Topology Schema

A full description of the overall molecule its geometry, fragments, and charges.

Required Keys

The following properties are required for a topology.

Key Name	Description	Field Type
symbols	(nat, ) atom symbols in title case.	array[string]
geometry	(3 * nat, ) vector of XYZ coordinates [a0] of the atoms.	array[number]
schema_name	No description provided.	string
schema_version	No description provided.	integer

Optional Keys

The following keys are optional for the topology specification.

Key Name	Description	Field Type
molecular_charge	The overall charge of the molecule.	number
molecular_multiplicity	The overall multiplicity of the molecule.	number
fix_com	Whether translation of geometry is allowed (fix F) or disallowed (fix T).	boolean
real	(nat, ) list describing if atoms are real (T) or ghost (F).	array[boolean]
connectivity	A list describing bonds within a molecule. Each element is a (atom1, atom2, order) tuple.	array[array]
fix_orientation	Whether rotation of geometry is allowed (fix F) or disallowed (fix T).	boolean
atom_labels	(nat, ) atom labels with any user tagging information.	array[string]
fragment_multiplicities	(nfr, ) list of multiplicities associated with each fragment tuple.	array[number]
fix_symmetry	Maximal point group symmetry at which geometry should be treated. Lowercase.	string
fragment_charges	(nfr, ) list of charges associated with each fragment tuple.	array[number]
mass_numbers	(nat, ) mass numbers for atoms, if known isotope, else -1.	array[number]
name	The name of the molecule.	string
masses	(nat, ) atom masses [u]; canonical weights assumed if not given.	array[number]
comment	Any additional comment one would attach to the molecule.	string
provenance	#/definitions/provenance	object
fragments	(nfr, <varies>) list of indices (0-indexed) grouping atoms into molecular fragments within the topology.	array[array]
atomic_numbers	(nat, ) atomic numbers, nuclear charge for atoms. Ghostedness should be indicated through ‘real’ field, not zeros here.	array[number]