Index _ | A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | V | X _ __init__() (cgbind.Cage method) (cgbind.CageSubstrateComplex method) (cgbind.Linker method) (cgbind.molecule.BaseStruct method) (cgbind.molecule.Molecule method) (cgbind.Substrate method) (cgbind.templates.Linker method) (cgbind.templates.Metal method) (cgbind.templates.Template method) A allow_permutations (cgbind.Config attribute) arch (cgbind.Linker attribute) atom_id (cgbind.templates.Metal attribute) atoms (cgbind.molecule.BaseStruct attribute) (cgbind.templates.Linker attribute) atoms_to_xyz_file() (in module cgbind.input_output) B BaseStruct (class in cgbind.molecule) bonds (cgbind.molecule.Molecule attribute) (cgbind.templates.Linker attribute) C Cage (class in cgbind) cage_template (cgbind.Linker attribute) CageSubstrateComplex (class in cgbind) calc_com() (in module cgbind.geom) calc_normalised_vector() (in module cgbind.geom) centre() (cgbind.molecule.BaseStruct method) charge (cgbind.molecule.BaseStruct attribute) com (cgbind.molecule.BaseStruct attribute) (cgbind.templates.Linker attribute) Config (class in cgbind) conformers (cgbind.molecule.Molecule attribute) coord (cgbind.templates.Metal attribute) coords (cgbind.templates.Linker attribute) D dr (cgbind.Linker attribute) E energy (cgbind.molecule.BaseStruct attribute) F find_mols_in_xyzs() (in module cgbind.templates) G gen_confs() (cgbind.Substrate method) get_atoms_from_file() (in module cgbind.input_output) get_cavity_vol() (cgbind.Cage method) get_centered_matrix() (in module cgbind.geom) get_centroid() (cgbind.Cage method) get_charges() (cgbind.Cage method) (cgbind.molecule.Molecule method) get_esp_cube() (cgbind.Cage method) get_m_m_dist() (cgbind.Cage method) get_max_escape_sphere() (cgbind.Cage method) get_metal_atom_ids() (cgbind.Cage method) get_num_h_bond_acceptors() (cgbind.Cage method) get_num_h_bond_donors() (cgbind.Cage method) get_num_rot_bonds() (cgbind.Cage method) get_rot_mat_kabsch() (in module cgbind.geom) get_template() (in module cgbind.templates) get_xmotif_coordinates() (cgbind.Linker method) I is_geom_reasonable() (in module cgbind.geom) L label (cgbind.templates.Metal attribute) Linker (class in cgbind) (class in cgbind.templates) M Metal (class in cgbind.templates) mol2file_to_atoms() (in module cgbind.input_output) mol_obj (cgbind.molecule.Molecule attribute) Molecule (class in cgbind.molecule) molfile_to_atoms() (in module cgbind.input_output) mult (cgbind.molecule.BaseStruct attribute) N n_atoms (cgbind.molecule.BaseStruct attribute) n_confs (cgbind.molecule.Molecule attribute) n_cores (cgbind.Config attribute) n_h_acceptors (cgbind.molecule.Molecule attribute) n_h_donors (cgbind.molecule.Molecule attribute) n_rot_bonds (cgbind.molecule.Molecule attribute) name (cgbind.molecule.BaseStruct attribute) O optimise() (cgbind.molecule.BaseStruct method) P print_esp_cube_file() (cgbind.Cage method) print_xyz_file() (cgbind.molecule.BaseStruct method) R reasonable_geometry (cgbind.molecule.BaseStruct attribute) rotation_matrix() (in module cgbind.geom) S save_template() (cgbind.templates.Template method) set_atoms() (cgbind.molecule.BaseStruct method) set_ranked_linker_possibilities() (cgbind.Linker method) shift_vec (cgbind.templates.Metal attribute) singlepoint() (cgbind.molecule.BaseStruct method) smiles (cgbind.molecule.Molecule attribute) solvent (cgbind.molecule.BaseStruct attribute) spherical_to_cart() (in module cgbind.geom) Substrate (class in cgbind) T Template (class in cgbind.templates) V volume (cgbind.molecule.Molecule attribute) X x_atoms (cgbind.Linker attribute) (cgbind.templates.Linker attribute) x_motifs (cgbind.Linker attribute) (cgbind.templates.Linker attribute) xyz_file_to_atoms() (in module cgbind.input_output) xyzfile_to_atoms() (in module cgbind.input_output)