from_arrays

qcelemental.molparse.from_arrays(*, geom=None, elea=None, elez=None, elem=None, mass=None, real=None, elbl=None, name=None, units='Angstrom', input_units_to_au=None, fix_com=None, fix_orientation=None, fix_symmetry=None, fragment_separators=None, fragment_charges=None, fragment_multiplicities=None, molecular_charge=None, molecular_multiplicity=None, comment=None, provenance=None, connectivity=None, fragment_files=None, hint_types=None, geom_hints=None, geom_unsettled=None, variables=None, domain='qm', missing_enabled_return='error', np_out=True, speclabel=True, tooclose=0.1, zero_ghost_fragments=False, nonphysical=False, mtol=0.001, copy=True, verbose=1)[source]

Compose a Molecule dict from unvalidated arrays and variables, returning dict.

See fields of Return molrec below. Required parameters (for QM XYZ) are geom and one of elem, elez, elbl (speclabel=True)

Parameters:

  • geom (Union[List[List[float]], numpy.ndarray]) – (nat, 3) or (3 * nat, ) ndarray or list o’lists of Cartesian coordinates.

  • fragment_separators (Union[List[int], numpy.ndarray]) – (nfr - 1, ) list of atom indices at which to split geom into fragments.

  • elbl (Union[List[str], numpy.ndarray]) – (nat, ) Label extending elem symbol, possibly conveying ghosting, isotope, mass, tagging information.

  • tooclose (float) – Interatom distance (native geom units) nearer than which atoms not allowed.

  • nonphysical (bool) – Do allow masses outside an element’s natural range to pass validation?

  • speclabel (bool) – If True, interpret elbl as potentially full nucleus spec including ghosting, isotope, mass, tagging information, e.g., @13C_mine or He4@4.01. If False, interpret elbl as only the user/tagging extension to nucleus label, e.g. _mine or 4 in the previous examples.

  • missing_enabled_return (str) – {‘minimal’, ‘none’, ‘error’} What to do when an enabled domain is of zero-length? Respectively, return a fully valid but empty molrec, return empty dictionary, or throw error.

  • np_out (bool) – When True, fields geom, elea, elez, elem, mass, real, elbl will be ndarray. Use False to get a json-able version.

Returns:

  • molrec (dict) – Molecule dictionary spec follows. Its principles are

    (1) contents are fully validated and defaulted - no error checking necessary,

    (2) contents may be mildly redundant - atomic numbers and element symbols present,

    (3) big system, nat-length single-type arrays, not small system, nat-number heterogeneous objects,

    (4) some fields are optional (e.g., fix_symmetry) but largely self-describing so units or fix_com must be present.

    (5) apart from some mild optional fields, _all_ fields will be present (corollary of “fully validated and defaulted”) - no need to check for every key. in some cases like efp, keys will appear in blocks, so pre-handshake there will be a few hint keys and post-handshake they will be joined by full qm-like molrec.

    (6) molrec should be idempotent through this function (equiv to schema validator) but are not idempotent throughout its life. if fields permit, frame may be changed. Future? if fields permit, mol may be symmetrized. Coordinates and angles may change units or range if program returns them in only one form.

  • name (str, optional) – Label for molecule; should be valid Python identifier.

  • units ({‘Angstrom’, ‘Bohr’}) – Units for geom.

  • input_units_to_au (float, optional) – If units=’Angstrom’, overrides consumer’s value for [A]–>[a0] conversion.

  • fix_com (bool) – Whether translation of geom is allowed or disallowed.

  • fix_orientation (bool) – Whether rotation of geom is allowed or disallowed.

  • fix_symmetry (str, optional) – Maximal point group symmetry which geom should be treated. Lowercase.

  • geom (ndarray of float) – (3 * nat, ) Cartesian coordinates in units.

  • elea (ndarray of int) – (nat, ) Mass number for atoms, if known isotope, else -1.

  • elez (ndarray of int) – (nat, ) Number of protons, nuclear charge for atoms.

  • elem (ndarray of str) – (nat, ) Element symbol for atoms.

  • mass (ndarray of float) – (nat, ) Atomic mass [u] for atoms.

  • real (ndarray of bool) – (nat, ) Real/ghostedness for atoms.

  • elbl (ndarray of str) – (nat, ) Label with any tagging information from element spec.

  • fragment_separators (list of int) – (nfr - 1, ) list of atom indices at which to split geom into fragments.

  • fragment_charges (list of float) – (nfr, ) list of charge allocated to each fragment.

  • fragment_multiplicities (list of int) – (nfr, ) list of multiplicity allocated to each fragment.

  • molecular_charge (float) – total charge on system.

  • molecular_multiplicity (int) – total multiplicity on system.

  • comment (str, optional) – Additional comment for molecule.

  • provenance (dict of str) – Accumulated history of molecule, with fields “creator”, “version”, “routine”.

  • connectivity (list of tuples of int, optional) – (nbond, 3) list of (0-indexed) (atomA, atomB, bond_order) (int, int, double) tuples

  • EFP extension (this + units is minimal)

  • fragment_files (list of str) – (nfr, ) lowercased names of efp meat fragment files.

  • hint_types ({‘xyzabc’, ‘points’}) – (nfr, ) type of fragment orientation hint.

  • geom_hints (list of lists of float) – (nfr, ) inner lists have length 6 (xyzabc; to orient the center) or 9 (points; to orient the first three atoms) of the EFP fragment.

  • QMVZ extension (geom_unsettled replaces geom)

  • geom_unsettled (list of lists of str) – (nat, ) all-string Cartesian and/or zmat anchor and value contents mixing anchors, values, and variables.

  • variables (list of pairs) – (nvar, 2) pairs of variables (str) and values (float). May be incomplete.

Raises:

qcelemental.ValidationError – For most anything wrong.