Definition of chemical bonds

After reading a molecule from an XYZ file, there is no information on the connectivity of the atoms defined. However, this information is required for calculating bond and also several atom features. In addition to defining the bonds separately and specifying them in an SD file, BONAFIDE provides two options to introduce bond information to 3D molecules and conformer ensembles:

• Internally define chemical bonds

• Attach a SMILES string

Internally determine chemical bonds

It is possible to automatically define chemical bonds with the determine_bonds() method after reading a molecule from an XYZ file. This method implements RDKit’s rdkit.Chem.rdDetermineBonds.DetermineBonds and assigns atom connectivity and bond information. This is done for all conformers in case multiple have been provided.

>>> from bonafide import AtomBondFeaturizer
>>> f = AtomBondFeaturizer()
>>> f.read_input("diclo.xyz", "diclofenac", input_format="file")
>>> f.determine_bonds()

Several optional arguments can be passed to modify the exact procedure of bond determination (see the API documentation).

Attaching a SMILES string

Alternatively, it is possible to attach a SMILES string to a 3D conformer ensemble, which exactly defines the chemical bonding between the atoms (within the SMILE system). This is done through the attach_smiles() method. By using the default align=True, the atom indices (atom order) of the initially read molecule are preserved; if set to False, the atoms are reordered according to the SMILES string.

>>> from bonafide import AtomBondFeaturizer
>>> f = AtomBondFeaturizer()
>>> f.read_input("diclo.xyz", "diclofenac", input_format="file")
>>> f.attach_smiles("O=C(O)Cc1ccccc1Nc1c(Cl)cccc1Cl")