spindry.Molecule

class spindry.Molecule(atoms, bonds, position_matrix)[source]

Molecule to optimize.

Parameters:

atoms (tuple[Atom, ...]) – Atoms that define the molecule.
bonds (tuple[Bond, ...]) – Bonds between atoms that define the molecule.
position_matrix (np.ndarray) – A (n, 3) matrix holding the position of every atom in the Molecule.

Methods

`get_atoms`	Yield the atoms in the molecule, ordered as input.
`get_bonds`	Yield the bonds in the molecule, ordered as input.
`get_centroid`	Return the centroid.
`get_num_atoms`	Return the number of atoms in the molecule.
`get_position_matrix`	Return a matrix holding the atomic positions.
`get_subunits`	Get connected graphs based on Molecule separated by bonds.
`with_displacement`	Return a displaced clone Molecule.
`with_position_matrix`	Return clone Molecule with new position matrix.
`write_pdb_file`	Write basic .pdb file of Molecule to path.
`write_xyz_content`	Write basic .xyz file content of Molecule.
`write_xyz_file`	Write basic .xyz file of Molecule to path.

Attributes

Yield the atoms in the molecule, ordered as input.

Yield the bonds in the molecule, ordered as input.

get_centroid(atom_ids=None)[source]

Return the centroid.

Parameters:: atom_ids (tuple | set | None) – iterable of int, optional The ids of atoms which are used to calculate the centroid. Can be a single int, if a single atom is to be used, or None if all atoms are to be used.
Returns:: The centroid of atoms specified by atom_ids.
Raises:: If atom_ids has a length of 0. –
Return type:: float

get_num_atoms()[source]

Return the number of atoms in the molecule.

get_position_matrix()[source]

Return a matrix holding the atomic positions.

Returns:: The array has the shape (n, 3). Each row holds the x, y and z coordinates of an atom.
Return type:: ndarray

get_subunits(bond_pair_ids)[source]

Get connected graphs based on Molecule separated by bonds.

Parameters:: bond_pair_ids (tuple) – iterable of tuple of ints Iterable of pairs of atom ids with bond between them to optimize.
Returns:: The subunits of mol split by bonds defined by bond_pair_ids. Key is subunit identifier, Value is iterable of atom ids in subunit.
Return type:: subunits

with_displacement(displacement)[source]

Return a displaced clone Molecule.

Parameters:: displacement (ndarray) – The displacement vector to be applied.
Return type:: Molecule

with_position_matrix(position_matrix)[source]

Return clone Molecule with new position matrix.

Parameters:: position_matrix (ndarray) – A position matrix of the clone. The shape of the matrix is (n, 3).
Return type:: Molecule

write_pdb_file(path)[source]

Write basic .pdb file of Molecule to path.

write_xyz_content()[source]

Write basic .xyz file content of Molecule.

write_xyz_file(path)[source]

Write basic .xyz file of Molecule to path.

Connectivity is not maintained in this file type!