spyrmsd.molecule module

class spyrmsd.molecule.Molecule(atomicnums: ndarray | List[int], coordinates: ndarray | List[List[float]], adjacency_matrix: ndarray | List[List[int]] | None = None)

Bases: object

center_of_geometry() → ndarray

Center of geometry.

Returns:

Center of geometry

Return type:

np.ndarray

center_of_mass() → ndarray

Center of mass.

Returns:

Center of mass

Return type:

np.ndarray

Notes

Atomic masses are cached.

classmethod from_rdkit(rdmol, adjacency: bool = True)

Constructor from RDKit molecule.

Parameters:

• rdmol – RDKit molecule

• adjacency – Flag to compute the adjacency matrix

Returns:

spyrmsd Molecule

Return type:

spyrmsd.molecule.Molecule

rotate(angle: float, axis: ndarray | List[float], units: str = 'rad') → None

Rotate molecule.

Parameters:

• angle (float) – Rotation angle

• axis (np.ndarray) – Axis of rotation (in 3D)

• units ({“rad”, “deg”}) – Units of the angle (radians rad or degrees deg)

strip() → None

Strip hydrogen atoms.

to_graph()

Convert molecule to graph.

Returns:

Molecular graph.

Return type:

Graph

Notes

If the molecule does not have an associated adjacency matrix, a simple bond perception is used.

The molecular graph is cached per backend.

translate(vector: ndarray | List[float]) → None

Translate molecule.

Parameters:

vector (np.ndarray) – Translation vector (in 3D)

spyrmsd.molecule.coords_from_molecule(mol: Molecule, center: bool = False) → ndarray

Atomic coordinates from molecule.

Parameters:

• mol (molecule.Molecule) – Molecule

• center (bool) – Center flag

Returns:

Atomic coordinates (possibly centred)

Return type:

np.ndarray

Notes

Atomic coordinates are centred according to the center of geometry, not the center of mass.