openbabel — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited openbabel (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
This skill provides practical Open Babel command patterns for common chemistry data tasks.
Check installation through uvx:
uvx --from openbabel obabel -VTypical conversion syntax:
uvx --from openbabel obabel input.ext -i<input_format> -o<output_format> -O output.extConvert XYZ to PDB:
uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdbOpen Babel supports a large set of chemistry formats (e.g., xyz, mol, mol2, pdb, smi, Gaussian gjf/log/fchk, etc.).
Generate methane (3D coordinates required):
uvx --from openbabel obabel -:C --gen3d -omol -O C.molGenerate a single carbon atom:
uvx --from openbabel obabel -:[C] --gen3d -omol -O C.molGenerate methyl radical:
uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.molImportant: quote SMILES when they contain brackets or special characters.
Equivalent explicit form:
uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.moluvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smiGenerate PNG:
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.pngGenerate SVG:
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svgConvert Gaussian log directly to image:
uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.pngGenerate Gaussian input from SMILES, then patch header with sed:
uvx --from openbabel obabel -:CC --gen3d -ogjf | sed "1c %nproc=28\n#opt b3lyp/6-31g(d,p)" > CC.gjfGenerate next-step input from a previous Gaussian log:
uvx --from openbabel obabel CC.log -ilog -ogjf | sed "1c %nproc=28\n#freq b3lyp/6-31g(d,p)" > CC2.gjfWhen using this skill for users:
-i and -o format flags for reproducibility.--gen3d when converting SMILES to coordinate-bearing structures.%nproc, method/basis) after generation.uvx --from openbabel obabel ... consistently to minimize local dependency setup.~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.