A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for computational workflows. USE WHEN you need to convert between chemical file formats (e.g., xyz, pdb, mol, smi, gjf), generate 3D structures from SMILES using `--gen3d`, render molecule images (PNG/SVG), or extract geometries from simulation logs to build new inputs.
This skill provides practical Open Babel command patterns for common chemistry data tasks.
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
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.).
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
uvx --from openbabel-wheel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi
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
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
When 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-wheel obabel ... consistently to minimize local dependency setup.Open Babel can generate 3D molecular geometries from SMILES for use as
input to Packmol or as single-molecule starting structures for GPUMD
liquid / molecular simulations. Convert the output to extxyz with dpdata
or ASE before using as GPUMD model.xyz.