QCElemental API

qcelemental Package

Main init for QCElemental

Functions

compare(expected, computed[, label, quiet, …])

Returns True if two integers, strings, booleans, or integer arrays are element-wise equal.

compare_recursive(expected, computed[, …])

Recursively compares nested structures such as dictionaries and lists.

compare_values(expected, computed[, label, …])

Returns True if two floats or float arrays are element-wise equal within a tolerance.

Classes

ChoicesError(msg[, choices])

Error called for problems with syntax input file.

CovalentRadii([context])

Covalent radii sets.

DataUnavailableError(dataset, atom)

Error when dataset incomplete and otherwise valid query can’t be fulfilled.

Datum(label, units, data, *[, comment, doi, …])

Facilitates the storage of quantum chemical results by labeling them with basic metadata.

MoleculeFormatError(msg)

Error called when a molparse.from_string contains unparsable lines.

NotAnElementError(atom)

Error when element or nuclide can’t be identified.

PhysicalConstantsContext([context])

CODATA 2014 physical constants set from NIST.

ValidationError(msg)

Error called for problems with syntax input file.

VanderWaalsRadii([context])

Van der Waals radii sets.

Variables

constants

CODATA 2014 physical constants set from NIST.

periodictable

Nuclear and mass data about chemical elements from NIST.

vdwradii

Van der Waals radii sets.

Class Inheritance Diagram

Inheritance diagram of qcelemental.exceptions.ChoicesError, qcelemental.covalent_radii.CovalentRadii, qcelemental.exceptions.DataUnavailableError, qcelemental.datum.Datum, qcelemental.exceptions.MoleculeFormatError, qcelemental.exceptions.NotAnElementError, qcelemental.physical_constants.context.PhysicalConstantsContext, qcelemental.exceptions.ValidationError, qcelemental.vanderwaals_radii.VanderWaalsRadii

qcelemental.periodic_table Module

Periodic table class

Classes

PeriodicTable()

Nuclear and mass data about chemical elements from NIST.

Class Inheritance Diagram

Inheritance diagram of qcelemental.periodic_table.PeriodicTable

qcelemental.physical_constants Package

Units handlers

Classes

PhysicalConstantsContext([context])

CODATA 2014 physical constants set from NIST.

Class Inheritance Diagram

Inheritance diagram of qcelemental.physical_constants.context.PhysicalConstantsContext

qcelemental.covalent_radii Module

Contains covalent radii

Classes

CovalentRadii([context])

Covalent radii sets.

Class Inheritance Diagram

Inheritance diagram of qcelemental.covalent_radii.CovalentRadii

qcelemental.molparse Package

Functions

contiguize_from_fragment_pattern(frag_pattern, *)

Take (nat, ?) array-like arrays and return with atoms arranged by (nfr, ?) frag_pattern.

from_arrays(*[, geom, elea, elez, elem, …])

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

from_input_arrays(*[, enable_qm, …])

Compose a Molecule dict from unvalidated arrays and variables in multiple domains.

from_schema(molschema, *[, verbose])

Construct molecule dictionary representation from non-Psi4 schema.

from_string(molstr[, dtype, name, fix_com, …])

Construct a molecule dictionary from any recognized string format.

parse_nucleus_label(label)

Separate molecule nucleus string into fields.

reconcile_nucleus

Forms consistent set of nucleus descriptors from all information from arguments, supplemented by the periodic table.

to_schema(molrec, dtype[, units, np_out, copy])

Translate molparse internal Molecule spec into dictionary from other schemas.

to_string(molrec, dtype[, units, …])

Format a string representation of QM molecule.

validate_and_fill_chgmult(zeff, …[, …])

Forms molecular and fragment charge and multiplicity specification by completing and reconciling information from argument, supplemented by physical constraints and sensible defaults.

qcelemental.testing Module

Functions

compare(expected, computed[, label, quiet, …])

Returns True if two integers, strings, booleans, or integer arrays are element-wise equal.

compare_molrecs(expected, computed[, label, …])

Function to compare Molecule dictionaries.

compare_recursive(expected, computed[, …])

Recursively compares nested structures such as dictionaries and lists.

compare_values(expected, computed[, label, …])

Returns True if two floats or float arrays are element-wise equal within a tolerance.

tnm()

Returns the name of the calling function, usually name of test case.