dpdata.rdkit package

Submodules

dpdata.rdkit.sanitize module

exception dpdata.rdkit.sanitize.SanitizeError(content='Sanitization Failed.')

Bases: Exception

class dpdata.rdkit.sanitize.Sanitizer(level='medium', raise_errors=True, verbose=False)

Bases: object

Methods

sanitize(mol)

Sanitize mol according to self.level.

sanitize(mol)

Sanitize mol according to self.level. If failed, return None.

dpdata.rdkit.sanitize.assign_formal_charge_for_atom(atom, verbose=False)

Assigen formal charge according to 8-electron rule for element B,C,N,O,S,P,As.

dpdata.rdkit.sanitize.contain_hetero_aromatic(mol)

dpdata.rdkit.sanitize.convert_by_obabel(mol, cache_dir='/home/docs/checkouts/readthedocs.org/user_builds/dpdata/checkouts/latest/docs/.cache', obabel_path='obabel')

dpdata.rdkit.sanitize.get_explicit_valence(atom, verbose=False)

dpdata.rdkit.sanitize.get_terminal_NR2s(atom)

dpdata.rdkit.sanitize.get_terminal_oxygens(atom)

dpdata.rdkit.sanitize.is_terminal_NR2(N_atom)

dpdata.rdkit.sanitize.is_terminal_nitrogen(N_atom)

dpdata.rdkit.sanitize.is_terminal_oxygen(O_atom)

dpdata.rdkit.sanitize.kekulize_aromatic_heterocycles(mol_in, assign_formal_charge=True, sanitize=True)

dpdata.rdkit.sanitize.mol_edit_log(mol, i, j)

dpdata.rdkit.sanitize.print_atoms(mol)

dpdata.rdkit.sanitize.print_bonds(mol)

dpdata.rdkit.sanitize.regularize_carbon_bond_order(atom, verbose=True)

dpdata.rdkit.sanitize.regularize_formal_charges(mol, sanitize=True, verbose=False)

Regularize formal charges of atoms.

dpdata.rdkit.sanitize.regularize_nitrogen_bond_order(atom, verbose=True)

dpdata.rdkit.sanitize.sanitize_carboxyl(mol)

dpdata.rdkit.sanitize.sanitize_carboxyl_Catom(C_atom, verbose=True)

dpdata.rdkit.sanitize.sanitize_guanidine(mol)

dpdata.rdkit.sanitize.sanitize_guanidine_Catom(C_atom, verbose=True)

dpdata.rdkit.sanitize.sanitize_mol(mol, verbose=False)

dpdata.rdkit.sanitize.sanitize_nitrine_Natom(atom, verbose=True)

dpdata.rdkit.sanitize.sanitize_nitro(mol)

dpdata.rdkit.sanitize.sanitize_nitro_Natom(N_atom, verbose=True)

dpdata.rdkit.sanitize.sanitize_phosphate(mol)

dpdata.rdkit.sanitize.sanitize_phosphate_Patom(P_atom, verbose=True)

dpdata.rdkit.sanitize.sanitize_sulfate(mol)

dpdata.rdkit.sanitize.sanitize_sulfate_Satom(S_atom, verbose=True)

dpdata.rdkit.sanitize.super_sanitize_mol(mol, name=None, verbose=True)

dpdata.rdkit.utils module

dpdata.rdkit.utils.check_molecule_list(mols)

dpdata.rdkit.utils.check_same_atom(atom_1, atom_2)

dpdata.rdkit.utils.check_same_molecule(mol_1, mol_2)

dpdata.rdkit.utils.combine_molecules(mols)

dpdata.rdkit.utils.mol_to_system_data(mol)

dpdata.rdkit.utils.system_data_to_mol(data)