Open Babel — Molecular Format Conversion

When to Use

• User needs to convert between molecular file formats (SMILES, mol2, sdf, pdb, xyz, cif)
• User wants to generate 3D coordinates from SMILES
• User needs to add/remove hydrogens
• User wants to perceive bond orders from a 3D structure
• User needs canonical SMILES or InChI identifiers

Prerequisites

1. Open Babel installed (obabel -V)
2. For Python scripting: openbabel or openbabel-wheel package

Workflow Steps — CLI

Convert between formats

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "convert_format",
  "command": "obabel input.mol2 -O output.pdb",
  "system_name": "format_convert"
})

Common CLI Commands

SMILES to 3D structure

obabel -:"CCO" -O ethanol.xyz --gen3d
# Generates 3D coordinates using force field optimization

Add hydrogens

obabel input.pdb -O output.pdb -h
# -h adds hydrogens at pH 7.4

Remove hydrogens

obabel input.pdb -O output.pdb -d

Batch conversion

obabel *.mol2 -O output_.pdb -m
# -m produces one output file per input molecule

Generate conformers

obabel input.sdf -O conformers.sdf --conformer --nconf 50 --writeconformers

Get canonical SMILES

obabel input.mol2 -O output.smi -ocan

Energy minimization

obabel input.xyz -O minimized.xyz --minimize --ff MMFF94 --steps 2500

Supported Formats (most common)

Format	Extension	Notes
SMILES	.smi	1D string representation
SDF/MOL	.sdf, .mol	2D/3D with bond orders
PDB	.pdb	Protein Data Bank format
MOL2	.mol2	Tripos format with charges
XYZ	.xyz	Simple Cartesian coordinates
CIF	.cif	Crystallographic Information File
CML	.cml	Chemical Markup Language
InChI	-	IUPAC identifier (use -oinchi)
POSCAR	.vasp	VASP structure (limited support)
GJF/COM	.gjf, .com	Gaussian input

Python API

from openbabel import openbabel as ob

conv = ob.OBConversion()
conv.SetInFormat("smi")
conv.SetOutFormat("mol2")

mol = ob.OBMol()
conv.ReadString(mol, "c1ccccc1")  # benzene

# Generate 3D
builder = ob.OBBuilder()
builder.Build(mol)

# Force field optimization
ff = ob.OBForceField.FindForceField("MMFF94")
ff.Setup(mol)
ff.ConjugateGradients(500)
ff.GetCoordinates(mol)

conv.WriteFile(mol, "benzene.mol2")

Parameter Guidance

Flag	Purpose
--gen3d	Generate 3D coordinates from 2D/SMILES
-h	Add hydrogens
-d	Delete hydrogens
--minimize	Energy minimization with force field
--ff MMFF94	Force field: MMFF94, UFF, Ghemical
-m	Multiple output files (one per molecule)
--conformer	Conformer search
-ocan	Output canonical SMILES

Common Pitfalls

1. No 3D coordinates from SMILES — SMILES are 1D strings. Use --gen3d to create 3D structures.
2. Bond order loss — XYZ format has no bond information. Converting xyz to mol2 requires bond perception (-b flag).
3. Wrong protonation — default -h adds H at pH 7.4. Specify pH with -p <pH> if needed.
4. Large molecule conformers — --gen3d gives one conformation. For proper conformer sampling, use RDKit (molecular/rdkit/SKILL.md).
5. Periodic structures — Open Babel's support for periodic systems (CIF/POSCAR) is limited. Use pymatgen or ASE for crystals.
6. Force field coverage — MMFF94 covers organic molecules well but may not have parameters for transition metals.