Index _ | A | B | C | D | F | G | I | L | M | N | P | R | S | T | U _ __call__() (bindflow.preparation.solvent.Solvate method) (bindflow.preparation.system_builder.MakeInputs method) __cluster_validation__() (bindflow.orchestration.generate_scheduler.FrontEnd method) (bindflow.orchestration.generate_scheduler.Scheduler method) (bindflow.orchestration.generate_scheduler.SlurmScheduler method) __init__() (bindflow.mdp.mdp.MDP method) (bindflow.mdp.mdp.StepMDP method) (bindflow.orchestration.generate_scheduler.FrontEnd method) (bindflow.orchestration.generate_scheduler.Scheduler method) (bindflow.orchestration.generate_scheduler.SlurmScheduler method) (bindflow.preparation.solvent.Solvate method) (bindflow.preparation.system_builder.CRYST1 method) (bindflow.preparation.system_builder.MakeInputs method) (bindflow.utils.tools.DotDict method) A approach_flow() (in module bindflow.orchestration.flow_builder) archive() (in module bindflow.utils.tools) B bindflow.mdp.mdp module bindflow.orchestration.flow_builder module bindflow.orchestration.generate_scheduler module bindflow.preparation.system_builder module bindflow.runners module bindflow.utils.tools module build_snakemake() (bindflow.orchestration.generate_scheduler.FrontEnd method) (bindflow.orchestration.generate_scheduler.Scheduler method) (bindflow.orchestration.generate_scheduler.SlurmScheduler method) C calculate() (in module bindflow.runners) center_xtc() (in module bindflow.utils.tools) clean() (bindflow.preparation.solvent.Solvate method) (bindflow.preparation.system_builder.MakeInputs method) config_validator() (in module bindflow.utils.tools) CRYST1 (class in bindflow.preparation.system_builder) D DotDict (class in bindflow.utils.tools) F find_xtc() (in module bindflow.utils.tools) from_pdb() (bindflow.preparation.system_builder.CRYST1 method) FrontEnd (class in bindflow.orchestration.generate_scheduler) G generate_approach_snake_file() (in module bindflow.orchestration.flow_builder) get_gmx_ff() (in module bindflow.preparation.system_builder) gmx_command() (in module bindflow.utils.tools) gmx_process() (bindflow.preparation.system_builder.MakeInputs method) gmx_runner() (in module bindflow.utils.tools) I input_helper() (in module bindflow.utils.tools) L list_if_file() (in module bindflow.utils.tools) M make_bindflow_dir() (in module bindflow.preparation.system_builder) make_fep_dir_structure() (in module bindflow.mdp.mdp) make_system() (bindflow.preparation.system_builder.MakeInputs method) MakeInputs (class in bindflow.preparation.system_builder) MDP (class in bindflow.mdp.mdp) module bindflow.mdp.mdp bindflow.orchestration.flow_builder bindflow.orchestration.generate_scheduler bindflow.preparation.system_builder bindflow.runners bindflow.utils.tools N natsort() (in module bindflow.utils.tools) P paths_exist() (in module bindflow.utils.tools) R readParmEDMolecule() (in module bindflow.utils.tools) run() (in module bindflow.utils.tools) S Scheduler (class in bindflow.orchestration.generate_scheduler) slurm_validation() (in module bindflow.orchestration.generate_scheduler) SlurmScheduler (class in bindflow.orchestration.generate_scheduler) small_mol_process() (bindflow.preparation.system_builder.MakeInputs method) Solvate (class in bindflow.preparation.solvent) StepMDP (class in bindflow.mdp.mdp) submit() (bindflow.orchestration.generate_scheduler.FrontEnd method) (bindflow.orchestration.generate_scheduler.Scheduler method) (bindflow.orchestration.generate_scheduler.SlurmScheduler method) sum_uncertainty_propagation() (in module bindflow.utils.tools) system_combiner() (in module bindflow.preparation.system_builder) T to_json() (bindflow.orchestration.generate_scheduler.Scheduler method) U unarchive() (in module bindflow.utils.tools) update_nwindows_config() (in module bindflow.orchestration.flow_builder)
