Index

A

ab_dist() (in module pyar.scan) add_one() (in module pyar.aggregator) affinity_propagation_clustering() (in module pyar.selection.clustering) agglomerative_clustering() (in module pyar.selection.clustering) aggregate() (in module pyar.aggregator) (in module pyar.workflows.aggregate) aggregate_from_formulas() (in module pyar.aggregator) (in module pyar.workflows.aggregate) AggregateResult (class in pyar.workflow_results) AggregateRunState (class in pyar.state.aggregate) AggregateStateError Aimnet2 (class in pyar.backends.aimnet_2) aimnet2_optimized_xyz_file (pyar.backends.xtb_aimnet2.XtbAimnet2 property) Aimnet2EnergyGradientProvider (class in pyar.energy_gradient_providers)

AIQM1 (class in pyar.backends.aiqm1_mlatom) aiqm1_optimized_xyz_file (pyar.backends.xtb_aiqm1.XtbAIQM1 property) align() (in module pyar.core.geometry) (pyar.core.molecule.Molecule method) aligned() (pyar.core.molecule.Molecule method) analyse_reaction_trace() (in module pyar.reaction_analysis) ANI (class in pyar.backends.ani) ANICalculationFailed ANIInterface (class in pyar.backends.ani) apply_geometry_result() (in module pyar.optimiser) argument_parse() (in module pyar.cli) (in module pyar.scripts.react) (in module pyar.scripts.reaction_trace) as_coordinates_array() (in module pyar.io.xyz) average() (in module pyar.scripts.similarity)

B

backend_family() (in module pyar.backend_capabilities) backend_supports_geometry_optimization() (in module pyar.backend_capabilities) backend_supports_staged_optimization() (in module pyar.backend_capabilities) BackendCapabilities (class in pyar.backend_capabilities) bond_changes() (in module pyar.reaction_trace)

broken() (in module pyar.sampling.trial_generator) build_gamma_schedule() (in module pyar.workflows.reaction) build_geometry() (in module pyar.optimiser) build_reaction_request() (in module pyar.workflows.reaction) build_xtb_command() (in module pyar.backends.xtb_utils) bulk_optimize() (in module pyar.optimiser)

C

calc_engrad (pyar.backends.xtb_turbo.XtbTurbo property) calc_fingerprint_distance() (in module pyar.selection.deduplication) calculate() (pyar.backends.ani.ANI method) (pyar.backends.geometric.PyarGeometricCalculator method) calculate_angle() (in module pyar.property) calculate_dihedral() (in module pyar.property) calculate_energy_gradient() (pyar.backends.xtb_turbo.XtbTurbo method) calculate_index_from_xyz() (in module pyar.scripts.react) calculate_properties() (in module pyar.scripts.descriptor) canonicalize_quaternion() (in module pyar.sampling.rotation) centroid (pyar.core.molecule.Molecule property) centroid_norm (pyar.sampling.metrics.SphereCoverageMetrics attribute) check_close_contact() (in module pyar.sampling.trial_generator) check_for_the_finished_jobs_on_restart() (in module pyar.aggregator) check_stop_signal() (in module pyar.aggregator) combine_multiplicity() (in module pyar.molecule_merge)

complete_cycle() (pyar.state.reaction.ReactionRunState method) (pyar.state.solvation.SolvationRunState method) complete_pathway() (pyar.state.aggregate.AggregateRunState method) completed_pathway_count() (pyar.state.aggregate.AggregateRunState method) coordinates (pyar.core.molecule.Molecule property) copy() (pyar.core.molecule.Molecule method) covering_radius_degrees (pyar.sampling.metrics.RotationCoverageMetrics attribute) (pyar.sampling.metrics.SphereCoverageMetrics attribute) create() (pyar.state.aggregate.AggregateRunState class method) (pyar.state.reaction.ReactionRunState class method) (pyar.state.solvation.SolvationRunState class method) create_combined_descriptor() (in module pyar.scripts.descriptor) create_composite_molecule() (in module pyar.sampling.trial_generator) create_composite_molecule_wrapper() (in module pyar.scripts.explore) create_trial_geometries() (in module pyar.sampling.trial_generator) current_seed_molecules() (pyar.state.solvation.SolvationRunState method) current_survivor_molecules() (pyar.state.reaction.ReactionRunState method)

D

dbscan_clustering() (in module pyar.selection.clustering)

determine_dbscan_params() (in module pyar.selection.clustering) distance() (in module pyar.property)

E

ellipsoid_wall_potential() (in module pyar.sampling.trial_generator) energy (pyar.backends.aimnet_2.Aimnet2 property) (pyar.backends.aiqm1_mlatom.AIQM1 property) (pyar.backends.xtb.Xtb property) (pyar.backends.xtb_aimnet2.XtbAimnet2 property) (pyar.backends.xtb_aiqm1.XtbAIQM1 property) energy_gradient (pyar.backend_capabilities.BackendCapabilities attribute) energy_hartree (pyar.energy_gradient_providers.EnergyGradientResult attribute) EnergyGradientProvider (class in pyar.energy_gradient_providers)

EnergyGradientResult (class in pyar.energy_gradient_providers) Euclidean_distance() (in module pyar.scripts.similarity) evaluate() (pyar.energy_gradient_providers.Aimnet2EnergyGradientProvider method) (pyar.energy_gradient_providers.EnergyGradientProvider method) (pyar.energy_gradient_providers.GaussianEnergyGradientProvider method) (pyar.energy_gradient_providers.OrcaEnergyGradientProvider method) (pyar.energy_gradient_providers.XtbEnergyGradientProvider method) expand_formula_to_aggregate_inputs() (in module pyar.aggregator) (in module pyar.workflows.aggregate)

F

family (pyar.backend_capabilities.BackendCapabilities attribute) fibonacci_sphere() (in module pyar.sampling.sphere) finish() (pyar.state.aggregate.AggregateRunState method) (pyar.state.reaction.ReactionRunState method) (pyar.state.solvation.SolvationRunState method)

format_gamma_id() (in module pyar.workflows.reaction) from_ase_atoms() (pyar.core.molecule.Molecule class method) from_xyz() (pyar.core.molecule.Molecule class method)

G

Gaussian (class in pyar.backends.gaussian) gaussian_mixture_clustering() (in module pyar.selection.clustering) GaussianEnergyGradientProvider (class in pyar.energy_gradient_providers) generate_chemical_pathway() (in module pyar.scripts.explore) generate_directions() (in module pyar.sampling.sphere) generate_guess_for_bonding() (in module pyar.scan) generate_guess_for_bonding_brute_force() (in module pyar.scan) generate_labels() (in module pyar.selection.clustering) generate_molecule_from_formula() (in module pyar.aggregator) (in module pyar.workflows.aggregate) generate_orientations() (in module pyar.aggregator) generate_points() (in module pyar.sampling.trial_generator) generate_trial_vectors() (in module pyar.sampling.trial_generator) Geometric (class in pyar.backends.geometric) get_average_radius() (in module pyar.property) get_backend_capabilities() (in module pyar.backend_capabilities) get_bond_matrix() (in module pyar.property) get_centre_of_mass() (in module pyar.property) get_centroid() (in module pyar.property) get_connectivity() (in module pyar.property) (in module pyar.sampling.trial_generator)

get_coordinates() (pyar.backends.psi4.Psi4 method) get_coords() (pyar.backends.babel.OBabel method) (pyar.backends.gaussian.Gaussian method) (pyar.backends.mlatom_aiqm1.MlatomAiqm1 method) (pyar.backends.mopac.Mopac method) get_distance_list() (in module pyar.property) get_distance_matrix() (in module pyar.property) get_energy() (pyar.backends.babel.OBabel method) (pyar.backends.gaussian.Gaussian method) (pyar.backends.mlatom_aiqm1.MlatomAiqm1 method) (pyar.backends.mopac.Mopac method) (pyar.backends.orca.Orca method) (pyar.backends.orca_aiqm1.OrcaAIQM1 method) (pyar.backends.psi4.Psi4 method) get_energy_gradient_provider() (in module pyar.energy_gradient_providers) get_principal_axes() (in module pyar.property) get_std_of_radius() (in module pyar.property) get_the_best_molecule() (in module pyar.selection.clustering) gradient_hartree_per_bohr (pyar.energy_gradient_providers.EnergyGradientResult attribute) Grigoryan_Springborg() (in module pyar.scripts.similarity)

H

halton_quaternions() (in module pyar.sampling.rotation)

hdbscan_clustering() (in module pyar.selection.clustering) hydrogen_bond_analysis() (in module pyar.property)

I

implemented_properties (pyar.backends.ani.ANI attribute) (pyar.backends.geometric.PyarGeometricCalculator attribute) index_elements() (in module pyar.scripts.similarity) infer_bonds() (in module pyar.reaction_trace)

initialize_reaction_run() (in module pyar.workflows.reaction) is_bonded() (pyar.core.molecule.Molecule method) is_cycle_exceeded() (in module pyar.optimiser) is_success() (in module pyar.optimiser) is_usable() (in module pyar.optimiser)

K

kmeans_clustering() (in module pyar.selection.clustering)

L

latin_hypercube_sphere() (in module pyar.sampling.sphere) load() (pyar.state.aggregate.AggregateRunState class method) (pyar.state.reaction.ReactionRunState class method) (pyar.state.solvation.SolvationRunState class method)

load_trace_records() (in module pyar.reaction_trace)

M

main() (in module pyar.backends.aimnet_2) (in module pyar.backends.aiqm1_mlatom) (in module pyar.backends.ani) (in module pyar.backends.babel) (in module pyar.backends.gaussian) (in module pyar.backends.geometric) (in module pyar.backends.mlatom_aiqm1) (in module pyar.backends.mlopt) (in module pyar.backends.mopac) (in module pyar.backends.orca) (in module pyar.backends.orca_aiqm1) (in module pyar.backends.psi4) (in module pyar.backends.xtb) (in module pyar.backends.xtb_aimnet2) (in module pyar.backends.xtb_aiqm1) (in module pyar.backends.xtb_turbo) (in module pyar.cli) (in module pyar.core.molecule) (in module pyar.optimiser) (in module pyar.sampling.trial_generator) (in module pyar.scripts.benchmark_clustering) (in module pyar.scripts.benchmark_orientations) (in module pyar.scripts.clustering) (in module pyar.scripts.descriptor) (in module pyar.scripts.energy_table) (in module pyar.scripts.explore) (in module pyar.scripts.optimiser) (in module pyar.scripts.react) (in module pyar.scripts.reaction_trace) (in module pyar.scripts.similarity) (in module pyar.scripts.trial_generation) (in module pyar.workflows.reaction) make_inchi_string_from_xyz() (in module pyar.backends.babel) make_smile_string_from_xyz() (in module pyar.backends.babel) maximin_select() (in module pyar.sampling.sphere) mean_covering_distance_degrees (pyar.sampling.metrics.RotationCoverageMetrics attribute) (pyar.sampling.metrics.SphereCoverageMetrics attribute) mean_nearest_neighbor_degrees (pyar.sampling.metrics.RotationCoverageMetrics attribute) (pyar.sampling.metrics.SphereCoverageMetrics attribute) mean_shift_clustering() (in module pyar.selection.clustering) merge_two_molecules() (in module pyar.sampling.trial_generator) merged_with() (in module pyar.molecule_merge) (pyar.core.molecule.Molecule method) metadata (pyar.workflow_results.WorkflowResult attribute) migrate_legacy() (pyar.state.reaction.ReactionRunState class method) min_interfragment_distance() (in module pyar.reaction_trace) minimum_separation() (in module pyar.sampling.trial_generator) minimum_separation_degrees (pyar.sampling.metrics.RotationCoverageMetrics attribute) (pyar.sampling.metrics.SphereCoverageMetrics attribute) MlatomAiqm1 (class in pyar.backends.mlatom_aiqm1) module pyar.aggregator pyar.backend_capabilities pyar.backends pyar.backends.aimnet_2 pyar.backends.aiqm1_mlatom pyar.backends.ani pyar.backends.babel pyar.backends.gaussian pyar.backends.geometric pyar.backends.mlatom_aiqm1 pyar.backends.mlopt pyar.backends.mopac pyar.backends.orca pyar.backends.orca_aiqm1 pyar.backends.psi4 pyar.backends.xtb pyar.backends.xtb_aimnet2 pyar.backends.xtb_aiqm1 pyar.backends.xtb_turbo pyar.backends.xtb_utils pyar.cli pyar.core.geometry pyar.core.molecule pyar.energy_gradient_providers pyar.io.xyz pyar.molecule_merge pyar.optimiser pyar.property pyar.reaction_analysis pyar.reaction_trace pyar.sampling.metrics pyar.sampling.rotation pyar.sampling.sphere pyar.sampling.trial_generator pyar.scan pyar.scripts pyar.scripts.benchmark_clustering pyar.scripts.benchmark_orientations pyar.scripts.clustering pyar.scripts.descriptor pyar.scripts.energy_table pyar.scripts.explore pyar.scripts.optimiser pyar.scripts.react pyar.scripts.reaction_trace pyar.scripts.similarity pyar.scripts.trial_generation pyar.selection.basin_memory pyar.selection.clustering pyar.selection.deduplication pyar.selection.diversity pyar.solvation_state pyar.state.aggregate pyar.state.reaction pyar.state.solvation pyar.workflow_results pyar.workflows.aggregate pyar.workflows.reaction pyar.workflows.solvation

mol_to_turbomole_coord() (pyar.core.molecule.Molecule method) mol_to_xyz() (pyar.core.molecule.Molecule method) Molecule (class in pyar.core.molecule) moments_of_inertia_tensor (pyar.core.molecule.Molecule property) moments_of_inertia_tensor() (in module pyar.core.geometry) Mopac (class in pyar.backends.mopac) move_to_centre_of_mass() (in module pyar.core.geometry) (pyar.core.molecule.Molecule method) move_to_origin() (in module pyar.core.geometry) (pyar.core.molecule.Molecule method) moved_to_centre_of_mass() (pyar.core.molecule.Molecule method) moved_to_origin() (pyar.core.molecule.Molecule method)

N

native_optimization (pyar.backend_capabilities.BackendCapabilities attribute)

O

OBabel (class in pyar.backends.babel) old_path_to_new_path() (in module pyar.aggregator) optics_clustering() (in module pyar.selection.clustering) optimise() (in module pyar.optimiser) optimize() (pyar.backends.aimnet_2.Aimnet2 method) (pyar.backends.aiqm1_mlatom.AIQM1 method) (pyar.backends.ani.ANIInterface method) (pyar.backends.babel.OBabel method) (pyar.backends.gaussian.Gaussian method) (pyar.backends.geometric.Geometric method) (pyar.backends.mlatom_aiqm1.MlatomAiqm1 method) (pyar.backends.mopac.Mopac method) (pyar.backends.orca.Orca method) (pyar.backends.orca_aiqm1.OrcaAIQM1 method) (pyar.backends.psi4.Psi4 method) (pyar.backends.xtb.Xtb method) (pyar.backends.xtb_aimnet2.XtbAimnet2 method) (pyar.backends.xtb_aiqm1.XtbAIQM1 method) (pyar.backends.xtb_turbo.XtbTurbo method)

optimize_all() (in module pyar.workflows.reaction) optimized_coordinates (pyar.backends.aimnet_2.Aimnet2 property) (pyar.backends.aiqm1_mlatom.AIQM1 property) (pyar.backends.xtb.Xtb property) (pyar.backends.xtb_aimnet2.XtbAimnet2 property) (pyar.backends.xtb_aiqm1.XtbAIQM1 property) Orca (class in pyar.backends.orca) OrcaAIQM1 (class in pyar.backends.orca_aiqm1) OrcaEnergyGradientProvider (class in pyar.energy_gradient_providers)

P

parse_arguments() (in module pyar.scripts.explore) parse_formula() (in module pyar.scripts.explore) parse_xyz() (in module pyar.core.molecule) (in module pyar.io.xyz) pending_molecules() (pyar.state.reaction.ReactionRunState method) plot_points() (in module pyar.sampling.trial_generator) plot_reaction_trace() (in module pyar.reaction_analysis) polar_to_cartesian() (in module pyar.sampling.trial_generator) prepare_input() (pyar.backends.aimnet_2.Aimnet2 method) (pyar.backends.aiqm1_mlatom.AIQM1 method) (pyar.backends.gaussian.Gaussian method) (pyar.backends.mlatom_aiqm1.MlatomAiqm1 method) (pyar.backends.mopac.Mopac method) (pyar.backends.orca.Orca method) (pyar.backends.orca_aiqm1.OrcaAIQM1 method) (pyar.backends.psi4.Psi4 method) prepare_keyword() (pyar.backends.orca_aiqm1.OrcaAIQM1 method) print_energy_table() (in module pyar.selection.clustering) (in module pyar.selection.diversity) print_header() (in module pyar.workflows.reaction) process_files() (in module pyar.scripts.similarity) Psi4 (class in pyar.backends.psi4) pyar.aggregator module pyar.backend_capabilities module pyar.backends module pyar.backends.aimnet_2 module pyar.backends.aiqm1_mlatom module pyar.backends.ani module pyar.backends.babel module pyar.backends.gaussian module pyar.backends.geometric module pyar.backends.mlatom_aiqm1 module pyar.backends.mlopt module pyar.backends.mopac module pyar.backends.orca module pyar.backends.orca_aiqm1 module pyar.backends.psi4 module pyar.backends.xtb module pyar.backends.xtb_aimnet2 module pyar.backends.xtb_aiqm1 module pyar.backends.xtb_turbo module pyar.backends.xtb_utils module pyar.cli module pyar.core.geometry module pyar.core.molecule module pyar.energy_gradient_providers module

pyar.io.xyz module pyar.molecule_merge module pyar.optimiser module pyar.property module pyar.reaction_analysis module pyar.reaction_trace module pyar.sampling.metrics module pyar.sampling.rotation module pyar.sampling.sphere module pyar.sampling.trial_generator module pyar.scan module pyar.scripts module pyar.scripts.benchmark_clustering module pyar.scripts.benchmark_orientations module pyar.scripts.clustering module pyar.scripts.descriptor module pyar.scripts.energy_table module pyar.scripts.explore module pyar.scripts.optimiser module pyar.scripts.react module pyar.scripts.reaction_trace module pyar.scripts.similarity module pyar.scripts.trial_generation module pyar.selection.basin_memory module pyar.selection.clustering module pyar.selection.deduplication module pyar.selection.diversity module pyar.solvation_state module pyar.state.aggregate module pyar.state.reaction module pyar.state.solvation module pyar.workflow_results module pyar.workflows.aggregate module pyar.workflows.reaction module pyar.workflows.solvation module PyarGeometricCalculator (class in pyar.backends.geometric)

Q

quaternion_coverage_metrics() (in module pyar.sampling.metrics)

quaternions_to_euler_zxz() (in module pyar.sampling.rotation)

R

random_quaternions() (in module pyar.sampling.rotation) random_sphere() (in module pyar.sampling.sphere) rbf_kernel_clustering() (in module pyar.selection.clustering) react() (in module pyar.workflows.reaction) ReactionResult (class in pyar.workflow_results) ReactionRunState (class in pyar.state.reaction) ReactionStateError ReactionTraceRecorder (class in pyar.reaction_trace) read_file() (in module pyar.scripts.similarity) read_legacy_checkpoint() (in module pyar.state.reaction) read_molecule_from_file() (pyar.backends.mlatom_aiqm1.MlatomAiqm1 method) read_old_path() (in module pyar.aggregator) read_orientations() (in module pyar.aggregator) read_xyz() (in module pyar.core.molecule) (in module pyar.io.xyz) record() (pyar.reaction_trace.ReactionTraceRecorder method) record_job() (pyar.state.reaction.ReactionRunState method)

record_product() (pyar.state.reaction.ReactionRunState method) record_selected_basins() (in module pyar.selection.basin_memory) register_backend_capabilities() (in module pyar.backend_capabilities) register_energy_gradient_provider() (in module pyar.energy_gradient_providers) relax_without_afir_bias() (in module pyar.workflows.reaction) remaining_gamma_schedule() (pyar.state.reaction.ReactionRunState method) remaining_pathway_labels() (pyar.state.aggregate.AggregateRunState method) remove_similar() (in module pyar.selection.deduplication) require_executable() (in module pyar.backends) rotate_3d() (in module pyar.core.geometry) (pyar.core.molecule.Molecule method) rotated_3d() (pyar.core.molecule.Molecule method) rotation_matrix() (in module pyar.core.geometry) RotationCoverageMetrics (class in pyar.sampling.metrics) run_command() (in module pyar.backends) run_directory (pyar.workflow_results.WorkflowResult attribute) run_output() (in module pyar.backends)

S

save() (pyar.state.aggregate.AggregateRunState method) (pyar.state.reaction.ReactionRunState method) (pyar.state.solvation.SolvationRunState method) saved_product_identities() (pyar.state.reaction.ReactionRunState method) scan_distance() (in module pyar.scan) select_best_from_each_cluster() (in module pyar.selection.clustering) select_pathways() (in module pyar.aggregator) selected_paths (pyar.workflow_results.WorkflowResult attribute) set_gamma() (pyar.backends.orca_aiqm1.OrcaAIQM1 method) SF (class in pyar.backends) singlepoint() (pyar.backends.ani.ANIInterface method) solvate() (in module pyar.aggregator) (in module pyar.workflows.solvation) SolvationResult (class in pyar.workflow_results) SolvationRunState (class in pyar.state.solvation)

SolvationStateError spectral_clustering() (in module pyar.selection.clustering) sphere_coverage_metrics() (in module pyar.sampling.metrics) SphereCoverageMetrics (class in pyar.sampling.metrics) spherical_to_cartesian() (in module pyar.sampling.trial_generator) split_atoms_lists() (pyar.core.molecule.Molecule method) split_coordinates() (pyar.core.molecule.Molecule method) split_covalent_radii_list() (pyar.core.molecule.Molecule method) staged_optimization (pyar.backend_capabilities.BackendCapabilities attribute) state_path (pyar.workflow_results.WorkflowResult attribute) status (pyar.workflow_results.WorkflowResult attribute) supported_geometry_backends() (in module pyar.backend_capabilities) supported_options (pyar.backend_capabilities.BackendCapabilities attribute) supports_charge (pyar.backend_capabilities.BackendCapabilities attribute) supports_multiplicity (pyar.backend_capabilities.BackendCapabilities attribute)

T

to_ase_atoms() (pyar.core.molecule.Molecule method) to_dict() (pyar.workflow_results.WorkflowResult method)

translate() (in module pyar.core.geometry) (pyar.core.molecule.Molecule method) translated() (pyar.core.molecule.Molecule method)

U

uniq() (in module pyar.scripts.similarity)

unsupported_qc_options() (in module pyar.backend_capabilities) update_id() (in module pyar.aggregator)

V

validate_fragments() (in module pyar.io.xyz) validate_progress() (pyar.state.aggregate.AggregateRunState method) (pyar.state.solvation.SolvationRunState method)

validate_request() (pyar.state.aggregate.AggregateRunState method) (pyar.state.reaction.ReactionRunState method) (pyar.state.solvation.SolvationRunState method) validate_trace_record() (in module pyar.reaction_trace)

W

which() (in module pyar.backends) with_gamma() (in module pyar.workflows.reaction) without_afir_bias() (in module pyar.workflows.reaction) workflow (pyar.workflow_results.WorkflowResult attribute) WorkflowResult (class in pyar.workflow_results)

write_csv_file() (in module pyar.optimiser) write_trial_vectors() (in module pyar.sampling.trial_generator) write_turbomole_coord() (in module pyar.io.xyz) write_xyz() (in module pyar.backends) (in module pyar.io.xyz)

X

Xtb (class in pyar.backends.xtb) xtb_optimized_xyz_file (pyar.backends.xtb_aimnet2.XtbAimnet2 property) (pyar.backends.xtb_aiqm1.XtbAIQM1 property) xtb_parallel_args() (in module pyar.backends.xtb_utils) XtbAimnet2 (class in pyar.backends.xtb_aimnet2)

XtbAIQM1 (class in pyar.backends.xtb_aiqm1) XtbEnergyGradientProvider (class in pyar.energy_gradient_providers) XtbTurbo (class in pyar.backends.xtb_turbo) xyz_to_mopac_input() (in module pyar.backends.babel) xyz_to_sdf_file() (in module pyar.backends.babel) XYZParseError