XpongeCPP

Preview beta: XpongeCPP is currently a preview release and is under active beta testing.

预览版说明：XpongeCPP 当前仍处于预览阶段，正在进行 Beta 测试。

Docs / 文档入口

XpongeCPP is a new C++ implementation of common Xponge workflows with a thin Python compatibility layer.

The original Xponge repository is used only as a reference implementation and regression baseline. This repository does not share the original Python object model internally.

Installation

PyPI-style installation target

The packaging target is:

pip install XpongeCPP

After installation, both of these should work:

import XpongeCPP
import Xponge

The wheel is configured to include both:

  • src/XpongeCPP
  • src/Xponge

so old Xponge package-name imports can continue to work after installation.

Automatic optional chemistry dependencies

The package now declares a practical default dependency set for pip users:

  • numpy
  • geometric
  • matplotlib
  • PubChemPy
  • MDAnalysis
  • rdkit
  • pyscf on non-Windows platforms
  • mokda-xpongelib (imported as XpongeLib)

Windows automatically skips pyscf through environment markers.

mokda-xpongelib is included so legacy gaff.parmchk2_gaff(...) workflows can resolve the XpongeLib bridge automatically after installation.

See:

GitHub Actions packaging matrix

The repository CI currently builds packages on:

  • Linux x64: ubuntu-24.04
  • Linux arm64: ubuntu-24.04-arm
  • macOS Intel: macos-15-intel
  • macOS arm64: macos-15
  • Windows x64: windows-2025

Validation is split into two layers:

  • all platforms run a minimal wheel smoke test with numpy installed
  • Linux x64 additionally runs a full dependency install smoke test

This keeps wheel validation broad across operating systems and CPU architectures without making every matrix job depend on the full optional chemistry stack.

v1 Scope

  • Amber-first force-field workflows.
  • Flat C++ storage with Molecule, Residue, and ResidueType view semantics.
  • Common Python entry points such as load_pdb, load_mol2, Add_Solvent_Box, Set_Box_Padding, Save_SPONGE_Input, and Assign.
  • Numeric equivalence goals for SPONGE input, not byte-for-byte compatibility.

Amber lipid force fields

Both Lipid17 and Lipid21 are packaged. Import exactly one lipid base family:

import XpongeCPP.forcefield.amber.ff14sb
import XpongeCPP.forcefield.amber.gaff2
import XpongeCPP.forcefield.amber.lipid21  # or lipid17

Either lipid import automatically registers the shared PI/phosphoinositide/LysoPL extension. Input remains Amber's split-residue representation, such as PA + SPM + SA; full lipid names such as PSM and POPC are not automatically split. The extension's mixed Lipid/GLYCAM/phosphate/GAFF2 provenance is reported when it is loaded.

Within one Python process, ff14sb/ff19sb, gaff/gaff2, and lipid17/lipid21 are mutually exclusive pairs. Different families may be combined; use separate processes to compare alternatives in the same family.

Development Environments

The lightweight development path still uses rtk uv:

rtk uv pip install -e . --force-reinstall --no-cache-dir
rtk uv run pytest -q

Full Assign validation needs optional chemistry backends. Use pixi for a reproducible environment with RDKit, PubChemPy, and PySCF:

pixi run install-dev
pixi run test-assign-full
pixi run test-resp
pixi run test

Bundled SPONGE HDF5 I/O is implemented in the native C++ backend. Its build dependencies match SPONGE: HighFive and the HDF5 C library. The pixi environment installs both automatically. Manual source builds must provide a discoverable HDF5 C installation; when HighFive is unavailable, CMake fetches the pinned HighFive 3.3.0 source archive automatically.

The default SPONGE input format remains the legacy raw-text layout. Bundled input v2 can be selected from the common API, while both format-specific entry points remain available:

XpongeCPP.save_sponge_input(molecule, "system", "inputs", format="bundle")
XpongeCPP.save_sponge_input_raw(molecule, "system", "inputs")
XpongeCPP.save_sponge_input_bundle(molecule, "system", "inputs")

RESP supports a multi-backend strategy:

  • default backend: PySCF
  • optional backend: Psi4
  • shared dispatch layer: XpongeCPP.qm

Example:

assign.calculate_charge("resp", backend="pyscf")
assign.calculate_charge("resp", backend="psi4")

from XpongeCPP import qm

qm.run_scf(assign, backend="pyscf")
qm.optimize_geometry(assign, backend="pyscf")

For Windows RESP workflows, install Psi4 separately and select it explicitly:

conda install -c conda-forge psi4
pip install XpongeCPP

PubChem network tests remain opt-in through the test environment; default Pixi tests use local mocks or dependency checks and do not require live network access.

Documentation

Packaging roadmap note

The current repository uses a hand-written GitHub Actions workflow plus scripts/build_pypi.py for packaging validation. We are deliberately keeping this simpler workflow for now because it makes the Xponge/XpongeCPP dual package layout and the minimal-vs-full smoke split easy to audit.

cibuildwheel is still a good future option once the wheel matrix and release policy stabilize further, but it is not the current default.

Project links

Data verified by PyPI on Jul 29, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.2.9)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for simbayuhao from gravatar.com simbayuhao

Credits

Author: The XpongeCPP contributors

GitHub Statistics

Data verified by PyPI on Jul 29, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

Apache Software License (Apache License 2.0)

Requires

Python <3.13, >=3.10

Provides Extra

dev

Tags

molecular-dynamics molecular-mechanics Xponge-origin-1.7b8

Classifiers

Report project as malware

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BLAKE2b-256 93ab1df3ec04fb80e00f8e506bb4c2119cc84421ebc0fdbf1ca69606ae2cde0b

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Provenance

The following attestation bundles were made for xpongecpp-0.2.0-cp310-cp310-macosx_15_0_arm64.whl:

Publisher: publish-pypi.yml on SPONGEMM/XpongeCPP

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

0.2.9

16 files

0.2.8

16 files

0.2.7

16 files

0.2.6

16 files

0.2.5

16 files

0.2.4

16 files

0.2.1

16 files

This release

0.2.0 This release

16 files

0.1.5

6 files

0.1.4

6 files

0.1.3

6 files

0.1.2

6 files

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