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_fe_range (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_mode (batter.config.run.RunSection attribute) batch_srun_extra (batter.config.run.RunSection attribute) 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) 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) 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_steps1 (batter.config.simulation.SimulationConfig attribute) dic_steps2 (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) eq_steps1 (batter.config.simulation.SimulationConfig attribute) eq_steps2 (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) from_sections() (batter.config.simulation.SimulationConfig class 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) 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() (batter.config.run.RunConfig class method) 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) model_validate_yaml() (batter.config.run.RunConfig class method) N n_steps_dict (batter.config.simulation.SimulationConfig attribute) 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) num_equil_extends (batter.config.run.FESimArgs attribute) (batter.config.run.MDSimArgs attribute) (batter.config.simulation.SimulationConfig attribute) num_fe_extends (batter.config.run.FESimArgs 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) 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 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_enable (batter.config.run.FESimArgs attribute) remd_nstlim (batter.config.simulation.SimulationConfig attribute) remd_numexchg (batter.config.simulation.SimulationConfig attribute) resolve_paths() (batter.config.run.CreateArgs method) (batter.config.run.RunSection method) resolved_sim_config() (batter.config.run.RunConfig method) 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 sdr_dist (batter.config.simulation.SimulationConfig attribute) slurm (batter.config.run.RunSection attribute) slurm_header_dir (batter.config.run.RunSection attribute) solv_shell (batter.config.run.CreateArgs attribute) (batter.config.simulation.SimulationConfig attribute) steps1 (batter.config.run.FESimArgs attribute) steps2 (batter.config.run.FESimArgs 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.config.simulation.SimulationConfig 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) with_base_dir() (batter.config.run.RunConfig method)