Molecule schema

Required Keys

There are no required fields for the Molecule specification.

Optional Keys

The following keys are optional for the Molecule specification.

Key Name	Description	Field Type
atom_labels	Additional per-atom labels as an array of strings. Typical use is in model conversions, such as Elemental <-> Molpro and not typically something which should be user assigned. See the comments field for general human-consumable text to affix to the molecule.	array[string]
atomic_numbers	An optional ordered 1-D array-like object of atomic numbers of shape (nat,). Index matches the 0-indexed indices of all other per-atom settings like symbols and real. Values are inferred from the symbols list if not explicitly set. Ghostedness should be indicated through real field, not zeros here.	array[number]
comment	Additional comments for this molecule. Intended for pure human/user consumption and clarity.	string
connectivity	A list of bonds within the molecule. Each entry is a tuple of (atom_index_A, atom_index_B, bond_order) where the atom_index matches the 0-indexed indices of all other per-atom settings like symbols and real. Bonds may be freely reordered and inverted.	array[array]
extras	Additional information to bundle with the molecule. Use for schema development and scratch space.	object
geometry	An ordered (natom*ndim,) array for XYZ atomic coordinates. Default unit is Angstrom.	array[number]
geometry_units	Units for atomic geometry. Defaults to Angstroms.	string
identifiers	An optional dictionary of additional identifiers by which this molecule can be referenced, such as INCHI, canonical SMILES, etc. See the :class:Identifiers model for more details.	object
mass_numbers	An optional ordered 1-D array-like object of atomic mass numbers of shape (nat). Index matches the 0-indexed indices of all other per-atom settings like symbols and real. Values are inferred from the most common isotopes of the symbols list if not explicitly set. If single isotope not (yet) known for an atom, -1 is placeholder.	array[number]
masses	The ordered array of particle masses. Index order matches the 0-indexed indices of all other per-atom fields like symbols and real. If this is not provided, the mass of each atom is inferred from its most common isotope. If this is provided, it must be the same length as symbols but can accept None entries for standard masses to infer from the same index in the symbols field.	array[number]
masses_units	Units for atomic masses. Defaults to unified atomic mass unit.	string
molecular_charge	The net electrostatic charge of the molecule. Default unit is elementary charge.	number
molecular_charge_units	Units for molecular charge. Defaults to elementary charge.	string
name	Common or human-readable name to assign to this molecule. This field can be arbitrary; see identifiers for well- defined labels.	string
ndim	Number of spatial dimensions.	integer
provenance	The provenance information about how this object (and its attributes) were generated, provided, and manipulated.	object
schema_name	The MMSchema specification to which this model conforms. Explicitly fixed as mmschema_molecule.	string
schema_version	The version number of schema_name to which this model conforms.	integer
substructs	A list of (name, num) of connected atoms constituting the building block (e.g. monomer) of the structure (e.g. a polymer). Order follows atomic indices from 0 till Natoms-1. E.g. [(‘ALA’, 4), …] means atom1 belongs to aminoacid alanine with residue number 4. Substruct name is max 4 characters.	array[array]
symbols	An ordered (natom,) array-like object of particle symbols. The index of this attribute sets the order for all other per- particle setting like geometry and the first dimension of geometry.	array[string]
velocities	An ordered (natoms*ndim,) array for XYZ atomic velocities. Default unit is Angstroms/femtoseconds.	array[number]
velocities_units	Units for atomic velocities. Defaults to Angstroms/femtoseconds.	string