Openbabel

Open Babel

This skill provides practical Open Babel command patterns for common chemistry data tasks.

Quick Start

Check installation through uvx:

uvx --from openbabel obabel -V

Typical conversion syntax:

uvx --from openbabel obabel input.ext -i<input_format> -o<output_format> -O output.ext

Core Tasks

1) File format conversion

Convert XYZ to PDB:

uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdb

Open Babel supports a large set of chemistry formats (e.g., xyz, mol, mol2, pdb, smi, Gaussian gjf/log/fchk, etc.).

2) Build structures from SMILES

Generate methane (3D coordinates required):

uvx --from openbabel obabel -:C --gen3d -omol -O C.mol

Generate a single carbon atom:

uvx --from openbabel obabel -:[C] --gen3d -omol -O C.mol

Generate methyl radical:

uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.mol

> Important: quote SMILES when they contain brackets or special characters.

Equivalent explicit form:

uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol

3) Export SMILES from one or more structure files

uvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi

4) Render 2D structure images

Generate PNG:

uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.png

Generate SVG:

uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svg

Convert Gaussian log directly to image:

uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.png

5) Gaussian workflow helper

Generate 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.gjf

Generate 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.gjf

Agent Checklist

When using this skill for users:

• Confirm source file(s) and desired target format.
• Prefer explicit -i and -o format flags for reproducibility.
• Add --gen3d when converting SMILES to coordinate-bearing structures.
• Quote SMILES strings that contain brackets/parentheses.
• For Gaussian workflows, verify route section and resource lines (%nproc, method/basis) after generation.
• Use uvx --from openbabel obabel ... consistently to minimize local dependency setup.

References

• Open Babel project: https://openbabel.org/
• Open Babel GitHub: https://github.com/openbabel/openbabel
• openbabel package: https://pypi.org/project/openbabel/