QCElemental API

qcelemental Package

Functions

compare(expected, computed[, label, ...])	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	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[, strict])	Error when element or nuclide can't be identified.
PhysicalConstantsContext([context])	CODATA 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 physical constants set from NIST.
covalentradii	Covalent radii sets.
periodictable	Nuclear and mass data about chemical elements from NIST.
vdwradii	Van der Waals radii sets.

Class Inheritance Diagram

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, *[, nonphysical, 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([A, Z, E, mass, real, ...])	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.molutil Package

Functions

B787(cgeom, rgeom, cuniq, runiq[, do_plot, ...])	Use Kabsch algorithm to find best alignment of geometry cgeom onto rgeom while sampling atom mappings restricted by runiq and cuniq.
compute_scramble(nat[, do_resort, do_shift, ...])	Generate a random or directed translation, rotation, and atom shuffling.
guess_connectivity(symbols, geometry[, ...])	Finds connected atoms based off of a covalent radii metric.
kabsch_align(rgeom, cgeom[, weight])	Finds optimal translation and rotation to align cgeom onto rgeom via Kabsch algorithm by minimizing the norm of the residual, \(|| R - U * C ||\).
molecular_formula_from_symbols(symbols[, order])	Returns the molecular formula for a list of symbols.
order_molecular_formula(formula[, order])	Reorders a molecular formula.

qcelemental.testing Module

Functions

compare(expected, computed[, label, ...])	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.

qcelemental.models Package

Classes

AlignmentMill	Facilitates the application of the simple transformation operations defined by shift, rotation, atommap arrays and mirror boolean as recipe to the data structures describing Cartesian molecular coordinates.
AtomicInput	The MolSSI Quantum Chemistry Schema
AtomicResult	Results from a CMS program execution.
AtomicResultProperties	Named properties of quantum chemistry computations following the MolSSI QCSchema.
AutodocBaseSettings	Old class for pydantic docstring before autodoc-pydantic came about.
BasisSet	A quantum chemistry basis description.
ComputeError	Complete description of the error from an unsuccessful program execution.
DriverEnum(value)	Allowed computation driver values.
FailedOperation	Record indicating that a given operation (program, procedure, etc.) has failed and containing the reason and input data which generated the failure.
Molecule	The physical Cartesian representation of the molecular system.
OptimizationInput	QCSchema input directive for geometry optimization.
OptimizationResult	QCSchema results model for geometry optimization.
ProtoModel	QCSchema extension of pydantic.BaseModel.
Provenance	Provenance information.
Result	QC Result Schema.
ResultInput	QC Input Schema.
ResultProperties	QC Result Properties Schema.

Class Inheritance Diagram