spyrmsd.optional.obabel module

spyrmsd.optional.obabel.adjacency_matrix(mol) → ndarray[source]

Adjacency matrix from OpenBabel molecule.

Parameters

mol – Molecule

Returns

Adjacency matrix of the molecule

Return type

np.ndarray

spyrmsd.optional.obabel.bonds(mol) → List[Tuple[int, int]][source]

List of bonds

Parameters

mol – Molecule

Returns

List of bonds

Return type

List[Tuple[int, int]]

Notes

A bond is defined by a tuple of (0-based) indices of two atoms.

spyrmsd.optional.obabel.load(fname: str)[source]

Load molecule from file.

Parameters

fname (str) – File name

Return type

Molecule

spyrmsd.optional.obabel.loadall(fname: str)[source]

Load molecules from file.

Parameters

fname (str) – File name

Return type

List of molecules

spyrmsd.optional.obabel.numatoms(mol) → int[source]

Number of atoms.

Parameters

mol – Molecule

Returns

Number of atoms

Return type

int

spyrmsd.optional.obabel.numbonds(mol) → int[source]

Number of bonds.

Parameters

mol – Molecule

Returns

Number of bonds

Return type

int

spyrmsd.optional.obabel.to_molecule(mol, adjacency: bool = True)[source]

Transform molecule to pyrmsd molecule.

Parameters

  • mol – Molecule

  • adjacency (boolean, optional) – Flag to decide wether to build the adjacency matrix from molecule

Returns

pyrmsd molecule

Return type

pyrmsd.molecule.Molecule