kickstart

kickstart is a command-line toolkit for stochastic molecular structure generation and refinement.

This repository is published as a source-available, binary-distributed research artifact for the Supplementary Information (SI) of the manuscript:

Closing the gap between theory and experiment in vibrational spectroscopy via physics-informed theory engineering

Scientific context

In the SI workflow (Supplementary Note 1), kickstart is used to explore CHON molecular space (typically < 12 heavy atoms) by combining:

• random coordinate kicking,
• distance-geometry filtering,
• evolutionary refinement,
• force-field-based geometry optimization.

This generation stage is part of the Theory Engineering pipeline used to build a quasi-experimental IR library.

What is included

• kickstart: orchestration and search workflow entry point.
• kickgen: random structure generation from an input molecule.
• kickmut: random bond-mutation structure generation.

Distribution model and reproducibility

• This project is distributed in binary-first mode for Linux x86_64.
• Official release binaries are built with musl, statically linked, and have no runtime dynamic-library dependency.
• Source code is provided for transparency and method inspection.
• For SI verification, use the release binaries and the release-specific example assets.

Documentation

• User guide: user-guide.md

Quick start (Linux x86_64)

1. Download assets from the GitHub Release page:

   https://github.com/spdkit/kickstart/releases/tag/v0.1.0

2. Make binaries executable:

chmod +x kickstart kickgen kickmut

3. Sanity check:

./kickstart --help
./kickgen --help
./kickmut --help

Minimal usage

./kickgen input.mol2 output_gen.mol2 -n 10
./kickmut input.mol2 output_mut.mol2 -n 5 -m 2
./kickstart --print

Citation

If you use this artifact, please cite:

1. the associated manuscript, and
2. the exact GitHub release tag used in your SI or benchmark.