter.config.simulation.SimulationConfig attribute) param_charge (batter.config.run.CreateArgs attribute) param_method (batter.config.run.CreateArgs attribute) param_outdir (batter.config.run.CreateArgs attribute) PDB_LigandProcessing (class in batter.param.ligand) prepare_ligand_parameters() (batter.param.ligand.LigandProcessing method) prepare_ligand_parameters_amberff() (batter.param.ligand.LigandProcessing method) prepare_ligand_parameters_openff() (batter.param.ligand.LigandProcessing method) protein_align (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) protein_input (batter.config.run.CreateArgs attribute) protocol (batter.config.run.RunConfig attribute) R rbfe (batter.config.run.RunConfig attribute) rec_com_force (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) receptor_ff (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) receptor_segment (batter.config.simulation.SimulationConfig attribute) release_eq (batter.config.simulation.SimulationConfig attribute) remd (batter.config.run.FESimArgs attribute) (batter.config.run.RunSection attribute) (batter.config.simulation.SimulationConfig attribute) remd_nstlim (batter.config.simulation.SimulationConfig attribute) rest (batter.config.simulation.SimulationConfig attribute) retain_lig_prot (batter.config.run.CreateArgs attribute) rng (batter.config.simulation.SimulationConfig attribute) rocklin_correction (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) run (batter.config.run.RunConfig attribute) run_id (batter.config.run.RunSection attribute) S SDF_LigandProcessing (class in batter.param.ligand) sdr_dist (batter.config.simulation.SimulationConfig attribute) slurm (batter.config.run.RunSection attribute) slurm_header_dir (batter.config.run.RunSection attribute) (batter.config.simulation.SimulationConfig attribute) smiles (batter.param.ligand.LigandProcessing property) solv_shell (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) system_coordinate (batter.config.run.CreateArgs attribute) system_input (batter.config.run.CreateArgs attribute) system_name (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) system_type (batter.config.run.RunSection attribute) T temperature (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) ti_points (batter.config.simulation.SimulationConfig attribute) to_dict() (batter.param.ligand.LigandProcessing method) U unbound_threshold (batter.config.run.FESimArgs attribute) (batter.config.simulation.SimulationConfig attribute) V version (batter.config.run.RunConfig attribute) W water_model (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute)