Index A | B | C | D | E | F | G | I | M | N | O | P | R | S | T | W | X | Y A add_conformer() (bbprepared.Ensemble method) AllNonHSelector (class in bbprepared.selectors) AllSelector (class in bbprepared.selectors) AngleRange (class in bbprepared.generators) B bbprepared module bbprepared.generators module bbprepared.selectors module BindersSelector (class in bbprepared.selectors) BondRange (class in bbprepared.generators) ByIdSelector (class in bbprepared.selectors) BySmartsSelector (class in bbprepared.selectors) C calculate_all_scores() (bbprepared.DitopicFitter method) (bbprepared.MinimiseAngle method) (bbprepared.Planarfy method) (bbprepared.Process method) (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) calculate_score() (bbprepared.DitopicFitter method) (bbprepared.MinimiseAngle method) (bbprepared.Planarfy method) (bbprepared.Process method) (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) calculate_value() (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) clone() (bbprepared.PanelBuildingBlock method) ClosestFGs (class in bbprepared) Conformer (class in bbprepared) conformer_id (bbprepared.Conformer attribute) D DeletersSelector (class in bbprepared.selectors) DitopicFitter (class in bbprepared) E EnergyCalculator (class in bbprepared) Ensemble (class in bbprepared) ETKDG (class in bbprepared.generators) expected_num_atoms (bbprepared.generators.AngleRange attribute) (bbprepared.generators.BondRange attribute) (bbprepared.generators.TorsionRange attribute) F function (bbprepared.EnergyCalculator attribute) (bbprepared.Optimiser attribute) FurthestFGs (class in bbprepared) G generate_conformers() (bbprepared.generators.ETKDG method) (bbprepared.generators.Generator method) (bbprepared.generators.GeometryScanner method) (bbprepared.generators.SelectorDistanceScanner method) (bbprepared.generators.TorsionScanner method) Generator (class in bbprepared.generators) GeometryScanner (class in bbprepared.generators) get_all_scores() (bbprepared.DitopicFitter method) (bbprepared.MinimiseAngle method) (bbprepared.Planarfy method) (bbprepared.Process method) (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) get_all_scores_by_id() (bbprepared.DitopicFitter method) (bbprepared.MinimiseAngle method) (bbprepared.Planarfy method) (bbprepared.Process method) (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) get_atomic_positions() (bbprepared.PanelBuildingBlock method) (bbprepared.selectors.AllNonHSelector method) (bbprepared.selectors.AllSelector method) (bbprepared.selectors.BindersSelector method) (bbprepared.selectors.ByIdSelector method) (bbprepared.selectors.BySmartsSelector method) (bbprepared.selectors.DeletersSelector method) (bbprepared.selectors.NotPlacersSelector method) (bbprepared.selectors.NullSelector method) (bbprepared.selectors.Selector method) (bbprepared.selectors.XCOMXSelector method) get_atoms() (bbprepared.PanelBuildingBlock method) get_base_molecule() (bbprepared.Ensemble method) get_best() (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) get_best_id() (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) get_bonders() (bbprepared.PanelBuildingBlock method) get_bonds() (bbprepared.PanelBuildingBlock method) get_canonical_atom_ids() (bbprepared.PanelBuildingBlock method) get_centroid() (bbprepared.PanelBuildingBlock method) get_concave_direction() (bbprepared.PanelBuildingBlock method) get_conformer() (bbprepared.Ensemble method) get_conformers() (bbprepared.Ensemble method) get_core_atom_ids() (bbprepared.PanelBuildingBlock method) get_data() (bbprepared.DitopicFitter method) (bbprepared.MinimiseAngle method) (bbprepared.Planarfy method) (bbprepared.Process method) (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) get_direction() (bbprepared.PanelBuildingBlock method) get_functional_groups() (bbprepared.PanelBuildingBlock method) get_long_axis() (bbprepared.PanelBuildingBlock method) get_lowest_energy_conformer() (bbprepared.Ensemble method) get_maximum_diameter() (bbprepared.PanelBuildingBlock method) get_minimum() (bbprepared.DitopicFitter method) (bbprepared.MinimiseAngle method) (bbprepared.Planarfy method) (bbprepared.Process method) (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) get_minimum_id() (bbprepared.DitopicFitter method) (bbprepared.MinimiseAngle method) (bbprepared.Planarfy method) (bbprepared.Process method) (bbprepared.TargetProcess method) (bbprepared.TargetTorsion method) get_molecule_num_atoms() (bbprepared.Ensemble method) get_num_atoms() (bbprepared.PanelBuildingBlock method) get_num_bonds() (bbprepared.PanelBuildingBlock method) get_num_conformers() (bbprepared.Ensemble method) get_num_functional_groups() (bbprepared.PanelBuildingBlock method) get_num_placers() (bbprepared.PanelBuildingBlock method) get_placer_ids() (bbprepared.PanelBuildingBlock method) get_plane_normal() (bbprepared.PanelBuildingBlock method) get_position_matrix() (bbprepared.PanelBuildingBlock method) I init() (bbprepared.PanelBuildingBlock class method) init_from_atomlite() (bbprepared.PanelBuildingBlock class method) init_from_file() (bbprepared.PanelBuildingBlock class method) init_from_molecule() (bbprepared.PanelBuildingBlock class method) init_from_rdkit_mol() (bbprepared.PanelBuildingBlock class method) init_from_vabene_molecule() (bbprepared.PanelBuildingBlock class method) M MinimiseAngle (class in bbprepared) Modifier (class in bbprepared) modify() (bbprepared.ClosestFGs method) (bbprepared.FurthestFGs method) (bbprepared.Modifier method) (bbprepared.RandomFGs method) (bbprepared.ReorientC1Panel method) (bbprepared.ReorientC2Panel method) (bbprepared.ReorientPanel method) module bbprepared bbprepared.generators bbprepared.selectors molecule (bbprepared.Conformer attribute) N name (bbprepared.EnergyCalculator attribute) (bbprepared.Optimiser attribute) NotPlacersSelector (class in bbprepared.selectors) NullSelector (class in bbprepared.selectors) O optimise_conformers() (bbprepared.Ensemble method) Optimiser (class in bbprepared) P PanelBuildingBlock (class in bbprepared) permutation (bbprepared.Conformer attribute) Planarfy (class in bbprepared) Process (class in bbprepared) R RandomFGs (class in bbprepared) reassign_functional_groups() (bbprepared.ReorientC1Panel method) (bbprepared.ReorientC2Panel method) (bbprepared.ReorientPanel method) ReorientC1Panel (class in bbprepared) ReorientC2Panel (class in bbprepared) ReorientPanel (class in bbprepared) S scanned_ids (bbprepared.generators.AngleRange attribute) (bbprepared.generators.BondRange attribute) (bbprepared.generators.TorsionRange attribute) scanned_range (bbprepared.generators.AngleRange attribute) (bbprepared.generators.BondRange attribute) (bbprepared.generators.TorsionRange attribute) score (bbprepared.Conformer attribute) select_atoms() (bbprepared.selectors.AllNonHSelector method) (bbprepared.selectors.AllSelector method) (bbprepared.selectors.BindersSelector method) (bbprepared.selectors.ByIdSelector method) (bbprepared.selectors.BySmartsSelector method) (bbprepared.selectors.DeletersSelector method) (bbprepared.selectors.NotPlacersSelector method) (bbprepared.selectors.NullSelector method) (bbprepared.selectors.Selector method) (bbprepared.selectors.XCOMXSelector method) Selector (class in bbprepared.selectors) SelectorDistanceScanner (class in bbprepared.generators) show_long_axis() (bbprepared.PanelBuildingBlock method) smarts (bbprepared.generators.AngleRange attribute) (bbprepared.generators.BondRange attribute) (bbprepared.generators.TorsionRange attribute) source (bbprepared.Conformer attribute) T TargetProcess (class in bbprepared) TargetTorsion (class in bbprepared) to_atomlite() (bbprepared.PanelBuildingBlock method) to_rdkit_mol() (bbprepared.PanelBuildingBlock method) TorsionRange (class in bbprepared.generators) TorsionScanner (class in bbprepared.generators) W with_canonical_atom_ordering() (bbprepared.PanelBuildingBlock method) with_centroid() (bbprepared.PanelBuildingBlock method) with_displacement() (bbprepared.PanelBuildingBlock method) with_functional_groups() (bbprepared.PanelBuildingBlock method) with_position_matrix() (bbprepared.PanelBuildingBlock method) with_rotation_about_axis() (bbprepared.PanelBuildingBlock method) with_rotation_between_vectors() (bbprepared.PanelBuildingBlock method) with_rotation_to_minimize_angle() (bbprepared.PanelBuildingBlock method) with_structure_from_atomlite() (bbprepared.PanelBuildingBlock method) with_structure_from_file() (bbprepared.PanelBuildingBlock method) write() (bbprepared.PanelBuildingBlock method) X XCOMXSelector (class in bbprepared.selectors) Y yield_conformers() (bbprepared.Ensemble method) yield_stepwise() (bbprepared.selectors.AllNonHSelector method) (bbprepared.selectors.AllSelector method) (bbprepared.selectors.BindersSelector method) (bbprepared.selectors.ByIdSelector method) (bbprepared.selectors.BySmartsSelector method) (bbprepared.selectors.DeletersSelector method) (bbprepared.selectors.NotPlacersSelector method) (bbprepared.selectors.NullSelector method) (bbprepared.selectors.Selector method) (bbprepared.selectors.XCOMXSelector method)