Index

A

Aligner (class in stko) AlignmentPotential (class in stko)

AlkyneAngle (class in stko.molecule_analysis) assign_FF() (stko.GulpUFFMDOptimizer method) (stko.GulpUFFOptimizer method)

C

C5N1Planarity (class in stko.molecule_analysis) C6Planarity (class in stko.molecule_analysis) calculate() (stko.ConstructedMoleculeTorsionCalculator method) (stko.KabschRmsdCalculator method) (stko.MatchedTorsionCalculator method) (stko.MMFFEnergy method) (stko.molecule_analysis.SubgroupAnalyser method) (stko.OpenBabelEnergy method) (stko.OpenMMEnergy method) (stko.OrcaEnergy method) (stko.PlanarityCalculator method) (stko.RmsdCalculator method) (stko.RmsdMappedCalculator method) (stko.ShapeCalculator method) (stko.TorsionCalculator method) (stko.UFFEnergy method) (stko.XTBEnergy method) calculate_angle() (in module stko) calculate_angles() (stko.molecule_analysis.GeometryAnalyser method) calculate_bonds() (stko.molecule_analysis.GeometryAnalyser method) calculate_dihedral() (in module stko)

calculate_torsions() (stko.molecule_analysis.GeometryAnalyser method) CalculatorError cap_absolute_value() (in module stko) clone() (stko.Du method) (stko.functional_groups.ThreeSiteFG method) (stko.Network method) (stko.PositionedAtom method) (stko.UnitCell method) CNCFactory (class in stko.functional_groups) CNNFactory (class in stko.functional_groups) Collapser (class in stko) CollapserMC (class in stko) compute_potential() (stko.AlignmentPotential method) ConstructedAnalyser (class in stko.molecule_analysis) ConstructedMoleculeT (in module stko) ConstructedMoleculeTorsionCalculator (class in stko) ConstructedMoleculeTorsionResults (class in stko) content (stko.MAEExtractor attribute) ConvergenceError ConversionError count_bbs (stko.topology_functions.NamedIntermediate attribute)

D

decompose() (stko.molecule_analysis.DecomposeMOC method) DecomposeMOC (class in stko.molecule_analysis) DifferentAtomError

DifferentMoleculeError DitopicThreeSiteAnalyser (class in stko.molecule_analysis) Du (class in stko)

E

electron_affinity (stko.XTBExtractor attribute) energies (stko.MAEExtractor attribute) EnergyResults (class in stko) ETKDG (class in stko) ExpectedMetalError

extract_conformers() (stko.MAEExtractor method) extract_energy() (stko.MAEExtractor method) extract_final_energy() (stko.GulpUFFMDOptimizer method) (stko.GulpUFFOptimizer method) extract_topology() (stko.TopologyExtractor method)

F

fermi_level (stko.XTBExtractor attribute) ForceFieldError ForceFieldSetupError

frequencies (stko.XTBExtractor attribute) full_dipole_moment (stko.XTBExtractor attribute) full_quadrupole_moment (stko.XTBExtractor attribute)

G

GeometryAnalyser (class in stko.molecule_analysis) get_a() (stko.UnitCell method) get_adjacent_centroids() (stko.molecule_analysis.DitopicThreeSiteAnalyser method) get_alpha() (stko.UnitCell method) get_approximate_cell_size() (in module stko) get_asphericity() (stko.ShapeResults method) get_atom() (stko.PositionedAtom method) get_atom_distance() (in module stko) get_atom_ids() (stko.functional_groups.ThreeSiteFG method) (stko.Torsion method) get_atom_plane() (stko.PlanarityResults method) get_atomic_number() (stko.Du method) (stko.PositionedAtom method) get_atoms() (stko.functional_groups.ThreeSiteFG method) (stko.Torsion method) get_available_reactions() (stko.topology_functions.UnreactedTopologyGraph method) get_avg_centroid_distance() (stko.molecule_analysis.GeometryAnalyser method) get_b() (stko.UnitCell method) get_beta() (stko.UnitCell method) get_binder() (stko.functional_groups.ThreeSiteFG method) get_binder_adjacent_torsion() (stko.molecule_analysis.DitopicThreeSiteAnalyser method) get_binder_angles() (stko.molecule_analysis.DitopicThreeSiteAnalyser method) get_binder_binder_angle() (stko.molecule_analysis.DitopicThreeSiteAnalyser method) get_binder_centroid_angle() (stko.molecule_analysis.DitopicThreeSiteAnalyser method) get_binder_distance() (stko.molecule_analysis.DitopicThreeSiteAnalyser method) get_bonder_ids() (stko.functional_groups.ThreeSiteFG method) get_bonders() (stko.functional_groups.ThreeSiteFG method) get_building_block() (stko.TorsionInfo method) get_building_block_atom_ids() (stko.molecule_analysis.ConstructedAnalyser method) get_building_block_centroids() (stko.molecule_analysis.ConstructedAnalyser method) get_building_block_id() (stko.TorsionInfo method) get_building_block_torsion() (stko.TorsionInfo method) get_c() (stko.UnitCell method) get_cell_matrix() (stko.UnitCell method) get_charge() (stko.Du method) (stko.PositionedAtom method) get_connected_components() (stko.Network method) get_connected_graphs() (stko.TopologyExtractor method) get_connectivities() (stko.TopologyInfo method) get_core_atom_ids() (stko.functional_groups.ThreeSiteFG method) get_deleter_ids() (stko.functional_groups.ThreeSiteFG method) get_deleters() (stko.functional_groups.ThreeSiteFG method) get_eccentricity() (stko.ShapeResults method) get_edge_pairs() (stko.TopologyInfo method) get_electron_affinity() (stko.XTBResults method) get_energy() (stko.EnergyResults method) (stko.MMFFEnergy method) (stko.OpenBabelEnergy method) (stko.OpenMMEnergy method) (stko.OrcaEnergy method) (stko.UFFEnergy method) (stko.XTBEnergy method) get_fermi_level() (stko.XTBResults method) get_frequencies() (stko.XTBResults method) get_from_parameters() (in module stko) get_full_dipole_moments() (stko.XTBResults method) get_full_quadrupole_moments() (stko.XTBResults method) get_functional_groups() (stko.functional_groups.CNCFactory method) (stko.functional_groups.CNNFactory method) (stko.functional_groups.NNNFactory method) (stko.functional_groups.ThreeSiteFactory method) get_gamma() (stko.UnitCell method) get_graph() (stko.Network method) get_halfbite_angles() (stko.molecule_analysis.DitopicThreeSiteAnalyser method) get_homo_lumo_gap() (stko.XTBResults method) get_homo_lumo_orbitals() (stko.XTBResults method) get_id() (stko.Du method) (stko.PositionedAtom method)

get_inertial_shape_factor() (stko.ShapeResults method) get_ionisation_potential() (stko.XTBResults method) get_max_diameter() (stko.molecule_analysis.GeometryAnalyser method) get_metal_atoms() (in module stko) get_metal_centroid_metal_angle() (stko.molecule_analysis.GeometryAnalyser method) get_metal_distances() (stko.molecule_analysis.GeometryAnalyser method) get_min_atom_atom_distance() (stko.molecule_analysis.GeometryAnalyser method) get_min_centroid_distance() (stko.molecule_analysis.GeometryAnalyser method) get_molecule() (stko.ConstructedMoleculeTorsionResults method) (stko.TorsionResults method) get_named_intermediates() (stko.topology_functions.UnreactedTopologyGraph method) get_neigh1() (stko.functional_groups.ThreeSiteFG method) get_neigh2() (stko.functional_groups.ThreeSiteFG method) get_nodes() (stko.Network method) get_npr1() (stko.ShapeResults method) get_npr2() (stko.ShapeResults method) get_num_bonders() (stko.functional_groups.ThreeSiteFG method) get_placer_ids() (stko.functional_groups.ThreeSiteFG method) get_planarity_parameter() (stko.PlanarityResults method) get_plane_deviation() (stko.PlanarityResults method) get_plane_deviation_span() (stko.PlanarityResults method) get_pmi1() (stko.ShapeResults method) get_pmi2() (stko.ShapeResults method) get_pmi3() (stko.ShapeResults method) get_position() (stko.PositionedAtom method) get_present_building_blocks() (stko.topology_functions.UnreactedTopologyGraph method) get_qdip_quadrupole_moments() (stko.XTBResults method) get_qonly_dipole_moments() (stko.XTBResults method) get_qonly_quadrupole_moments() (stko.XTBResults method) get_radius_gyration() (stko.molecule_analysis.GeometryAnalyser method) get_radius_of_gyration() (stko.ShapeResults method) get_reacted_smiles() (stko.topology_functions.UnreactedTopologyGraph method) get_reaction_results() (stko.topology_functions.UnreactedTopologyGraph method) get_results() (stko.ConstructedMoleculeTorsionCalculator method) (stko.KabschRmsdCalculator method) (stko.MatchedTorsionCalculator method) (stko.MMFFEnergy method) (stko.OpenBabelEnergy method) (stko.OrcaEnergy method) (stko.PlanarityCalculator method) (stko.RmsdCalculator method) (stko.RmsdMappedCalculator method) (stko.ShapeCalculator method) (stko.TorsionCalculator method) (stko.UFFEnergy method) (stko.XTBEnergy method) get_rmsd() (stko.RmsdResults method) get_spherocity_index() (stko.ShapeResults method) get_torsion() (stko.TorsionInfo method) get_torsion_angles() (stko.ConstructedMoleculeTorsionResults method) (stko.TorsionResults method) get_torsion_info_angles() (in module stko) get_torsion_infos() (stko.ConstructedMoleculeTorsionResults method) get_torsion_infos_by_building_block() (stko.ConstructedMoleculeTorsionResults method) get_torsions() (stko.ConstructedMoleculeTorsionResults method) (stko.TorsionResults method) get_total_energy() (stko.OrcaResults method) (stko.XTBResults method) get_total_free_energy() (stko.XTBResults method) get_total_sasa() (stko.XTBResults method) get_unit_string() (stko.EnergyResults method) get_universe() (stko.MDAnalysis method) get_vector_1() (stko.UnitCell method) get_vector_2() (stko.UnitCell method) get_vector_3() (stko.UnitCell method) get_vertex_positions() (stko.TopologyInfo method) get_zmatrix() (stko.ZMatrix method) GulpUFFMDOptimizer (class in stko) GulpUFFOptimizer (class in stko)

H

homo_lumo_gap (stko.XTBExtractor attribute)

homo_lumo_occ (stko.XTBExtractor attribute)

I

incomplete (stko.XTB attribute) init_from_molecule() (stko.Network class method) InputError intermediate_name (stko.topology_functions.NamedIntermediate attribute)

IntermediatePool (class in stko.topology_functions) intermediates (stko.topology_functions.IntermediatePool attribute) InvalidSolventError ionisation_potential (stko.XTBExtractor attribute) is_valid_xtb_solvent() (in module stko)

K

KabschRmsdCalculator (class in stko)

L

LewisStructureError

lowest_energy_conformers() (stko.MAEExtractor method)

M

MacroModelForceField (class in stko) MacroModelMD (class in stko) mae_path (stko.MAEExtractor attribute) MAEExtractor (class in stko) maegz_path (stko.MAEExtractor attribute) maegz_to_mae() (stko.MAEExtractor method) MatchedTorsionCalculator (class in stko) MDAnalysis (class in stko) measure() (stko.molecule_analysis.AlkyneAngle method) (stko.molecule_analysis.C5N1Planarity method) (stko.molecule_analysis.C6Planarity method) (stko.molecule_analysis.Subgroup method) (stko.molecule_analysis.X5Planarity method) merge_stk_molecules() (in module stko.molecular_utilities) MetalOptimizer (class in stko)

min_energy (stko.MAEExtractor attribute) MMFF (class in stko) MMFFEnergy (class in stko) module stko stko.functional_groups stko.molecular_utilities stko.molecule_analysis stko.topology_functions mol_from_mae_file() (in module stko) molecule (stko.topology_functions.NamedIntermediate attribute) MoleculeSplitter (class in stko) MoleculeT (in module stko) MoleculeTransformer (class in stko) move_generated_macromodel_files() (in module stko)

N

NamedIntermediate (class in stko.topology_functions) Network (class in stko) NNNFactory (class in stko.functional_groups)

NotCompletedError NotStartedError NullOptimizer (class in stko) num_atoms (stko.topology_functions.NamedIntermediate attribute)

O

OpenBabel (class in stko) OpenBabelEnergy (class in stko) OpenMMEnergy (class in stko) OpenMMForceField (class in stko) OpenMMMD (class in stko) optimize() (stko.Aligner method) (stko.Collapser method) (stko.CollapserMC method) (stko.ETKDG method) (stko.GulpUFFMDOptimizer method) (stko.GulpUFFOptimizer method) (stko.MacroModelForceField method) (stko.MacroModelMD method) (stko.MetalOptimizer method) (stko.MMFF method) (stko.NullOptimizer method) (stko.OpenBabel method) (stko.OpenMMForceField method) (stko.OpenMMMD method) (stko.Optimizer method) (stko.OptimizerSequence method) (stko.OptWriterSequence method) (stko.TryCatchOptimizer method) (stko.UFF method) (stko.XTB method) (stko.XTBCREST method) (stko.XTBFF method) (stko.XTBFFCREST method)

Optimizer (class in stko) OptimizerError OptimizerSequence (class in stko) OptWriterSequence (class in stko) OrcaEnergy (class in stko) OrcaExtractor (class in stko) OrcaResults (class in stko) output_file (stko.OrcaExtractor attribute) (stko.XTBExtractor attribute) output_lines (stko.OrcaExtractor attribute) (stko.XTBExtractor attribute)

P

p_optimize() (stko.Collapser method) (stko.CollapserMC method) (stko.GulpUFFMDOptimizer method) (stko.GulpUFFOptimizer method) path (stko.MAEExtractor attribute)

PathError PlanarityCalculator (class in stko) PlanarityResults (class in stko) PositionedAtom (class in stko) present_bbs (stko.topology_functions.NamedIntermediate attribute)

Q

qdip_quadrupole_moment (stko.XTBExtractor attribute)

qonly_dipole_moment (stko.XTBExtractor attribute) qonly_quadrupole_moment (stko.XTBExtractor attribute)

R

RmsdCalculator (class in stko)

RmsdMappedCalculator (class in stko) RmsdResults (class in stko)

S

separate_molecule() (in module stko.molecular_utilities) SettingConflictError ShapeCalculator (class in stko) ShapeResults (class in stko) split() (stko.MoleculeSplitter method) stko module stko.functional_groups module

stko.molecular_utilities module stko.molecule_analysis module stko.topology_functions module Subgroup (class in stko.molecule_analysis) SubgroupAnalyser (class in stko.molecule_analysis)

T

ThreeSiteFactory (class in stko.functional_groups) ThreeSiteFG (class in stko.functional_groups) TopologyExtractor (class in stko) TopologyInfo (class in stko) Torsion (class in stko) TorsionCalculator (class in stko) TorsionInfo (class in stko)

TorsionResults (class in stko) total_energy (stko.OrcaExtractor attribute) (stko.XTBExtractor attribute) total_free_energy (stko.XTBExtractor attribute) total_sasa (stko.XTBExtractor attribute) transform() (stko.MoleculeTransformer method) TryCatchOptimizer (class in stko)

U

UFF (class in stko) UFFEnergy (class in stko) unit_vector() (in module stko)

UnitCell (class in stko) UnreactedTopologyGraph (class in stko.topology_functions) update_stk_from_rdkit_conformer() (in module stko.molecular_utilities)

V

vector_angle() (in module stko)

W

with_atoms() (stko.functional_groups.ThreeSiteFG method) with_cell_from_cif() (stko.UnitCell method) with_cell_from_turbomole() (stko.UnitCell method) with_cell_from_vectors() (stko.UnitCell method) with_deleted_bonds() (stko.Network method)

with_deleted_elements() (stko.Network method) with_id() (stko.PositionedAtom method) with_ids() (stko.functional_groups.ThreeSiteFG method) WrapperNotInstalledError write() (stko.TopologyInfo method)

X

X5Planarity (class in stko.molecule_analysis) XTB (class in stko) XTBCREST (class in stko) XTBEnergy (class in stko)

XTBExtractor (class in stko) XTBFF (class in stko) XTBFFCREST (class in stko) XTBResults (class in stko)

Y

yield_constructed_molecules() (stko.topology_functions.UnreactedTopologyGraph method)

Z

ZMatrix (class in stko)