Repository

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Open File Format Repository

Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry, and many related areas.

Many file formats have formal, published specifications (e.g., CML or PDB) but realistically, such specifications evolve, many files are passed around which do not adhere to these specifications, and without example reference files, the details of file format specifications are not always clear.

This repository is an open resource of test files in various chemical file formats. All have been made available either under the GNU General Public License (GPL) or a Creative Commons license which permits reuse and distribution (with attribution).

Importantly these files can be used for testing import/export routines in many chemical programs, not just Open Babel. By providing such a resource, we hope that developers of chemical software will minimize bugs when translating chemical and molecular data between different file formats and different representations. Additionally, we hope to encourage the community of chemical software developers to support open, well-defined file formats to facilitate interconversion and collaboration in the chemical sciences.

The repository is performed in combination with this website, which includes a full file format database including as much information as known on various chemical file formats, including some example files and descriptions of the assumed format used by Open Babel for such informal formats as XYZ or Free Form Fractional.

Discussion of this project and announcements of new files and releases of the repository will occur on the OpenBabel-Repository mailing list. To subscribe to the mailing list, go to the list information page. We intend to release a version of the repository at least twice per year (in early January and early June).

Repository Currently Contains Examples Of:

(in alphabetical order)

  • Biosym CAR files
  • Chemical Resource Kit 2D and 3D
  • CML version 1 and version 2
  • Daylight SMILES
  • DMol3 coordinates
  • GAMESS-US output
  • Gaussian 98 output
  • Ghemical files
  • Jaguar output
  • MacroModel conformers
  • MDL Molfile
  • MOPAC version 7 output
  • MPQC output
  • PDB files
  • Q-Chem output
  • ShelX INS files
  • Sybyl Mol2 files
  • XYZ coordinates and trajectories

Contributions are requested in a wide variety of chemical and molecular file formats -- preferably with a pointer towards a file format specification. Contributions must include a full description of the program used to generate the file and the name of the format used.

Contributions should be made through the test file tracker. Notification of new submissions will be automatically posted to the OpenBabel-Repository mailing list.

For example:

  • File1.pdb is a Protein Data Bank file generated by WizzyChem, version 2.0.13.
  • Benzenedithiol.mzq is an MZQ file generated by WizzyChem, version 3.0.17. The MZQ format is specified at http://wizzychem.com/ and Benzenedithiol.mol is the same file in MDL Molfile v2000 format.
  • HMZ.mol2 is a Sybyl Mol2 file generated by ABChem, version 0.9.
  • 1ABC.mmcif is an mmCIF file produced by CrystalGrinder, 2003.

Suggestions, comments? Contact the openbabel-discuss mailing list.