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claude-code

Computational-chemistry-agent-skills openbabel

install
source · Clone the upstream repo
git clone https://github.com/jinzhezenggroup/computational-chemistry-agent-skills
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/data-processing/openbabel" ~/.claude/skills/jinzhezenggroup-computational-chemistry-agent-skills-openbabel && rm -rf "$T"
manifest: data-processing/openbabel/SKILL.md
source content

Open Babel

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

Quick Start

Check installation through uvx:

uvx --from openbabel-wheel obabel -V

Typical conversion syntax:

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

Generate a single carbon atom:

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

Generate methyl radical:

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

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

Equivalent explicit form:

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

3) Export SMILES from one or more structure files

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

4) Render 2D structure images

Generate PNG:

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

Generate SVG:

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

Convert Gaussian log directly to image:

uvx --from openbabel-wheel 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-wheel 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-wheel 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:

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

References