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Chemical Formats

Tools to convert chemical formats

Overview

​Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation.
Labii is developing a list of widgets that can convert one chemical format to other chemical formats. Here is a list of widgets:
Widget
Type
Description
​Obabel​
Section
Convert chemical formats with Open Babel
Section
Resolve a structure identifier to a file

Obabel

Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats. This widget uses the Obabel function from the Open Babel to convert nearly all the chemical formats and it very practical to quickly move from one program to another.
To convert format:
  1. 1.
    Copy and paste the data into the Input field.
  2. 2.
    You can also load the data from one of the Chemical Drawing widget by selecting a section.
  3. 3.
    Make sure the Input format is correct
  4. 4.
    Select the Output format
  5. 5.
    Click the Submit
  6. 6.
    Copy or click Download to download the transformed data.
Supported formats:
  • mol -- MDL MOL format
  • pdb -- Protein Data Bank format
  • smi -- SMILES format
  • xyz -- XYZ cartesian coordinates format
  • CONFIG -- DL-POLY CONFIG
  • CONTCAR -- VASP format
  • HISTORY -- DL-POLY HISTORY
  • POSCAR -- VASP format
  • VASP -- VASP format
  • abinit -- ABINIT Output Format
  • acesin -- ACES input format
  • acesout -- ACES output format
  • acr -- ACR format
  • adf -- ADF cartesian input format
  • adfout -- ADF output format
  • alc -- Alchemy format
  • arc -- Accelrys/MSI Biosym/Insight II CAR format
  • ascii -- ASCII format
  • axsf -- XCrySDen Structure Format
  • bgf -- MSI BGF format
  • box -- Dock 3.5 Box format
  • bs -- Ball and Stick format
  • c09out -- Crystal 09 output format
  • c3d1 -- Chem3D Cartesian 1 format
  • c3d2 -- Chem3D Cartesian 2 format
  • cac -- CAChe MolStruct format
  • caccrt -- Cacao Cartesian format
  • cache -- CAChe MolStruct format
  • cacint -- Cacao Internal format
  • can -- Canonical SMILES format
  • car -- Accelrys/MSI Biosym/Insight II CAR format
  • castep -- CASTEP format
  • ccc -- CCC format
  • cdx -- ChemDraw binary format
  • cdxml -- ChemDraw CDXML format
  • cht -- Chemtool format
  • cif -- Crystallographic Information File
  • ck -- ChemKin format
  • cml -- Chemical Markup Language
  • cmlr -- CML Reaction format
  • com -- Gaussian 98/03 Input
  • copy -- Copy raw text
  • crk2d -- Chemical Resource Kit diagram(2D)
  • crk3d -- Chemical Resource Kit 3D format
  • csr -- Accelrys/MSI Quanta CSR format
  • cssr -- CSD CSSR format
  • ct -- ChemDraw Connection Table format
  • cub -- Gaussian cube format
  • cube -- Gaussian cube format
  • dat -- Generic Output file format
  • dmol -- DMol3 coordinates format
  • dx -- OpenDX cube format for APBS
  • ent -- Protein Data Bank format
  • fa -- FASTA format
  • fasta -- FASTA format
  • fch -- Gaussian formatted checkpoint file format
  • fchk -- Gaussian formatted checkpoint file format
  • fck -- Gaussian formatted checkpoint file format
  • feat -- Feature format
  • fh -- Fenske-Hall Z-Matrix format
  • fhiaims -- FHIaims XYZ format
  • fix -- SMILES FIX format
  • fps -- FPS text fingerprint format (Dalke)
  • fpt -- Fingerprint format
  • fract -- Free Form Fractional format
  • fs -- Fastsearch format
  • fsa -- FASTA format
  • g03 -- Gaussian Output
  • g09 -- Gaussian Output
  • g92 -- Gaussian Output
  • g94 -- Gaussian Output
  • g98 -- Gaussian Output
  • gal -- Gaussian Output
  • gam -- GAMESS Output
  • gamess -- GAMESS Output
  • gamin -- GAMESS Input
  • gamout -- GAMESS Output
  • gau -- Gaussian 98/03 Input
  • gjc -- Gaussian 98/03 Input
  • gjf -- Gaussian 98/03 Input
  • got -- GULP format
  • gpr -- Ghemical format
  • gr96 -- GROMOS96 format
  • gro -- GRO format
  • gukin -- GAMESS-UK Input
  • gukout -- GAMESS-UK Output
  • gzmat -- Gaussian Z-Matrix Input
  • hin -- HyperChem HIN format
  • inchi -- InChI format
  • inchikey -- InChIKey
  • inp -- GAMESS Input
  • ins -- ShelX format
  • jin -- Jaguar input format
  • jout -- Jaguar output format
  • k -- Compare molecules using InChI
  • lmpdat -- The LAMMPS data format
  • log -- Generic Output file format
  • mcdl -- MCDL format
  • mcif -- Macromolecular Crystallographic Info
  • mdl -- MDL MOL format
  • ml2 -- Sybyl Mol2 format
  • mmcif -- Macromolecular Crystallographic Info
  • mmd -- MacroModel format
  • mmod -- MacroModel format
  • mna -- Multilevel Neighborhoods of Atoms (MNA)
  • mol2 -- Sybyl Mol2 format
  • mold -- Molden format
  • molden -- Molden format
  • molf -- Molden format
  • molreport -- Open Babel molecule report
  • moo -- MOPAC Output format
  • mop -- MOPAC Cartesian format
  • mopcrt -- MOPAC Cartesian format
  • mopin -- MOPAC Internal
  • mopout -- MOPAC Output format
  • mp -- Molpro input format
  • mpc -- MOPAC Cartesian format
  • mpd -- MolPrint2D format
  • mpo -- Molpro output format
  • mpqc -- MPQC output format
  • mpqcin -- MPQC simplified input format
  • mrv -- Chemical Markup Language
  • msi -- Accelrys/MSI Cerius II MSI format
  • msms -- M.F. Sanner's MSMS input format
  • nul -- Outputs nothing
  • nw -- NWChem input format
  • nwo -- NWChem output format
  • out -- Generic Output file format
  • outmol -- DMol3 coordinates format
  • output -- Generic Output file format
  • pc -- PubChem format
  • pcm -- PCModel Format
  • pdbqt -- AutoDock PDQBT format
  • png -- PNG 2D depiction
  • pos -- POS cartesian coordinates format
  • pov -- POV-Ray input format
  • pqr -- PQR format
  • pqs -- Parallel Quantum Solutions format
  • prep -- Amber Prep format
  • pwscf -- PWscf format
  • qcin -- Q-Chem input format
  • qcout -- Q-Chem output format
  • report -- Open Babel report format
  • res -- ShelX format
  • rsmi -- Reaction SMILES format
  • rxn -- MDL RXN format
  • sd -- MDL MOL format
  • sdf -- MDL MOL format
  • smiles -- SMILES format
  • svg -- SVG 2D depiction
  • sy2 -- Sybyl Mol2 format
  • t41 -- ADF TAPE41 format
  • 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
  • vmol -- ViewMol format
  • xed -- XED format
  • xml -- General XML format
  • xsf -- XCrySDen Structure Format
  • xtc -- XTC format
  • yob -- YASARA.org YOB format
  • zin -- ZINDO input format

CACTVS Formats

CACTVS is known as CADD Group Chemoinformatics Tools and User Services (https://cactus.nci.nih.gov/). The NCI/CADD group is a research unit within the Chemical Biology Laboratory at the National Cancer Institute.
The chemoinformatic toolkit CACTVS can resolve a structure identifier into a chemical format.
Click the Submit to convert the file format. The file can be downloaded by clicking the Download button.
Supported formats:
  • alc -- Alchemy format
  • cdxml -- ChemDraw CDXML format
  • cerius -- MSI Cerius II format
  • charmm -- Chemistry at HARvard Macromolecular Mechanics file format
  • cif -- Crystallographic Information File
  • cml -- Chemical Markup Language
  • ctx -- Gaussian input data file
  • gjf -- Gaussian 98/03 Input
  • gromacs -- GROMACS file format
  • hyperchem -- HyperChem file format
  • jme -- Java Molecule Editor format
  • maestro -- Schroedinger MacroModel structure file format
  • mol -- MDL MOL format
  • mol2 -- Sybyl Mol2 format
  • mrv -- Chemical Markup Language
  • pdb -- Protein Data Bank format
  • sdf -- MDL MOL format
  • sdf3000 -- Symyx Structure Data Format 3000
  • sln -- SYBYL Line Notation
  • smiles -- SMILES format
  • xyz -- XYZ cartesian coordinates format
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Last modified 1yr ago