Molecule¶

class Molecule(atoms, bonds)[source]¶

Bases: object

A molecular graph.

Parameters:	atoms (`tuple` of `Atom`) – The atoms of the molecule. bonds (`iterable` of `Bond`) – The bonds of the molecule.

Methods

`get_atoms`(self[, atom_ids])	Yield the atoms of the molecule.
`get_bonds`(self[, bond_ids])	Yield the bonds of the molecule.
`get_num_atoms`(self)	Return the number of atoms in the molecule.
`get_num_bonds`(self)	Return the number of bonds in the molecule.

get_atoms(self, atom_ids=None)[source]¶

Yield the atoms of the molecule.

Parameters:	atom_ids (`iterable` of `int`) – The ids of the atoms which should be yielded. Can be an `int`, if only one atom should be yielded.
Yields:	`Atom` – An atom of the molecule.

get_bonds(self, bond_ids=None)[source]¶

Yield the bonds of the molecule.

Parameters:	bond_ids (`iterable` of `int`) – The ids of bonds which should be yielded. Can be an `int`, if only one bond should be yielded.
Yields:	`Bond` – A bond of the molecule.

get_num_atoms(self)[source]¶

Return the number of atoms in the molecule.

Returns:	The number of atoms in the molecule.
Return type:	`int`

get_num_bonds(self)[source]¶

Return the number of bonds in the molecule.

Returns:	The number of bonds in the molecule.
Return type:	`int`