Gaussian Molecular Box
Export a Multiwfn molecular box PDB and render its length, width, and height as a PNG from Gaussian formatted checkpoint (.fch) files. Use for Gaussian FCH molecular dimensions and box visualization.
Install
$ agentstack add skill-nanhuai-x-gaussian-molecule-workflow-gaussian-molecular-box ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
Security review
✓ PassedNo issues found. Passed automated security review. · v0.1.0 How review works →
- ✓ Prompt-injection patterns
- ✓ Secret / credential exfiltration
- ✓ Dangerous shell & filesystem operations
- ✓ Untrusted network calls
- ✓ Known-malicious package signatures
What it can access
- ✓ Network access No
- ✓ Filesystem access No
- ✓ Shell / process execution No
- ✓ Environment & secrets No
- ✓ Dynamic code execution No
From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.
Verified badge
Passed review? Show it. Paste this badge into your README, it links to the public security report.
Links to your public security report.[](https://agentstack.voostack.com/security/report/skill-nanhuai-x-gaussian-molecule-workflow-gaussian-molecular-box) Reliability & compatibility
Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
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Gaussian molecular box and dimensions
Use this skill when a Gaussian .fch file needs a PDB with box dimensions and a molecular-box image.
Preconditions
- Inputs are
fch/.fch; results go tooutput//. - Resolve Multiwfn from
MULTIWFN_BIN, thenPATH, then a user-provided installation path. - Python 3, NumPy, and Matplotlib are required for rendering
_BOX.png.
Isolated workflow
Run the bundled exporter from the analysis folder:
python /scripts/run_box.py --input fch --output outputThe bundled renderer and Multiwfn input template are self-contained.
- Create an isolated working directory for exactly one molecule; do not allow a root-level or prior molecule's
new.pdbto satisfy the run. - Run Multiwfn's molecular-box/PDB sequence and verify that a new
new.pdbwas generated in that isolated directory. Stop on a non-zero exit or a missing new file; never suppress Multiwfn failures. A known Multiwfn 3.8 Windows EOF return after theExporting new.pdb file finished!marker is accepted only when the PDB is present and itsCRYST1record is valid. - Copy the verified file into
output//new.pdbandoutput//.pdb. - Read the
CRYST1record in.pdbfor X/Y/Z dimensions, save_box_dimensions.txt, and render an atom-plus-wireframe figure as_BOX.pngwith NumPy and Matplotlib. - Verify both PDB files and the PNG are readable, then report the three dimensions with their units.
Meaning of dimensions
The PDB CRYST1 box is the output of this skill. Electron-density-isosurface dimensions are a separate, optional quantity and should be generated and labelled through $gaussian-esp-vmd; never present the two definitions as interchangeable.
Failure handling
- Missing NumPy or Matplotlib: retain the valid PDB outputs and report that only the PNG stage is unavailable.
- Missing
CRYST1: stop before plotting and preserve the Multiwfn log for diagnosis. - Preserve outputs unless overwrite was explicitly approved; use quiet per-molecule logs and a final summary. The box dimensions are distinct from the ESP isosurface dimensions.
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: Nanhuai-X
- Source: Nanhuai-X/gaussian-molecule-workflow
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.