Chemical table file

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ctab
File extension:	`.mol, .sd, .sdf`
Type of format:	chemical file format

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MDL publishes a specification of their Connection Table formats, which include Molfile and SD formats.

1 Molfiles
- 1.1 Example
2 RGfiles
3 Rxnfiles
4 SDfiles
5 RDfiles
6 XDfiles
7 Clipboard
8 References
9 External links

[edit] Molfiles

A MDL Molfile is a file format created (and owned) by MDL, for holding information about the atoms, bonds, connectivity and coordinates of a molecule. The molfile consists of some header information, the Connection Table (CT) containing atom info, then bond connections and types, followed by sections for more complex information.

The molfile is sufficiently common that most, if not all, cheminformatics software systems/applications are able to read the format, though not always to the same degree.

There are different versions, the current de facto standard is the V2000 molfile, though more recently the V3000 format has been circulating in large-enough volumes to be an issue for those unable to read V3000-format files.

[edit] Example

This is what the Molfile of benzene created in ChemSketch looks like when opened with a text editor.

 benzene
 ACD/Labs0812062058
 
  6  6  0  0  0  0  0  0  0  0  1 V2000
    1.9050   -0.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9050   -2.1232    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7531   -0.1282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7531   -2.7882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3987   -0.7932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3987   -2.1232    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0

1: header
2: general information: 6 atoms, 6 bonds, ..., V2000 standard
3-8: x, y, z, element, extra information
9-14: bonding information (each bond listed): 1st atom, 2nd atom, type, extra information

[edit] RGfiles

[edit] Rxnfiles

[edit] SDfiles

SDF - one of a family of file formats from MDL holding chemical data, especially structure information.

SDF stands for structure-data file and actually wraps the molfile (MDL_Molfile) format. Multiple compounds are separated by a Delimiter, a line of four dollar signs ( $$$$ ). A feature of SDF is the possibility of storing associated data items.

[edit] RDfiles

[edit] XDfiles

[edit] Clipboard

[edit] References

Dalby, A.; Nourse, J. G.; Hounshell, W. D.; Gushurst, A. K. I.; Grier, D. L. et al. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32, 244-255.