SYMBOL INDEX (2321 symbols across 196 files)

FILE: devtools/data/fix_rbfe_results.py
  function untar (line 18) | def untar(fn):
  function retar (line 24) | def retar(loc, name):
  function replace_settings (line 30) | def replace_settings(fn, new_settings):
  function fix_rbfe_results (line 45) | def fix_rbfe_results():

FILE: devtools/data/gen_serialized_results.py
  function get_molecule (line 61) | def get_molecule(smi, name):
  function get_hif2a_inputs (line 69) | def get_hif2a_inputs():
  function execute_and_serialize (line 82) | def execute_and_serialize(
  function generate_md_settings (line 134) | def generate_md_settings():
  function generate_md_json (line 144) | def generate_md_json(smc):
  function generate_abfe_settings (line 152) | def generate_abfe_settings():
  function generate_abfe_json (line 177) | def generate_abfe_json():
  function generate_ahfe_settings (line 198) | def generate_ahfe_settings():
  function generate_ahfe_json (line 226) | def generate_ahfe_json(smc):
  function generate_rfe_settings (line 236) | def generate_rfe_settings():
  function generate_rfe_json (line 245) | def generate_rfe_json(smcA, smcB):
  function generate_septop_settings (line 260) | def generate_septop_settings():
  function generate_septop_json (line 285) | def generate_septop_json():

FILE: docs/_ext/sass.py
  function configure_path (line 28) | def configure_path(conf_dir: str, src: Optional[Union[PathLike, Path]]) ...
  function get_targets (line 38) | def get_targets(app: Sphinx) -> dict[Path, Path]:
  function build_sass_sources (line 53) | def build_sass_sources(app: Sphinx, env: BuildEnvironment):
  function setup (line 70) | def setup(app: Sphinx):

FILE: src/openfe/analysis/plotting.py
  function plot_lambda_transition_matrix (line 13) | def plot_lambda_transition_matrix(matrix: npt.NDArray) -> Axes:
  function plot_convergence (line 141) | def plot_convergence(
  function plot_replica_timeseries (line 239) | def plot_replica_timeseries(
  function plot_2D_rmsd (line 279) | def plot_2D_rmsd(data: list[list[float]], vmax=5.0) -> plt.Figure:
  function plot_ligand_COM_drift (line 336) | def plot_ligand_COM_drift(time: list[float], data: list[list[float]]):
  function plot_ligand_RMSD (line 350) | def plot_ligand_RMSD(time: list[float], data: list[list[float]]):

FILE: src/openfe/data/_downloader.py
  function retrieve_registry_data (line 6) | def retrieve_registry_data(zenodo_registry: list[dict], path: str) -> None:

FILE: src/openfe/due.py
  class InactiveDueCreditCollector (line 30) | class InactiveDueCreditCollector(object):
    method _donothing (line 33) | def _donothing(self, *args, **kwargs):
    method dcite (line 37) | def dcite(self, *args, **kwargs):
    method __repr__ (line 48) | def __repr__(self):
  function _donothing_func (line 52) | def _donothing_func(*args, **kwargs):

FILE: src/openfe/protocols/openmm_afe/abfe_units.py
  class ComplexComponentsMixin (line 47) | class ComplexComponentsMixin:
    method _get_components (line 48) | def _get_components(self):
  class ComplexSettingsMixin (line 83) | class ComplexSettingsMixin:
    method _get_settings (line 84) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
  class ABFEComplexSetupUnit (line 126) | class ABFEComplexSetupUnit(ComplexComponentsMixin, ComplexSettingsMixin,...
    method _get_mda_universe (line 135) | def _get_mda_universe(
    method _get_idxs_from_residxs (line 182) | def _get_idxs_from_residxs(
    method _get_boresch_restraint (line 215) | def _get_boresch_restraint(
    method _add_restraints (line 270) | def _add_restraints(
  class ABFEComplexSimUnit (line 403) | class ABFEComplexSimUnit(
  class ABFEComplexAnalysisUnit (line 415) | class ABFEComplexAnalysisUnit(ComplexSettingsMixin, BaseAbsoluteMultiSta...
  class SolventComponentsMixin (line 424) | class SolventComponentsMixin:
    method _get_components (line 425) | def _get_components(self):
  class SolventSettingsMixin (line 453) | class SolventSettingsMixin:
    method _get_settings (line 454) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
  class ABFESolventSetupUnit (line 494) | class ABFESolventSetupUnit(SolventComponentsMixin, SolventSettingsMixin,...
  class ABFESolventSimUnit (line 503) | class ABFESolventSimUnit(
  class ABFESolventAnalysisUnit (line 515) | class ABFESolventAnalysisUnit(SolventSettingsMixin, BaseAbsoluteMultiSta...

FILE: src/openfe/protocols/openmm_afe/afe_protocol_results.py
  class AbsoluteProtocolResultMixin (line 33) | class AbsoluteProtocolResultMixin:
    method __init__ (line 37) | def __init__(self, **data):
    method get_forward_and_reverse_energy_analysis (line 48) | def get_forward_and_reverse_energy_analysis(
    method get_overlap_matrices (line 104) | def get_overlap_matrices(self) -> dict[str, list[dict[str, npt.NDArray...
    method get_replica_transition_statistics (line 135) | def get_replica_transition_statistics(self) -> dict[str, list[dict[str...
    method get_replica_states (line 173) | def get_replica_states(self) -> dict[str, list[npt.NDArray]]:
    method equilibration_iterations (line 224) | def equilibration_iterations(self) -> dict[str, list[float]]:
    method production_iterations (line 247) | def production_iterations(self) -> dict[str, list[float]]:
    method selection_indices (line 272) | def selection_indices(self) -> dict[str, list[Optional[npt.NDArray]]]:
  class AbsoluteSolvationProtocolResult (line 297) | class AbsoluteSolvationProtocolResult(gufe.ProtocolResult, AbsoluteProto...
    method get_individual_estimates (line 305) | def get_individual_estimates(self) -> dict[str, list[tuple[Quantity, Q...
    method get_estimate (line 328) | def get_estimate(self):
    method get_uncertainty (line 352) | def get_uncertainty(self):
  class AbsoluteBindingProtocolResult (line 379) | class AbsoluteBindingProtocolResult(gufe.ProtocolResult, AbsoluteProtoco...
    method get_individual_estimates (line 387) | def get_individual_estimates(
    method _add_complex_standard_state_corr (line 434) | def _add_complex_standard_state_corr(
    method get_estimate (line 472) | def get_estimate(self) -> Quantity:
    method get_uncertainty (line 501) | def get_uncertainty(self) -> Quantity:
    method restraint_geometries (line 533) | def restraint_geometries(self) -> list[BoreschRestraintGeometry]:

FILE: src/openfe/protocols/openmm_afe/ahfe_units.py
  class VacuumComponentsMixin (line 27) | class VacuumComponentsMixin:
    method _get_components (line 28) | def _get_components(self):
  class VacuumSettingsMixin (line 61) | class VacuumSettingsMixin:
    method _get_settings (line 62) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
  class AHFEVacuumSetupUnit (line 102) | class AHFEVacuumSetupUnit(VacuumComponentsMixin, VacuumSettingsMixin, Ba...
  class AHFEVacuumSimUnit (line 111) | class AHFEVacuumSimUnit(
  class AHFEVacuumAnalysisUnit (line 123) | class AHFEVacuumAnalysisUnit(VacuumSettingsMixin, BaseAbsoluteMultiState...
  class SolventComponentsMixin (line 132) | class SolventComponentsMixin:
    method _get_components (line 133) | def _get_components(self):
  class SolventSettingsMixin (line 162) | class SolventSettingsMixin:
    method _get_settings (line 163) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
  class AHFESolventSetupUnit (line 203) | class AHFESolventSetupUnit(SolventComponentsMixin, SolventSettingsMixin,...
  class AHFESolventSimUnit (line 212) | class AHFESolventSimUnit(
  class AHFESolventAnalysisUnit (line 224) | class AHFESolventAnalysisUnit(SolventSettingsMixin, BaseAbsoluteMultiSta...

FILE: src/openfe/protocols/openmm_afe/base_afe_units.py
  class AbsoluteUnitMixin (line 95) | class AbsoluteUnitMixin:
    method _prepare (line 96) | def _prepare(
    method _get_settings (line 127) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
    method _verify_execution_environment (line 154) | def _verify_execution_environment(
  class BaseAbsoluteSetupUnit (line 174) | class BaseAbsoluteSetupUnit(gufe.ProtocolUnit, AbsoluteUnitMixin):
    method _get_components (line 180) | def _get_components(
    method _get_alchemical_indices (line 198) | def _get_alchemical_indices(
    method _pre_equilibrate (line 233) | def _pre_equilibrate(
    method _assign_partial_charges (line 352) | def _assign_partial_charges(
    method _get_system_generator (line 379) | def _get_system_generator(
    method _get_modeller (line 424) | def _get_modeller(
    method _get_omm_objects (line 468) | def _get_omm_objects(
    method _add_restraints (line 537) | def _add_restraints(
    method _get_alchemical_system (line 555) | def _get_alchemical_system(
    method _subsample_topology (line 622) | def _subsample_topology(
    method run (line 659) | def run(
    method _execute (line 795) | def _execute(
  class BaseAbsoluteMultiStateSimulationUnit (line 815) | class BaseAbsoluteMultiStateSimulationUnit(gufe.ProtocolUnit, AbsoluteUn...
    method _check_restart (line 817) | def _check_restart(output_settings: SettingsBaseModel, shared_path: pa...
    method _get_components (line 861) | def _get_components(
    method _get_lambda_schedule (line 878) | def _get_lambda_schedule(
    method _get_states (line 913) | def _get_states(
    method _get_integrator (line 994) | def _get_integrator(
    method _get_reporter (line 1051) | def _get_reporter(
    method _get_sampler (line 1123) | def _get_sampler(
    method _run_simulation (line 1275) | def _run_simulation(
    method run (line 1351) | def run(
    method _execute (line 1515) | def _execute(
  class BaseAbsoluteMultiStateAnalysisUnit (line 1556) | class BaseAbsoluteMultiStateAnalysisUnit(gufe.ProtocolUnit, AbsoluteUnit...
    method _analyze_multistate_energies (line 1558) | def _analyze_multistate_energies(
    method run (line 1604) | def run(
    method _execute (line 1663) | def _execute(

FILE: src/openfe/protocols/openmm_afe/equil_afe_settings.py
  class AlchemicalSettings (line 44) | class AlchemicalSettings(SettingsBaseModel):
  class LambdaSettings (line 90) | class LambdaSettings(SettingsBaseModel):
    method must_be_between_0_and_1 (line 147) | def must_be_between_0_and_1(cls, v):
    method must_be_monotonic (line 157) | def must_be_monotonic(cls, v):
  class ABFEPreEquilOutputSettings (line 171) | class ABFEPreEquilOutputSettings(MDOutputSettings):
    method must_be_all (line 207) | def must_be_all(cls, v):
  class AbsoluteSolvationSettings (line 218) | class AbsoluteSolvationSettings(SettingsBaseModel):
    method must_be_positive (line 235) | def must_be_positive(cls, v):
  class AbsoluteBindingSettings (line 329) | class AbsoluteBindingSettings(SettingsBaseModel):
    method must_be_positive (line 346) | def must_be_positive(cls, v):

FILE: src/openfe/protocols/openmm_afe/equil_binding_afe_method.py
  class AbsoluteBindingProtocol (line 99) | class AbsoluteBindingProtocol(gufe.Protocol):
    method _default_settings (line 117) | def _default_settings(cls):
    method _adaptive_settings (line 214) | def _adaptive_settings(
    method _validate_endstates (line 254) | def _validate_endstates(
    method _validate_lambda_schedule (line 320) | def _validate_lambda_schedule(
    method _validate (line 381) | def _validate(
    method _create (line 472) | def _create(
    method _gather (line 543) | def _gather(

FILE: src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py
  class AbsoluteSolvationProtocol (line 106) | class AbsoluteSolvationProtocol(gufe.Protocol):
    method _default_settings (line 124) | def _default_settings(cls):
    method _validate_endstates (line 206) | def _validate_endstates(
    method _validate_lambda_schedule (line 290) | def _validate_lambda_schedule(
    method _validate (line 363) | def _validate(
    method _create (line 435) | def _create(
    method _gather (line 507) | def _gather(

FILE: src/openfe/protocols/openmm_md/plain_md_methods.py
  class PlainMDProtocolResult (line 69) | class PlainMDProtocolResult(gufe.ProtocolResult):
    method __init__ (line 77) | def __init__(self, **data):
    method get_estimate (line 83) | def get_estimate(self):
    method get_uncertainty (line 93) | def get_uncertainty(self):
    method get_traj_filename (line 98) | def get_traj_filename(self) -> list[pathlib.Path]:
    method get_pdb_filename (line 111) | def get_pdb_filename(self) -> list[pathlib.Path]:
  class PlainMDProtocol (line 125) | class PlainMDProtocol(gufe.Protocol):
    method _default_settings (line 142) | def _default_settings(cls):
    method _validate (line 173) | def _validate(
    method _create (line 225) | def _create(
    method _gather (line 276) | def _gather(self, protocol_dag_results: Iterable[gufe.ProtocolDAGResul...
  class PlainMDUnitMixin (line 299) | class PlainMDUnitMixin:
    method _prepare (line 300) | def _prepare(
  class PlainMDSetupUnit (line 331) | class PlainMDSetupUnit(PlainMDUnitMixin, gufe.ProtocolUnit):
    method _assign_partial_charges (line 337) | def _assign_partial_charges(
    method run (line 362) | def run(
    method _execute (line 528) | def _execute(
  class PlainMDSimulationUnit (line 548) | class PlainMDSimulationUnit(PlainMDUnitMixin, gufe.ProtocolUnit):
    method _check_restart (line 554) | def _check_restart(output_settings: MDOutputSettings, shared_path: pat...
    method _verify_execution_environment (line 576) | def _verify_execution_environment(
    method _save_pdb_subset (line 596) | def _save_pdb_subset(
    method _run_dynamics (line 619) | def _run_dynamics(
    method _get_remaining_steps (line 658) | def _get_remaining_steps(
    method _run_MD (line 696) | def _run_MD(
    method run (line 911) | def run(
    method _execute (line 1057) | def _execute(

FILE: src/openfe/protocols/openmm_md/plain_md_settings.py
  class PlainMDProtocolSettings (line 25) | class PlainMDProtocolSettings(Settings):
    method must_be_positive (line 34) | def must_be_positive(cls, v):

FILE: src/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py
  class LambdaProtocol (line 15) | class LambdaProtocol(object):
    method __init__ (line 46) | def __init__(self, functions='default', windows=10, lambda_schedule=No...
    method _validate_schedule (line 155) | def _validate_schedule(schedule, windows):
    method _validate_functions (line 194) | def _validate_functions(self, n=10):
    method _check_for_naked_charges (line 232) | def _check_for_naked_charges(self):
    method get_functions (line 262) | def get_functions(self):
    method plot_functions (line 265) | def plot_functions(self, lambda_schedule=None):
  class RelativeAlchemicalState (line 292) | class RelativeAlchemicalState(AlchemicalState):
    class _LambdaParameter (line 315) | class _LambdaParameter(AlchemicalState._LambdaParameter):
    method set_alchemical_parameters (line 327) | def set_alchemical_parameters(self, global_lambda,

FILE: src/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py
  class HybridCompatibilityMixin (line 29) | class HybridCompatibilityMixin:
    method __init__ (line 35) | def __init__(
    method setup (line 46) | def setup(self, reporter, lambda_protocol,
  class HybridRepexSampler (line 169) | class HybridRepexSampler(HybridCompatibilityMixin,
    method __init__ (line 176) | def __init__(
  class HybridSAMSSampler (line 191) | class HybridSAMSSampler(HybridCompatibilityMixin, sams.SAMSSampler):
    method __init__ (line 197) | def __init__(
  class HybridMultiStateSampler (line 212) | class HybridMultiStateSampler(HybridCompatibilityMixin,
    method __init__ (line 218) | def __init__(
  function create_endstates (line 233) | def create_endstates(first_thermostate, last_thermostate):
  function minimize (line 306) | def minimize(thermodynamic_state: states.ThermodynamicState,

FILE: src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py
  class HybridTopologyFactory (line 24) | class HybridTopologyFactory:
    method __init__ (line 85) | def __init__(self,
    method _verify_cmap_compatibility (line 236) | def _verify_cmap_compatibility(
    method _handle_cmap_torsion_force (line 287) | def _handle_cmap_torsion_force(self):
    method _check_bounds (line 385) | def _check_bounds(value, varname, minmax=(0, 1)):
    method _invert_dict (line 407) | def _invert_dict(dictionary):
    method _set_mappings (line 418) | def _set_mappings(self, old_to_new_map, core_old_to_new_map):
    method _check_and_store_system_forces (line 465) | def _check_and_store_system_forces(self):
    method _add_particles (line 501) | def _add_particles(self):
    method _handle_box (line 548) | def _handle_box(self):
    method _set_atom_classes (line 570) | def _set_atom_classes(self):
    method _generate_dict_from_exceptions (line 613) | def _generate_dict_from_exceptions(force):
    method _validate_disjoint_sets (line 637) | def _validate_disjoint_sets(self):
    method _handle_constraints (line 673) | def _handle_constraints(self):
    method _copy_threeparticleavg (line 715) | def _copy_threeparticleavg(atm_map, env_atoms, vs):
    method _handle_virtual_sites (line 747) | def _handle_virtual_sites(self):
    method _add_bond_force_terms (line 803) | def _add_bond_force_terms(self):
    method _add_angle_force_terms (line 838) | def _add_angle_force_terms(self):
    method _add_torsion_force_terms (line 878) | def _add_torsion_force_terms(self):
    method _nonbonded_custom (line 922) | def _nonbonded_custom(v2):
    method _nonbonded_custom_sterics_common (line 958) | def _nonbonded_custom_sterics_common():
    method _nonbonded_custom_mixing_rules (line 984) | def _nonbonded_custom_mixing_rules():
    method _translate_nonbonded_method_to_custom (line 1011) | def _translate_nonbonded_method_to_custom(standard_nonbonded_method):
    method _add_nonbonded_force_terms (line 1041) | def _add_nonbonded_force_terms(self):
    method _find_bond_parameters (line 1162) | def _find_bond_parameters(bond_force, index1, index2):
    method _handle_harmonic_bonds (line 1190) | def _handle_harmonic_bonds(self):
    method _find_angle_parameters (line 1325) | def _find_angle_parameters(angle_force, indices):
    method _handle_harmonic_angles (line 1356) | def _handle_harmonic_angles(self):
    method _find_torsion_parameters (line 1527) | def _find_torsion_parameters(torsion_force, indices):
    method _handle_periodic_torsion_force (line 1561) | def _handle_periodic_torsion_force(self):
    method _handle_nonbonded (line 1680) | def _handle_nonbonded(self):
    method _handle_interaction_groups (line 1842) | def _handle_interaction_groups(self):
    method _handle_hybrid_exceptions (line 1892) | def _handle_hybrid_exceptions(self):
    method _find_exception (line 2009) | def _find_exception(force, index1, index2):
    method _handle_original_exceptions (line 2037) | def _handle_original_exceptions(self):
    method _handle_old_new_exceptions (line 2221) | def _handle_old_new_exceptions(self):
    method _compute_hybrid_positions (line 2363) | def _compute_hybrid_positions(self):
    method _create_mdtraj_topology (line 2402) | def _create_mdtraj_topology(self):
    method _create_hybrid_topology (line 2497) | def _create_hybrid_topology(self):
    method old_positions (line 2578) | def old_positions(self, hybrid_positions):
    method new_positions (line 2605) | def new_positions(self, hybrid_positions):
    method hybrid_system (line 2633) | def hybrid_system(self):
    method new_to_hybrid_atom_map (line 2645) | def new_to_hybrid_atom_map(self):
    method old_to_hybrid_atom_map (line 2657) | def old_to_hybrid_atom_map(self):
    method hybrid_positions (line 2669) | def hybrid_positions(self):
    method hybrid_topology (line 2684) | def hybrid_topology(self):
    method omm_hybrid_topology (line 2698) | def omm_hybrid_topology(self):
    method has_virtual_sites (line 2716) | def has_virtual_sites(self):

FILE: src/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py
  function _get_ion_and_water_parameters (line 29) | def _get_ion_and_water_parameters(
  function _fix_alchemical_water_atom_mapping (line 96) | def _fix_alchemical_water_atom_mapping(
  function handle_alchemical_waters (line 125) | def handle_alchemical_waters(
  function get_alchemical_waters (line 225) | def get_alchemical_waters(
  function combined_topology (line 297) | def combined_topology(topology1: app.Topology,
  function _get_indices (line 385) | def _get_indices(topology, resids):
  function _remove_constraints (line 406) | def _remove_constraints(old_to_new_atom_map, old_system, old_topology,
  function get_system_mappings (line 525) | def get_system_mappings(old_to_new_atom_map,
  function set_and_check_new_positions (line 668) | def set_and_check_new_positions(mapping, old_topology, new_topology,

FILE: src/openfe/protocols/openmm_rfe/equil_rfe_settings.py
  class LambdaSettings (line 34) | class LambdaSettings(SettingsBaseModel):
  class AlchemicalSettings (line 51) | class AlchemicalSettings(SettingsBaseModel):
  class RelativeHybridTopologyProtocolSettings (line 105) | class RelativeHybridTopologyProtocolSettings(Settings):
    method must_be_positive (line 114) | def must_be_positive(cls, v):

FILE: src/openfe/protocols/openmm_rfe/hybridtop_protocol_results.py
  class RelativeHybridTopologyProtocolResult (line 22) | class RelativeHybridTopologyProtocolResult(gufe.ProtocolResult):
    method __init__ (line 27) | def __init__(self, **data):
    method compute_mean_estimate (line 35) | def compute_mean_estimate(dGs: list[Quantity]) -> Quantity:
    method get_estimate (line 43) | def get_estimate(self) -> Quantity:
    method compute_uncertainty (line 57) | def compute_uncertainty(dGs: list[Quantity]) -> Quantity:
    method get_uncertainty (line 65) | def get_uncertainty(self) -> Quantity:
    method get_individual_estimates (line 73) | def get_individual_estimates(self) -> list[tuple[Quantity, Quantity]]:
    method get_forward_and_reverse_energy_analysis (line 90) | def get_forward_and_reverse_energy_analysis(
    method get_overlap_matrices (line 137) | def get_overlap_matrices(self) -> list[dict[str, npt.NDArray]]:
    method get_replica_transition_statistics (line 157) | def get_replica_transition_statistics(self) -> list[dict[str, npt.NDAr...
    method get_replica_states (line 184) | def get_replica_states(self) -> list[npt.NDArray]:
    method equilibration_iterations (line 215) | def equilibration_iterations(self) -> list[float]:
    method production_iterations (line 230) | def production_iterations(self) -> list[float]:

FILE: src/openfe/protocols/openmm_rfe/hybridtop_protocols.py
  class RelativeHybridTopologyProtocol (line 85) | class RelativeHybridTopologyProtocol(gufe.Protocol):
    method _default_settings (line 105) | def _default_settings(cls):
    method _adaptive_settings (line 138) | def _adaptive_settings(
    method _validate_endstates (line 211) | def _validate_endstates(
    method _validate_mapping (line 255) | def _validate_mapping(
    method _validate_smcs (line 318) | def _validate_smcs(
    method _validate_charge_difference (line 371) | def _validate_charge_difference(
    method _validate_simulation_settings (line 448) | def _validate_simulation_settings(
    method _validate (line 514) | def _validate(
    method _create (line 600) | def _create(
    method _gather (line 660) | def _gather(self, protocol_dag_results: Iterable[gufe.ProtocolDAGResul...

FILE: src/openfe/protocols/openmm_rfe/hybridtop_units.py
  class HybridTopologyUnitMixin (line 84) | class HybridTopologyUnitMixin:
    method _prepare (line 85) | def _prepare(
    method _get_settings (line 116) | def _get_settings(
    method _verify_execution_environment (line 147) | def _verify_execution_environment(
  class HybridTopologySetupUnit (line 167) | class HybridTopologySetupUnit(gufe.ProtocolUnit, HybridTopologyUnitMixin):
    method _get_components (line 173) | def _get_components(
    method _assign_partial_charges (line 208) | def _assign_partial_charges(
    method _get_system_generator (line 235) | def _get_system_generator(
    method _create_stateA_system (line 280) | def _create_stateA_system(
    method _create_stateB_system (line 337) | def _create_stateB_system(
    method _handle_net_charge (line 385) | def _handle_net_charge(
    method _get_omm_objects (line 431) | def _get_omm_objects(
    method _get_alchemical_system (line 581) | def _get_alchemical_system(
    method _subsample_topology (line 644) | def _subsample_topology(
    method run (line 704) | def run(
    method _execute (line 825) | def _execute(
  class HybridTopologyMultiStateSimulationUnit (line 843) | class HybridTopologyMultiStateSimulationUnit(gufe.ProtocolUnit, HybridTo...
    method _check_restart (line 850) | def _check_restart(output_settings: SettingsBaseModel, shared_path: pa...
    method _get_integrator (line 893) | def _get_integrator(
    method _get_reporter (line 948) | def _get_reporter(
    method _get_sampler (line 1014) | def _get_sampler(
    method _run_simulation (line 1181) | def _run_simulation(
    method run (line 1265) | def run(
    method _execute (line 1417) | def _execute(
  class HybridTopologyMultiStateAnalysisUnit (line 1449) | class HybridTopologyMultiStateAnalysisUnit(gufe.ProtocolUnit, HybridTopo...
    method _analyze_multistate_energies (line 1455) | def _analyze_multistate_energies(
    method _structural_analysis (line 1502) | def _structural_analysis(
    method run (line 1569) | def run(
    method _execute (line 1649) | def _execute(

FILE: src/openfe/protocols/openmm_septop/base_units.py
  function _pre_equilibrate (line 78) | def _pre_equilibrate(
  class SepTopUnitMixin (line 233) | class SepTopUnitMixin:
    method _prepare (line 238) | def _prepare(
    method _get_settings (line 269) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
    method _verify_execution_environment (line 296) | def _verify_execution_environment(
  class BaseSepTopSetupUnit (line 316) | class BaseSepTopSetupUnit(gufe.ProtocolUnit, SepTopUnitMixin):
    method _get_alchemical_system (line 321) | def _get_alchemical_system(
    method _get_components (line 400) | def _get_components(
    method _get_system_generator (line 417) | def _get_system_generator(
    method _assign_partial_charges (line 455) | def _assign_partial_charges(
    method _get_modeller (line 480) | def _get_modeller(
    method _get_omm_objects (line 541) | def _get_omm_objects(
    method _get_atom_indices (line 584) | def _get_atom_indices(
    method get_smc_comps (line 614) | def get_smc_comps(
    method get_system (line 637) | def get_system(
    method _subsample_topology (line 685) | def _subsample_topology(
    method _execute (line 722) | def _execute(
  class BaseSepTopRunUnit (line 742) | class BaseSepTopRunUnit(gufe.ProtocolUnit, SepTopUnitMixin):
    method _check_restart (line 748) | def _check_restart(output_settings: SettingsBaseModel, shared_path: pa...
    method _get_components (line 792) | def _get_components(
    method _get_lambda_schedule (line 810) | def _get_lambda_schedule(
    method _get_states (line 831) | def _get_states(
    method _get_integrator (line 891) | def _get_integrator(
    method _get_reporter (line 942) | def _get_reporter(
    method _get_sampler (line 1014) | def _get_sampler(
    method _run_simulation (line 1165) | def _run_simulation(
    method run (line 1246) | def run(
    method _execute (line 1425) | def _execute(
  class BaseSepTopAnalysisUnit (line 1458) | class BaseSepTopAnalysisUnit(gufe.ProtocolUnit, SepTopUnitMixin):
    method _analyze_multistate_energies (line 1460) | def _analyze_multistate_energies(
    method run (line 1506) | def run(
    method _execute (line 1565) | def _execute(

FILE: src/openfe/protocols/openmm_septop/equil_septop_method.py
  function _check_alchemical_charge_difference (line 110) | def _check_alchemical_charge_difference(
  class SepTopProtocol (line 142) | class SepTopProtocol(gufe.Protocol):
    method _default_settings (line 162) | def _default_settings(cls):
    method _adaptive_settings (line 273) | def _adaptive_settings(
    method _validate_endstates (line 313) | def _validate_endstates(
    method _validate_lambda_schedule (line 385) | def _validate_lambda_schedule(
    method _validate (line 461) | def _validate(
    method _create (line 514) | def _create(
    method _gather (line 594) | def _gather(

FILE: src/openfe/protocols/openmm_septop/equil_septop_settings.py
  class LambdaSettings (line 40) | class LambdaSettings(SettingsBaseModel):
    method must_be_between_0_and_1 (line 139) | def must_be_between_0_and_1(cls, v):
    method must_be_monotonically_increasing_A (line 153) | def must_be_monotonically_increasing_A(cls, v):
    method must_be_monotonically_decreasing_B (line 172) | def must_be_monotonically_decreasing_B(cls, v):
  class SepTopEquilOutputSettings (line 187) | class SepTopEquilOutputSettings(MDOutputSettings):
    method must_be_all (line 239) | def must_be_all(cls, v):
  class SepTopSettings (line 246) | class SepTopSettings(SettingsBaseModel):
    method must_be_positive (line 263) | def must_be_positive(cls, v):

FILE: src/openfe/protocols/openmm_septop/septop_protocol_results.py
  class SepTopProtocolResult (line 30) | class SepTopProtocolResult(gufe.ProtocolResult):
    method __init__ (line 33) | def __init__(self, **data):
    method get_individual_estimates (line 44) | def get_individual_estimates(
    method _add_complex_standard_state_corr (line 101) | def _add_complex_standard_state_corr(
    method _add_solvent_standard_state_corr (line 145) | def _add_solvent_standard_state_corr(
    method get_estimate (line 183) | def get_estimate(self) -> Quantity:
    method get_uncertainty (line 219) | def get_uncertainty(self) -> Quantity:
    method get_forward_and_reverse_energy_analysis (line 256) | def get_forward_and_reverse_energy_analysis(
    method get_overlap_matrices (line 310) | def get_overlap_matrices(self) -> dict[str, list[dict[str, npt.NDArray...
    method get_replica_transition_statistics (line 339) | def get_replica_transition_statistics(
    method get_replica_states (line 377) | def get_replica_states(self) -> dict[str, list[npt.NDArray]]:
    method equilibration_iterations (line 423) | def equilibration_iterations(self) -> dict[str, list[float]]:
    method production_iterations (line 444) | def production_iterations(self) -> dict[str, list[float]]:
    method restraint_geometries (line 467) | def restraint_geometries(
    method selection_indices (line 495) | def selection_indices(self) -> dict[str, list[Optional[npt.NDArray]]]:

FILE: src/openfe/protocols/openmm_septop/septop_units.py
  class SepTopComplexMixin (line 66) | class SepTopComplexMixin:
    method _get_components (line 71) | def _get_components(self):
    method _get_settings (line 102) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
  class SepTopSolventMixin (line 150) | class SepTopSolventMixin:
    method _get_components (line 155) | def _get_components(self):
    method _get_settings (line 188) | def _get_settings(self) -> dict[str, SettingsBaseModel]:
  class SepTopComplexSetupUnit (line 236) | class SepTopComplexSetupUnit(SepTopComplexMixin, BaseSepTopSetupUnit):
    method get_system_AB (line 243) | def get_system_AB(
    method _get_selection_atom_indices (line 301) | def _get_selection_atom_indices(
    method _update_positions (line 335) | def _update_positions(
    method _get_mda_universe (line 375) | def _get_mda_universe(
    method _get_boresch_restraint (line 423) | def _get_boresch_restraint(
    method _add_restraints (line 477) | def _add_restraints(
    method run (line 638) | def run(
  class SepTopSolventSetupUnit (line 876) | class SepTopSolventSetupUnit(SepTopSolventMixin, BaseSepTopSetupUnit):
    method _update_positions (line 884) | def _update_positions(
    method _add_restraints (line 930) | def _add_restraints(
    method run (line 1014) | def run(
  class SepTopSolventRunUnit (line 1152) | class SepTopSolventRunUnit(SepTopSolventMixin, BaseSepTopRunUnit):
    method _get_lambda_schedule (line 1159) | def _get_lambda_schedule(
  class SepTopComplexRunUnit (line 1187) | class SepTopComplexRunUnit(SepTopComplexMixin, BaseSepTopRunUnit):
    method _get_lambda_schedule (line 1194) | def _get_lambda_schedule(
  class SepTopSolventAnalysisUnit (line 1223) | class SepTopSolventAnalysisUnit(SepTopSolventMixin, BaseSepTopAnalysisUn...
  class SepTopComplexAnalysisUnit (line 1231) | class SepTopComplexAnalysisUnit(SepTopComplexMixin, BaseSepTopAnalysisUn...

FILE: src/openfe/protocols/openmm_septop/utils.py
  class SepTopParameterState (line 5) | class SepTopParameterState(GlobalParameterState):
    class _LambdaParameter (line 53) | class _LambdaParameter(states.GlobalParameterState.GlobalParameter):
      method __init__ (line 57) | def __init__(self, parameter_name):
      method lambda_validator (line 61) | def lambda_validator(self, instance, parameter_value):

FILE: src/openfe/protocols/openmm_utils/charge_generation.py
  function assign_offmol_espaloma_charges (line 74) | def assign_offmol_espaloma_charges(offmol: OFFMol, toolkit_registry: Too...
  function assign_offmol_nagl_charges (line 112) | def assign_offmol_nagl_charges(
  function assign_offmol_am1bcc_charges (line 164) | def assign_offmol_am1bcc_charges(
  function _generate_offmol_conformers (line 207) | def _generate_offmol_conformers(
  function assign_offmol_partial_charges (line 286) | def assign_offmol_partial_charges(
  function bulk_assign_partial_charges (line 441) | def bulk_assign_partial_charges(

FILE: src/openfe/protocols/openmm_utils/mdtraj_utils.py
  function mdtraj_from_openmm (line 10) | def mdtraj_from_openmm(

FILE: src/openfe/protocols/openmm_utils/multistate_analysis.py
  class MultistateEquilFEAnalysis (line 61) | class MultistateEquilFEAnalysis:
    method __init__ (line 87) | def __init__(
    method plot (line 105) | def plot(self, filepath: Path, filename_prefix: str):
    method _analyze (line 156) | def _analyze(self, forward_reverse_samples: int):
    method _get_free_energy (line 198) | def _get_free_energy(
    method get_equil_free_energy (line 266) | def get_equil_free_energy(self) -> tuple[Quantity, Quantity]:
    method get_forward_and_reverse_analysis (line 285) | def get_forward_and_reverse_analysis(
    method get_overlap_matrix (line 378) | def get_overlap_matrix(self) -> dict[str, npt.NDArray]:
    method get_exchanges (line 394) | def get_exchanges(self) -> dict[str, npt.NDArray]:
    method replica_states (line 417) | def replica_states(self):
    method equilibration_iterations (line 424) | def equilibration_iterations(self):
    method production_iterations (line 431) | def production_iterations(self):
    method free_energy (line 438) | def free_energy(self):
    method free_energy_error (line 445) | def free_energy_error(self):
    method forward_and_reverse_free_energies (line 452) | def forward_and_reverse_free_energies(self):
    method free_energy_overlaps (line 460) | def free_energy_overlaps(self):
    method replica_exchange_statistics (line 468) | def replica_exchange_statistics(self):
    method unit_results_dict (line 483) | def unit_results_dict(self):
    method close (line 498) | def close(self):

FILE: src/openfe/protocols/openmm_utils/omm_compute.py
  function get_openmm_platform (line 12) | def get_openmm_platform(

FILE: src/openfe/protocols/openmm_utils/omm_settings.py
  class BaseSolvationSettings (line 47) | class BaseSolvationSettings(SettingsBaseModel):
  class OpenMMSolvationSettings (line 55) | class OpenMMSolvationSettings(BaseSolvationSettings):
    method supported_vectors (line 184) | def supported_vectors(cls, v):
    method is_positive_distance (line 192) | def is_positive_distance(cls, v):
    method positive_solvent_number (line 206) | def positive_solvent_number(cls, v):
    method box_size_properties (line 217) | def box_size_properties(cls, v):
  class BasePartialChargeSettings (line 228) | class BasePartialChargeSettings(SettingsBaseModel):
  class OpenFFPartialChargeSettings (line 236) | class OpenFFPartialChargeSettings(BasePartialChargeSettings):
  class OpenMMEngineSettings (line 319) | class OpenMMEngineSettings(SettingsBaseModel):
    method supported_sampler (line 350) | def supported_sampler(cls, v):
  class IntegratorSettings (line 358) | class IntegratorSettings(SettingsBaseModel):
    method must_be_positive_or_zero (line 414) | def must_be_positive_or_zero(cls, v):
    method must_be_positive (line 424) | def must_be_positive(cls, v):
    method is_time (line 431) | def is_time(cls, v):
    method must_be_inverse_time (line 438) | def must_be_inverse_time(cls, v):
    method validate_surface_tension (line 444) | def validate_surface_tension(self):
  class OutputSettings (line 457) | class OutputSettings(SettingsBaseModel):
    method must_be_positive (line 487) | def must_be_positive(cls, v):
  class MultiStateOutputSettings (line 494) | class MultiStateOutputSettings(OutputSettings):
    method must_be_positive (line 533) | def must_be_positive(cls, v):
  class SimulationSettings (line 543) | class SimulationSettings(SettingsBaseModel):
    method is_time (line 564) | def is_time(cls, v):
    method must_be_positive (line 571) | def must_be_positive(cls, v):
  class MultiStateSimulationSettings (line 578) | class MultiStateSimulationSettings(SimulationSettings):
    method supported_flatness (line 661) | def supported_flatness(cls, v):
    method supported_sampler (line 669) | def supported_sampler(cls, v):
    method must_be_positive (line 677) | def must_be_positive(cls, v):
    method must_be_zero_or_positive (line 689) | def must_be_zero_or_positive(cls, v):
  class MDSimulationSettings (line 699) | class MDSimulationSettings(SimulationSettings):
  class MDOutputSettings (line 715) | class MDOutputSettings(OutputSettings):

FILE: src/openfe/protocols/openmm_utils/serialization.py
  function serialize (line 13) | def serialize(item, filename: pathlib.Path):
  function deserialize (line 43) | def deserialize(filename: pathlib.Path):
  function make_vec3_box (line 75) | def make_vec3_box(dimensions: NanometerArrayQuantity) -> Vec3:

FILE: src/openfe/protocols/openmm_utils/settings_validation.py
  function validate_openmm_solvation_settings (line 20) | def validate_openmm_solvation_settings(settings: OpenMMSolvationSettings...
  function validate_timestep (line 55) | def validate_timestep(hmass: float, timestep: Quantity):
  function get_simsteps (line 80) | def get_simsteps(sim_length: Quantity, timestep: Quantity, mc_steps: int...
  function divmod_time (line 117) | def divmod_time(
  function divmod_time_and_check (line 146) | def divmod_time_and_check(
  function convert_checkpoint_interval_to_iterations (line 184) | def convert_checkpoint_interval_to_iterations(
  function convert_steps_per_iteration (line 220) | def convert_steps_per_iteration(
  function convert_real_time_analysis_iterations (line 244) | def convert_real_time_analysis_iterations(
  function convert_target_error_from_kcal_per_mole_to_kT (line 287) | def convert_target_error_from_kcal_per_mole_to_kT(

FILE: src/openfe/protocols/openmm_utils/system_creation.py
  function get_system_generator (line 35) | def get_system_generator(
  function get_omm_modeller (line 154) | def get_omm_modeller(

FILE: src/openfe/protocols/openmm_utils/system_validation.py
  function get_alchemical_components (line 30) | def get_alchemical_components(
  function validate_solvent (line 88) | def validate_solvent(state: ChemicalSystem, nonbonded_method: str):
  function validate_protein (line 143) | def validate_protein(state: ChemicalSystem):
  function validate_barostat (line 165) | def validate_barostat(state: ChemicalSystem, barostat: str):
  function get_components (line 215) | def get_components(state: ChemicalSystem) -> ParseCompRet:
  function assert_multistate_system_equality (line 250) | def assert_multistate_system_equality(
  function validate_chemical_system (line 353) | def validate_chemical_system(system: ChemicalSystem):

FILE: src/openfe/protocols/restraint_utils/geometry/base.py
  class BaseRestraintGeometry (line 16) | class BaseRestraintGeometry(BaseModel, abc.ABC):
  class HostGuestRestraintGeometry (line 24) | class HostGuestRestraintGeometry(BaseRestraintGeometry):
    method positive_idxs (line 46) | def positive_idxs(cls, v):

FILE: src/openfe/protocols/restraint_utils/geometry/boresch/geometry.py
  class BoreschRestraintGeometry (line 31) | class BoreschRestraintGeometry(HostGuestRestraintGeometry):
  function _get_restraint_distances (line 74) | def _get_restraint_distances(
  function find_boresch_restraint (line 136) | def find_boresch_restraint(

FILE: src/openfe/protocols/restraint_utils/geometry/boresch/guest.py
  function _sort_by_distance_from_atom (line 26) | def _sort_by_distance_from_atom(
  function _bonded_angles_from_pool (line 59) | def _bonded_angles_from_pool(
  function _get_guest_atom_pool (line 125) | def _get_guest_atom_pool(
  function find_guest_atom_candidates (line 173) | def find_guest_atom_candidates(

FILE: src/openfe/protocols/restraint_utils/geometry/boresch/host.py
  function _host_atoms_search (line 35) | def _host_atoms_search(
  function find_host_atom_candidates (line 84) | def find_host_atom_candidates(
  class EvaluateBoreschAtoms (line 200) | class EvaluateBoreschAtoms(AnalysisBase):
    method __init__ (line 215) | def __init__(
    method _prepare (line 236) | def _prepare(self):
    method _single_frame (line 246) | def _single_frame(self):
    method _conclude (line 281) | def _conclude(self):
  class EvaluateHostAtoms1 (line 335) | class EvaluateHostAtoms1(AnalysisBase):
    method __init__ (line 354) | def __init__(
    method _prepare (line 375) | def _prepare(self):
    method _single_frame (line 390) | def _single_frame(self):
    method _conclude (line 420) | def _conclude(self):
  class EvaluateHostAtoms2 (line 464) | class EvaluateHostAtoms2(EvaluateHostAtoms1):
    method _prepare (line 483) | def _prepare(self):
    method _single_frame (line 498) | def _single_frame(self):
    method _conclude (line 527) | def _conclude(self):
  function _get_lowest_variance_restraint_hostanchor (line 554) | def _get_lowest_variance_restraint_hostanchor(
  function find_host_anchor_bonded (line 622) | def find_host_anchor_bonded(
  function find_host_anchor_multi (line 697) | def find_host_anchor_multi(

FILE: src/openfe/protocols/restraint_utils/geometry/flatbottom.py
  class FlatBottomDistanceGeometry (line 24) | class FlatBottomDistanceGeometry(DistanceRestraintGeometry):
  class COMDistanceAnalysis (line 33) | class COMDistanceAnalysis(AnalysisBase):
    method __init__ (line 47) | def __init__(self, group1, group2, **kwargs):
    method _prepare (line 53) | def _prepare(self):
    method _single_frame (line 56) | def _single_frame(self):
    method _conclude (line 64) | def _conclude(self):
  function get_flatbottom_distance_restraint (line 68) | def get_flatbottom_distance_restraint(

FILE: src/openfe/protocols/restraint_utils/geometry/harmonic.py
  class DistanceRestraintGeometry (line 20) | class DistanceRestraintGeometry(HostGuestRestraintGeometry):
  function get_distance_restraint (line 26) | def get_distance_restraint(
  function get_molecule_centers_restraint (line 69) | def get_molecule_centers_restraint(

FILE: src/openfe/protocols/restraint_utils/geometry/utils.py
  function _get_mda_selection (line 35) | def _get_mda_selection(
  function get_aromatic_rings (line 76) | def get_aromatic_rings(rdmol: Chem.Mol) -> list[set[int]]:
  function get_aromatic_atom_idxs (line 110) | def get_aromatic_atom_idxs(rdmol: Chem.Mol) -> list[int]:
  function get_heavy_atom_idxs (line 129) | def get_heavy_atom_idxs(rdmol: Chem.Mol) -> list[int]:
  function get_central_atom_idx (line 146) | def get_central_atom_idx(rdmol: Chem.Mol) -> int:
  function is_collinear (line 189) | def is_collinear(
  function _wrap_angle (line 249) | def _wrap_angle(angle: Quantity) -> Quantity:
  function check_angle_not_flat (line 271) | def check_angle_not_flat(
  function check_dihedral_bounds (line 318) | def check_dihedral_bounds(
  function check_angular_variance (line 353) | def check_angular_variance(
  class CentroidDistanceSort (line 391) | class CentroidDistanceSort(AnalysisBase):
    method __init__ (line 418) | def __init__(
    method _prepare (line 437) | def _prepare(self):
    method _single_frame (line 440) | def _single_frame(self):
    method _conclude (line 447) | def _conclude(self):
  class FindHostAtoms (line 452) | class FindHostAtoms(AnalysisBase):
    method __init__ (line 476) | def __init__(
    method _prepare (line 496) | def _prepare(self):
    method _single_frame (line 499) | def _single_frame(self):
    method _conclude (line 515) | def _conclude(self):
  function get_local_rmsf (line 520) | def get_local_rmsf(atomgroup: mda.AtomGroup):  # -> ArrayQuantity:
  function _atomgroup_has_bonds (line 553) | def _atomgroup_has_bonds(atomgroup: Union[mda.AtomGroup, mda.Universe]) ...
  function stable_secondary_structure_selection (line 577) | def stable_secondary_structure_selection(
  function protein_chain_selection (line 718) | def protein_chain_selection(

FILE: src/openfe/protocols/restraint_utils/openmm/omm_forces.py
  function get_boresch_energy_function (line 15) | def get_boresch_energy_function(
  function get_periodic_boresch_energy_function (line 44) | def get_periodic_boresch_energy_function(
  function get_custom_compound_bond_force (line 74) | def get_custom_compound_bond_force(
  function add_force_in_separate_group (line 92) | def add_force_in_separate_group(

FILE: src/openfe/protocols/restraint_utils/openmm/omm_restraints.py
  class RestraintParameterState (line 54) | class RestraintParameterState(GlobalParameterState):
    method lambda_restraints (line 83) | def lambda_restraints(self, instance, new_value):
  class BaseHostGuestRestraints (line 91) | class BaseHostGuestRestraints(abc.ABC):
    method __init__ (line 107) | def __init__(
    method _verify_inputs (line 114) | def _verify_inputs(self):
    method _verify_geometry (line 122) | def _verify_geometry(self, geometry):
    method add_force (line 131) | def add_force(
    method get_standard_state_correction (line 154) | def get_standard_state_correction(
    method _get_force (line 180) | def _get_force(
  class SingleBondMixin (line 192) | class SingleBondMixin:
    method _verify_geometry (line 198) | def _verify_geometry(self, geometry: HostGuestRestraintGeometry):
  class BaseRadiallySymmetricRestraintForce (line 209) | class BaseRadiallySymmetricRestraintForce(BaseHostGuestRestraints):
    method add_force (line 220) | def add_force(
    method get_standard_state_correction (line 248) | def get_standard_state_correction(
    method _get_force (line 279) | def _get_force(self, geometry, controlling_parameter_name: str):
  class HarmonicBondRestraint (line 283) | class HarmonicBondRestraint(SingleBondMixin, BaseRadiallySymmetricRestra...
    method _get_force (line 297) | def _get_force(
  class FlatBottomBondRestraint (line 329) | class FlatBottomBondRestraint(SingleBondMixin, BaseRadiallySymmetricRest...
    method _get_force (line 346) | def _get_force(
  class CentroidHarmonicRestraint (line 380) | class CentroidHarmonicRestraint(BaseRadiallySymmetricRestraintForce):
    method _get_force (line 394) | def _get_force(
  class CentroidFlatBottomRestraint (line 426) | class CentroidFlatBottomRestraint(BaseRadiallySymmetricRestraintForce):
    method _get_force (line 440) | def _get_force(
  class BoreschRestraint (line 476) | class BoreschRestraint(BaseHostGuestRestraints):
    method add_force (line 538) | def add_force(
    method _get_force (line 569) | def _get_force(
    method get_standard_state_correction (line 629) | def get_standard_state_correction(

FILE: src/openfe/protocols/restraint_utils/settings.py
  class BaseRestraintSettings (line 27) | class BaseRestraintSettings(SettingsBaseModel):
  class DistanceRestraintSettings (line 35) | class DistanceRestraintSettings(BaseRestraintSettings):
    method positive_idxs (line 65) | def positive_idxs(cls, v):
  class FlatBottomRestraintSettings (line 72) | class FlatBottomRestraintSettings(DistanceRestraintSettings):
    method positive_value (line 85) | def positive_value(cls, v):
  class BoreschRestraintSettings (line 92) | class BoreschRestraintSettings(BaseRestraintSettings):

FILE: src/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py
  class AbstractAlchemicalNetworkPlanner (line 10) | class AbstractAlchemicalNetworkPlanner(abc.ABC):
    method __call__ (line 16) | def __call__(self, *args, **kwargs) -> AlchemicalNetwork:

FILE: src/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py
  class RelativeAlchemicalNetworkPlanner (line 41) | class RelativeAlchemicalNetworkPlanner(AbstractAlchemicalNetworkPlanner,...
    method __init__ (line 44) | def __init__(
    method __call__ (line 92) | def __call__(self, *args, **kwargs) -> AlchemicalNetwork: ...  # -no-cov-
    method mappers (line 95) | def mappers(self) -> Iterable[LigandAtomMapper]:
    method mapping_scorer (line 99) | def mapping_scorer(self) -> Callable:
    method ligand_network_planner (line 103) | def ligand_network_planner(self) -> Callable:
    method transformation_protocol (line 107) | def transformation_protocol(self) -> Protocol:
    method chemical_system_generator_type (line 111) | def chemical_system_generator_type(
    method _construct_ligand_network (line 116) | def _construct_ligand_network(self, ligands: Iterable[SmallMoleculeCom...
    method _build_transformations (line 123) | def _build_transformations(
    method _build_transformation (line 181) | def _build_transformation(
  class RHFEAlchemicalNetworkPlanner (line 220) | class RHFEAlchemicalNetworkPlanner(RelativeAlchemicalNetworkPlanner):
    method __init__ (line 229) | def __init__(
    method __call__ (line 245) | def __call__(
  class RBFEAlchemicalNetworkPlanner (line 284) | class RBFEAlchemicalNetworkPlanner(RelativeAlchemicalNetworkPlanner):
    method __init__ (line 293) | def __init__(
    method _build_transformation (line 309) | def _build_transformation(
    method __call__ (line 345) | def __call__(

FILE: src/openfe/setup/atom_mapping/ligandatommapper.py
  class LigandAtomMapper (line 12) | class LigandAtomMapper(gufe.AtomMapper):
    method _mappings_generator (line 21) | def _mappings_generator(
    method suggest_mappings (line 41) | def suggest_mappings(

FILE: src/openfe/setup/atom_mapping/perses_mapper.py
  class PersesAtomMapper (line 28) | class PersesAtomMapper(LigandAtomMapper):
    method _to_dict (line 34) | def _to_dict(self) -> dict:
    method _from_dict (line 45) | def _from_dict(cls, dct: dict):
    method _defaults (line 52) | def _defaults(cls):
    method __init__ (line 56) | def __init__(
    method _mappings_generator (line 89) | def _mappings_generator(self, componentA, componentB):

FILE: src/openfe/setup/atom_mapping/perses_scorers.py
  function _get_all_mapped_atoms_with (line 21) | def _get_all_mapped_atoms_with(
  function default_perses_scorer (line 39) | def default_perses_scorer(

FILE: src/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py
  class RFEComponentLabels (line 12) | class RFEComponentLabels(str, Enum):
  class AbstractChemicalSystemGenerator (line 19) | class AbstractChemicalSystemGenerator(abc.ABC):
    method __call__ (line 25) | def __call__(self, *args, **kwargs) -> Iterable[ChemicalSystem]:

FILE: src/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py
  class EasyChemicalSystemGenerator (line 21) | class EasyChemicalSystemGenerator(AbstractChemicalSystemGenerator):
    method __init__ (line 22) | def __init__(
    method __call__ (line 73) | def __call__(self, component: SmallMoleculeComponent) -> Iterable[Chem...

FILE: src/openfe/setup/ligand_network_planning.py
  function _hasten_lomap (line 27) | def _hasten_lomap(mapper, ligands):
  function generate_radial_network (line 49) | def generate_radial_network(
  function generate_maximal_network (line 157) | def generate_maximal_network(
  function generate_minimal_spanning_network (line 208) | def generate_minimal_spanning_network(
  function generate_minimal_redundant_network (line 252) | def generate_minimal_redundant_network(
  function generate_network_from_names (line 306) | def generate_network_from_names(
  function generate_network_from_indices (line 346) | def generate_network_from_indices(
  function load_orion_network (line 381) | def load_orion_network(
  function load_fepplus_network (line 427) | def load_fepplus_network(

FILE: src/openfe/storage/metadatastore.py
  class MetadataStore (line 12) | class MetadataStore(collections.abc.Mapping):
    method __init__ (line 13) | def __init__(self, external_store):
    method store_metadata (line 18) | def store_metadata(self, location: str, metadata: Metadata):
    method load_all_metadata (line 22) | def load_all_metadata(self) -> Dict[str, Metadata]:
    method __delitem__ (line 26) | def __delitem__(self, location):
    method __getitem__ (line 29) | def __getitem__(self, location):
    method __iter__ (line 32) | def __iter__(self):
    method __len__ (line 35) | def __len__(self):
  class JSONMetadataStore (line 39) | class JSONMetadataStore(MetadataStore):
    method _dump_file (line 43) | def _dump_file(self):
    method store_metadata (line 48) | def store_metadata(self, location: str, metadata: Metadata):
    method load_all_metadata (line 52) | def load_all_metadata(self):
    method __delitem__ (line 63) | def __delitem__(self, location):
  class PerFileJSONMetadataStore (line 68) | class PerFileJSONMetadataStore(MetadataStore):
    method _metadata_path (line 71) | def _metadata_path(self, location):
    method store_metadata (line 74) | def store_metadata(self, location: str, metadata: Metadata):
    method load_all_metadata (line 84) | def load_all_metadata(self):
    method __delitem__ (line 98) | def __delitem__(self, location):

FILE: src/openfe/storage/resultclient.py
  class _ResultContainer (line 21) | class _ResultContainer(abc.ABC):
    method __init__ (line 26) | def __init__(self, parent, path_component):
    method __eq__ (line 31) | def __eq__(self, other):
    method _to_path_component (line 35) | def _to_path_component(item: Any) -> str:
    method __getitem__ (line 45) | def __getitem__(self, item):
    method __truediv__ (line 58) | def __truediv__(self, item):
    method _load_next_level (line 62) | def _load_next_level(self, item):
    method __iter__ (line 65) | def __iter__(self):
    method load_stream (line 70) | def load_stream(self, location, *, allow_changed=False):
    method load_bytes (line 73) | def load_bytes(self, location, *, allow_changed=False):
    method path (line 80) | def path(self):
    method result_server (line 84) | def result_server(self):
    method __repr__ (line 87) | def __repr__(self):
  class ResultClient (line 92) | class ResultClient(_ResultContainer):
    method __init__ (line 93) | def __init__(self, external_store):
    method delete (line 101) | def delete(self, location):
    method _gufe_key_to_storage_key (line 105) | def _gufe_key_to_storage_key(prefix: str, key: str):
    method _store_gufe_tokenizable (line 130) | def _store_gufe_tokenizable(self, prefix, obj):
    method store_transformation (line 143) | def store_transformation(self, transformation):
    method store_network (line 153) | def store_network(self, network):
    method _load_gufe_tokenizable (line 163) | def _load_gufe_tokenizable(self, prefix, gufe_key):
    method load_transformation (line 207) | def load_transformation(self, key: str):
    method load_network (line 222) | def load_network(self, key: str):
    method _load_next_level (line 237) | def _load_next_level(self, transformation):
    method path (line 243) | def path(self):
    method result_server (line 247) | def result_server(self):
  class TransformationResult (line 251) | class TransformationResult(_ResultContainer):
    method __init__ (line 252) | def __init__(self, parent, transformation):
    method _load_next_level (line 256) | def _load_next_level(self, clone):
  class CloneResult (line 260) | class CloneResult(_ResultContainer):
    method __init__ (line 261) | def __init__(self, parent, clone):
    method _to_path_component (line 266) | def _to_path_component(item):
    method _load_next_level (line 269) | def _load_next_level(self, extension):
  class ExtensionResult (line 273) | class ExtensionResult(_ResultContainer):
    method __init__ (line 274) | def __init__(self, parent, extension):
    method _to_path_component (line 279) | def _to_path_component(item):
    method __getitem__ (line 282) | def __getitem__(self, filename):
    method _load_next_level (line 286) | def _load_next_level(self, filename):

FILE: src/openfe/storage/resultserver.py
  class ResultServer (line 9) | class ResultServer:
    method __init__ (line 16) | def __init__(self, external_store, metadata_store):
    method _store_metadata (line 20) | def _store_metadata(self, location):
    method store_bytes (line 24) | def store_bytes(self, location, byte_data):
    method store_path (line 28) | def store_path(self, location, path):
    method delete (line 32) | def delete(self, location):
    method validate (line 36) | def validate(self, location, allow_changed=False):
    method __iter__ (line 51) | def __iter__(self):
    method find_missing_files (line 54) | def find_missing_files(self):
    method load_stream (line 58) | def load_stream(self, location, allow_changed=False):

FILE: src/openfe/tests/analysis/test_plotting.py
  function test_mbar_overlap_plot_high_warn (line 111) | def test_mbar_overlap_plot_high_warn(matrix):
  function test_mbar_overlap_plot (line 155) | def test_mbar_overlap_plot():
  function test_plot_2D_rmsd (line 161) | def test_plot_2D_rmsd(num):

FILE: src/openfe/tests/conftest.py
  class SlowTests (line 31) | class SlowTests:
    method __init__ (line 65) | def __init__(self, config):
    method _modify_slow (line 69) | def _modify_slow(items, config):
    method _modify_integration (line 80) | def _modify_integration(items, config):
    method pytest_collection_modifyitems (line 90) | def pytest_collection_modifyitems(self, items, config):
  function pytest_addoption (line 108) | def pytest_addoption(parser):
  function pytest_configure (line 113) | def pytest_configure(config):
  function mol_from_smiles (line 119) | def mol_from_smiles(smiles: str) -> Chem.Mol:
  function simple_mapping (line 127) | def simple_mapping():
  function other_mapping (line 143) | def other_mapping():
  function lomap_basic_test_files_dir (line 159) | def lomap_basic_test_files_dir(tmp_path_factory):
  function atom_mapping_basic_test_files (line 176) | def atom_mapping_basic_test_files():
  function lomap_old_mapper (line 199) | def lomap_old_mapper() -> AtomMapper:
  function benzene_toluene_topology (line 217) | def benzene_toluene_topology():
  function benzene_modifications (line 226) | def benzene_modifications():
  function charged_benzene_modifications (line 237) | def charged_benzene_modifications():
  function T4L_septop_reference_xml (line 248) | def T4L_septop_reference_xml():
  function serialization_template (line 255) | def serialization_template():
  function benzene_transforms (line 265) | def benzene_transforms():
  function T4_protein_component_pdb (line 277) | def T4_protein_component_pdb() -> str:
  function T4_protein_component (line 283) | def T4_protein_component(T4_protein_component_pdb) -> gufe.ProteinCompon...
  function a2a_protein_membrane_pdb (line 288) | def a2a_protein_membrane_pdb():
  function a2a_protein_membrane_component (line 294) | def a2a_protein_membrane_component(a2a_protein_membrane_pdb) -> openfe.P...
  function eg5_protein_pdb (line 299) | def eg5_protein_pdb():
  function eg5_ligands_sdf (line 305) | def eg5_ligands_sdf():
  function eg5_cofactor_sdf (line 311) | def eg5_cofactor_sdf():
  function eg5_protein (line 317) | def eg5_protein(eg5_protein_pdb) -> openfe.ProteinComponent:
  function eg5_ligands (line 322) | def eg5_ligands(eg5_ligands_sdf) -> list[SmallMoleculeComponent]:
  function eg5_cofactor (line 327) | def eg5_cofactor(eg5_cofactor_sdf) -> SmallMoleculeComponent:
  function a2a_ligands_sdf (line 332) | def a2a_ligands_sdf():
  function a2a_ligands (line 338) | def a2a_ligands(a2a_ligands_sdf):
  function orion_network (line 345) | def orion_network():
  function fepplus_network (line 351) | def fepplus_network():
  function CN_molecule (line 357) | def CN_molecule() -> list[SmallMoleculeComponent]:
  function am1bcc_ref_charges (line 371) | def am1bcc_ref_charges():
  function chlorobenzene (line 409) | def chlorobenzene():
  function fluorobenzene (line 416) | def fluorobenzene():
  function ethane (line 423) | def ethane():
  function chloroethane (line 430) | def chloroethane():
  function fluoroethane (line 437) | def fluoroethane():
  function benzene (line 444) | def benzene():
  function chlorobenzene_to_fluorobenzene_mapping (line 451) | def chlorobenzene_to_fluorobenzene_mapping(chlorobenzene, fluorobenzene):
  function chloroethane_to_ethane_mapping (line 475) | def chloroethane_to_ethane_mapping(chloroethane, ethane):
  function chloroethane_to_fluoroethane_mapping (line 494) | def chloroethane_to_fluoroethane_mapping(chloroethane, fluoroethane):
  function chlorobenzene_to_benzene_mapping (line 514) | def chlorobenzene_to_benzene_mapping(chlorobenzene, benzene):
  function t4_lysozyme_solvated (line 537) | def t4_lysozyme_solvated():
  function apply_box_vectors_and_fix_nb_force (line 544) | def apply_box_vectors_and_fix_nb_force(
  function htf_cmap_chlorobenzene_to_fluorobenzene (line 594) | def htf_cmap_chlorobenzene_to_fluorobenzene(
  function htf_chloro_fluoroethane (line 634) | def htf_chloro_fluoroethane(chloroethane, fluoroethane, chloroethane_to_...
  function htf_chloro_ethane (line 669) | def htf_chloro_ethane(chloroethane, ethane, chloroethane_to_ethane_mappi...
  function htf_chlorobenzene_fluorobenzene (line 705) | def htf_chlorobenzene_fluorobenzene(
  function htf_chlorobenzene_benzene (line 749) | def htf_chlorobenzene_benzene(

FILE: src/openfe/tests/dev/serialization_test_templates.py
  function mol_from_smiles (line 28) | def mol_from_smiles(smiles: str) -> Chem.Mol:

FILE: src/openfe/tests/protocols/conftest.py
  function benzene_vacuum_system (line 31) | def benzene_vacuum_system(benzene_modifications):
  function benzene_system (line 38) | def benzene_system(benzene_modifications):
  function benzene_complex_system (line 52) | def benzene_complex_system(benzene_modifications, T4_protein_component):
  function toluene_vacuum_system (line 67) | def toluene_vacuum_system(benzene_modifications):
  function toluene_system (line 74) | def toluene_system(benzene_modifications):
  function toluene_complex_system (line 86) | def toluene_complex_system(benzene_modifications, T4_protein_component):
  function benzene_to_toluene_mapping (line 99) | def benzene_to_toluene_mapping(benzene_modifications):
  function benzene_charges (line 109) | def benzene_charges():
  function benzene_to_benzoic_mapping (line 120) | def benzene_to_benzoic_mapping(benzene_charges):
  function benzoic_to_benzene_mapping (line 128) | def benzoic_to_benzene_mapping(benzene_charges):
  function benzene_to_aniline_mapping (line 136) | def benzene_to_aniline_mapping(benzene_charges):
  function aniline_to_benzene_mapping (line 144) | def aniline_to_benzene_mapping(benzene_charges):
  function aniline_to_benzoic_mapping (line 152) | def aniline_to_benzoic_mapping(benzene_charges):
  function benzene_many_solv_system (line 160) | def benzene_many_solv_system(benzene_modifications):
  function toluene_many_solv_system (line 190) | def toluene_many_solv_system(benzene_modifications):
  function rfe_transformation_json (line 219) | def rfe_transformation_json() -> str:
  function afe_solv_transformation_json (line 231) | def afe_solv_transformation_json() -> str:
  function abfe_transformation_json_path (line 245) | def abfe_transformation_json_path() -> str:
  function md_json (line 258) | def md_json() -> str:
  function septop_json (line 272) | def septop_json() -> str:
  function industry_benchmark_files (line 295) | def industry_benchmark_files():
  function t4_lysozyme_trajectory_dir (line 314) | def t4_lysozyme_trajectory_dir():
  function simulation_nc (line 323) | def simulation_nc():
  function htop_trajectory_path (line 339) | def htop_trajectory_path():
  function htop_checkpoint_path (line 348) | def htop_checkpoint_path():
  function ahfe_vac_trajectory_path (line 357) | def ahfe_vac_trajectory_path():
  function vac_checkpoint_path (line 366) | def vac_checkpoint_path():
  function ahfe_solv_trajectory_path (line 375) | def ahfe_solv_trajectory_path():
  function ahfe_solv_checkpoint_path (line 384) | def ahfe_solv_checkpoint_path():
  function septop_solv_trajectory_path (line 393) | def septop_solv_trajectory_path():
  function septop_solv_checkpoint_path (line 402) | def septop_solv_checkpoint_path():
  function plain_md_checkpoint_path (line 418) | def plain_md_checkpoint_path():
  function available_platforms (line 424) | def available_platforms() -> set[str]:
  function get_available_openmm_platforms (line 432) | def get_available_openmm_platforms() -> set[str]:
  class ModGufeTokenizableTestsMixin (line 460) | class ModGufeTokenizableTestsMixin(GufeTokenizableTestsMixin):
    method test_repr (line 466) | def test_repr(self, instance):
  function compute_energy (line 474) | def compute_energy(

FILE: src/openfe/tests/protocols/openmm_abfe/conftest.py
  function benzene_complex_dag (line 10) | def benzene_complex_dag(benzene_modifications, T4_protein_component):

FILE: src/openfe/tests/protocols/openmm_abfe/test_abfe_energies.py
  class AlchemStateRest (line 27) | class AlchemStateRest(AlchemicalState):
  function get_alchemical_energy_components (line 38) | def get_alchemical_energy_components(alchemical_system, alchemical_state...
  class TestT4EnergiesRegression (line 105) | class TestT4EnergiesRegression:
    method t4_reference_system (line 113) | def t4_reference_system(self):
    method t4_validation_data (line 120) | def t4_validation_data(self, benzene_modifications, T4_protein_compone...
    method get_energy_components (line 158) | def get_energy_components(
    method test_energies_regression (line 182) | def test_energies_regression(self, lambda_val, t4_reference_system, t4...
    method test_lambda_scale (line 209) | def test_lambda_scale(self, t4_validation_data):

FILE: src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
  function default_settings (line 49) | def default_settings():
  function benzene_wcharges (line 54) | def benzene_wcharges(benzene_modifications):
  function test_create_default_protocol (line 60) | def test_create_default_protocol(default_settings):
  function test_serialize_protocol (line 68) | def test_serialize_protocol(default_settings):
  function test_repeat_units (line 78) | def test_repeat_units(benzene_modifications, T4_protein_component):
  function test_create_independent_repeat_ids (line 127) | def test_create_independent_repeat_ids(benzene_modifications, T4_protein...
  function test_mda_universe_error (line 165) | def test_mda_universe_error():
  class TestT4LysozymeDryRun (line 176) | class TestT4LysozymeDryRun:
    method set_platform (line 191) | def set_platform(self, get_available_openmm_platforms):
    method protocol (line 219) | def protocol(self, settings):
    method settings (line 225) | def settings(self):
    method dag (line 239) | def dag(self, protocol, benzene_wcharges, T4_protein_component):
    method complex_setup_units (line 262) | def complex_setup_units(self, dag):
    method complex_sim_units (line 266) | def complex_sim_units(self, dag):
    method solvent_setup_units (line 270) | def solvent_setup_units(self, dag):
    method solvent_sim_units (line 274) | def solvent_sim_units(self, dag):
    method test_number_of_units (line 277) | def test_number_of_units(
    method _assert_force_num (line 289) | def _assert_force_num(self, system, forcetype, number):
    method _assert_expected_alchemical_forces (line 293) | def _assert_expected_alchemical_forces(self, system, phase: str, setti...
    method _assert_expected_nonalchemical_forces (line 337) | def _assert_expected_nonalchemical_forces(self, system, phase: str, se...
    method _verify_sampler (line 376) | def _verify_sampler(self, sampler, phase: str, settings):
    method _check_box_vectors (line 391) | def _check_box_vectors(self, system):
    method _test_dodecahedron_vectors (line 395) | def _test_dodecahedron_vectors(system):
    method _test_cubic_vectors (line 414) | def _test_cubic_vectors(system):
    method _test_energies (line 431) | def _test_energies(reference_system, alchemical_system, alchemical_reg...
    method test_complex_dry_run (line 453) | def test_complex_dry_run(self, complex_setup_units, complex_sim_units,...
    method test_solvent_dry_run (line 514) | def test_solvent_dry_run(self, solvent_setup_units, solvent_sim_units,...
  class TestT4LysozymeTIP4PExtraSettingsDryRun (line 581) | class TestT4LysozymeTIP4PExtraSettingsDryRun(TestT4LysozymeDryRun):
    method settings (line 590) | def settings(self):
  function test_user_charges (line 617) | def test_user_charges(benzene_modifications, T4_protein_component, tmp_p...
  class TestA2AMembraneDryRun (line 690) | class TestA2AMembraneDryRun(TestT4LysozymeDryRun):
    method settings (line 716) | def settings(self):
    method dag (line 727) | def dag(self, settings, a2a_ligands, a2a_protein_membrane_component):
    method _check_box_vectors (line 757) | def _check_box_vectors(self, system):
    method _test_orthogonal_vectors (line 761) | def _test_orthogonal_vectors(system):

FILE: src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol_results.py
  function patcher (line 23) | def patcher():
  function test_gather (line 86) | def test_gather(benzene_complex_dag, patcher, tmp_path):
  function test_unit_tagging (line 104) | def test_unit_tagging(benzene_complex_dag, patcher, tmp_path):
  class TestProtocolResult (line 145) | class TestProtocolResult:
    method protocolresult (line 147) | def protocolresult(self, abfe_transformation_json_path):
    method test_reload_protocol_result (line 153) | def test_reload_protocol_result(self, afe_solv_transformation_json):
    method test_get_estimate (line 160) | def test_get_estimate(self, protocolresult):
    method test_get_uncertainty (line 168) | def test_get_uncertainty(self, protocolresult):
    method test_get_individual (line 176) | def test_get_individual(self, protocolresult):
    method test_get_forwards_etc (line 188) | def test_get_forwards_etc(self, key, protocolresult):
    method test_get_frwd_reverse_none_return (line 211) | def test_get_frwd_reverse_none_return(self, key, protocolresult):
    method test_get_overlap_matrices (line 223) | def test_get_overlap_matrices(self, key, n_rep, protocolresult):
    method test_get_replica_transition_statistics (line 235) | def test_get_replica_transition_statistics(self, n_rep, key, protocolr...
    method test_equilibration_iterations (line 248) | def test_equilibration_iterations(self, key, protocolresult):
    method test_production_iterations (line 257) | def test_production_iterations(self, key, protocolresult):
    method test_filenotfound_replica_states (line 265) | def test_filenotfound_replica_states(self, protocolresult):
    method test_restraint_geometry (line 271) | def test_restraint_geometry(self, protocolresult):
    method test_selection_indices (line 292) | def test_selection_indices(self, key, protocolresult, expected_size):

FILE: src/openfe/tests/protocols/openmm_abfe/test_abfe_settings.py
  function default_settings (line 13) | def default_settings():
  function test_create_default_settings (line 17) | def test_create_default_settings():
  function test_negative_repeats_settings (line 22) | def test_negative_repeats_settings(default_settings):
  function test_incorrect_window_settings (line 34) | def test_incorrect_window_settings(val, default_settings):
  function test_monotonic_lambda_windows (line 63) | def test_monotonic_lambda_windows(val, default_settings):
  function test_equil_not_all_complex (line 73) | def test_equil_not_all_complex(default_settings):
  function test_equil_not_all_solvent (line 78) | def test_equil_not_all_solvent(default_settings):
  function test_adaptive_settings_no_protein_membrane (line 83) | def test_adaptive_settings_no_protein_membrane(toluene_complex_system, d...
  function test_adaptive_settings_with_protein_membrane (line 95) | def test_adaptive_settings_with_protein_membrane(a2a_protein_membrane_co...

FILE: src/openfe/tests/protocols/openmm_abfe/test_abfe_slow.py
  function test_openmm_run_engine (line 21) | def test_openmm_run_engine(

FILE: src/openfe/tests/protocols/openmm_abfe/test_abfe_tokenization.py
  function protocol (line 23) | def protocol():
  function protocol_units (line 28) | def protocol_units(protocol, benzene_complex_system, T4_protein_component):
  function _filter_units (line 41) | def _filter_units(pus, classtype):
  function complex_protocol_setup_unit (line 48) | def complex_protocol_setup_unit(protocol_units):
  function complex_protocol_sim_unit (line 53) | def complex_protocol_sim_unit(protocol_units):
  function complex_protocol_analysis_unit (line 58) | def complex_protocol_analysis_unit(protocol_units):
  function solvent_protocol_setup_unit (line 63) | def solvent_protocol_setup_unit(protocol_units):
  function solvent_protocol_sim_unit (line 68) | def solvent_protocol_sim_unit(protocol_units):
  function solvent_protocol_analysis_unit (line 73) | def solvent_protocol_analysis_unit(protocol_units):
  function protocol_result (line 78) | def protocol_result(abfe_transformation_json_path):
  class TestAbsoluteBindingProtocol (line 84) | class TestAbsoluteBindingProtocol(ModGufeTokenizableTestsMixin):
    method instance (line 90) | def instance(self, protocol):
  class TestABFESolventSetupUnit (line 94) | class TestABFESolventSetupUnit(ModGufeTokenizableTestsMixin):
    method instance (line 100) | def instance(self, solvent_protocol_setup_unit):
  class TestABFESolventSimUnit (line 104) | class TestABFESolventSimUnit(ModGufeTokenizableTestsMixin):
    method instance (line 110) | def instance(self, solvent_protocol_sim_unit):
  class TestABFESolventAnalysisUnit (line 114) | class TestABFESolventAnalysisUnit(ModGufeTokenizableTestsMixin):
    method instance (line 120) | def instance(self, solvent_protocol_analysis_unit):
  class TestABFEComplexSetupUnit (line 124) | class TestABFEComplexSetupUnit(ModGufeTokenizableTestsMixin):
    method instance (line 130) | def instance(self, complex_protocol_setup_unit):
  class TestABFEComplexSimUnit (line 134) | class TestABFEComplexSimUnit(ModGufeTokenizableTestsMixin):
    method instance (line 140) | def instance(self, complex_protocol_sim_unit):
  class TestABFEComplexAnalysisUnit (line 144) | class TestABFEComplexAnalysisUnit(ModGufeTokenizableTestsMixin):
    method instance (line 150) | def instance(self, complex_protocol_analysis_unit):
  class TestAbsoluteBindingProtocolResult (line 154) | class TestAbsoluteBindingProtocolResult(ModGufeTokenizableTestsMixin):
    method instance (line 160) | def instance(self, protocol_result):

FILE: src/openfe/tests/protocols/openmm_abfe/test_abfe_validation.py
  function default_settings (line 13) | def default_settings():
  function test_validate_complex_lambda_schedule_naked_charge (line 23) | def test_validate_complex_lambda_schedule_naked_charge(val, default_sett...
  function test_validate_solvent_lambda_schedule_naked_charge (line 47) | def test_validate_solvent_lambda_schedule_naked_charge(val, default_sett...
  function test_validate_lambda_schedule_nreplicas (line 71) | def test_validate_lambda_schedule_nreplicas(val, default_settings):
  function test_validate_lambda_schedule_nwindows (line 95) | def test_validate_lambda_schedule_nwindows(val, default_settings):
  function test_validate_no_protcomp (line 115) | def test_validate_no_protcomp(
  function test_validate_endstates_nosolvcomp_stateA (line 134) | def test_validate_endstates_nosolvcomp_stateA(benzene_modifications, T4_...
  function test_validate_endstates_nosolvcomp_stateB (line 154) | def test_validate_endstates_nosolvcomp_stateB(benzene_modifications, T4_...
  function test_validate_endstates_multiple_uniqueA (line 174) | def test_validate_endstates_multiple_uniqueA(benzene_modifications, T4_p...
  function test_validate_solvent_endstates_solvent_dissapearing (line 195) | def test_validate_solvent_endstates_solvent_dissapearing(
  function test_validate_endstates_unique_stateB (line 220) | def test_validate_endstates_unique_stateB(benzene_modifications, T4_prot...
  function test_charged_endstate (line 241) | def test_charged_endstate(charged_benzene_modifications, T4_protein_comp...
  function test_validate_fail_extends (line 262) | def test_validate_fail_extends(benzene_modifications, T4_protein_compone...
  function test_high_timestep (line 287) | def test_high_timestep(benzene_modifications, T4_protein_component):
  function test_validate_warnings (line 312) | def test_validate_warnings(benzene_modifications, T4_protein_component, ...

FILE: src/openfe/tests/protocols/openmm_abfe/utils.py
  function _get_units (line 26) | def _get_units(protocol_units, unit_type):

FILE: src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol.py
  function protocol_dry_settings (line 41) | def protocol_dry_settings():
  function default_settings (line 50) | def default_settings():
  function test_create_default_protocol (line 54) | def test_create_default_protocol(default_settings):
  function test_serialize_protocol (line 60) | def test_serialize_protocol(default_settings):
  function test_bad_sampler (line 68) | def test_bad_sampler():
  function test_repeat_units (line 86) | def test_repeat_units(benzene_system):
  function test_create_independent_repeat_ids (line 120) | def test_create_independent_repeat_ids(benzene_system):
  function _assert_num_forces (line 149) | def _assert_num_forces(system, forcetype, number):
  function _verify_alchemical_sterics_force_parameters (line 158) | def _verify_alchemical_sterics_force_parameters(
  function test_setup_dry_sim_vac_benzene (line 198) | def test_setup_dry_sim_vac_benzene(benzene_system, method, protocol_dry_...
  function test_alchemical_settings_setup_vacuum (line 279) | def test_alchemical_settings_setup_vacuum(
  function test_confgen_fail_AFE (line 341) | def test_confgen_fail_AFE(benzene_system, protocol_dry_settings, tmp_path):
  function test_setup_solv_benzene (line 369) | def test_setup_solv_benzene(benzene_system, protocol_dry_settings, tmp_p...
  function test_dry_run_vsite_fail (line 412) | def test_dry_run_vsite_fail(benzene_system, tmp_path, protocol_dry_setti...
  function test_setup_dry_sim_solv_benzene_tip4p (line 460) | def test_setup_dry_sim_solv_benzene_tip4p(benzene_system, protocol_dry_s...
  function test_dry_run_solv_benzene_noncubic (line 509) | def test_dry_run_solv_benzene_noncubic(benzene_system, protocol_dry_sett...
  function test_dry_run_solv_user_charges_benzene (line 547) | def test_dry_run_solv_user_charges_benzene(benzene_modifications, protoc...
  function test_dry_run_charge_backends (line 647) | def test_dry_run_charge_backends(
  function benzene_solvation_dag (line 693) | def benzene_solvation_dag(benzene_system, protocol_dry_settings):
  function test_dry_run_vacuum_write_frequency (line 712) | def test_dry_run_vacuum_write_frequency(

FILE: src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol_results.py
  function protocol_dry_settings (line 22) | def protocol_dry_settings():
  function benzene_solvation_dag (line 31) | def benzene_solvation_dag(benzene_system, protocol_dry_settings):
  function patcher (line 43) | def patcher():
  function test_gather (line 106) | def test_gather(benzene_solvation_dag, patcher, tmp_path):
  function test_unit_tagging (line 124) | def test_unit_tagging(benzene_solvation_dag, patcher, tmp_path):
  class TestProtocolResult (line 165) | class TestProtocolResult:
    method protocolresult (line 167) | def protocolresult(self, afe_solv_transformation_json):
    method test_reload_protocol_result (line 174) | def test_reload_protocol_result(self, afe_solv_transformation_json):
    method test_get_estimate (line 181) | def test_get_estimate(self, protocolresult):
    method test_get_uncertainty (line 189) | def test_get_uncertainty(self, protocolresult):
    method test_get_individual (line 197) | def test_get_individual(self, protocolresult):
    method test_get_forwards_etc (line 209) | def test_get_forwards_etc(self, key, protocolresult):
    method test_get_frwd_reverse_none_return (line 224) | def test_get_frwd_reverse_none_return(self, key, protocolresult):
    method test_get_overlap_matrices (line 236) | def test_get_overlap_matrices(self, key, protocolresult):
    method test_get_replica_transition_statistics (line 248) | def test_get_replica_transition_statistics(self, key, protocolresult):
    method test_equilibration_iterations (line 261) | def test_equilibration_iterations(self, key, protocolresult):
    method test_production_iterations (line 270) | def test_production_iterations(self, key, protocolresult):
    method test_filenotfound_replica_states (line 278) | def test_filenotfound_replica_states(self, protocolresult):

FILE: src/openfe/tests/protocols/openmm_ahfe/test_ahfe_resume.py
  function protocol_settings (line 29) | def protocol_settings():
  function test_verify_execution_environment (line 51) | def test_verify_execution_environment():
  function test_verify_execution_environment_fail (line 62) | def test_verify_execution_environment_fail():
  function test_verify_execution_env_missing_key (line 74) | def test_verify_execution_env_missing_key():
  function test_solvent_check_restart (line 90) | def test_solvent_check_restart(protocol_settings, ahfe_solv_trajectory_p...
  function test_vacuum_check_restart (line 106) | def test_vacuum_check_restart(protocol_settings, ahfe_vac_trajectory_path):
  function test_check_restart_one_file_missing (line 122) | def test_check_restart_one_file_missing(protocol_settings, ahfe_vac_traj...
  class TestCheckpointResuming (line 133) | class TestCheckpointResuming:
    method protocol_dag (line 135) | def protocol_dag(
    method _check_sampler (line 160) | def _check_sampler(sampler, num_iterations: int):
    method _get_positions (line 171) | def _get_positions(dataset):
    method _copy_simfiles (line 179) | def _copy_simfiles(cwd: pathlib.Path, filepath):
    method test_resume (line 183) | def test_resume(
    method test_resume_fail_particles (line 271) | def test_resume_fail_particles(
    method test_resume_fail_constraints (line 311) | def test_resume_fail_constraints(
    method test_resume_fail_forces (line 353) | def test_resume_fail_forces(
    method test_resume_differ_barostat (line 393) | def test_resume_differ_barostat(
    method test_resume_differ_forces (line 449) | def test_resume_differ_forces(
    method test_resume_bad_files (line 512) | def test_resume_bad_files(

FILE: src/openfe/tests/protocols/openmm_ahfe/test_ahfe_settings.py
  function default_settings (line 12) | def default_settings():
  function test_create_default_settings (line 16) | def test_create_default_settings():
  function test_invalid_protocol_repeats (line 21) | def test_invalid_protocol_repeats():
  function test_incorrect_window_settings (line 34) | def test_incorrect_window_settings(val, default_settings):
  function test_monotonic_lambda_windows (line 49) | def test_monotonic_lambda_windows(val, default_settings):

FILE: src/openfe/tests/protocols/openmm_ahfe/test_ahfe_slow.py
  function test_openmm_run_engine (line 20) | def test_openmm_run_engine(

FILE: src/openfe/tests/protocols/openmm_ahfe/test_ahfe_tokenization.py
  function protocol (line 23) | def protocol():
  function protocol_units (line 30) | def protocol_units(protocol, benzene_system):
  function _filter_units (line 39) | def _filter_units(pus, classtype):
  function solvent_protocol_setup_unit (line 46) | def solvent_protocol_setup_unit(protocol_units):
  function solvent_protocol_sim_unit (line 51) | def solvent_protocol_sim_unit(protocol_units):
  function solvent_protocol_analysis_unit (line 56) | def solvent_protocol_analysis_unit(protocol_units):
  function vacuum_protocol_setup_unit (line 61) | def vacuum_protocol_setup_unit(protocol_units):
  function vacuum_protocol_sim_unit (line 66) | def vacuum_protocol_sim_unit(protocol_units):
  function vacuum_protocol_analysis_unit (line 71) | def vacuum_protocol_analysis_unit(protocol_units):
  function protocol_result (line 76) | def protocol_result(afe_solv_transformation_json):
  class TestAbsoluteSolvationProtocol (line 82) | class TestAbsoluteSolvationProtocol(ModGufeTokenizableTestsMixin):
    method instance (line 88) | def instance(self, protocol):
  class TestAHFESolventSetupUnit (line 92) | class TestAHFESolventSetupUnit(ModGufeTokenizableTestsMixin):
    method instance (line 98) | def instance(self, solvent_protocol_setup_unit):
  class TestAHFESolventSimUnit (line 102) | class TestAHFESolventSimUnit(ModGufeTokenizableTestsMixin):
    method instance (line 108) | def instance(self, solvent_protocol_sim_unit):
  class TestAHFESolventAnalysisUnit (line 112) | class TestAHFESolventAnalysisUnit(ModGufeTokenizableTestsMixin):
    method instance (line 118) | def instance(self, solvent_protocol_analysis_unit):
  class TestAHFEVacuumSetupUnit (line 122) | class TestAHFEVacuumSetupUnit(ModGufeTokenizableTestsMixin):
    method instance (line 128) | def instance(self, vacuum_protocol_setup_unit):
  class TestAHFEVacuumSimUnit (line 132) | class TestAHFEVacuumSimUnit(ModGufeTokenizableTestsMixin):
    method instance (line 138) | def instance(self, vacuum_protocol_sim_unit):
  class TestAHFEVacuumAnalysisUnit (line 142) | class TestAHFEVacuumAnalysisUnit(ModGufeTokenizableTestsMixin):
    method instance (line 148) | def instance(self, vacuum_protocol_analysis_unit):
  class TestAbsoluteSolvationProtocolResult (line 152) | class TestAbsoluteSolvationProtocolResult(ModGufeTokenizableTestsMixin):
    method instance (line 158) | def instance(self, protocol_result):

FILE: src/openfe/tests/protocols/openmm_ahfe/test_ahfe_validation.py
  function default_settings (line 16) | def default_settings():
  function stateA (line 21) | def stateA(benzene_modifications):
  function stateB (line 28) | def stateB():
  function test_validate_lambda_schedule_naked_charge (line 38) | def test_validate_lambda_schedule_naked_charge(val, default_settings):
  function test_validate_lambda_schedule_nreplicas (line 68) | def test_validate_lambda_schedule_nreplicas(val, default_settings):
  function test_validate_lambda_schedule_nwindows (line 91) | def test_validate_lambda_schedule_nwindows(val, default_settings):
  function test_validate_lambda_schedule_nonzero_restraints (line 116) | def test_validate_lambda_schedule_nonzero_restraints(val, default_settin...
  function test_validate_endstates_protcomp (line 133) | def test_validate_endstates_protcomp(benzene_modifications, T4_protein_c...
  function test_validate_endstates_nosolvcomp_stateA (line 154) | def test_validate_endstates_nosolvcomp_stateA(benzene_modifications, T4_...
  function test_validate_endstates_nosolvcomp_stateB (line 173) | def test_validate_endstates_nosolvcomp_stateB(benzene_modifications, T4_...
  function test_validate_alchem_comps_appearingB (line 192) | def test_validate_alchem_comps_appearingB(benzene_modifications):
  function test_validate_alchem_comps_multi (line 208) | def test_validate_alchem_comps_multi(benzene_modifications):
  function test_validate_alchem_nonsmc (line 227) | def test_validate_alchem_nonsmc(benzene_modifications):
  function test_charged_alchem_comp (line 246) | def test_charged_alchem_comp(charged_benzene_modifications):
  function test_extends_error (line 266) | def test_extends_error(default_settings, stateA, stateB):
  function test_vac_bad_nonbonded (line 276) | def test_vac_bad_nonbonded(stateA, stateB):
  function test_vac_nvt_error (line 285) | def test_vac_nvt_error(stateA, stateB):
  function test_mapping_warning (line 294) | def test_mapping_warning(benzene_modifications, default_settings, stateA...
  function test_high_timestep (line 308) | def test_high_timestep(phase, stateA, stateB):

FILE: src/openfe/tests/protocols/openmm_ahfe/utils.py
  function _get_units (line 27) | def _get_units(protocol_units, unit_type):

FILE: src/openfe/tests/protocols/openmm_md/test_plain_md_protocol.py
  function vac_settings (line 40) | def vac_settings():
  function test_get_remaining_steps (line 58) | def test_get_remaining_steps(inputs, expected):
  function test_create_default_settings (line 66) | def test_create_default_settings():
  function test_create_default_protocol (line 72) | def test_create_default_protocol():
  function test_invalid_protocol_repeats (line 81) | def test_invalid_protocol_repeats():
  function test_serialize_protocol (line 87) | def test_serialize_protocol():
  function test_create_independent_repeat_ids (line 99) | def test_create_independent_repeat_ids(benzene_system):
  function test_dry_run_default_vacuum (line 127) | def test_dry_run_default_vacuum(benzene_vacuum_system, vac_settings, tmp...
  function test_dry_run_logger_output (line 155) | def test_dry_run_logger_output(benzene_vacuum_system, vac_settings, tmp_...
  function test_dry_run_ffcache_none_vacuum (line 206) | def test_dry_run_ffcache_none_vacuum(benzene_vacuum_system, vac_settings...
  function test_dry_run_gaff_vacuum (line 224) | def test_dry_run_gaff_vacuum(benzene_vacuum_system, vac_settings, tmp_pa...
  function test_dry_run_espaloma_vacuum_user_charges (line 243) | def test_dry_run_espaloma_vacuum_user_charges(benzene_modifications, vac...
  function test_dry_run_charge_backends (line 303) | def test_dry_run_charge_backends(
  function test_dry_many_molecules_solvent (line 332) | def test_dry_many_molecules_solvent(benzene_many_solv_system, tmp_path):
  function test_dry_run_ligand_tip4p (line 418) | def test_dry_run_ligand_tip4p(benzene_system, tmp_path):
  function test_dry_run_complex (line 450) | def test_dry_run_complex(benzene_complex_system, tmp_path):
  function test_hightimestep (line 485) | def test_hightimestep(benzene_vacuum_system, tmp_path):
  function test_vaccuum_PME_error (line 501) | def test_vaccuum_PME_error(benzene_vacuum_system):
  function test_multiple_basesolvents_error (line 515) | def test_multiple_basesolvents_error(a2a_protein_membrane_component):
  function test_states_not_matching_error (line 534) | def test_states_not_matching_error(benzene_vacuum_system, toluene_vacuum...
  function test_mapping_warning (line 545) | def test_mapping_warning(benzene_vacuum_system, tmp_path):
  function solvent_protocol_dag (line 564) | def solvent_protocol_dag(benzene_system):
  function test_unit_tagging (line 576) | def test_unit_tagging(benzene_system, tmp_path):
  function test_gather (line 611) | def test_gather(solvent_protocol_dag, tmp_path):
  class TestProtocolResult (line 636) | class TestProtocolResult:
    method protocolresult (line 638) | def protocolresult(self, md_json):
    method test_reload_protocol_result (line 645) | def test_reload_protocol_result(self, md_json):
    method test_get_estimate (line 652) | def test_get_estimate(self, protocolresult):
    method test_get_uncertainty (line 657) | def test_get_uncertainty(self, protocolresult):
    method test_get_traj_filename (line 662) | def test_get_traj_filename(self, protocolresult):
    method test_get_pdb_filename (line 668) | def test_get_pdb_filename(self, protocolresult):

FILE: src/openfe/tests/protocols/openmm_md/test_plain_md_resume.py
  function vacuum_protocol_settings (line 27) | def vacuum_protocol_settings():
  function test_verify_execution_environment (line 41) | def test_verify_execution_environment():
  function test_verify_execution_environment_fail (line 52) | def test_verify_execution_environment_fail():
  function test_verify_execution_env_missing_key (line 64) | def test_verify_execution_env_missing_key():
  function test_check_restart (line 80) | def test_check_restart(vacuum_protocol_settings, plain_md_checkpoint_path):
  class TestPlainMDResume (line 98) | class TestPlainMDResume:
    method protocol_dag (line 100) | def protocol_dag(self, vacuum_protocol_settings, benzene_vacuum_system):
    method test_resume (line 108) | def test_resume(

FILE: src/openfe/tests/protocols/openmm_md/test_plain_md_slow.py
  function test_vacuum_sim (line 14) | def test_vacuum_sim(
  function test_complex_solvent_sim_gpu (line 81) | def test_complex_solvent_sim_gpu(

FILE: src/openfe/tests/protocols/openmm_md/test_plain_md_tokenization.py
  function protocol (line 13) | def protocol():
  function protocol_units (line 18) | def protocol_units(protocol, benzene_system):
  function protocol_setup_unit (line 28) | def protocol_setup_unit(protocol, protocol_units):
  function protocol_simulation_unit (line 35) | def protocol_simulation_unit(protocol, protocol_units):
  function protocol_result (line 42) | def protocol_result(md_json):
  class TestPlainMDProtocol (line 48) | class TestPlainMDProtocol(GufeTokenizableTestsMixin):
    method instance (line 54) | def instance(self, protocol):
    method test_repr (line 57) | def test_repr(self, instance):
  class TestPlainMDSetupUnit (line 65) | class TestPlainMDSetupUnit(GufeTokenizableTestsMixin):
    method instance (line 71) | def instance(self, protocol_setup_unit):
    method test_repr (line 74) | def test_repr(self, instance):
  class TestPlainMDSimulationUnit (line 82) | class TestPlainMDSimulationUnit(GufeTokenizableTestsMixin):
    method instance (line 88) | def instance(self, protocol_simulation_unit):
    method test_repr (line 91) | def test_repr(self, instance):
  class TestPlainMDProtocolResult (line 96) | class TestPlainMDProtocolResult(GufeTokenizableTestsMixin):
    method instance (line 102) | def instance(self, protocol_result):
    method test_repr (line 105) | def test_repr(self, instance):

FILE: src/openfe/tests/protocols/openmm_rfe/helpers.py
  function make_htf (line 15) | def make_htf(
  function _make_system_with_cmap (line 137) | def _make_system_with_cmap(

FILE: src/openfe/tests/protocols/openmm_rfe/test_hybrid_factory.py
  function test_cmap_system_no_dummy_pme_energy (line 13) | def test_cmap_system_no_dummy_pme_energy(htf_cmap_chlorobenzene_to_fluor...
  function test_cmap_missing_cmap_error (line 68) | def test_cmap_missing_cmap_error():
  function test_verify_cmap_incompatible_maps_error (line 89) | def test_verify_cmap_incompatible_maps_error():
  function test_verify_cmap_incompatible_torsions_error (line 103) | def test_verify_cmap_incompatible_torsions_error():
  function test_cmap_maps_incompatible_error (line 120) | def test_cmap_maps_incompatible_error():
  function test_cmap_torsions_incompatible_error (line 143) | def test_cmap_torsions_incompatible_error():
  function test_cmap_map_index_incompatible_error (line 184) | def test_cmap_map_index_incompatible_error():
  function test_cmap_in_alchemical_region_error (line 213) | def test_cmap_in_alchemical_region_error():
  function test_softcore_parameters (line 235) | def test_softcore_parameters(chloroethane_to_fluoroethane_mapping, softc...
  function test_particles_mass_no_dummy (line 257) | def test_particles_mass_no_dummy(htf_chloro_fluoroethane):
  function test_particle_mass_dummy (line 277) | def test_particle_mass_dummy(htf_chloro_ethane):
  function test_constraints_count_no_dummy (line 299) | def test_constraints_count_no_dummy(htf_chloro_fluoroethane):
  function test_constraints_count_dummy (line 304) | def test_constraints_count_dummy(htf_chloro_ethane):
  function test_hybrid_forces_no_dummy (line 309) | def test_hybrid_forces_no_dummy(htf_chloro_fluoroethane):
  function test_hybrid_forces_dummy (line 328) | def test_hybrid_forces_dummy(htf_chloro_ethane):
  function test_bond_force_no_dummy (line 344) | def test_bond_force_no_dummy(htf_chloro_fluoroethane):
  function test_bond_force_dummy (line 383) | def test_bond_force_dummy(htf_chloro_ethane):
  function test_angle_force_no_dummy (line 433) | def test_angle_force_no_dummy(htf_chloro_fluoroethane):
  function test_angle_force_dummy (line 473) | def test_angle_force_dummy(htf_chloro_ethane):
  function test_torsion_force_no_dummy (line 538) | def test_torsion_force_no_dummy(htf_chloro_fluoroethane):
  function test_torsion_force_dummy (line 619) | def test_torsion_force_dummy(htf_chloro_ethane):
  function test_nonbonded_force_no_dummy (line 700) | def test_nonbonded_force_no_dummy(htf_chloro_fluoroethane):
  function test_nonbonded_force_dummy (line 736) | def test_nonbonded_force_dummy(htf_chloro_ethane):
  function test_nonbonded_offsets_no_dummy (line 792) | def test_nonbonded_offsets_no_dummy(htf_chloro_fluoroethane):
  function test_nonbonded_offsets_dummy (line 821) | def test_nonbonded_offsets_dummy(htf_chloro_ethane):
  function test_nonbonded_exceptions_no_dummy (line 858) | def test_nonbonded_exceptions_no_dummy(htf_chloro_fluoroethane):
  function test_nonbonded_exceptions_dummy (line 919) | def test_nonbonded_exceptions_dummy(htf_chloro_ethane):
  function test_nonbonded_exception_offsets_no_dummy (line 1001) | def test_nonbonded_exception_offsets_no_dummy(htf_chloro_fluoroethane):
  function test_nonbonded_exception_offsets_dummy (line 1095) | def test_nonbonded_exception_offsets_dummy(htf_chloro_ethane):
  function test_custom_nb_force_no_dummy (line 1197) | def test_custom_nb_force_no_dummy(htf_chloro_fluoroethane):
  function test_custom_nb_force_dummy (line 1243) | def test_custom_nb_force_dummy(htf_chloro_ethane):
  function test_custom_nb_exclusions_no_dummy (line 1309) | def test_custom_nb_exclusions_no_dummy(htf_chloro_fluoroethane):
  function test_custom_nb_exclusions_dummy (line 1333) | def test_custom_nb_exclusions_dummy(htf_chloro_ethane):
  function test_custom_nb_interation_groups_no_dummy (line 1359) | def test_custom_nb_interation_groups_no_dummy(htf_chloro_fluoroethane):
  function test_custom_nb_interation_groups_dummy (line 1391) | def test_custom_nb_interation_groups_dummy(htf_chloro_ethane):
  function test_custom_sterics_force_no_dummy (line 1425) | def test_custom_sterics_force_no_dummy(htf_chloro_fluoroethane):
  function test_custom_sterics_force_dummy (line 1450) | def test_custom_sterics_force_dummy(htf_chloro_ethane):
  function test_vacuum_system_energy_no_dummy (line 1551) | def test_vacuum_system_energy_no_dummy(htf_chloro_fluoroethane):
  function test_vacuum_system_energy_dummy (line 1608) | def test_vacuum_system_energy_dummy(htf_chloro_ethane):
  function test_system_energy_pme_no_dummy (line 1683) | def test_system_energy_pme_no_dummy(htf_chlorobenzene_fluorobenzene):
  function test_system_interaction_groups_no_dummy (line 1732) | def test_system_interaction_groups_no_dummy(htf_chlorobenzene_fluorobenz...
  function test_system_interaction_groups_dummy (line 1764) | def test_system_interaction_groups_dummy(htf_chlorobenzene_benzene):
  function test_system_energy_pme_dummy (line 1796) | def test_system_energy_pme_dummy(htf_chlorobenzene_benzene):

FILE: src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py
  function _get_units (line 54) | def _get_units(protocol_units, unit_type):
  function vac_settings (line 62) | def vac_settings():
  function solv_settings (line 71) | def solv_settings():
  function test_compute_platform_warn (line 78) | def test_compute_platform_warn():
  function test_append_topology (line 83) | def test_append_topology(benzene_complex_system, toluene_complex_system):
  function test_append_topology_no_exclude (line 112) | def test_append_topology_no_exclude(benzene_complex_system, toluene_comp...
  function test_create_default_settings (line 141) | def test_create_default_settings():
  function test_adaptive_settings_no_initial (line 147) | def test_adaptive_settings_no_initial(benzene_system, toluene_system, be...
  function test_create_default_protocol (line 159) | def test_create_default_protocol():
  function test_invalid_protocol_repeats (line 168) | def test_invalid_protocol_repeats():
  function test_serialize_protocol (line 174) | def test_serialize_protocol():
  function test_repeat_units (line 186) | def test_repeat_units(benzene_system, toluene_system, benzene_to_toluene...
  function test_create_independent_repeat_ids (line 222) | def test_create_independent_repeat_ids(benzene_system, toluene_system, b...
  function test_bad_sampler (line 250) | def test_bad_sampler():
  function test_setup_dry_sim_default_vacuum (line 272) | def test_setup_dry_sim_default_vacuum(
  function test_setup_gaff_vacuum (line 355) | def test_setup_gaff_vacuum(
  function test_dry_many_molecules_solvent (line 380) | def test_dry_many_molecules_solvent(
  function test_setup_core_element_change (line 471) | def test_setup_core_element_change(vac_settings, tmp_path):
  function test_dry_run_ligand (line 504) | def test_dry_run_ligand(
  function test_confgen_mocked_fail (line 547) | def test_confgen_mocked_fail(
  function tip4p_hybrid_factory (line 567) | def tip4p_hybrid_factory(
  function test_tip4p_particle_count (line 610) | def test_tip4p_particle_count(tip4p_hybrid_factory):
  function test_tip4p_num_waters (line 625) | def test_tip4p_num_waters(tip4p_hybrid_factory):
  function test_tip4p_check_vsite_parameters (line 642) | def test_tip4p_check_vsite_parameters(tip4p_hybrid_factory):
  function test_setup_ligand_system_cutoff (line 692) | def test_setup_ligand_system_cutoff(
  function test_setup_charge_backends (line 755) | def test_setup_charge_backends(
  function test_setup_same_mol_different_charges (line 817) | def test_setup_same_mol_different_charges(benzene_modifications, vac_set...
  function test_setup_user_charges (line 881) | def test_setup_user_charges(benzene_modifications, vac_settings, tmp_path):
  function test_virtual_sites_no_reassign (line 1001) | def test_virtual_sites_no_reassign(
  function test_setup_dodecahdron_ligand_box (line 1046) | def test_setup_dodecahdron_ligand_box(
  function test_dry_run_complex (line 1083) | def test_dry_run_complex(
  function test_dry_run_membrane_complex (line 1129) | def test_dry_run_membrane_complex(
  function test_lambda_schedule_default (line 1218) | def test_lambda_schedule_default():
  function test_lambda_schedule (line 1224) | def test_lambda_schedule(windows):
  function test_setup_ligand_overlap_warning (line 1231) | def test_setup_ligand_overlap_warning(
  function solvent_protocol_dag (line 1271) | def solvent_protocol_dag(benzene_system, toluene_system, benzene_to_tolu...
  function unit_mock_patcher (line 1284) | def unit_mock_patcher():
  function test_unit_tagging (line 1325) | def test_unit_tagging(solvent_protocol_dag, unit_mock_patcher, tmp_path):
  function test_gather (line 1364) | def test_gather(solvent_protocol_dag, unit_mock_patcher, tmp_path):
  class TestConstraintRemoval (line 1382) | class TestConstraintRemoval:
    method make_systems (line 1384) | def make_systems(
    method test_remove_constraints_lengthchange (line 1443) | def test_remove_constraints_lengthchange(self, benzene_modifications, ...
    method test_constraint_to_harmonic (line 1492) | def test_constraint_to_harmonic(self, benzene_modifications, reverse):
    method test_constraint_to_harmonic_nitrile (line 1527) | def test_constraint_to_harmonic_nitrile(self, benzene_modifications, r...
    method test_non_H_constraint_fail (line 1564) | def test_non_H_constraint_fail(self, benzene_modifications, reverse):
    method test_double_constraint_fail (line 1606) | def test_double_constraint_fail(self):
  function tyk2_xml (line 1641) | def tyk2_xml(tmp_path_factory):
  function tyk2_reference_xml (line 1687) | def tyk2_reference_xml():
  class TestTyk2XmlRegression (line 1696) | class TestTyk2XmlRegression:
    method test_particles (line 1700) | def test_particles(tyk2_xml, tyk2_reference_xml):
    method test_constraints (line 1711) | def test_constraints(tyk2_xml, tyk2_reference_xml):
  class TestProtocolResult (line 1723) | class TestProtocolResult:
    method protocolresult (line 1725) | def protocolresult(self, rfe_transformation_json):
    method test_reload_protocol_result (line 1732) | def test_reload_protocol_result(self, rfe_transformation_json):
    method test_get_estimate (line 1739) | def test_get_estimate(self, protocolresult):
    method test_get_uncertainty (line 1747) | def test_get_uncertainty(self, protocolresult):
    method test_get_individual (line 1755) | def test_get_individual(self, protocolresult):
    method test_get_forwards_etc (line 1764) | def test_get_forwards_etc(self, protocolresult):
    method test_none_foward_reverse_energies (line 1779) | def test_none_foward_reverse_energies(self, protocolresult):
    method test_get_overlap_matrices (line 1790) | def test_get_overlap_matrices(self, protocolresult):
    method test_get_replica_transition_statistics (line 1800) | def test_get_replica_transition_statistics(self, protocolresult):
    method test_equilibration_iterations (line 1811) | def test_equilibration_iterations(self, protocolresult):
    method test_production_iterations (line 1818) | def test_production_iterations(self, protocolresult):
    method test_filenotfound_replica_states (line 1825) | def test_filenotfound_replica_states(self, protocolresult):
  function benzene_solvent_openmm_system (line 1833) | def benzene_solvent_openmm_system(benzene_modifications):
  function benzene_tip4p_solvent_openmm_system (line 1867) | def benzene_tip4p_solvent_openmm_system(benzene_modifications):
  function benzene_self_system_mapping (line 1907) | def benzene_self_system_mapping(benzene_solvent_openmm_system):
  function test_get_ion_water_parameters_unknownresname (line 1942) | def test_get_ion_water_parameters_unknownresname(ion, water, benzene_sol...
  function test_get_alchemical_waters_no_waters (line 1953) | def test_get_alchemical_waters_no_waters(
  function test_handle_alchemwats_incorrect_count (line 1966) | def test_handle_alchemwats_incorrect_count(
  function test_handle_alchemwats_too_many_nbf (line 1987) | def test_handle_alchemwats_too_many_nbf(
  function test_handle_alchemwats_vsite_water (line 2011) | def test_handle_alchemwats_vsite_water(
  function test_handle_alchemwats_incorrect_atom (line 2033) | def test_handle_alchemwats_incorrect_atom(
  function test_handle_alchemical_wats (line 2061) | def test_handle_alchemical_wats(
  function _assert_total_charge (line 2107) | def _assert_total_charge(system, atom_classes, chgA, chgB):
  function test_dry_run_alchemwater_solvent (line 2147) | def test_dry_run_alchemwater_solvent(benzene_to_benzoic_mapping, solv_se...
  function test_setup_complex_alchemwater_totcharge (line 2196) | def test_setup_complex_alchemwater_totcharge(
  function test_structural_analysis_error (line 2253) | def test_structural_analysis_error(tmp_path):
  function test_dry_run_vacuum_write_frequency (line 2273) | def test_dry_run_vacuum_write_frequency(

FILE: src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_resume.py
  function protocol_settings (line 37) | def protocol_settings():
  function test_verify_execution_environment (line 51) | def test_verify_execution_environment():
  function test_verify_execution_environment_fail (line 62) | def test_verify_execution_environment_fail():
  function test_verify_execution_env_missing_key (line 74) | def test_verify_execution_env_missing_key():
  function test_check_restart (line 90) | def test_check_restart(protocol_settings, htop_trajectory_path):
  class TestCheckpointResuming (line 106) | class TestCheckpointResuming:
    method protocol_dag (line 108) | def protocol_dag(
    method _check_sampler (line 118) | def _check_sampler(sampler, num_iterations: int):
    method _get_positions (line 129) | def _get_positions(dataset):
    method _copy_simfiles (line 137) | def _copy_simfiles(basedir: pathlib.Path, filepath):
    method test_resume (line 141) | def test_resume(self, protocol_dag, htop_trajectory_path, htop_checkpo...
    method test_resume_fail_particles (line 223) | def test_resume_fail_particles(
    method test_resume_fail_constraints (line 257) | def test_resume_fail_constraints(
    method test_resume_fail_forces (line 297) | def test_resume_fail_forces(
    method test_resume_differ_barostat (line 335) | def test_resume_differ_barostat(
    method test_resume_differ_forces (line 380) | def test_resume_differ_forces(
    method test_resume_bad_files (line 428) | def test_resume_bad_files(
    method test_missing_file (line 468) | def test_missing_file(

FILE: src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_slow.py
  function test_openmm_run_engine (line 19) | def test_openmm_run_engine(
  function test_run_eg5_sim (line 131) | def test_run_eg5_sim(eg5_protein, eg5_ligands, eg5_cofactor, tmp_path):
  function test_run_dodecahedron_sim (line 176) | def test_run_dodecahedron_sim(benzene_system, toluene_system, benzene_to...

FILE: src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_tokenization.py
  function rfe_protocol (line 24) | def rfe_protocol():
  function rfe_protocol_other_input_units (line 31) | def rfe_protocol_other_input_units():
  function protocol_units (line 39) | def protocol_units(rfe_protocol, benzene_system, toluene_system, benzene...
  function protocol_setup_unit (line 49) | def protocol_setup_unit(protocol_units):
  function protocol_simulation_unit (line 56) | def protocol_simulation_unit(protocol_units):
  function protocol_analysis_unit (line 63) | def protocol_analysis_unit(protocol_units):
  class TestRelativeHybridTopologyProtocolResult (line 70) | class TestRelativeHybridTopologyProtocolResult(GufeTokenizableTestsMixin):
    method instance (line 76) | def instance(self):
  class TestRelativeHybridTopologyProtocolOtherInputUnits (line 80) | class TestRelativeHybridTopologyProtocolOtherInputUnits(GufeTokenizableT...
    method instance (line 86) | def instance(self, rfe_protocol_other_input_units):
    method test_repr (line 89) | def test_repr(self, instance):
  class TestRelativeHybridTopologyProtocol (line 97) | class TestRelativeHybridTopologyProtocol(GufeTokenizableTestsMixin):
    method instance (line 103) | def instance(self, rfe_protocol):
    method test_repr (line 106) | def test_repr(self, instance):
  class TestHybridTopologySetupUnit (line 114) | class TestHybridTopologySetupUnit(GufeTokenizableTestsMixin):
    method instance (line 120) | def instance(self, protocol_setup_unit):
    method test_key_stable (line 123) | def test_key_stable(self):
    method test_repr (line 126) | def test_repr(self, instance):
  class TestHybridTopologyMultiStateSimulationUnit (line 134) | class TestHybridTopologyMultiStateSimulationUnit(GufeTokenizableTestsMix...
    method instance (line 140) | def instance(self, protocol_simulation_unit):
    method test_key_stable (line 143) | def test_key_stable(self):
    method test_repr (line 146) | def test_repr(self, instance):
  class TestHybridTopologyMultiStateAnalysisUnit (line 154) | class TestHybridTopologyMultiStateAnalysisUnit(GufeTokenizableTestsMixin):
    method instance (line 160) | def instance(self, protocol_analysis_unit):
    method test_key_stable (line 163) | def test_key_stable(self):
    method test_repr (line 166) | def test_repr(self, instance):

FILE: src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_validation.py
  function vac_settings (line 14) | def vac_settings():
  function solv_settings (line 23) | def solv_settings():
  function test_invalid_protocol_repeats (line 30) | def test_invalid_protocol_repeats():
  function test_endstate_two_alchemcomp_stateA (line 37) | def test_endstate_two_alchemcomp_stateA(state, benzene_modifications):
  function test_endstates_not_smc (line 62) | def test_endstates_not_smc(state, benzene_modifications):
  function test_validate_mapping_none_mapping (line 86) | def test_validate_mapping_none_mapping():
  function test_validate_mapping_multi_mapping (line 92) | def test_validate_mapping_multi_mapping(benzene_to_toluene_mapping):
  function test_validate_mapping_alchem_not_in (line 101) | def test_validate_mapping_alchem_not_in(state, benzene_to_toluene_mapping):
  function test_vaccuum_PME_error (line 116) | def test_vaccuum_PME_error(
  function test_multiple_basesolvents_error (line 130) | def test_multiple_basesolvents_error(a2a_protein_membrane_component, a2a...
  function test_smcs_same_charge_passes (line 160) | def test_smcs_same_charge_passes(charge, benzene_modifications):
  function test_smcs_different_charges_none_not_none (line 174) | def test_smcs_different_charges_none_not_none(benzene_modifications):
  function test_smcs_different_charges_all (line 190) | def test_smcs_different_charges_all(benzene_modifications):
  function test_smcs_different_charges_different_endstates (line 206) | def test_smcs_different_charges_different_endstates(benzene_modifications):
  function test_solvent_nocutoff_error (line 223) | def test_solvent_nocutoff_error(
  function test_nonwater_solvent_error (line 241) | def test_nonwater_solvent_error(
  function test_too_many_solv_comps_error (line 268) | def test_too_many_solv_comps_error(
  function test_bad_solv_settings (line 301) | def test_bad_solv_settings(
  function test_too_many_prot_comps_error (line 322) | def test_too_many_prot_comps_error(
  function test_element_change_warning (line 359) | def test_element_change_warning(atom_mapping_basic_test_files):
  function test_charge_difference_no_corr (line 381) | def test_charge_difference_no_corr(benzene_to_benzoic_mapping):
  function test_charge_difference_no_solvent (line 396) | def test_charge_difference_no_solvent(benzene_to_benzoic_mapping):
  function test_charge_difference_no_pme (line 408) | def test_charge_difference_no_pme(benzene_to_benzoic_mapping):
  function test_greater_than_one_charge_difference_error (line 420) | def test_greater_than_one_charge_difference_error(aniline_to_benzoic_map...
  function test_get_charge_difference (line 440) | def test_get_charge_difference(mapping_name, result, request, caplog):
  function test_hightimestep (line 461) | def test_hightimestep(
  function test_time_per_iteration_divmod (line 482) | def test_time_per_iteration_divmod(
  function test_simsteps_not_timestep_divisible (line 505) | def test_simsteps_not_timestep_divisible(
  function test_simsteps_not_mcstep_divisible (line 527) | def test_simsteps_not_mcstep_divisible(
  function test_checkpoint_interval_not_divisible_time_per_iter (line 548) | def test_checkpoint_interval_not_divisible_time_per_iter(
  function test_pos_vel_write_frequency_not_divisible (line 570) | def test_pos_vel_write_frequency_not_divisible(
  function test_real_time_analysis_not_divisible (line 594) | def test_real_time_analysis_not_divisible(
  function test_n_replicas_not_n_windows (line 615) | def test_n_replicas_not_n_windows(

FILE: src/openfe/tests/protocols/openmm_septop/conftest.py
  function protocol_dry_settings (line 10) | def protocol_dry_settings():
  function benzene_toluene_dag (line 19) | def benzene_toluene_dag(

FILE: src/openfe/tests/protocols/openmm_septop/test_septop_protocol.py
  function default_settings (line 67) | def default_settings():
  function test_create_default_protocol (line 72) | def test_create_default_protocol(default_settings):
  function test_serialize_protocol (line 81) | def test_serialize_protocol(default_settings):
  function test_repeat_units (line 91) | def test_repeat_units(benzene_complex_system, toluene_complex_system, de...
  function test_create_independent_repeat_ids (line 132) | def test_create_independent_repeat_ids(
  function compute_interaction_energy (line 167) | def compute_interaction_energy(
  function three_particle_system (line 187) | def three_particle_system():
  class TestNonbondedInteractions (line 225) | class TestNonbondedInteractions:
    method test_one_ligand (line 226) | def test_one_ligand(self, three_particle_system):
    method test_two_ligands (line 278) | def test_two_ligands(self, three_particle_system):
    method test_two_ligands_charges (line 337) | def test_two_ligands_charges(self, three_particle_system):
  function test_dry_run_benzene_toluene (line 365) | def test_dry_run_benzene_toluene(benzene_toluene_dag, tmp_path):
  function test_dry_run_methods (line 461) | def test_dry_run_methods(
  function test_dry_run_ligand_system_pressure (line 518) | def test_dry_run_ligand_system_pressure(
  function test_virtual_sites_no_reassign (line 562) | def test_virtual_sites_no_reassign(
  function test_dry_run_ligand_system_cutoff (line 615) | def test_dry_run_ligand_system_cutoff(
  function test_dry_run_benzene_toluene_tip4p (line 655) | def test_dry_run_benzene_toluene_tip4p(
  function test_dry_run_benzene_toluene_noncubic (line 706) | def test_dry_run_benzene_toluene_noncubic(
  function test_dry_run_solv_user_charges_benzene_toluene (line 755) | def test_dry_run_solv_user_charges_benzene_toluene(
  function test_high_timestep (line 863) | def test_high_timestep(
  function test_bad_sampler (line 886) | def test_bad_sampler():
  function T4L_xml (line 905) | def T4L_xml(
  class TestT4LXmlRegression (line 935) | class TestT4LXmlRegression:
    method test_particles (line 939) | def test_particles(T4L_xml, T4L_septop_reference_xml):
    method test_constraints (line 953) | def test_constraints(T4L_xml, T4L_septop_reference_xml):
  class TestA2AMembraneDryRun (line 973) | class TestA2AMembraneDryRun:
    method settings (line 981) | def settings(self):
    method dag (line 992) | def dag(self, settings, a2a_ligands, a2a_protein_membrane_component):
    method complex_setup_units (line 1024) | def complex_setup_units(self, dag):
    method complex_run_units (line 1028) | def complex_run_units(self, dag):
    method complex_analysis_unit (line 1032) | def complex_analysis_unit(self, dag):
    method solvent_setup_units (line 1036) | def solvent_setup_units(self, dag):
    method solvent_run_units (line 1040) | def solvent_run_units(self, dag):
    method solvent_analysis_unit (line 1044) | def solvent_analysis_unit(self, dag):
    method test_number_of_units (line 1047) | def test_number_of_units(
    method _assert_force_num (line 1056) | def _assert_force_num(self, system, forcetype, number):
    method _assert_expected_alchemical_forces (line 1060) | def _assert_expected_alchemical_forces(self, system, complexed: bool, ...
    method _assert_expected_nonalchemical_forces (line 1103) | def _assert_expected_nonalchemical_forces(self, system, complexed: boo...
    method _verify_sampler (line 1139) | def _verify_sampler(self, sampler, complexed: bool, settings):
    method _test_orthogonal_vectors (line 1158) | def _test_orthogonal_vectors(system):
    method _test_cubic_vectors (line 1183) | def _test_cubic_vectors(system):
    method test_complex_dry_run (line 1199) | def test_complex_dry_run(self, complex_setup_units, complex_run_units,...
    method test_solvent_dry_run (line 1244) | def test_solvent_dry_run(self, solvent_setup_units, solvent_run_units,...

FILE: src/openfe/tests/protocols/openmm_septop/test_septop_protocol_results.py
  function patcher (line 60) | def patcher():
  function test_unit_tagging (line 129) | def test_unit_tagging(benzene_toluene_dag, patcher, tmp_path):
  function test_gather (line 171) | def test_gather(benzene_toluene_dag, patcher, tmp_path):
  class TestProtocolResult (line 189) | class TestProtocolResult:
    method protocolresult (line 191) | def protocolresult(self, septop_json):
    method test_reload_protocol_result (line 198) | def test_reload_protocol_result(self, septop_json):
    method test_get_estimate (line 205) | def test_get_estimate(self, protocolresult):
    method test_get_uncertainty (line 213) | def test_get_uncertainty(self, protocolresult):
    method test_get_individual (line 220) | def test_get_individual(self, protocolresult):
    method test_get_forwards_etc (line 231) | def test_get_forwards_etc(self, protocolresult):
    method test_get_overlap_matrices (line 253) | def test_get_overlap_matrices(self, key, protocolresult):
    method test_get_replica_transition_statistics (line 269) | def test_get_replica_transition_statistics(self, key, protocolresult):
    method test_equilibration_iterations (line 286) | def test_equilibration_iterations(self, key, protocolresult):
    method test_production_iterations (line 295) | def test_production_iterations(self, key, protocolresult):
    method test_selection_indices (line 310) | def test_selection_indices(self, key, protocolresult, expected_size):
    method test_filenotfound_replica_states (line 319) | def test_filenotfound_replica_states(self, protocolresult):
    method test_restraint_geometry (line 325) | def test_restraint_geometry(self, protocolresult):

FILE: src/openfe/tests/protocols/openmm_septop/test_septop_resume.py
  function protocol_settings (line 35) | def protocol_settings():
  function test_verify_execution_environment (line 59) | def test_verify_execution_environment():
  function test_verify_execution_environment_fail (line 70) | def test_verify_execution_environment_fail():
  function test_verify_execution_env_missing_key (line 82) | def test_verify_execution_env_missing_key():
  function test_check_restart (line 98) | def test_check_restart(protocol_settings, septop_solv_trajectory_path):
  function test_check_restart_one_file_missing (line 114) | def test_check_restart_one_file_missing(protocol_settings, septop_solv_t...
  class TestCheckpointResuming (line 125) | class TestCheckpointResuming:
    method protocol_dag (line 127) | def protocol_dag(
    method protocol_units (line 142) | def protocol_units(self, protocol_dag):
    method setup_results (line 150) | def setup_results(self, protocol_units, tmp_path):
    method pdb_file (line 160) | def pdb_file(self, setup_results):
    method _check_sampler (line 164) | def _check_sampler(sampler, num_iterations: int):
    method _get_positions (line 175) | def _get_positions(dataset):
    method _copy_simfiles (line 184) | def _copy_simfiles(cwd: pathlib.Path, filepath):
    method test_resume (line 188) | def test_resume(
    method test_resume_fail_particles (line 271) | def test_resume_fail_particles(
    method test_resume_fail_constraints (line 309) | def test_resume_fail_constraints(
    method test_resume_fail_forces (line 349) | def test_resume_fail_forces(
    method test_resume_differ_barostat (line 387) | def test_resume_differ_barostat(
    method test_resume_differ_forces (line 437) | def test_resume_differ_forces(
    method test_resume_bad_files (line 494) | def test_resume_bad_files(

FILE: src/openfe/tests/protocols/openmm_septop/test_septop_settings.py
  function protocol_dry_settings (line 14) | def protocol_dry_settings():
  function default_settings (line 23) | def default_settings():
  function test_create_default_settings (line 28) | def test_create_default_settings():
  function test_incorrect_window_settings (line 41) | def test_incorrect_window_settings(val, default_settings):
  function test_monotonic_lambda_windows_A (line 70) | def test_monotonic_lambda_windows_A(val, default_settings):
  function test_monotonic_lambda_windows_B (line 100) | def test_monotonic_lambda_windows_B(val, default_settings):
  function test_output_induces_not_all (line 110) | def test_output_induces_not_all(default_settings):
  function test_adaptive_settings_no_protein_membrane (line 117) | def test_adaptive_settings_no_protein_membrane(toluene_complex_system, d...
  function test_adaptive_settings_with_protein_membrane (line 127) | def test_adaptive_settings_with_protein_membrane(a2a_protein_membrane_co...

FILE: src/openfe/tests/protocols/openmm_septop/test_septop_slow.py
  function default_settings (line 26) | def default_settings():
  function compare_energies (line 32) | def compare_energies(alchemical_system, positions):
  function test_lambda_energies (line 104) | def test_lambda_energies(
  function test_openmm_run_engine (line 214) | def test_openmm_run_engine(
  function test_restraints_solvent (line 297) | def test_restraints_solvent(

FILE: src/openfe/tests/protocols/openmm_septop/test_septop_tokenization.py
  function protocol (line 13) | def protocol():
  function protocol_units (line 18) | def protocol_units(protocol, benzene_complex_system, toluene_complex_sys...
  function solvent_setup_protocol_unit (line 28) | def solvent_setup_protocol_unit(protocol_units):
  function solvent_run_protocol_unit (line 35) | def solvent_run_protocol_unit(protocol_units):
  function solvent_analysis_protocol_unit (line 42) | def solvent_analysis_protocol_unit(protocol_units):
  function complex_setup_protocol_unit (line 49) | def complex_setup_protocol_unit(protocol_units):
  function complex_run_protocol_unit (line 56) | def complex_run_protocol_unit(protocol_units):
  function complex_analysis_protocol_unit (line 63) | def complex_analysis_protocol_unit(protocol_units):
  function protocol_result (line 70) | def protocol_result(septop_json):
  class TestSepTopProtocol (line 79) | class TestSepTopProtocol(GufeTokenizableTestsMixin):
    method instance (line 85) | def instance(self, protocol):
    method test_repr (line 88) | def test_repr(self, instance):
  class TestSepTopSolventSetupUnit (line 96) | class TestSepTopSolventSetupUnit(GufeTokenizableTestsMixin):
    method instance (line 104) | def instance(self, solvent_setup_protocol_unit):
    method test_repr (line 107) | def test_repr(self, instance):
  class TestSepTopSolventRunUnit (line 115) | class TestSepTopSolventRunUnit(GufeTokenizableTestsMixin):
    method instance (line 121) | def instance(self, solvent_run_protocol_unit):
    method test_repr (line 124) | def test_repr(self, instance):
  class TestSepTopSolventAnalysisUnit (line 132) | class TestSepTopSolventAnalysisUnit(GufeTokenizableTestsMixin):
    method instance (line 138) | def instance(self, solvent_analysis_protocol_unit):
    method test_repr (line 141) | def test_repr(self, instance):
  class TestSepTopComplexSetupUnit (line 149) | class TestSepTopComplexSetupUnit(GufeTokenizableTestsMixin):
    method instance (line 157) | def instance(self, complex_setup_protocol_unit):
    method test_repr (line 160) | def test_repr(self, instance):
  class TestSepTopComplexRunUnit (line 168) | class TestSepTopComplexRunUnit(GufeTokenizableTestsMixin):
    method instance (line 174) | def instance(self, complex_run_protocol_unit):
    method test_repr (line 177) | def test_repr(self, instance):
  class TestSepTopComplexAnalysisUnit (line 185) | class TestSepTopComplexAnalysisUnit(GufeTokenizableTestsMixin):
    method instance (line 191) | def instance(self, complex_analysis_protocol_unit):
    method test_repr (line 194) | def test_repr(self, instance):
  class TestSepTopProtocolResult (line 202) | class TestSepTopProtocolResult(GufeTokenizableTestsMixin):
    method instance (line 208) | def instance(self, protocol_result):
    method test_repr (line 211) | def test_repr(self, instance):

FILE: src/openfe/tests/protocols/openmm_septop/test_septop_validation.py
  function default_settings (line 17) | def default_settings():
  function test_validate_lambda_schedule_nreplicas (line 35) | def test_validate_lambda_schedule_nreplicas(val, default_settings):
  function test_validate_lambda_schedule_nwindows (line 61) | def test_validate_lambda_schedule_nwindows(val, default_settings):
  function test_validate_lambda_schedule_nakedcharge (line 91) | def test_validate_lambda_schedule_nakedcharge(val, default_settings):
  function test_check_alchem_charge_diff (line 118) | def test_check_alchem_charge_diff(charged_benzene_modifications):
  function test_charge_error_create (line 127) | def test_charge_error_create(charged_benzene_modifications, T4_protein_c...
  function test_validate_endstates_protcomp (line 162) | def test_validate_endstates_protcomp(request, system_A, system_B, fail_e...
  function T4L_benzene_vacuum (line 171) | def T4L_benzene_vacuum(benzene_modifications, T4_protein_component):
  function test_validate_endstates_nosolvcomp (line 187) | def test_validate_endstates_nosolvcomp(
  function T4L_system (line 201) | def T4L_system(T4_protein_component):
  function test_validate_alchem_comps_missing (line 217) | def test_validate_alchem_comps_missing(
  function test_validate_alchem_comps_toomanyA (line 238) | def test_validate_alchem_comps_toomanyA(
  function test_validate_alchem_nonsmc (line 273) | def test_validate_alchem_nonsmc(

FILE: src/openfe/tests/protocols/openmm_septop/utils.py
  function _get_units (line 26) | def _get_units(protocol_units, unit_type):

FILE: src/openfe/tests/protocols/restraints/test_geometry_base.py
  function test_hostguest_geometry (line 9) | def test_hostguest_geometry():
  function test_hostguest_positiveidxs_validator (line 18) | def test_hostguest_positiveidxs_validator():

FILE: src/openfe/tests/protocols/restraints/test_geometry_boresch.py
  function eg5_protein_ligand_universe (line 21) | def eg5_protein_ligand_universe(eg5_protein_pdb, eg5_ligands):
  function test_get_boresch_missing_atoms (line 29) | def test_get_boresch_missing_atoms(eg5_protein_ligand_universe, eg5_liga...
  function test_boresch_too_few_host_atoms_found (line 47) | def test_boresch_too_few_host_atoms_found(eg5_protein_ligand_universe, e...
  function test_boresch_restraint_user_defined (line 64) | def test_boresch_restraint_user_defined(eg5_protein_ligand_universe, eg5...
  function test_boresch_no_guest_atoms_found_ethane (line 95) | def test_boresch_no_guest_atoms_found_ethane(eg5_protein_pdb):
  function test_boresch_no_guest_atoms_found_collinear (line 117) | def test_boresch_no_guest_atoms_found_collinear(eg5_protein_pdb):
  function test_boresch_no_host_atom_pool (line 135) | def test_boresch_no_host_atom_pool(eg5_protein_ligand_universe, eg5_liga...
  function test_boresch_no_host_anchor (line 153) | def test_boresch_no_host_anchor(eg5_protein_ligand_universe, eg5_ligands):
  function test_get_boresch_restraint_single_frame (line 175) | def test_get_boresch_restraint_single_frame(eg5_protein_ligand_universe,...
  function test_get_boresch_restraint_dssp (line 205) | def test_get_boresch_restraint_dssp(eg5_protein_ligand_universe, eg5_lig...
  function test_get_boresch_restrain_industry_benchmark_systems (line 283) | def test_get_boresch_restrain_industry_benchmark_systems(system, industr...

FILE: src/openfe/tests/protocols/restraints/test_geometry_boresch_guest.py
  function test_get_bond_angle_aromatic (line 31) | def test_get_bond_angle_aromatic(eg5_ligands, aromatic, expected):
  function test_sort_by_distance (line 45) | def test_sort_by_distance(eg5_ligands):
  function test_get_guest_atom_pool (line 51) | def test_get_guest_atom_pool(eg5_ligands):
  function test_get_guest_atom_pool_all_heavy (line 66) | def test_get_guest_atom_pool_all_heavy(eg5_ligands):
  function test_get_guest_atom_pool_no_atoms (line 85) | def test_get_guest_atom_pool_no_atoms(eg5_ligands):
  function test_find_guest_atoms_normal (line 97) | def test_find_guest_atoms_normal(eg5_ligands):
  function test_find_guest_atoms_no_atom_pool (line 108) | def test_find_guest_atoms_no_atom_pool():

FILE: src/openfe/tests/protocols/restraints/test_geometry_boresch_host.py
  function eg5_protein_ligand_universe (line 31) | def eg5_protein_ligand_universe(eg5_protein_pdb, eg5_ligands):
  function eg5_protein_ligand_universe_bonded (line 40) | def eg5_protein_ligand_universe_bonded(eg5_protein_pdb, eg5_ligands):
  function test_host_atom_candidates_dssp (line 50) | def test_host_atom_candidates_dssp(eg5_protein_ligand_universe):
  function test_host_atom_candidates_dssp_too_few_atoms (line 75) | def test_host_atom_candidates_dssp_too_few_atoms(eg5_protein_ligand_univ...
  function test_host_atom_candidate_small_search (line 96) | def test_host_atom_candidate_small_search(eg5_protein_ligand_universe):
  function test_evaluate_host1_bad_ref (line 110) | def test_evaluate_host1_bad_ref(eg5_protein_ligand_universe):
  function test_evaluate_host1_good (line 121) | def test_evaluate_host1_good(eg5_protein_ligand_universe):
  function test_evaluate_host2_good (line 156) | def test_evaluate_host2_good(eg5_protein_ligand_universe):
  class TestFindAnchorMulti (line 185) | class TestFindAnchorMulti:
    method universe (line 195) | def universe(self, eg5_protein_ligand_universe):
    method host_anchor (line 199) | def host_anchor(self, universe):
    method test_anchor_regression (line 209) | def test_anchor_regression(self, host_anchor):
    method test_host_guest_bond_distance (line 213) | def test_host_guest_bond_distance(self, host_anchor, universe):
    method test_host_distances (line 223) | def test_host_distances(self, host_anchor, universe):
    method test_not_collinear (line 237) | def test_not_collinear(self, host_anchor, universe):
    method test_angles (line 250) | def test_angles(self, host_anchor, universe):
    method test_dihedrals (line 271) | def test_dihedrals(self, host_anchor, universe):
  class TestFindAnchorBonded (line 299) | class TestFindAnchorBonded(TestFindAnchorMulti):
    method universe (line 307) | def universe(self, eg5_protein_ligand_universe_bonded):
    method host_anchor (line 311) | def host_anchor(self, universe):
  class TestFindAnchorBondedTrajectory (line 326) | class TestFindAnchorBondedTrajectory(TestFindAnchorMulti):
    method universe (line 335) | def universe(self, t4_lysozyme_trajectory_dir):
    method host_anchor (line 346) | def host_anchor(self, universe):
  function test_boresch_evaluation_noatomgroup_error (line 356) | def test_boresch_evaluation_noatomgroup_error():
  function test_boresch_evaluation_incorrectnumber_error (line 366) | def test_boresch_evaluation_incorrectnumber_error(eg5_protein_ligand_uni...
  function test_find_host_anchor_multi_none (line 378) | def test_find_host_anchor_multi_none(eg5_protein_ligand_universe):
  function test_find_host_anchor_bonded_none (line 394) | def test_find_host_anchor_bonded_none(eg5_protein_ligand_universe_bonded):
  function test_find_host_anchor_bonded_nobonds_none (line 410) | def test_find_host_anchor_bonded_nobonds_none(eg5_protein_ligand_universe):

FILE: src/openfe/tests/protocols/restraints/test_geometry_flatbottom.py
  function eg5_protein_ligand_universe (line 15) | def eg5_protein_ligand_universe(eg5_protein_pdb, eg5_ligands):
  function test_no_atoms_found (line 23) | def test_no_atoms_found(eg5_protein_ligand_universe):
  function test_get_flatbottom_restraint_from_selection (line 41) | def test_get_flatbottom_restraint_from_selection(eg5_protein_ligand_univ...
  function test_get_flatbottom_restraint_from_atoms (line 61) | def test_get_flatbottom_restraint_from_atoms(eg5_protein_ligand_universe):

FILE: src/openfe/tests/protocols/restraints/test_geometry_harmonic.py
  function eg5_protein_ligand_universe (line 15) | def eg5_protein_ligand_universe(eg5_protein_pdb, eg5_ligands):
  function test_hostguest_geometry (line 23) | def test_hostguest_geometry():
  function test_get_distance_restraint_selection (line 32) | def test_get_distance_restraint_selection(eg5_protein_ligand_universe):
  function test_get_distance_restraint_atom_list (line 51) | def test_get_distance_restraint_atom_list(eg5_protein_ligand_universe):
  function test_get_molecule_centers_restraint (line 69) | def test_get_molecule_centers_restraint(eg5_ligands):

FILE: src/openfe/tests/protocols/restraints/test_geometry_utils.py
  function eg5_pdb_universe (line 38) | def eg5_pdb_universe(eg5_protein_pdb):
  function eg5_protein_ligand_universe (line 43) | def eg5_protein_ligand_universe(eg5_protein_pdb, eg5_ligands):
  function beta_barrel_universe (line 52) | def beta_barrel_universe():
  function test_mda_selection_none_error (line 58) | def test_mda_selection_none_error(eg5_pdb_universe):
  function test_mda_selection_both_args_error (line 63) | def test_mda_selection_both_args_error(eg5_pdb_universe):
  function test_mda_selection_universe_atom_list (line 68) | def test_mda_selection_universe_atom_list(eg5_pdb_universe):
  function test_mda_selection_atomgroup_string (line 73) | def test_mda_selection_atomgroup_string(eg5_pdb_universe):
  function test_aromatic_rings (line 94) | def test_aromatic_rings(smiles, expected):
  function test_heavy_atoms (line 137) | def test_heavy_atoms(smiles, nheavy, nlight):
  function test_central_idx (line 168) | def test_central_idx(smiles, idx):
  function test_central_atom_disconnected (line 176) | def test_central_atom_disconnected():
  function test_collinear_too_few_atoms (line 183) | def test_collinear_too_few_atoms():
  function test_collinear_index_match_error_length (line 188) | def test_collinear_index_match_error_length():
  function test_collinear_index_match_error_index (line 196) | def test_collinear_index_match_error_index():
  function test_is_collinear_three_atoms (line 220) | def test_is_collinear_three_atoms(arr, thresh, truth):
  function test_is_collinear_three_atoms_dimensions (line 242) | def test_is_collinear_three_atoms_dimensions(arr, truth, dims):
  function test_is_collinear_four_atoms (line 276) | def test_is_collinear_four_atoms(arr, tresh, truth):
  function test_wrap_angle_degrees (line 287) | def test_wrap_angle_degrees():
  function test_wrap_angle_radians (line 307) | def test_wrap_angle_radians(angle, expected):
  function test_angle_not_flat (line 319) | def test_angle_not_flat(limit, force, temperature):
  function test_check_dihedral_bounds (line 344) | def test_check_dihedral_bounds(dihed, expected):
  function test_check_dihedral_bounds_defined (line 357) | def test_check_dihedral_bounds_defined(dihed, lower, upper, expected):
  function test_angular_variance (line 362) | def test_angular_variance():
  function test_atomgroup_has_bonds (line 384) | def test_atomgroup_has_bonds(eg5_protein_pdb):
  function t4_lysozyme_trajectory_universe (line 405) | def t4_lysozyme_trajectory_universe(t4_lysozyme_trajectory_dir):
  function test_atomgroup_has_bonds_ions (line 418) | def test_atomgroup_has_bonds_ions(t4_lysozyme_trajectory_universe):
  function test_centroid_distance_sort (line 432) | def test_centroid_distance_sort(eg5_protein_ligand_universe):
  function test_find_host_atoms (line 444) | def test_find_host_atoms(eg5_protein_ligand_universe):
  function test_get_rmsf_single_frame (line 464) | def test_get_rmsf_single_frame(eg5_protein_ligand_universe):
  function test_get_rmsf_trajectory (line 475) | def test_get_rmsf_trajectory(t4_lysozyme_trajectory_universe):
  class TestStableSelection (line 509) | class TestStableSelection:
    method test_stable_ss_selection (line 510) | def test_stable_ss_selection(self, t4_lysozyme_trajectory_universe):
    method test_small_chain (line 525) | def test_small_chain(self, t4_lysozyme_trajectory_universe):
    method test_bad_dssp (line 537) | def test_bad_dssp(self, t4_lysozyme_trajectory_universe):
    method test_beta_dssp (line 554) | def test_beta_dssp(self, beta_barrel_universe):
  function test_protein_chain_selection (line 565) | def test_protein_chain_selection(eg5_protein_ligand_universe):
  function test_protein_chain_selection_subchain (line 580) | def test_protein_chain_selection_subchain(eg5_pdb_universe):
  function test_protein_chain_selection_nochains (line 593) | def test_protein_chain_selection_nochains(eg5_pdb_universe):
  function test_protein_chain_selection_trim_too_large (line 607) | def test_protein_chain_selection_trim_too_large(eg5_pdb_universe):

FILE: src/openfe/tests/protocols/restraints/test_omm_restraints.py
  function test_parameter_state_default (line 33) | def test_parameter_state_default():
  function test_parameter_state_suffix (line 40) | def test_parameter_state_suffix(suffix, lambda_var):
  function test_single_bond_mixin (line 67) | def test_single_bond_mixin(restraint, geometry_settings):
  function test_verify_inputs (line 80) | def test_verify_inputs():
  function test_verify_geometry (line 89) | def test_verify_geometry():
  function tyk2_protein_ligand_system (line 101) | def tyk2_protein_ligand_system(industry_benchmark_files):
  function tyk2_rdkit_ligand (line 109) | def tyk2_rdkit_ligand(industry_benchmark_files):
  function test_harmonic_add_force (line 120) | def test_harmonic_add_force(tyk2_protein_ligand_system):
  function test_flatbottom_add_force (line 153) | def test_flatbottom_add_force(tyk2_protein_ligand_system):
  function test_centriod_harmonic_add_force (line 191) | def test_centriod_harmonic_add_force(tyk2_protein_ligand_system):
  function test_centroid_flat_bottom_add_force (line 229) | def test_centroid_flat_bottom_add_force(tyk2_protein_ligand_system):
  function test_add_boresch_force (line 272) | def test_add_boresch_force(tyk2_protein_ligand_system, tyk2_rdkit_ligand):
  function test_get_boresch_state_correction (line 316) | def test_get_boresch_state_correction(tyk2_protein_ligand_system, tyk2_r...

FILE: src/openfe/tests/protocols/restraints/test_openmm_forces.py
  function test_boresch_energy_function (line 17) | def test_boresch_energy_function(param):
  function test_periodic_boresch_energy_function (line 35) | def test_periodic_boresch_energy_function(param):
  function test_custom_compound_force (line 53) | def test_custom_compound_force(num_atoms):
  function test_add_force_in_separate_group (line 74) | def test_add_force_in_separate_group(groups, expected):
  function test_add_too_many_force_groups (line 105) | def test_add_too_many_force_groups():

FILE: src/openfe/tests/protocols/restraints/test_settings.py
  function test_distance_restraint_settings_default (line 17) | def test_distance_restraint_settings_default():
  function test_distance_restraint_negative_idxs (line 28) | def test_distance_restraint_negative_idxs():
  function test_flatbottom_restraint_settings_default (line 41) | def test_flatbottom_restraint_settings_default():
  function test_flatbottom_restraint_negative_well (line 52) | def test_flatbottom_restraint_negative_well():
  function test_boresch_restraint_settings_default (line 64) | def test_boresch_restraint_settings_default():

FILE: src/openfe/tests/protocols/test_openmm_settings.py
  class TestOMMSettingsFromStrings (line 14) | class TestOMMSettingsFromStrings:
    method test_system_settings (line 16) | def test_system_settings(self):
    method test_solvation_settings (line 23) | def test_solvation_settings(self):
    method test_alchemical_sampler_settings (line 30) | def test_alchemical_sampler_settings(self):
    method test_integator_settings (line 34) | def test_integator_settings(self):
    method test_simulation_settings (line 47) | def test_simulation_settings(self):
  class TestEquilRFESettingsFromString (line 60) | class TestEquilRFESettingsFromString:
    method test_alchemical_settings (line 61) | def test_alchemical_settings(self):
  class TestOpenMMSolvationSettings (line 69) | class TestOpenMMSolvationSettings:
    method test_unreduced_box_vectors (line 70) | def test_unreduced_box_vectors(self):
    method test_non_positive_solvent (line 90) | def test_non_positive_solvent(self, n_solv):
    method test_box_size_properties_non_1d (line 96) | def test_box_size_properties_non_1d(self):
  class TestOpenMMEngineSettings (line 103) | class TestOpenMMEngineSettings:
    method test_ok_platforms (line 105) | def test_ok_platforms(self, platform):
    method test_fail_platform (line 109) | def test_fail_platform(self):

FILE: src/openfe/tests/protocols/test_openmmutils.py
  function test_validate_ommsolvation_settings_unique_settings (line 60) | def test_validate_ommsolvation_settings_unique_settings(
  function test_validate_ommsolvation_settings_shape_conflicts (line 82) | def test_validate_ommsolvation_settings_shape_conflicts(
  function test_validate_timestep (line 98) | def test_validate_timestep():
  function test_get_simsteps (line 111) | def test_get_simsteps(s, ts, mc, es):
  function test_get_simsteps_indivisible_simtime (line 117) | def test_get_simsteps_indivisible_simtime():
  function test_mc_indivisible (line 124) | def test_mc_indivisible():
  function test_get_alchemical_components (line 131) | def test_get_alchemical_components(benzene_modifications, T4_protein_com...
  function test_duplicate_chemical_components (line 159) | def test_duplicate_chemical_components(benzene_modifications):
  function test_validate_solvent_nocutoff (line 174) | def test_validate_solvent_nocutoff(benzene_modifications):
  function test_validate_solvent_multiple_solvent (line 183) | def test_validate_solvent_multiple_solvent(benzene_modifications):
  function test_validate_solvent_multiple_solvated (line 196) | def test_validate_solvent_multiple_solvated(benzene_modifications, a2a_p...
  function test_not_water_solvent (line 209) | def test_not_water_solvent(benzene_modifications):
  function test_multiple_proteins (line 218) | def test_multiple_proteins(T4_protein_component):
  function test_membrane_protein_warns_with_non_membrane_barostat (line 225) | def test_membrane_protein_warns_with_non_membrane_barostat(a2a_protein_m...
  function test_non_membrane_protein_warns_with_membrane_barostat (line 234) | def test_non_membrane_protein_warns_with_membrane_barostat(T4_protein_co...
  function test_get_components_gas (line 243) | def test_get_components_gas(benzene_modifications):
  function test_components_solvent (line 258) | def test_components_solvent(benzene_modifications):
  function test_components_complex (line 274) | def test_components_complex(T4_protein_component, benzene_modifications):
  function test_validate_chemical_system (line 291) | def test_validate_chemical_system(a2a_protein_membrane_pdb):
  function get_settings (line 316) | def get_settings():
  class TestFEAnalysis (line 327) | class TestFEAnalysis:
    method reporter (line 330) | def reporter(self):
    method analyzer (line 344) | def analyzer(self, reporter):
    method test_free_energies (line 351) | def test_free_energies(self, analyzer):
    method test_plots (line 411) | def test_plots(self, analyzer, tmp_path):
    method test_plot_convergence_bad_units (line 418) | def test_plot_convergence_bad_units(self, analyzer):
    method test_analyze_unknown_method_warning_and_error (line 425) | def test_analyze_unknown_method_warning_and_error(self, reporter):
  class TestSystemCreation (line 437) | class TestSystemCreation:
    method test_system_generator_nosolv_nocache (line 438) | def test_system_generator_nosolv_nocache(self, get_settings):
    method test_system_generator_solv_cache (line 460) | def test_system_generator_solv_cache(self, get_settings):
    method test_system_generator_membrane (line 484) | def test_system_generator_membrane(self, get_settings):
    method test_get_omm_modeller_complex (line 506) | def test_get_omm_modeller_complex(
    method test_get_omm_modeller_membrane_box (line 538) | def test_get_omm_modeller_membrane_box(
    method ligand_mol_and_generator (line 594) | def ligand_mol_and_generator(self, get_settings):
    method test_get_omm_modeller_ligand_no_neutralize (line 609) | def test_get_omm_modeller_ligand_no_neutralize(self, ligand_mol_and_ge...
    method test_omm_modeller_ligand_n_solv (line 642) | def test_omm_modeller_ligand_n_solv(
    method test_omm_modeller_box_size (line 669) | def test_omm_modeller_box_size(self, ligand_mol_and_generator):
    method test_omm_modeller_box_vectors (line 695) | def test_omm_modeller_box_vectors(self, ligand_mol_and_generator):
  function test_convert_steps_per_iteration (line 722) | def test_convert_steps_per_iteration():
  function test_convert_steps_per_iteration_failure (line 735) | def test_convert_steps_per_iteration_failure():
  function test_convert_real_time_analysis_iterations (line 747) | def test_convert_real_time_analysis_iterations():
  function test_convert_real_time_analysis_iterations_interval_fail (line 761) | def test_convert_real_time_analysis_iterations_interval_fail():
  function test_convert_real_time_analysis_iterations_min_interval_fail (line 775) | def test_convert_real_time_analysis_iterations_min_interval_fail():
  function test_convert_real_time_analysis_iterations_None (line 789) | def test_convert_real_time_analysis_iterations_None():
  function test_convert_target_error_from_kcal_per_mole_to_kT (line 804) | def test_convert_target_error_from_kcal_per_mole_to_kT():
  function test_convert_target_error_from_kcal_per_mole_to_kT_zero (line 813) | def test_convert_target_error_from_kcal_per_mole_to_kT_zero():
  class TestOFFPartialCharge (line 823) | class TestOFFPartialCharge:
    method uncharged_mol (line 825) | def uncharged_mol(self, CN_molecule):
    method test_offmol_chg_gen_charged_overwrite (line 829) | def test_offmol_chg_gen_charged_overwrite(self, overwrite, uncharged_m...
    method test_unknown_method (line 845) | def test_unknown_method(self, uncharged_mol):
    method test_incompatible_backend_am1bcc (line 865) | def test_incompatible_backend_am1bcc(self, method, backend, uncharged_...
    method test_no_conformers (line 876) | def test_no_conformers(self, uncharged_mol):
    method test_too_many_existing_conformers (line 889) | def test_too_many_existing_conformers(self, uncharged_mol):
    method test_too_many_requested_conformers (line 906) | def test_too_many_requested_conformers(self, uncharged_mol):
    method test_am1bcc_no_conformer (line 917) | def test_am1bcc_no_conformer(self, uncharged_mol):
    method test_am1bcc_conformer_nochange (line 928) | def test_am1bcc_conformer_nochange(self, eg5_ligands):
    method test_latest_production_nagl (line 968) | def test_latest_production_nagl(self, uncharged_mol):
    method test_no_production_nagl (line 983) | def test_no_production_nagl(self, uncharged_mol):
    method test_am1bcc_reference (line 1076) | def test_am1bcc_reference(
    method test_nagl_oechem_not_openeye_error (line 1105) | def test_nagl_oechem_not_openeye_error(self, uncharged_mol):
    method test_nagl_import_error (line 1120) | def test_nagl_import_error(self, monkeypatch, uncharged_mol):
    method test_espaloma_import_error (line 1137) | def test_espaloma_import_error(self, monkeypatch, uncharged_mol):
    method test_openeye_import_error (line 1154) | def test_openeye_import_error(self, monkeypatch, uncharged_mol):
  function test_forward_backwards_failure (line 1177) | def test_forward_backwards_failure(simulation_nc):

FILE: src/openfe/tests/protocols/test_openmmutils_serialization.py
  function test_serialize_creates_parent_directory (line 11) | def test_serialize_creates_parent_directory(tmp_path):
  function test_serialize_xml (line 20) | def test_serialize_xml(tmp_path):
  function test_serialize_bz2 (line 29) | def test_serialize_bz2(tmp_path):
  function test_deserialize_xml (line 41) | def test_deserialize_xml(tmp_path):
  function test_deserialize_bz2 (line 52) | def test_deserialize_bz2(tmp_path):

FILE: src/openfe/tests/setup/alchemical_network_planner/edge_types.py
  function both_states_proteinC_edge (line 10) | def both_states_proteinC_edge(edge: Transformation) -> bool:
  function both_states_solventC_edge (line 14) | def both_states_solventC_edge(edge: Transformation) -> bool:
  function both_states_ligandC_edge (line 18) | def both_states_ligandC_edge(edge: Transformation) -> bool:
  function r_vacuum_edge (line 22) | def r_vacuum_edge(edge: Transformation) -> bool:
  function r_solvent_edge (line 30) | def r_solvent_edge(edge: Transformation) -> bool:
  function r_complex_edge (line 38) | def r_complex_edge(edge: Transformation) -> bool:

FILE: src/openfe/tests/setup/alchemical_network_planner/test_relative_alchemical_network_planner.py
  function test_rhfe_alchemical_network_planner_init (line 15) | def test_rhfe_alchemical_network_planner_init():
  function test_rbfe_alchemical_network_planner_init (line 20) | def test_rbfe_alchemical_network_planner_init():
  function test_rbfe_alchemical_network_planner_call (line 25) | def test_rbfe_alchemical_network_planner_call(atom_mapping_basic_test_fi...
  function test_rhfe_alchemical_network_planner_call_multigraph (line 74) | def test_rhfe_alchemical_network_planner_call_multigraph(atom_mapping_ba...
  function test_rhfe_alchemical_network_planner_call (line 105) | def test_rhfe_alchemical_network_planner_call(atom_mapping_basic_test_fi...

FILE: src/openfe/tests/setup/atom_mapping/conftest.py
  function _translate_lomap_mapping (line 16) | def _translate_lomap_mapping(atom_mapping_str: str) -> Dict[int, int]:
  function _get_atom_mapping_dict (line 21) | def _get_atom_mapping_dict(lomap_atom_mappings) -> Dict[Tuple[int, int],...
  function gufe_atom_mapping_matrix (line 29) | def gufe_atom_mapping_matrix(
  function mol_pair_to_shock_perses_mapper (line 50) | def mol_pair_to_shock_perses_mapper() -> Tuple[SmallMoleculeComponent, S...

FILE: src/openfe/tests/setup/atom_mapping/test_atommapper.py
  class TestAtomMapper (line 7) | class TestAtomMapper:
    method test_abstract_error (line 8) | def test_abstract_error(self, simple_mapping):
    method test_concrete_mapper (line 17) | def test_concrete_mapper(self, simple_mapping, other_mapping):
    method test_alchemical_charge_deprecation_warning (line 47) | def test_alchemical_charge_deprecation_warning(self, simple_mapping):

FILE: src/openfe/tests/setup/atom_mapping/test_lomap_atommapper.py
  function test_simple (line 14) | def test_simple(atom_mapping_basic_test_files, lomap_old_mapper):
  function test_distances (line 29) | def test_distances(atom_mapping_basic_test_files, lomap_old_mapper):
  function test_generator_length (line 51) | def test_generator_length(atom_mapping_basic_test_files, lomap_old_mapper):
  function test_bad_mapping (line 66) | def test_bad_mapping(atom_mapping_basic_test_files, lomap_old_mapper):
  function test_simple_no_element_changes (line 78) | def test_simple_no_element_changes(atom_mapping_basic_test_files, lomap_...
  function test_bas_mapping_no_element_changes (line 93) | def test_bas_mapping_no_element_changes(atom_mapping_basic_test_files, l...

FILE: src/openfe/tests/setup/atom_mapping/test_lomap_scorers.py
  function toluene_to_cyclohexane (line 21) | def toluene_to_cyclohexane(atom_mapping_basic_test_files):
  function toluene_to_methylnaphthalene (line 30) | def toluene_to_methylnaphthalene(atom_mapping_basic_test_files):
  function toluene_to_heptane (line 39) | def toluene_to_heptane(atom_mapping_basic_test_files):
  function methylnaphthalene_to_naphthol (line 51) | def methylnaphthalene_to_naphthol(atom_mapping_basic_test_files):
  function test_mcsr_zero (line 71) | def test_mcsr_zero(toluene_to_cyclohexane):
  function test_mcsr_nonzero (line 78) | def test_mcsr_nonzero(toluene_to_methylnaphthalene):
  function test_mcsr_custom_beta (line 84) | def test_mcsr_custom_beta(toluene_to_methylnaphthalene):
  function test_mcnar_score_pass (line 90) | def test_mcnar_score_pass(toluene_to_cyclohexane):
  function test_mcnar_score_fail (line 96) | def test_mcnar_score_fail(toluene_to_heptane):
  function test_atomic_number_score_pass (line 102) | def test_atomic_number_score_pass(toluene_to_cyclohexane):
  function test_atomic_number_score_fail (line 108) | def test_atomic_number_score_fail(methylnaphthalene_to_naphthol):
  function test_atomic_number_score_weights (line 115) | def test_atomic_number_score_weights(methylnaphthalene_to_naphthol):
  class TestSulfonamideRule (line 126) | class TestSulfonamideRule:
    method ethylbenzene (line 129) | def ethylbenzene():
    method sulfonamide (line 136) | def sulfonamide():
    method from_sulf_mapping (line 144) | def from_sulf_mapping():
    method test_sulfonamide_hit_backwards (line 171) | def test_sulfonamide_hit_backwards(ethylbenzene, sulfonamide, from_sul...
    method test_sulfonamide_hit_forwards (line 184) | def test_sulfonamide_hit_forwards(ethylbenzene, sulfonamide, from_sulf...
  function test_heterocycle_score (line 210) | def test_heterocycle_score(base, other, name, hit):
  function test_lomap_individual_scores (line 249) | def test_lomap_individual_scores(params, atom_mapping_basic_test_files):
  function test_lomap_regression (line 274) | def test_lomap_regression(
  function test_transmuting_methyl_into_ring_score (line 317) | def test_transmuting_methyl_into_ring_score():

FILE: src/openfe/tests/setup/atom_mapping/test_perses_atommapper.py
  function test_simple (line 12) | def test_simple(atom_mapping_basic_test_files):
  function test_generator_length (line 29) | def test_generator_length(atom_mapping_basic_test_files):
  function test_empty_atommappings (line 46) | def test_empty_atommappings(mol_pair_to_shock_perses_mapper):
  function test_dict_round_trip (line 62) | def test_dict_round_trip():

FILE: src/openfe/tests/setup/atom_mapping/test_perses_scorers.py
  function test_perses_normalization_not_using_positions (line 19) | def test_perses_normalization_not_using_positions(gufe_atom_mapping_matr...
  function test_perses_not_implemented_position_using (line 44) | def test_perses_not_implemented_position_using(gufe_atom_mapping_matrix):
  function test_perses_regression (line 61) | def test_perses_regression(gufe_atom_mapping_matrix):

FILE: src/openfe/tests/setup/chemicalsystem_generator/component_checks.py
  function ligandC_in_chem_sys (line 7) | def ligandC_in_chem_sys(chemical_system: ChemicalSystem) -> bool:
  function solventC_in_chem_sys (line 11) | def solventC_in_chem_sys(chemical_system: ChemicalSystem) -> bool:
  function proteinC_in_chem_sys (line 15) | def proteinC_in_chem_sys(chemical_system: ChemicalSystem) -> bool:
  function cofactorC_in_chem_sys (line 19) | def cofactorC_in_chem_sys(chemical_system: ChemicalSystem) -> bool:

FILE: src/openfe/tests/setup/chemicalsystem_generator/test_easy_chemicalsystem_generator.py
  function test_easy_chemical_system_generator_init (line 20) | def test_easy_chemical_system_generator_init(T4_protein_component):
  function test_build_vacuum_chemical_system (line 40) | def test_build_vacuum_chemical_system(ethane):
  function test_build_solvent_chemical_system (line 51) | def test_build_solvent_chemical_system(ethane):
  function test_build_protein_chemical_system (line 62) | def test_build_protein_chemical_system(ethane, T4_protein_component):
  function test_build_cofactor_chemical_system (line 76) | def test_build_cofactor_chemical_system(eg5_cofactor, eg5_ligands, eg5_p...
  function test_build_hydr_scenario_chemical_systems (line 88) | def test_build_hydr_scenario_chemical_systems(ethane):
  function test_build_binding_scenario_chemical_systems (line 100) | def test_build_binding_scenario_chemical_systems(ethane, T4_protein_comp...
  function test_build_hbinding_scenario_chemical_systems (line 115) | def test_build_hbinding_scenario_chemical_systems(ethane, T4_protein_com...

FILE: src/openfe/tests/setup/test_network_planning.py
  class BadMapper (line 13) | class BadMapper(openfe.setup.atom_mapping.LigandAtomMapper):
    method _defaults (line 15) | def _defaults(cls):
    method _to_dict (line 18) | def _to_dict(self):
    method _from_dict (line 22) | def _from_dict(cls, d):
    method _mappings_generator (line 25) | def _mappings_generator(self, molA, molB):
  function toluene_vs_others (line 30) | def toluene_vs_others(atom_mapping_basic_test_files):
  function simple_scorer (line 41) | def simple_scorer() -> Callable:
  function deterministic_toluene_mst_scorer (line 50) | def deterministic_toluene_mst_scorer() -> Callable:
  function deterministic_minimal_spanning_network (line 77) | def deterministic_minimal_spanning_network(
  function deterministic_minimal_redundant_network (line 93) | def deterministic_minimal_redundant_network(
  class TestRadialNetworkGenerator (line 109) | class TestRadialNetworkGenerator:
    method test_radial_network (line 111) | def test_radial_network(
    method test_radial_network_central_ligand_int_str (line 148) | def test_radial_network_central_ligand_int_str(
    method test_radial_network_bad_name (line 182) | def test_radial_network_bad_name(self, toluene_vs_others, lomap_old_ma...
    method test_radial_network_multiple_str (line 195) | def test_radial_network_multiple_str(self, toluene_vs_others, lomap_ol...
    method test_radial_network_index_error (line 208) | def test_radial_network_index_error(self, toluene_vs_others, lomap_old...
    method test_radial_network_self_central (line 221) | def test_radial_network_self_central(self, toluene_vs_others, lomap_ol...
    method test_radial_network_with_scorer (line 249) | def test_radial_network_with_scorer(self, toluene_vs_others, lomap_old...
    method test_radial_network_multiple_mappers_no_scorer (line 279) | def test_radial_network_multiple_mappers_no_scorer(self, toluene_vs_ot...
    method test_radial_network_no_mapping_failure (line 304) | def test_radial_network_no_mapping_failure(self, toluene_vs_others, lo...
  function test_generate_maximal_network (line 323) | def test_generate_maximal_network(
  class TestMinimalSpanningNetworkGenerator (line 369) | class TestMinimalSpanningNetworkGenerator:
    method test_minimal_spanning_network (line 371) | def test_minimal_spanning_network(
    method test_minimal_spanning_network_no_scorer_error (line 407) | def test_minimal_spanning_network_no_scorer_error(self, toluene_vs_oth...
    method test_minimal_spanning_network_connectedness (line 420) | def test_minimal_spanning_network_connectedness(self, deterministic_mi...
    method test_minimal_spanning_network_regression (line 430) | def test_minimal_spanning_network_regression(self, deterministic_minim...
    method test_minimal_spanning_network_unreachable (line 449) | def test_minimal_spanning_network_unreachable(
  class TestMinimalRedundantNetworkGenerator (line 468) | class TestMinimalRedundantNetworkGenerator:
    method test_minimal_redundant_network (line 469) | def test_minimal_redundant_network(
    method test_minimal_redundant_network_connectedness (line 488) | def test_minimal_redundant_network_connectedness(self, deterministic_m...
    method test_redundant_vs_spanning_network (line 499) | def test_redundant_vs_spanning_network(
    method test_minimal_redundant_network_edges (line 521) | def test_minimal_redundant_network_edges(self, deterministic_minimal_r...
    method test_minimal_redundant_network_redundant (line 548) | def test_minimal_redundant_network_redundant(self, deterministic_minim...
    method test_minimal_redundant_network_unreachable (line 554) | def test_minimal_redundant_network_unreachable(
  class TestGenerateNetworkFromNames (line 571) | class TestGenerateNetworkFromNames:
    method test_generate_network_from_names (line 572) | def test_generate_network_from_names(self, atom_mapping_basic_test_fil...
    method test_generate_network_from_names_bad_name_error (line 597) | def test_generate_network_from_names_bad_name_error(
    method test_generate_network_from_names_duplicate_name (line 614) | def test_generate_network_from_names_duplicate_name(
  class TestNetworkFromIndices (line 633) | class TestNetworkFromIndices:
    method test_network_from_indices (line 634) | def test_network_from_indices(self, atom_mapping_basic_test_files, lom...
    method test_network_from_indices_indexerror (line 657) | def test_network_from_indices_indexerror(self, atom_mapping_basic_test...
    method test_network_from_indices_disconnected_warning (line 669) | def test_network_from_indices_disconnected_warning(
  function test_network_from_external (line 690) | def test_network_from_external(file_fixture, loader, request, benzene_mo...
  function test_network_from_external_unknown_edge (line 722) | def test_network_from_external_unknown_edge(file_fixture, loader, reques...
  function test_bad_orion_network (line 746) | def test_bad_orion_network(benzene_modifications, tmp_path):
  function test_bad_edges_network (line 768) | def test_bad_edges_network(benzene_modifications, tmp_path):

FILE: src/openfe/tests/storage/conftest.py
  function solv_comp (line 9) | def solv_comp():
  function solvated_complex (line 14) | def solvated_complex(T4_protein_component, benzene_transforms, solv_comp):
  function solvated_ligand (line 25) | def solvated_ligand(benzene_transforms, solv_comp):
  function absolute_transformation (line 35) | def absolute_transformation(solvated_ligand, solvated_complex):
  function complex_equilibrium (line 45) | def complex_equilibrium(solvated_complex):
  function benzene_variants_star_map (line 53) | def benzene_variants_star_map(benzene_transforms, solv_comp, T4_protein_...

FILE: src/openfe/tests/storage/test_metadatastore.py
  function json_metadata (line 13) | def json_metadata(tmp_path):
  function per_file_metadata (line 23) | def per_file_metadata(tmp_path):
  class MetadataTests (line 36) | class MetadataTests:
    method test_store_metadata (line 39) | def test_store_metadata(self, metadata):
    method test_load_all_metadata (line 42) | def test_load_all_metadata(self):
    method test_delete (line 45) | def test_delete(self):
    method _test_load_all_metadata (line 48) | def _test_load_all_metadata(self, metadata):
    method _test_delete (line 54) | def _test_delete(self, metadata):
    method _test_iter (line 61) | def _test_iter(self, metadata):
    method _test_len (line 64) | def _test_len(self, metadata):
    method _test_getitem (line 67) | def _test_getitem(self, metadata):
  class TestJSONMetadataStore (line 71) | class TestJSONMetadataStore(MetadataTests):
    method test_store_metadata (line 72) | def test_store_metadata(self, json_metadata):
    method test_load_all_metadata (line 87) | def test_load_all_metadata(self, json_metadata):
    method test_load_all_metadata_nofile (line 90) | def test_load_all_metadata_nofile(self, tmp_path):
    method test_delete (line 97) | def test_delete(self, json_metadata):
    method test_iter (line 100) | def test_iter(self, json_metadata):
    method test_len (line 103) | def test_len(self, json_metadata):
    method test_getitem (line 106) | def test_getitem(self, json_metadata):
  class TestPerFileJSONMetadataStore (line 110) | class TestPerFileJSONMetadataStore(MetadataTests):
    method test_store_metadata (line 111) | def test_store_metadata(self, per_file_metadata):
    method test_load_all_metadata (line 123) | def test_load_all_metadata(self, per_file_metadata):
    method test_delete (line 126) | def test_delete(self, per_file_metadata):
    method test_iter (line 130) | def test_iter(self, per_file_metadata):
    method test_len (line 133) | def test_len(self, per_file_metadata):
    method test_getitem (line 136) | def test_getitem(self, per_file_metadata):
    method test_bad_metadata_contents (line 139) | def test_bad_metadata_contents(self, tmp_path):

FILE: src/openfe/tests/storage/test_resultclient.py
  function result_client (line 17) | def result_client():
  function _make_mock_transformation (line 42) | def _make_mock_transformation(hash_str):
  function test_load_file (line 48) | def test_load_file(result_client):
  class _ResultContainerTest (line 54) | class _ResultContainerTest:
    method get_container (line 56) | def get_container(result_client):
    method _getitem_object (line 59) | def _getitem_object(self, container):
    method test_iter (line 62) | def test_iter(self, result_client):
    method _get_key (line 66) | def _get_key(self, as_object, container):
    method test_getitem (line 77) | def test_getitem(self, as_object, result_client):
    method test_div (line 83) | def test_div(self, as_object, result_client):
    method test_caching (line 89) | def test_caching(self, result_client, load_with):
    method test_load_stream (line 109) | def test_load_stream(self, result_client):
    method test_load_bytes (line 115) | def test_load_bytes(self, result_client):
    method test_path (line 120) | def test_path(self, result_client):
    method test_result_server (line 124) | def test_result_server(self, result_client):
  class TestResultClient (line 129) | class TestResultClient(_ResultContainerTest):
    method get_container (line 140) | def get_container(result_client):
    method _getitem_object (line 143) | def _getitem_object(self, container):
    method test_store_protocol_dag_result (line 149) | def test_store_protocol_dag_result(self):
    method _test_store_load_same_process (line 153) | def _test_store_load_same_process(obj, store_func_name, load_func_name):
    method _test_store_load_different_process (line 165) | def _test_store_load_different_process(obj, store_func_name, load_func...
    method test_store_load_transformation_same_process (line 186) | def test_store_load_transformation_same_process(self, request, fixture):
    method test_store_load_transformation_different_process (line 198) | def test_store_load_transformation_different_process(self, request, fi...
    method test_store_load_network_same_process (line 207) | def test_store_load_network_same_process(self, request, fixture):
    method test_store_load_network_different_process (line 212) | def test_store_load_network_different_process(self, request, fixture):
    method test_delete (line 216) | def test_delete(self, result_client):
  class TestTransformationResults (line 224) | class TestTransformationResults(_ResultContainerTest):
    method get_container (line 234) | def get_container(result_client):
    method _getitem_object (line 242) | def _getitem_object(self, container):
  class TestCloneResults (line 246) | class TestCloneResults(_ResultContainerTest):
    method get_container (line 255) | def get_container(result_client):
    method _getitem_object (line 261) | def _getitem_object(self, container):
  class TestExtensionResults (line 265) | class TestExtensionResults(_ResultContainerTest):
    method get_container (line 273) | def get_container(result_client):
    method _get_key (line 279) | def _get_key(self, as_object, container):
    method test_div (line 287) | def test_div(self, result_client):
    method test_getitem (line 292) | def test_getitem(self, result_client):
    method test_caching (line 297) | def test_caching(self, result_client):

FILE: src/openfe/tests/storage/test_resultserver.py
  function result_server (line 14) | def result_server(tmp_path):
  class TestResultServer (line 22) | class TestResultServer:
    method test_store_bytes (line 23) | def test_store_bytes(self, result_server):
    method test_store_path (line 49) | def test_store_path(self, result_server, tmp_path):
    method test_iter (line 76) | def test_iter(self, result_server):
    method test_find_missing_files (line 79) | def test_find_missing_files(self, result_server):
    method test_load_stream (line 85) | def test_load_stream(self, result_server):
    method test_delete (line 91) | def test_delete(self, result_server, tmp_path):
    method test_load_stream_missing (line 100) | def test_load_stream_missing(self, result_server):
    method test_load_stream_error_bad_hash (line 104) | def test_load_stream_error_bad_hash(self, result_server):
    method test_load_stream_allow_bad_hash (line 110) | def test_load_stream_allow_bad_hash(self, result_server):

FILE: src/openfe/tests/utils/conftest.py
  class _NetworkTestContainer (line 14) | class _NetworkTestContainer(NamedTuple):
  function mols (line 25) | def mols():
  function std_edges (line 33) | def std_edges(mols):
  function simple_network (line 42) | def simple_network(mols, std_edges):
  function benzene_transforms (line 55) | def benzene_transforms():

FILE: src/openfe/tests/utils/test_atommapping_network_plotting.py
  function bound_args (line 18) | def bound_args(func, args, kwargs):
  function network_drawing (line 42) | def network_drawing(simple_network):
  function default_edge (line 58) | def default_edge(network_drawing):
  function default_node (line 64) | def default_node(network_drawing):
  class TestAtomMappingEdge (line 69) | class TestAtomMappingEdge:
    method test_draw_mapped_molecule (line 70) | def test_draw_mapped_molecule(self, default_edge):
    method test_get_image_extents (line 82) | def test_get_image_extents(self, default_edge):
    method test_select (line 87) | def test_select(self, default_edge, network_drawing):
    method test_select_mock_drawing (line 105) | def test_select_mock_drawing(self, edge_str, left_right, molA_to_molB,...
    method test_unselect (line 141) | def test_unselect(self, default_edge, network_drawing):
  class TestLigandNode (line 159) | class TestLigandNode:
    method setup_method (line 160) | def setup_method(self):
    method teardown_method (line 163) | def teardown_method(self):
    method test_register_artist (line 166) | def test_register_artist(self, default_node):
    method test_extent (line 172) | def test_extent(self, default_node):
    method test_xy (line 179) | def test_xy(self, default_node):
  function test_plot_atommapping_network (line 186) | def test_plot_atommapping_network(simple_network):

FILE: src/openfe/tests/utils/test_duecredit.py
  class TestDuecredit (line 15) | class TestDuecredit:
    method test_duecredit_protocol_collection (line 60) | def test_duecredit_protocol_collection(self, module, dois):
    method test_duecredit_active (line 65) | def test_duecredit_active(self):

FILE: src/openfe/tests/utils/test_log_control.py
  function logger (line 14) | def logger():
  class Test_MsgIncludesStringFilter (line 39) | class Test_MsgIncludesStringFilter:
    method test_single_string_blocks_matching_message (line 42) | def test_single_string_blocks_matching_message(self):
    method test_single_string_allows_non_matching_message (line 56) | def test_single_string_allows_non_matching_message(self):
    method test_list_of_strings_blocks_any_match (line 70) | def test_list_of_strings_blocks_any_match(self):
    method test_list_allows_non_matching_messages (line 96) | def test_list_allows_non_matching_messages(self):
    method test_substring_matching (line 110) | def test_substring_matching(self):
    method test_case_sensitive_matching (line 124) | def test_case_sensitive_matching(self):
  class Test_AppendMsgFilter (line 151) | class Test_AppendMsgFilter:
    method test_single_suffix_appends (line 154) | def test_single_suffix_appends(self):
    method test_multiple_suffixes_append_in_order (line 170) | def test_multiple_suffixes_append_in_order(self):
    method test_idempotent_single_suffix (line 185) | def test_idempotent_single_suffix(self):
    method test_idempotent_multiple_suffixes (line 200) | def test_idempotent_multiple_suffixes(self):
    method test_always_returns_true (line 215) | def test_always_returns_true(self):
  class Testlogging_control (line 230) | class Testlogging_control:
    method test__silence_message_single_string_single_logger (line 233) | def test__silence_message_single_string_single_logger(self, logger):
    method test__silence_message_multiple_strings_single_logger (line 245) | def test__silence_message_multiple_strings_single_logger(self, logger):
    method test__silence_message_single_string_multiple_loggers (line 258) | def test__silence_message_single_string_multiple_loggers(self):
    method test__silence_message_multiple_strings_multiple_loggers (line 278) | def test__silence_message_multiple_strings_multiple_loggers(self):
    method test__silence_logger_single (line 298) | def test__silence_logger_single(self, logger):
    method test__silence_logger_multiple (line 312) | def test__silence_logger_multiple(self):
    method test__silence_logger_custom_level (line 329) | def test__silence_logger_custom_level(self, logger):
    method test__append_logger_single_suffix_single_logger (line 344) | def test__append_logger_single_suffix_single_logger(self, logger):
    method test__append_logger_multiple_suffixes (line 355) | def test__append_logger_multiple_suffixes(self, logger):
    method test__append_logger_multiple_loggers (line 368) | def test__append_logger_multiple_loggers(self):
    method test_pymbar_example (line 387) | def test_pymbar_example(self, logger):
    method test_combining_multiple_controls (line 401) | def test_combining_multiple_controls(self, logger):
  class TestBaseLogFilter (line 415) | class TestBaseLogFilter:
    method test_cannot_instantiate_abstract_class (line 418) | def test_cannot_instantiate_abstract_class(self):
    method test_subclass_must_implement_filter (line 423) | def test_subclass_must_implement_filter(self):
    method test_subclass_with_filter_works (line 432) | def test_subclass_with_filter_works(self):
    method test_string_conversion_to_list (line 442) | def test_string_conversion_to_list(self):
    method test_list_stays_as_list (line 448) | def test_list_stays_as_list(self):
  class TestEdgeCases (line 455) | class TestEdgeCases:
    method test_empty_string (line 458) | def test_empty_string(self, logger):
    method test_empty_list (line 469) | def test_empty_list(self, logger):
    method test_special_characters_in_message (line 480) | def test_special_characters_in_message(self, logger):
    method test_unicode_characters (line 494) | def test_unicode_characters(self, logger):
    method test_very_long_message (line 507) | def test_very_long_message(self, logger):

FILE: src/openfe/tests/utils/test_network_plotting.py
  function _get_fig_ax (line 12) | def _get_fig_ax(fig):
  function mock_event (line 24) | def mock_event(event_name, xdata, ydata, fig=None):
  function make_mock_graph (line 42) | def make_mock_graph(fig=None):
  class TestNode (line 66) | class TestNode:
    method setup_method (line 67) | def setup_method(self):
    method teardown_method (line 72) | def teardown_method(self):
    method test_register_artist (line 75) | def test_register_artist(self):
    method test_extent (line 84) | def test_extent(self):
    method test_xy (line 87) | def test_xy(self):
    method test_unselect (line 90) | def test_unselect(self):
    method test_edge_select (line 98) | def test_edge_select(self):
    method test_update_location (line 105) | def test_update_location(self):
    method test_contains (line 119) | def test_contains(self, point, expected):
    method test_on_mousedown_in_rect (line 123) | def test_on_mousedown_in_rect(self):
    method test_on_mousedown_in_axes (line 134) | def test_on_mousedown_in_axes(self):
    method test_on_mousedown_out_axes (line 144) | def test_on_mousedown_out_axes(self):
    method test_on_drag (line 159) | def test_on_drag(self):
    method test_on_drag_do_nothing (line 180) | def test_on_drag_do_nothing(self):
    method test_on_drag_no_mousedown (line 189) | def test_on_drag_no_mousedown(self):
    method test_on_mouseup (line 199) | def test_on_mouseup(self):
    method test_blitting (line 209) | def test_blitting(self):
  class TestEdge (line 213) | class TestEdge:
    method setup_method (line 214) | def setup_method(self):
    method teardown_method (line 223) | def teardown_method(self):
    method test_register_artist (line 226) | def test_register_artist(self):
    method test_contains (line 242) | def test_contains(self, point, expected):
    method test_edge_xs_ys (line 246) | def test_edge_xs_ys(self):
    method _get_colors (line 249) | def _get_colors(self):
    method test_unselect (line 254) | def test_unselect(self):
    method test_select (line 271) | def test_select(self):
    method test_update_locations (line 287) | def test_update_locations(self):
  class TestEventHandler (line 297) | class TestEventHandler:
    method setup_method (line 298) | def setup_method(self):
    method teardown_method (line 311) | def teardown_method(self):
    method _mock_for_connections (line 314) | def _mock_for_connections(self):
    method test_connect (line 320) | def test_connect(self, event_type):
    method test_disconnect (line 343) | def test_disconnect(self, event_type):
    method _mock_contains (line 365) | def _mock_contains(self, mock_objs):
    method test_get_event_container_select_node (line 375) | def test_get_event_container_select_node(self, hit):
    method test_on_mousedown (line 397) | def test_on_mousedown(self, hit):
    method test_on_drag (line 413) | def test_on_drag(self, is_active):
    method test_on_mouseup_click_select (line 428) | def test_on_mouseup_click_select(self, has_selected):
    method test_on_mouseup_click_not_select (line 457) | def test_on_mouseup_click_not_select(self, has_selected):
    method test_on_mouseup_drag (line 479) | def test_on_mouseup_drag(self, has_selected):
  class TestGraphDrawing (line 504) | class TestGraphDrawing:
    method setup_method (line 505) | def setup_method(self):
    method test_init (line 517) | def test_init(self):
    method test_init_custom_ax (line 526) | def test_init_custom_ax(self):
    method test_register_node_error (line 533) | def test_register_node_error(self):
    method test_edges_for_node (line 548) | def test_edges_for_node(self, node, edges):
    method test_get_nodes_extent (line 552) | def test_get_nodes_extent(self):
    method test_reset_bounds (line 555) | def test_reset_bounds(self):
    method test_draw (line 564) | def test_draw(self):

FILE: src/openfe/tests/utils/test_optional_imports.py
  function the_answer (line 10) | def the_answer():
  function test_requires_decorator (line 14) | def test_requires_decorator():

FILE: src/openfe/tests/utils/test_remove_oechem.py
  function test_remove_oechem (line 8) | def test_remove_oechem():

FILE: src/openfe/tests/utils/test_system_probe.py
  function fake_disk_usage (line 127) | def fake_disk_usage(path):
  function patch_system (line 135) | def patch_system():
  function test_get_hostname (line 219) | def test_get_hostname():
  function test_get_gpu_info (line 226) | def test_get_gpu_info():
  function test_get_psutil_info (line 253) | def test_get_psutil_info():
  function test_get_disk_usage (line 295) | def test_get_disk_usage():
  function test_get_disk_usage_with_path (line 318) | def test_get_disk_usage_with_path():
  function test_probe_system (line 340) | def test_probe_system():
  function test_probe_system_smoke_test (line 423) | def test_probe_system_smoke_test():
  function test_log_system_probe_unconfigured (line 428) | def test_log_system_probe_unconfigured():
  function test_log_system_probe (line 454) | def test_log_system_probe(caplog):
  function test_nvidia_smi_error (line 488) | def test_nvidia_smi_error(error_type, expected, caplog):

FILE: src/openfe/tests/utils/test_visualization_3D.py
  function maps (line 9) | def maps():
  function benzene_phenol_mapping (line 18) | def benzene_phenol_mapping(benzene_transforms, maps):
  function test_visualize_component_coords_give_iterable (line 26) | def test_visualize_component_coords_give_iterable(benzene_transforms):
  function test_visualize_component_coords_give_iterable_shift (line 35) | def test_visualize_component_coords_give_iterable_shift(benzene_transfor...
  function test_visualize_component_coords_reuse_view (line 44) | def test_visualize_component_coords_reuse_view(benzene_transforms):
  function test_visualize_3D_mapping (line 54) | def test_visualize_3D_mapping(benzene_phenol_mapping):

FILE: src/openfe/utils/atommapping_network_plotting.py
  class AtomMappingEdge (line 17) | class AtomMappingEdge(Edge):
    method __init__ (line 32) | def __init__(self, node_artist1: Node, node_artist2: Node, data: Dict):
    method _draw_mapped_molecule (line 37) | def _draw_mapped_molecule(
    method _get_image_extents (line 76) | def _get_image_extents(self):
    method select (line 90) | def select(self, event, graph):
    method unselect (line 113) | def unselect(self):
  class LigandNode (line 123) | class LigandNode(Node):
    method _make_artist (line 124) | def _make_artist(self, x, y, dx, dy):
    method register_artist (line 128) | def register_artist(self, ax):
    method extent (line 132) | def extent(self):
    method xy (line 139) | def xy(self):
  class AtomMappingNetworkDrawing (line 143) | class AtomMappingNetworkDrawing(GraphDrawing):
  function plot_atommapping_network (line 159) | def plot_atommapping_network(network: LigandNetwork):

FILE: src/openfe/utils/ligand_utils.py
  function get_alchemical_charge_difference (line 6) | def get_alchemical_charge_difference(mapping: LigandAtomMapping) -> int:

FILE: src/openfe/utils/logging_control.py
  class _BaseLogFilter (line 5) | class _BaseLogFilter(ABC):
    method __init__ (line 14) | def __init__(self, strings: str | list[str]) -> None:
    method filter (line 20) | def filter(self, record: logging.LogRecord) -> bool:
  class _MsgIncludesStringFilter (line 36) | class _MsgIncludesStringFilter(_BaseLogFilter):
    method filter (line 48) | def filter(self, record: logging.LogRecord) -> bool:
  class _AppendMsgFilter (line 67) | class _AppendMsgFilter(_BaseLogFilter):
    method __init__ (line 78) | def __init__(self, strings: str | list[str]) -> None:
    method filter (line 83) | def filter(self, record: logging.LogRecord) -> bool:
  function _silence_message (line 103) | def _silence_message(msg: str | list[str], logger_names: str | list[str]...
  function _silence_logger (line 128) | def _silence_logger(logger_names: str | list[str], level: int = logging....
  function _append_logger (line 149) | def _append_logger(suffix: str | list[str], logger_names: str | list[str...

FILE: src/openfe/utils/network_plotting.py
  class Node (line 26) | class Node:
    method __init__ (line 41) | def __init__(self, node, x: float, y: float, dx=0.1, dy=0.1):
    method _make_artist (line 49) | def _make_artist(self, x, y, dx, dy):
    method register_artist (line 52) | def register_artist(self, ax: MPL_Axes):
    method extent (line 57) | def extent(self) -> tuple[float, float, float, float]:
    method xy (line 63) | def xy(self) -> tuple[float, float]:
    method select (line 67) | def select(self, event: MPL_MouseEvent, graph: GraphDrawing):  # -no-cov-
    method unselect (line 71) | def unselect(self):
    method edge_select (line 75) | def edge_select(self, edge: Edge):
    method update_location (line 79) | def update_location(self, x: float, y: float):
    method contains (line 86) | def contains(self, event: MPL_MouseEvent) -> bool:
    method on_mousedown (line 90) | def on_mousedown(self, event: MPL_MouseEvent, graph: GraphDrawing):
    method on_drag (line 107) | def on_drag(self, event: MPL_MouseEvent, graph: GraphDrawing):
    method on_mouseup (line 131) | def on_mouseup(self, event: MPL_MouseEvent, graph: GraphDrawing):
  class Edge (line 139) | class Edge:
    method __init__ (line 156) | def __init__(self, node_artist1: Node, node_artist2: Node, data: dict):
    method _make_artist (line 162) | def _make_artist(self, node_artist1: Node, node_artist2: Node, data: d...
    method register_artist (line 166) | def register_artist(self, ax: MPL_Axes):
    method contains (line 170) | def contains(self, event: MPL_MouseEvent) -> bool:
    method _edge_xs_ys (line 175) | def _edge_xs_ys(node1: Node, node2: Node):
    method on_mousedown (line 186) | def on_mousedown(self, event: MPL_MouseEvent, graph: GraphDrawing):
    method on_drag (line 190) | def on_drag(self, event: MPL_MouseEvent, graph: GraphDrawing):
    method on_mouseup (line 194) | def on_mouseup(self, event: MPL_MouseEvent, graph: GraphDrawing):
    method unselect (line 198) | def unselect(self):
    method select (line 205) | def select(self, event: MPL_MouseEvent, graph: GraphDrawing):
    method update_locations (line 213) | def update_locations(self):
  class EventHandler (line 219) | class EventHandler:
    method __init__ (line 246) | def __init__(self, graph: GraphDrawing):
    method connect (line 253) | def connect(self, canvas: MPL_FigureCanvasBase):
    method disconnect (line 263) | def disconnect(self, canvas: MPL_FigureCanvasBase):
    method _get_event_container (line 269) | def _get_event_container(self, event: MPL_MouseEvent):
    method on_mousedown (line 285) | def on_mousedown(self, event: MPL_MouseEvent):
    method on_drag (line 296) | def on_drag(self, event: MPL_MouseEvent):
    method on_mouseup (line 303) | def on_mouseup(self, event: MPL_MouseEvent):
  class GraphDrawing (line 327) | class GraphDrawing:
    method __init__ (line 347) | def __init__(self, graph: nx.Graph, positions=None, ax=None):
    method _ipython_display_ (line 380) | def _ipython_display_(self):  # -no-cov-
    method edges_for_node (line 383) | def edges_for_node(self, node: Node) -> list[Edge]:
    method _get_nodes_extent (line 388) | def _get_nodes_extent(self):
    method reset_bounds (line 393) | def reset_bounds(self):
    method draw (line 407) | def draw(self):
    method _register_node (line 412) | def _register_node(self, node: Any, position: tuple[float, float]):
    method _register_edge (line 421) | def _register_edge(self, edge: tuple[Node, Node, dict]):

FILE: src/openfe/utils/optional_imports.py
  function requires_package (line 12) | def requires_package(package_name: str) -> Callable:

FILE: src/openfe/utils/remove_oechem.py
  function without_oechem_backend (line 10) | def without_oechem_backend():

FILE: src/openfe/utils/silence_root_logging.py
  function silence_root_logging (line 6) | def silence_root_logging():

FILE: src/openfe/utils/system_probe.py
  function _get_disk_usage (line 13) | def _get_disk_usage(
  function _get_psutil_info (line 127) | def _get_psutil_info() -> dict[str, dict[str, str]]:
  function _get_hostname (line 245) | def _get_hostname() -> str:
  function _get_gpu_info (line 276) | def _get_gpu_info() -> dict[str, dict[str, str]]:
  function _probe_system (line 387) | def _probe_system(paths: Optional[Iterable[pathlib.Path]] = None) -> dict:
  function log_system_probe (line 501) | def log_system_probe(level=logging.DEBUG, paths: Optional[Iterable[os.Pa...

FILE: src/openfe/utils/visualization_3D.py
  function _get_max_dist_in_x (line 22) | def _get_max_dist_in_x(atom_mapping: AtomMapping) -> float:
  function _translate (line 47) | def _translate(mol, shift: Union[Tuple[float, float, float], NDArray[np....
  function _add_spheres (line 72) | def _add_spheres(view: py3Dmol.view, mol1: Chem.Mol, mol2: Chem.Mol, map...
  function view_components_3d (line 112) | def view_components_3d(
  function view_mapping_3d (line 159) | def view_mapping_3d(

FILE: src/openfecli/cli.py
  class OpenFECLI (line 15) | class OpenFECLI(CLI):
    method get_loaders (line 19) | def get_loaders(self):
    method get_installed_plugins (line 24) | def get_installed_plugins(self):
  function main (line 42) | def main(log):

FILE: src/openfecli/clicktypes/hyphenchoice.py
  function _normalize_to_hyphen (line 4) | def _normalize_to_hyphen(string):
  class HyphenAwareChoice (line 8) | class HyphenAwareChoice(click.Choice):
    method __init__ (line 9) | def __init__(self, choices, case_sensitive=True):
    method convert (line 13) | def convert(self, value, param, ctx):

FILE: src/openfecli/commands/atommapping.py
  function allow_two_molecules (line 10) | def allow_two_molecules(ctx, param, value):
  function atommapping (line 26) | def atommapping(mol, mapper, output):
  function generate_mapping (line 44) | def generate_mapping(mapper, molA, molB):
  function atommapping_print_dict_main (line 69) | def atommapping_print_dict_main(mapper, molA, molB):
  function atommapping_visualize_main (line 75) | def atommapping_visualize_main(mapper, molA, molB, file, ext):

FILE: src/openfecli/commands/fetch.py
  class SingleModulePluginLoader (line 17) | class SingleModulePluginLoader(CLIPluginLoader):
    method __init__ (line 20) | def __init__(self, module_name, plugin_class):
    method _find_candidates (line 27) | def _find_candidates(self):
    method _make_nsdict (line 31) | def _make_nsdict(candidate):
  class FetchCLI (line 35) | class FetchCLI(CLI):
    method get_loaders (line 44) | def get_loaders(self):
    method get_installed_plugins (line 47) | def get_installed_plugins(self):
  function fetch (line 53) | def fetch():

FILE: src/openfecli/commands/gather.py
  function _get_column (line 18) | def _get_column(val: float | int) -> int:
  function format_estimate_uncertainty (line 46) | def format_estimate_uncertainty(
  function format_df_with_precision (line 100) | def format_df_with_precision(
  function is_results_json (line 179) | def is_results_json(fpath: os.PathLike | str) -> bool:
  function load_json (line 184) | def load_json(fpath: os.PathLike | str) -> dict:
  function _get_names (line 207) | def _get_names(result: dict) -> tuple[str, str]:
  function _get_type (line 237) | def _get_type(result: dict) -> Literal["vacuum", "solvent", "complex"]:
  function _legacy_get_type (line 266) | def _legacy_get_type(res_fn: os.PathLike | str) -> Literal["vacuum", "so...
  function _get_result_id (line 278) | def _get_result_id(
  function _load_valid_result_json (line 305) | def _load_valid_result_json(fpath: os.PathLike | str) -> tuple[tuple | N...
  function _generate_bad_legs_error_message (line 345) | def _generate_bad_legs_error_message(bad_legs: list[tuple[set[str], tupl...
  function _get_ddgs (line 371) | def _get_ddgs(legs: dict, allow_partial=False) -> pd.DataFrame:
  function _generate_ddg (line 440) | def _generate_ddg(legs: dict, allow_partial: bool) -> pd.DataFrame:
  function _generate_raw (line 469) | def _generate_raw(legs: dict, allow_partial=True) -> pd.DataFrame:
  function _check_legs_have_sufficient_repeats (line 506) | def _check_legs_have_sufficient_repeats(legs):
  function _generate_dg_mle (line 517) | def _generate_dg_mle(legs: dict, allow_partial: bool) -> pd.DataFrame:
  function _collect_result_jsons (line 612) | def _collect_result_jsons(results: List[os.PathLike | str]) -> List[path...
  function _get_legs_from_result_jsons (line 641) | def _get_legs_from_result_jsons(
  function rich_print_to_stdout (line 707) | def rich_print_to_stdout(df: pd.DataFrame) -> None:
  function gather (line 774) | def gather(

FILE: src/openfecli/commands/gather_abfe.py
  function _get_name (line 20) | def _get_name(result: dict) -> str:
  function _load_valid_result_json (line 45) | def _load_valid_result_json(fpath: os.PathLike | str) -> tuple[tuple | N...
  function _get_legs_from_result_jsons (line 88) | def _get_legs_from_result_jsons(
  function _error_std (line 151) | def _error_std(r):
  function _error_mbar (line 158) | def _error_mbar(r):
  function _generate_dg (line 169) | def _generate_dg(results_dict: dict[str, dict[str, list]], allow_partial...
  function _generate_dg_raw (line 211) | def _generate_dg_raw(results_dict: dict[str, dict[str, list]], allow_par...
  function gather_abfe (line 293) | def gather_abfe(

FILE: src/openfecli/commands/gather_septop.py
  function _load_valid_result_json (line 20) | def _load_valid_result_json(fpath: os.PathLike | str) -> tuple[tuple | N...
  function _get_legs_from_result_jsons (line 63) | def _get_legs_from_result_jsons(
  function _get_names (line 137) | def _get_names(result: dict) -> tuple[str, str]:
  function _error_std (line 164) | def _error_std(r):
  function _error_mbar (line 171) | def _error_mbar(r):
  function _get_ddgs (line 182) | def _get_ddgs(
  function _infer_unc_col_name (line 226) | def _infer_unc_col_name(df: pd.DataFrame) -> str:
  function _generate_ddg (line 233) | def _generate_ddg(results_dict, allow_partial: bool = False) -> pd.DataF...
  function _generate_dg_mle (line 241) | def _generate_dg_mle(
  function _generate_raw (line 291) | def _generate_raw(
  function gather_septop (line 379) | def gather_septop(

FILE: src/openfecli/commands/generate_partial_charges.py
  function charge_molecules (line 41) | def charge_molecules(molecules, yaml_settings, output, n_cores, overwrit...

FILE: src/openfecli/commands/plan_rbfe_network.py
  function plan_rbfe_network_main (line 21) | def plan_rbfe_network_main(
  function plan_rbfe_network (line 138) | def plan_rbfe_network(

FILE: src/openfecli/commands/plan_rhfe_network.py
  function plan_rhfe_network_main (line 22) | def plan_rhfe_network_main(
  function plan_rhfe_network (line 110) | def plan_rhfe_network(

FILE: src/openfecli/commands/quickrun.py
  function _format_exception (line 15) | def _format_exception(exception) -> str:
  function _hash_quickrun_inputs (line 20) | def _hash_quickrun_inputs(output, transformation):
  function quickrun (line 48) | def quickrun(transformation, work_dir, output, resume):

FILE: src/openfecli/commands/test.py
  function test (line 19) | def test(long, download_only):

FILE: src/openfecli/commands/view_ligand_network.py
  function view_ligand_network (line 13) | def view_ligand_network(ligand_network: os.PathLike):

FILE: src/openfecli/fetching.py
  class _Fetcher (line 12) | class _Fetcher:
    method __init__ (line 31) | def __init__(
    method resources (line 48) | def resources(self):
    method __call__ (line 51) | def __call__(self, directory: pathlib.Path):
    method plugin (line 55) | def plugin(self):
  class URLFetcher (line 96) | class URLFetcher(_Fetcher):
    method __call__ (line 105) | def __call__(self, dest_dir):
  class PkgResourceFetcher (line 120) | class PkgResourceFetcher(_Fetcher):
    method __call__ (line 129) | def __call__(self, dest_dir):
  class FetchablePlugin (line 154) | class FetchablePlugin(CommandPlugin):
    method __init__ (line 160) | def __init__(self, command, section, requires_ofe, fetcher):
    method filenames (line 170) | def filenames(self):

FILE: src/openfecli/parameters/mapper.py
  function _atommapper_from_openfe_setup (line 9) | def _atommapper_from_openfe_setup(user_input, context):
  function _atommapper_from_qualname (line 13) | def _atommapper_from_qualname(user_input, context):

FILE: src/openfecli/parameters/mol.py
  function _load_molecule_from_smiles (line 7) | def _load_molecule_from_smiles(user_input, context):
  function _load_molecule_from_sdf (line 25) | def _load_molecule_from_sdf(user_input, context):
  function _load_molecule_from_mol2 (line 37) | def _load_molecule_from_mol2(user_input, context):

FILE: src/openfecli/parameters/molecules.py
  function _smcs_from_sdf (line 12) | def _smcs_from_sdf(sdf):
  function _smcs_from_mol2 (line 22) | def _smcs_from_mol2(mol2):
  function load_molecules (line 31) | def load_molecules(file_or_directory):
  function molecule_getter (line 67) | def molecule_getter(user_input, context):

FILE: src/openfecli/parameters/output.py
  function get_file_and_extension (line 7) | def get_file_and_extension(user_input, context):

FILE: src/openfecli/parameters/output_dir.py
  function get_dir (line 8) | def get_dir(user_input, context):

FILE: src/openfecli/parameters/plan_network_options.py
  class MapperSelection (line 26) | class MapperSelection(BaseModel):
  class NetworkSelection (line 33) | class NetworkSelection(BaseModel):
  class PartialChargeSelection (line 40) | class PartialChargeSelection(BaseModel):
  class CliYaml (line 47) | class CliYaml(BaseModel):
  function parse_yaml_planner_options (line 55) | def parse_yaml_planner_options(contents: str) -> CliYaml:
  function load_yaml_planner_options (line 88) | def load_yaml_planner_options(path: Optional[str], context) -> PlanNetwo...

FILE: src/openfecli/parameters/protein.py
  function _contains_any_substring (line 13) | def _contains_any_substring(input: str, substrings: Iterable[str]) -> bool:
  function _load_protein_from_file (line 17) | def _load_protein_from_file(input_file, protein_class):
  function _get_protein (line 34) | def _get_protein(user_input, context):
  function _get_protein_membrane (line 40) | def _get_protein_membrane(user_input, context):

FILE: src/openfecli/parameters/utils.py
  function import_parameter (line 9) | def import_parameter(import_str: str):

FILE: src/openfecli/plan_alchemical_networks_utils.py
  function plan_alchemical_network_output (line 11) | def plan_alchemical_network_output(

FILE: src/openfecli/plugins.py
  class OFECommandPlugin (line 7) | class OFECommandPlugin(CommandPlugin):
    method __init__ (line 8) | def __init__(self, command, section, requires_ofe):

FILE: src/openfecli/tests/clicktypes/test_hyphenchoice.py
  class TestHyphenAwareChoice (line 7) | class TestHyphenAwareChoice:
    method test_init (line 9) | def test_init(self, value):
    method test_convert (line 14) | def test_convert(self, value):

FILE: src/openfecli/tests/commands/conftest.py
  function min_result_json (line 5) | def min_result_json():

FILE: src/openfecli/tests/commands/test_atommapping.py
  function molA_args (line 18) | def molA_args():
  function molB_args (line 23) | def molB_args():
  function mapper_args (line 28) | def mapper_args():
  function mols_AB (line 33) | def mols_AB(molA_args, molB_args):
  function print_test (line 37) | def print_test(mapper, molA, molB):
  function print_test_with_file (line 43) | def print_test_with_file(mapper, molA, molB, file, ext):
  function test_atommapping (line 50) | def test_atommapping(molA_args, molB_args, mapper_args, with_file):
  function test_atommapping_bad_number_of_mols (line 75) | def test_atommapping_bad_number_of_mols(molA_args, mapper_args):
  function test_atommapping_missing_mapper (line 83) | def test_atommapping_missing_mapper(molA_args, molB_args):
  function test_generate_mapping (line 92) | def test_generate_mapping(n_mappings, mols_AB):
  function test_atommapping_print_dict_main (line 107) | def test_atommapping_print_dict_main(capsys, mols_AB):
  function test_atommapping_visualize_main (line 117) | def test_atommapping_visualize_main(mols_AB):
  function test_atommapping_visualize_main_bad_extension (line 123) | def test_atommapping_visualize_main_bad_extension(mols_AB, tmp_path):

FILE: src/openfecli/tests/commands/test_charge_generation.py
  function yaml_nagl_settings (line 20) | def yaml_nagl_settings():
  function methane (line 30) | def methane() -> Molecule:
  function methane_with_charges (line 38) | def methane_with_charges(methane) -> Molecule:
  function test_missing_output (line 43) | def test_missing_output(methane, tmp_path):
  function test_write_charges_to_input (line 53) | def test_write_charges_to_input(methane, tmp_path):
  function test_charge_molecules_default (line 66) | def test_charge_molecules_default(methane, tmp_path, caplog):
  function test_charge_molecules_overwrite (line 93) | def test_charge_molecules_overwrite(
  function test_charge_settings (line 136) | def test_charge_settings(methane, tmp_path, caplog, yaml_nagl_settings, ...

FILE: src/openfecli/tests/commands/test_gather.py
  function test_format_estimate_uncertainty (line 59) | def test_format_estimate_uncertainty(est, unc, unc_prec, est_str, unc_str):
  function test_get_column (line 78) | def test_get_column(val, col):
  class TestResultLoading (line 82) | class TestResultLoading:
    method test_minimal_valid_results (line 83) | def test_minimal_valid_results(self, capsys, min_result_json):
    method test_skip_missing_unit_result (line 90) | def test_skip_missing_unit_result(self, capsys, min_result_json):
    method test_skip_missing_estimate (line 99) | def test_skip_missing_estimate(self, capsys, min_result_json):
    method test_skip_missing_uncertainty (line 108) | def test_skip_missing_uncertainty(self, capsys, min_result_json):
    method test_skip_all_failed_runs (line 117) | def test_skip_all_failed_runs(self, capsys, min_result_json):
    method test_missing_pr_data (line 125) | def test_missing_pr_data(self, capsys, min_result_json):
    method test_get_legs_from_result_jsons (line 133) | def test_get_legs_from_result_jsons(self, capsys, min_result_json):
  function test_no_results_found (line 144) | def test_no_results_found():
  function cmet_result_dir (line 241) | def cmet_result_dir() -> pathlib.Path:
  class TestGatherCMET (line 248) | class TestGatherCMET:
    method test_cmet_full_results (line 250) | def test_cmet_full_results(self, cmet_result_dir, report, file_regress...
    method test_cmet_missing_complex_leg (line 261) | def test_cmet_missing_complex_leg(self, cmet_result_dir, report, file_...
    method test_cmet_missing_edge (line 274) | def test_cmet_missing_edge(self, cmet_result_dir, report, file_regress...
    method test_cmet_failed_edge (line 285) | def test_cmet_failed_edge(self, cmet_result_dir, report, file_regressi...
    method test_cmet_too_few_edges_error (line 295) | def test_cmet_too_few_edges_error(self, cmet_result_dir, allow_partial):
    method test_cmet_missing_all_complex_legs_fail (line 309) | def test_cmet_missing_all_complex_legs_fail(self, cmet_result_dir, rep...
    method test_cmet_missing_all_complex_legs_allow_partial (line 320) | def test_cmet_missing_all_complex_legs_allow_partial(self, cmet_result...
    method test_pretty_print (line 331) | def test_pretty_print(self, cmet_result_dir, report, file_regression):
    method test_write_to_file (line 340) | def test_write_to_file(self, cmet_result_dir):
  function rbfe_results_serial_dir (line 352) | def rbfe_results_serial_dir() -> pathlib.Path:
  function rbfe_results_parallel_dir (line 362) | def rbfe_results_parallel_dir() -> pathlib.Path:
  function test_rbfe_gather (line 378) | def test_rbfe_gather(request, dataset, report, input_mode):
  function test_rbfe_gather_single_repeats_dg_error (line 407) | def test_rbfe_gather_single_repeats_dg_error(rbfe_results_parallel_dir):
  class TestRBFEGatherFailedEdges (line 421) | class TestRBFEGatherFailedEdges:
    method results_paths_serial_missing_legs (line 423) | def results_paths_serial_missing_legs(self, rbfe_results_serial_dir) -...
    method test_missing_leg_error (line 437) | def test_missing_leg_error(self, results_paths_serial_missing_legs: str):
    method test_missing_leg_allow_partial_disconnected (line 447) | def test_missing_leg_allow_partial_disconnected(self, results_paths_se...
    method test_allow_partial_msg_not_printed (line 455) | def test_allow_partial_msg_not_printed(self, results_paths_serial_miss...
  function abfe_result_dir (line 477) | def abfe_result_dir() -> pathlib.Path:
  class TestGatherABFE (line 484) | class TestGatherABFE:
    method test_abfe_full_results (line 487) | def test_abfe_full_results(self, abfe_result_dir, report, protocol_typ...
    method test_abfe_single_repeat (line 501) | def test_abfe_single_repeat(self, abfe_result_dir, report, protocol_ty...
  function septop_result_dir (line 514) | def septop_result_dir() -> pathlib.Path:
  class TestGatherSepTop (line 521) | class TestGatherSepTop:
    method test_septop_full_results (line 534) | def test_septop_full_results(self, version, septop_result_dir, report,...
    method test_septop_single_repeat (line 547) | def test_septop_single_repeat(self, version, septop_result_dir, report...

FILE: src/openfecli/tests/commands/test_ligand_network_viewer.py
  function test_view_ligand_network (line 12) | def test_view_ligand_network():

FILE: src/openfecli/tests/commands/test_plan_rbfe_network.py
  function mol_dir_args (line 36) | def mol_dir_args(tmp_path_factory):
  function dummy_charge_dir_args (line 47) | def dummy_charge_dir_args(tmp_path_factory):
  function protein_args (line 58) | def protein_args(T4_protein_component_pdb):
  function protein_membrane_args (line 64) | def protein_membrane_args(a2a_protein_membrane_pdb):
  function print_test_with_file (line 68) | def print_test_with_file(
  function validate_charges (line 82) | def validate_charges(smc):
  function ligs_23_55 (line 92) | def ligs_23_55() -> list[SmallMoleculeComponent]:
  function test_plan_rbfe_network_main (line 106) | def test_plan_rbfe_network_main(request, protein_fixture, ligs_23_55):
  function yaml_nagl_settings (line 148) | def yaml_nagl_settings():
  function test_plan_rbfe_network (line 162) | def test_plan_rbfe_network(mol_dir_args, request, protein_fixture, tmp_p...
  function test_plan_rbfe_network_n_repeats (line 225) | def test_plan_rbfe_network_n_repeats(mol_dir_args, protein_args, input_n...
  function test_plan_rbfe_network_charge_overwrite (line 251) | def test_plan_rbfe_network_charge_overwrite(dummy_charge_dir_args, prote...
  function eg5_files (line 290) | def eg5_files():
  function test_plan_rbfe_network_cofactors (line 303) | def test_plan_rbfe_network_cofactors(eg5_files, tmp_path, yaml_nagl_sett...
  function cdk8_files (line 339) | def cdk8_files():
  function test_plan_rbfe_network_charge_changes (line 347) | def test_plan_rbfe_network_charge_changes(cdk8_files, caplog):
  function lomap_yaml_settings (line 384) | def lomap_yaml_settings():
  function test_lomap_yaml_plan_rbfe_smoke_test (line 408) | def test_lomap_yaml_plan_rbfe_smoke_test(lomap_yaml_settings, cdk8_files...
  function custom_yaml_radial (line 427) | def custom_yaml_radial():
  function test_custom_yaml_plan_radial_smoke_test (line 451) | def test_custom_yaml_plan_radial_smoke_test(custom_yaml_radial, eg5_file...
  function test_plan_rbfe_invalid_membrane (line 469) | def test_plan_rbfe_invalid_membrane(eg5_files):
  function test_plan_rbfe_missing_protein_args (line 481) | def test_plan_rbfe_missing_protein_args(eg5_files):
  function test_plan_rbfe_too_many_protein_error (line 490) | def test_plan_rbfe_too_many_protein_error(eg5_files):

FILE: src/openfecli/tests/commands/test_plan_rhfe_network.py
  function mol_dir_args (line 24) | def mol_dir_args(tmp_path_factory):
  function dummy_charge_dir_args (line 35) | def dummy_charge_dir_args(tmp_path_factory):
  function print_test_with_file (line 45) | def print_test_with_file(mapping_scorer, ligand_network_planner, small_m...
  function validate_charges (line 52) | def validate_charges(smc):
  function test_plan_rhfe_network_main (line 68) | def test_plan_rhfe_network_main():
  function yaml_nagl_settings (line 105) | def yaml_nagl_settings():
  function test_plan_rhfe_network (line 121) | def test_plan_rhfe_network(mol_dir_args, tmp_path, yaml_nagl_settings):
  function custom_yaml_settings (line 172) | def custom_yaml_settings():
  function test_custom_yaml_plan_rhfe_smoke_test (line 199) | def test_custom_yaml_plan_rhfe_smoke_test(custom_yaml_settings, mol_dir_...
  function test_plan_rhfe_network_charge_overwrite (line 230) | def test_plan_rhfe_network_charge_overwrite(dummy_charge_dir_args, tmp_p...

FILE: src/openfecli/tests/commands/test_quickrun.py
  function json_file (line 18) | def json_file():
  function test_quickrun (line 26) | def test_quickrun(extra_args, json_file):
  function test_quickrun_interrupted (line 62) | def test_quickrun_interrupted(extra_args, json_file):
  function test_quickrun_output_file_exists (line 81) | def test_quickrun_output_file_exists(json_file):
  function test_quickrun_output_file_in_nonexistent_directory (line 91) | def test_quickrun_output_file_in_nonexistent_directory(json_file):
  function test_quickrun_dir_created_at_runtime (line 101) | def test_quickrun_dir_created_at_runtime(json_file):
  function test_quickrun_unit_error (line 111) | def test_quickrun_unit_error():
  function test_quickrun_existing_cache_error (line 126) | def test_quickrun_existing_cache_error(json_file):
  function test_quickrun_resume_from_cache (line 143) | def test_quickrun_resume_from_cache(json_file):
  function test_quickrun_resume_invalid_cache (line 161) | def test_quickrun_resume_invalid_cache(json_file):
  function test_quickrun_resume_missing_cache (line 179) | def test_quickrun_resume_missing_cache(json_file):

FILE: src/openfecli/tests/commands/test_test.py
  function mock_func (line 10) | def mock_func(args):
  function test_test (line 15) | def test_test(slow):

FILE: src/openfecli/tests/parameters/test_mapper.py
  function test_get_atommapper (line 15) | def test_get_atommapper(user_input, expected):
  function test_get_atommapper_error (line 19) | def test_get_atommapper_error():

FILE: src/openfecli/tests/parameters/test_mol.py
  function test_get_molecule_smiles (line 11) | def test_get_molecule_smiles():
  function test_get_molecule_sdf (line 18) | def test_get_molecule_sdf():
  function test_get_molecule_mol2 (line 29) | def test_get_molecule_mol2():
  function test_get_molecule_error (line 37) | def test_get_molecule_error():

FILE: src/openfecli/tests/parameters/test_molecules.py
  function test_get_dir_molecules_sdf (line 12) | def test_get_dir_molecules_sdf():
  function test_load_molecules_sdf_file (line 24) | def test_load_molecules_sdf_file():
  function test_get_dir_molecules_mol2 (line 33) | def test_get_dir_molecules_mol2():
  function test_get_molecule_error (line 47) | def test_get_molecule_error():

FILE: src/openfecli/tests/parameters/test_output.py
  function test_get_file_and_extension (line 13) | def test_get_file_and_extension(tmp_path, fname, expected_ext):

FILE: src/openfecli/tests/parameters/test_output_dir.py
  function test_get_output_dir (line 8) | def test_get_output_dir():

FILE: src/openfecli/tests/parameters/test_plan_network_options.py
  function full_yaml (line 9) | def full_yaml():
  function partial_mapper_yaml (line 22) | def partial_mapper_yaml():
  function partial_network_yaml (line 32) | def partial_network_yaml():
  function unsupported_field_yaml (line 42) | def unsupported_field_yaml():
  function test_loading_full_yaml (line 52) | def test_loading_full_yaml(full_yaml):
  function test_loading_mapper_yaml (line 63) | def test_loading_mapper_yaml(partial_mapper_yaml):
  function test_loading_network_yaml (line 72) | def test_loading_network_yaml(partial_network_yaml):
  function test_raise_unsupported_fields_warning (line 82) | def test_raise_unsupported_fields_warning(full_yaml, unsupported_field_y...

FILE: src/openfecli/tests/parameters/test_protein.py
  function test_load_protein_pdb (line 13) | def test_load_protein_pdb():
  function test_load_protein_pdbx (line 22) | def test_load_protein_pdbx():
  function test_load_protein_invalid_file_error (line 31) | def test_load_protein_invalid_file_error():
  function test_load_protein_with_membrane (line 36) | def test_load_protein_with_membrane(a2a_protein_membrane_pdb):
  function test_load_membrane_pdb (line 44) | def test_load_membrane_pdb(a2a_protein_membrane_pdb):
  function test_load_membrane_pdbx (line 50) | def test_load_membrane_pdbx():
  function test_load_membrane_with_protein_only (line 58) | def test_load_membrane_with_protein_only():

FILE: src/openfecli/tests/parameters/test_utils.py
  function test_import_parameter (line 19) | def test_import_parameter(import_str, expected):

FILE: src/openfecli/tests/test_cli.py
  function null_command (line 12) | def null_command():
  function null_command_context (line 25) | def null_command_context(cli):
  function cli (line 35) | def cli():
  class TestCLI (line 39) | class TestCLI:
    method test_invoke (line 40) | def test_invoke(self):
    method test_command_sections (line 49) | def test_command_sections(self, cli):
    method test_get_installed_plugins (line 57) | def test_get_installed_plugins(self, cli):
  function test_main_log (line 69) | def test_main_log(with_log):

FILE: src/openfecli/tests/test_fetchables.py
  function fetchable_test (line 12) | def fetchable_test(fetchable):
  function test_rbfe_tutorial (line 27) | def test_rbfe_tutorial():
  function test_rbfe_tutorial_results (line 32) | def test_rbfe_tutorial_results():

FILE: src/openfecli/tests/test_fetching.py
  class FetcherTester (line 8) | class FetcherTester:
    method fetcher (line 10) | def fetcher(self):
    method test_resources (line 13) | def test_resources(self):
    method test_plugin (line 16) | def test_plugin(self, fetcher):
    method test_call (line 22) | def test_call(self, fetcher, tmp_path):
  class TestURLFetcher (line 35) | class TestURLFetcher(FetcherTester):
    method fetcher (line 37) | def fetcher(self):
    method test_resources (line 46) | def test_resources(self, fetcher):
    method test_call (line 51) | def test_call(self, fetcher, tmp_path):
    method test_without_trailing_slash (line 55) | def test_without_trailing_slash(self, tmp_path):
  class TestPkgResourceFetcher (line 67) | class TestPkgResourceFetcher(FetcherTester):
    method fetcher (line 69) | def fetcher(self):
    method test_resources (line 78) | def test_resources(self, fetcher):

FILE: src/openfecli/tests/test_plugins.py
  function fake (line 7) | def fake():
  class TestOFECommandPlugin (line 11) | class TestOFECommandPlugin:
    method setup_method (line 12) | def setup_method(self):
    method test_plugin_setup (line 19) | def test_plugin_setup(self):

FILE: src/openfecli/tests/test_rbfe_tutorial.py
  function tyk2_ligands (line 27) | def tyk2_ligands():
  function tyk2_protein (line 33) | def tyk2_protein():
  function expected_transformations (line 39) | def expected_transformations():
  function test_plan_tyk2 (line 62) | def test_plan_tyk2(tyk2_ligands, tyk2_protein, expected_transformations):
  function ref_gather (line 95) | def ref_gather():
  function fake_setup_execute_results (line 112) | def fake_setup_execute_results():
  function fake_sim_execute_results (line 129) | def fake_sim_execute_results():
  function fake_analysis_execute_results (line 144) | def fake_analysis_execute_results():
  function test_run_tyk2 (line 160) | def test_run_tyk2(

FILE: src/openfecli/tests/test_utils.py
  function patch_root_logger (line 14) | def patch_root_logger():
  function test_import_thing (line 36) | def test_import_thing(import_string, expected):
  function test_import_thing_import_error (line 40) | def test_import_thing_import_error():
  function test_import_thing_attribute_error (line 45) | def test_import_thing_attribute_error():
  function test_should_configure_logger (line 63) | def test_should_configure_logger(logger_name, expected, with_adapter):
  function test_root_logger_level_configured (line 74) | def test_root_logger_level_configured():
  function test_configure_logger (line 84) | def test_configure_logger(with_handler):

FILE: src/openfecli/tests/utils.py
  function assert_click_success (line 8) | def assert_click_success(result: click.testing.Result):  # -no-cov-

FILE: src/openfecli/utils.py
  function import_thing (line 13) | def import_thing(import_string: str):
  function write (line 40) | def write(string: str):
  function _should_configure_logger (line 49) | def _should_configure_logger(logger: logging.Logger):
  function configure_logger (line 74) | def configure_logger(
  function print_duration (line 104) | def print_duration(function: Callable) -> Callable: