ball-py 0.1.0a5

Python bindings for BALL — Biochemical ALgorithms Library

BALL Python bindings (pybind11)

Minimal Python access to BALL's force-field evaluation surface. Wraps just enough to compute single-point AMBER and CHARMM-EEF1 energies on a PDB and return per-component breakdowns.

Originating need: serve as an oracle source for the proteon EVIDENT manifest, replacing the frozen BALL_CRAMBIN_RAW reference values in tests/oracle/test_ball_energy.py with live regeneration, and unblocking the open forcefield_charmm19_internal claim by enabling a CHARMM-EEF1 component oracle.

Surface

import ball

amber = ball.amber_energy("crambin.pdb")
# -> {bond_stretch, angle_bend, torsion, nonbonded, total, n_atoms}

charmm = ball.charmm_energy("crambin.pdb", use_eef1=True)
# -> {bond_stretch, angle_bend, torsion, improper_torsion,
#     vdw, nonbonded, solvation, total, n_atoms, use_eef1}

nonbonded_cutoff defaults to 1e6 (effectively NoCutoff), matching the convention proteon uses on its own side of the comparison.

Build

# from the repo root, after Qt6 / Boost / Eigen3 / FFTW3 dev libs are
# installed (libqt6base-dev libqt6core5compat6-dev libboost-all-dev
# libeigen3-dev libfftw3-dev on Ubuntu 22.04 / Debian bookworm):

mkdir build && cd build
cmake -DBALL_BUILD_PYTHON=ON ..
cmake --build . -j

# ball.cpython-3X-x86_64-linux-gnu.so lands in build/python/.
# At runtime the bindings need three env vars set:
#   PYTHONPATH       — find the .so
#   LD_LIBRARY_PATH  — find libBALL.so
#   BALL_DATA_PATH   — find the force-field parameter files
#                      (Amber/, CHARMM/, MMFF94/, ... — these live
#                       at the repo's `data/` directory)
PYTHONPATH=build/python \
LD_LIBRARY_PATH=build/lib \
BALL_DATA_PATH=$(pwd)/../data \
    python -c 'import ball; print(ball.amber_energy.__doc__)'

The wheel build (pip install . via scikit-build-core, see pyproject.toml) bundles the data files into the wheel and resolves BALL_DATA_PATH at install time, so end users of the published wheel do not set env vars manually.

The pybind11 dependency is fetched via CMake FetchContent at configure time (pinned to v2.13.6); no system pybind11 install required.

Test

cd build
PYTHONPATH=python ctest -R python_smoke --output-on-failure
# or directly:
PYTHONPATH=python python -m pytest ../python/tests -v

The smoke tests look for a 1crn.pdb fixture in this order:

1. $BALL_TEST_CRAMBIN env var (if set)
2. /scratch/TMAlign/proteon/test-pdbs/1crn.pdb (the proteon staging-parent layout)
3. <repo>/test/data/1crn.pdb
4. <repo>/data/1crn.pdb

Tests skip rather than fail when no fixture is locatable.

Known issues

These are component-level mapping bugs in the current bindings, not pipeline issues. The Python-side smoke test catches them via pytest.approx-style assertions in proteon's oracle test layer; here they are documented for whoever picks up the next iteration:

• angle_bend = 0 on both AMBER and CHARMM. Real bend terms on crambin should be tens of kJ/mol. Likely an option flag at setup() that gates bend-term registration; the binding currently passes only the cutoff options.
• CHARMM torsion == improper_torsion. Both report 39.7 kJ/mol on crambin in current testing — they should differ. Either getTorsionEnergy() already includes impropers (in which case the dict key is misleading) or one of the getters is reading the wrong component sum. Needs a quick read of BALL's CHARMM force-field initialisation to confirm.

Out of scope (for now)

• Minimization, dynamics, Monte Carlo
• NMR, QSAR, docking
• Trajectory I/O (DCD, XTC)
• Force-field parameter introspection
• Class-level bindings (e.g. ball.System, ball.Atom); the current binding is functional only

These can land later if a downstream consumer needs them. The current binding is sized to one job — sourcing oracle energies for proteon — and stays narrow on purpose. New bindings ship through the same wheel pipeline (pyproject.toml → scikit-build-core → cibuildwheel CI) so adding them is a small per-PR cost.

Why pybind11 and not the original SIP bindings

The original SIP bindings under source/PYTHON/EXTENSIONS/ were removed in the zomball modernization line (commits 1–5 on this fork). They were unmaintained, did not build with modern Qt/Boost, and covered far more surface than any current consumer needs. Restarting on pybind11 against the modernized C++ tree is cheaper than reviving SIP and produces a binding that matches today's Python packaging conventions.