xyz_to_rdkit

xyz_to_rdkit(symbols, positions, distance_tolerance=0.1, ignore_scale=False)

Convert a QCElemental molecule to an RDKit molecule.

Parameters:

symbolslist[str]

List of element symbols

positionsnumpy.ndarray

Matrix of the same length as symbols with x, y, and z coordinates in Angstroms

distance_tolerancefloat, optional, default=0.1

Additional tolerance for bond distance cutoffs (Angstroms) in determine_connectivity()

ignore_scalebool, optional, default=False

If True avoid an error when “H” is present and the minimum atomic distance is not between 0.8 Å and 1.5 Å.

Returns:

rdkit.Chem.Mol

RDKit molecule object