Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel -L formats" - List of File Formats Supported
This section provides a list of molecule file formats supported by Open Babel obtained by the 'obabel -L formats' command.
The main advantage of using Open Babel instead of other tools is that it supports a large number molecule file formats, total of 184.
You can use "obabel -L formats" command to get a list of File Formats Supported by Open Babel:
herong$ obabel -L formats abinit -- ABINIT Output Format [Read-only] acesin -- ACES input format [Write-only] acesout -- ACES output format [Read-only] acr -- ACR format [Read-only] adf -- ADF cartesian input format [Write-only] adfband -- ADF Band output format [Read-only] adfdftb -- ADF DFTB output format [Read-only] adfout -- ADF output format [Read-only] alc -- Alchemy format aoforce -- Turbomole AOFORCE output format [Read-only] arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] ascii -- ASCII format [Write-only] axsf -- XCrySDen Structure Format [Read-only] bgf -- MSI BGF format box -- Dock 3.5 Box format bs -- Ball and Stick format c09out -- Crystal 09 output format [Read-only] c3d1 -- Chem3D Cartesian 1 format c3d2 -- Chem3D Cartesian 2 format cac -- CAChe MolStruct format [Write-only] caccrt -- Cacao Cartesian format cache -- CAChe MolStruct format [Write-only] cacint -- Cacao Internal format [Write-only] can -- Canonical SMILES format car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] castep -- CASTEP format [Read-only] ccc -- CCC format [Read-only] cdjson -- ChemDoodle JSON cdx -- ChemDraw binary format [Read-only] cht -- Chemtool format [Write-only] cif -- Crystallographic Information File ck -- ChemKin format cof -- Culgi object file format com -- Gaussian Input [Write-only] CONFIG -- DL-POLY CONFIG CONTCAR -- VASP format CONTFF -- MDFF format copy -- Copy raw text [Write-only] crk2d -- Chemical Resource Kit diagram(2D) crk3d -- Chemical Resource Kit 3D format csr -- Accelrys/MSI Quanta CSR format [Write-only] cssr -- CSD CSSR format [Write-only] ct -- ChemDraw Connection Table format cub -- Gaussian cube format cube -- Gaussian cube format dallog -- DALTON output format [Read-only] dalmol -- DALTON input format dat -- Generic Output file format [Read-only] dmol -- DMol3 coordinates format dx -- OpenDX cube format for APBS ent -- Protein Data Bank format exyz -- Extended XYZ cartesian coordinates format fa -- FASTA format fasta -- FASTA format fch -- Gaussian formatted checkpoint file format [Read-only] fchk -- Gaussian formatted checkpoint file format [Read-only] fck -- Gaussian formatted checkpoint file format [Read-only] feat -- Feature format fh -- Fenske-Hall Z-Matrix format [Write-only] fhiaims -- FHIaims XYZ format fix -- SMILES FIX format [Write-only] fps -- FPS text fingerprint format (Dalke) [Write-only] fpt -- Fingerprint format [Write-only] fract -- Free Form Fractional format fs -- Fastsearch format fsa -- FASTA format g03 -- Gaussian Output [Read-only] g09 -- Gaussian Output [Read-only] g16 -- Gaussian Output [Read-only] g92 -- Gaussian Output [Read-only] g94 -- Gaussian Output [Read-only] g98 -- Gaussian Output [Read-only] gal -- Gaussian Output [Read-only] gam -- GAMESS Output [Read-only] gamess -- GAMESS Output [Read-only] gamin -- GAMESS Input gamout -- GAMESS Output [Read-only]
gau -- Gaussian Input [Write-only] gjc -- Gaussian Input [Write-only] gjf -- Gaussian Input [Write-only] got -- GULP format [Read-only] gpr -- Ghemical format gr96 -- GROMOS96 format [Write-only] gro -- GRO format gukin -- GAMESS-UK Input gukout -- GAMESS-UK Output gzmat -- Gaussian Z-Matrix Input hin -- HyperChem HIN format HISTORY -- DL-POLY HISTORY [Read-only] inchi -- InChI format inchikey -- InChIKey [Write-only] inp -- GAMESS Input ins -- ShelX format [Read-only] jin -- Jaguar input format jout -- Jaguar output format [Read-only] k -- Compare molecules using InChI [Write-only] lmpdat -- The LAMMPS data format [Write-only] log -- Generic Output file format [Read-only] lpmd -- LPMD format mae -- Maestro format maegz -- Maestro format mcdl -- MCDL format mcif -- Macromolecular Crystallographic Info MDFF -- MDFF format mdl -- MDL MOL format ml2 -- Sybyl Mol2 format mmcif -- Macromolecular Crystallographic Info mmd -- MacroModel format mmod -- MacroModel format mna -- Multilevel Neighborhoods of Atoms (MNA) [Write-only] mol -- MDL MOL format mol2 -- Sybyl Mol2 format mold -- Molden format molden -- Molden format molf -- Molden format molreport -- Open Babel molecule report [Write-only] moo -- MOPAC Output format [Read-only] mop -- MOPAC Cartesian format mopcrt -- MOPAC Cartesian format mopin -- MOPAC Internal mopout -- MOPAC Output format [Read-only] mp -- Molpro input format [Write-only] mpc -- MOPAC Cartesian format mpd -- MolPrint2D format [Write-only] mpo -- Molpro output format [Read-only] mpqc -- MPQC output format [Read-only] mpqcin -- MPQC simplified input format [Write-only] msi -- Accelrys/MSI Cerius II MSI format [Read-only] msms -- M.F. Sanner's MSMS input format [Write-only] nul -- Outputs nothing [Write-only] nw -- NWChem input format [Write-only] nwo -- NWChem output format [Read-only] orca -- ORCA output format [Read-only] orcainp -- ORCA input format [Write-only] out -- Generic Output file format [Read-only] outmol -- DMol3 coordinates format output -- Generic Output file format [Read-only] paint -- Painter format [Write-only] pcjson -- PubChem JSON pcm -- PCModel Format pdb -- Protein Data Bank format pdbqt -- AutoDock PDBQT format png -- PNG 2D depiction pointcloud -- Point cloud on VDW surface [Write-only] pos -- POS cartesian coordinates format [Read-only] POSCAR -- VASP format POSFF -- MDFF format pov -- POV-Ray input format [Write-only] pqr -- PQR format pqs -- Parallel Quantum Solutions format prep -- Amber Prep format [Read-only] pwscf -- PWscf format [Read-only] qcin -- Q-Chem input format [Write-only] qcout -- Q-Chem output format [Read-only] report -- Open Babel report format [Write-only] res -- ShelX format [Read-only] rinchi -- RInChI [Write-only] rsmi -- Reaction SMILES format rxn -- MDL RXN format sd -- MDL MOL format sdf -- MDL MOL format siesta -- SIESTA format [Read-only] smi -- SMILES format smiles -- SMILES format smy -- SMILES format using Smiley parser [Read-only] stl -- STL 3D-printing format [Write-only] svg -- SVG 2D depiction [Write-only] sy2 -- Sybyl Mol2 format t41 -- ADF TAPE41 format [Read-only] tdd -- Thermo format text -- Read and write raw text therm -- Thermo format tmol -- TurboMole Coordinate format txt -- Title format txyz -- Tinker XYZ format unixyz -- UniChem XYZ format VASP -- VASP format vmol -- ViewMol format wln -- Wiswesser Line Notation [Read-only] xed -- XED format [Write-only] xsf -- XCrySDen Structure Format [Read-only] xyz -- XYZ cartesian coordinates format yob -- YASARA.org YOB format zin -- ZINDO input format [Write-only]
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
►Using Open Babel Command: "obabel"
"obabel -i ..." - Input Data Format and Source
"obabel -o ... -O" - Output Data Format and Destination
"obabel -... --..." - Generic Conversion Options
"obabel" Command Option Argument Syntax
"obabel ... --gen2D" - Calculated 2D Coordinates
"obabel ... -f # -l #" - Split Large Molecule File
"obabel -h/-d" - Add/Remove Hydrogens in Molecule Data
"obabel --append ..." - Calculate Molecule Properties
►"obabel -L formats" - List of File Formats Supported
"obabel -a..." - Extra Options for Input Reading
"obabel -x..." - Extra Options for Output Writing
"obabel" vs. "babel" Open Babel Commands
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction