qcinf 0.4.0

Cheminformatics algorithms and structure utilities using standardized qcdata data structures.

Quantum Chemistry Informatics (qcinf)

Cheminformatics algorithms and structure utilities using standardized qcdata data structures.

The QC Suite of Programs

qcinf works in harmony with a suite of other quantum chemistry tools for fast, structured, and interoperable quantum chemistry.

• qcconst - Physical constants, conversion factors, and a periodic table with clear source information for every value.
• qcdata - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. Documentation
• qcinf - Cheminformatics algorithms and structure utilities using standardized qcdata data structures.
• qccodec - A package for translating between standardized qcdata data structures and native QC program inputs and outputs.
• qcop - A package for operating quantum chemistry programs using standardized qcdata data structures. Compatible with TeraChem, psi4, QChem, NWChem, ORCA, Molpro, geomeTRIC and many more.
• BigChem - A distributed application for running quantum chemistry calculations at scale across clusters of computers or the cloud. Bring multi-node scaling to your favorite quantum chemistry program.
• ChemCloud - A web application and associated Python client for exposing a BigChem cluster securely over the internet.

Installation

python -m pip install qcinf

To install with numba-accelerated kernels:

python -m pip install 'qcinf[fast]'

Additional backends can be added for conversion and compatibility features, including rdkit, openbabel, or install the whole suite with all:

python -m pip install 'qcinf[rdkit,openbabel]'

Or

python -m pip install 'qcinf[all]'

snapRMSD

snapRMSD is the native qcinf algorithm for symmetry-aware molecular RMSD. It uses bonded connectivity to find a connectivity-preserving atom assignment between two isomorphic structures, optionally aligns the structures, and returns the RMSD for the best assignment.

from qcdata import Structure
from qcinf import snap_rmsd

reference = Structure(
    symbols=["C", "H", "H", "H", "H"],
    geometry=[
        [0.0, 0.0, 0.0],
        [1.0, 1.0, 1.0],
        [-1.0, -1.0, 1.0],
        [-1.0, 1.0, -1.0],
        [1.0, -1.0, -1.0],
    ],
    connectivity=[(0, 1, 1.0), (0, 2, 1.0), (0, 3, 1.0), (0, 4, 1.0)],
)

candidate = Structure(
    symbols=["C", "H", "H", "H", "H"],
    geometry=[
        [0.0, 0.0, 0.0],
        [-1.0, 1.0, -1.0],
        [1.0, -1.0, -1.0],
        [1.0, 1.0, 1.0],
        [-1.0, -1.0, 1.0],
    ],
    connectivity=[(0, 1, 1.0), (0, 2, 1.0), (0, 3, 1.0), (0, 4, 1.0)],
)

rmsd = snap_rmsd(reference, candidate)

For the full result, use snap_rmsd_align_assign:

from qcinf import snap_rmsd_align_assign

rmsd, aligned_reference, assignment = snap_rmsd_align_assign(reference, candidate)

assignment[i] is the atom index in candidate matched to atom i in reference. The returned aligned_reference is a copy of reference with its geometry aligned to candidate.

Common options:

from qcinf import snap_align, snap_assign, snap_rmsd

# Compare structures without rotational/translational alignment.
rmsd = snap_rmsd(reference, candidate, align=False)

# Increase factoring depth for larger repeated peripheral groups.
rmsd = snap_rmsd(reference, candidate, factor_depth=2)

# Use the QCP alignment backend. Install with `qcinf[fast]` for numba acceleration.
rmsd = snap_rmsd(reference, candidate, alignment_backend="qcp")

# Return only the aligned structure or atom assignment.
aligned = snap_align(reference, candidate)
assignment = snap_assign(reference, candidate)

If a Structure does not include bonded connectivity, snapRMSD will infer it from covalent radii. For production workflows, pass validated connectivity on the structures or through a_connectivity= and b_connectivity= so the graph used for assignment is explicit and reproducible.

Development

Install the package with all optional dependencies:

uv sync --all-extras

Run tests to ensure your setup is working correctly:

bash scripts/tests.sh

Support

If you have any issues with qcinf or would like to request a feature, please open an issue.