molgrid.molecule module

class molgrid.molecule.Element(symbol=None, number=None)

Bases: object

Element class containing atomic properties

class molgrid.molecule.Atom(element, coordinate)

Bases: object

assign_coordinate(coordinate)

Assign coordinates to the atom

Parameters:

coordinate (list) – [x, y, z] coordinates

Raises:

• TypeError – If coordinate is not a list

• ValueError – If coordinate length is not 3

class molgrid.molecule.Molecule(atoms=None, charge=0, multiplicity=1)

Bases: object

Molecule class representing a collection of atoms

add_atom(atom)

Add an atom to the molecule

remove_atom(index)

Remove atom at given index

get_atom(index)

Get atom at given index

property coordinate

Get all atomic coordinates as Nx3 array

property mass

Get total molecular mass