blues.buildmol

blues.buildmol.add_atoms(atom_file)

Adds atoms and correct bonds to build molecule using an RDKit class

Parameters

• atom_file (string of file path) –

• Returns (RWMol object) –

blues.buildmol.build_molecule(atom_list, bo_matrix)

Takes .txt file, builds molecule and connection matrix specifying bonds, and builds the molecule with RDKit

Parameters

• atom_file (list of str) – Atomic symbols of molecule

• bo_matrix (np.ndarray) – Array containing bond orders between atoms in the style of a contact matrix.

Returns

object with structure and bonding based on JANPA’s Wiberg-Mayer bond index matrix

Return type

RWMol

blues.buildmol.draw_molecule(atom_list, bo_matrix)

Represents built molecule as 2 and 3 dimensional images and output INCHI and SMILES. Molecule is built from txt file containing ordered elements, bonds are added from Wiberg-Mayer matrix contained in JANPA output.

Parameters

• atom_file (list of str) – Atomic symbols of molecule

• bo_matrix (np.ndarray) – Array containing bond orders between atoms in the style of a contact matrix.

• Returns –

• ---------- –

• and 3d images as well as INCHI and SMILES strings for the molecule (2d) –