Molecule Module

Molecules

class czone.molecule.molecule.BaseMolecule(species=None, positions=None, **kwargs)

Bases: abc.ABC

Base abstract class for Molecule objects.

Molecule objects are intended to facilitate molecular atomic items, which are not easily generated in the Generation-Volume pair scheme. They are also intended to facilitate applications, for example, in surface chemistry studies. The molecule class mostly interfaces with other packages more suited for molecular generation.

BaseMolecules are typically not created directly.

atoms

Nx3 array of atom positions of atoms in molecule

Type

np.ndarray

species

Nx1 array of atomic numbers of atom in molecule

Type

np.ndarray

origin

Reference origin of molecule.

Type

np.ndarray

orientation

Reference orientation of molecule.

Type

np.ndarray

priority

Relative generation precedence of molecule.

Type

int

ase_atoms

Collection of atoms in molecule as ASE Atoms object

Type

Atoms

property ase_atoms

Collection of atoms in molecule as ASE Atoms object.

property atoms

Array of atomic positions of atoms lying within molecule.

checkIfInterior(testPoints: numpy.ndarray)

classmethod from_ase_atoms(atoms)

from_molecule(**kwargs)

Constructor for new Molecules from existing Molecule object

Parameters

**kwargs – “transformation”=List[BaseTransformation] to apply a series of transformations to the copied molecule.

classmethod from_pmg_molecule(atoms)

property orientation

property origin

populate_atoms()

property print_warnings

property priority

Relative generation precedence of molecule.

remove_atoms(indices, new_origin_idx=None)

reset_orientation()

Reset orientation to align with global XYZ. Does not transform molecule.

set_atoms(species, positions)

set_origin(point=None, idx=None) → None

Set the reference origin to global coordinate or to track specific atom.

Parameters

• point (np.ndarray) –

• idx (int) –

property species

Array of atomic numbers of atoms lying within molecule.

transform(transformation: czone.transform.transform.BaseTransform, transform_origin=True)

Transform molecule with given transformation.

Parameters

transformation (BaseTransform) – transformation to apply to molecule.

update_positions(positions)

update_species(species)

class czone.molecule.molecule.Molecule(species, positions, **kwargs)

Bases: czone.molecule.molecule.BaseMolecule

Standard object for representing molecules.