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.