Chemical table file
Chemical table file (CT File) is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms.
File formats
There are several file formats in the family.
The formats were created by MDL Information Systems (MDL), which was acquired by Symyx Technologies then merged with Accelrys Corp., and now called BIOVIA, a subsidiary of Dassault Systemes of Dassault Group[1]
CT File is an open format, BIOVIA publishes its specification.[2]
Molfile
| Filename extension |
.mol |
|---|---|
| Internet media type |
chemical/x-mdl-molfile |
| Type of format | chemical file format |
An MDL Molfile is a file format 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. It is also supported by some computational software such as Mathematica.
The current de facto standard version is molfile V2000; although, more recently, the V3000 format has been circulating widely enough to present a potential compatibility issue for those applications that are not yet V3000-capable.
Following are the contents of a Molfile of benzene created in ChemSketch, as seen in a text editor (Note: According to the official molfile specification,[3] the '$$$$' notation applied only to the SDF file – not to the molfile, so ChemSketch molfiles will not always function properly.):
benzene
ACD/Labs0812062058
6 6 0 0 0 0 0 0 0 0 1 V2000
1.9050 -0.7932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9050 -2.1232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7531 -0.1282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7531 -2.7882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3987 -0.7932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3987 -2.1232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 2 0 0 0 0
4 2 2 0 0 0 0
5 3 1 0 0 0 0
6 4 1 0 0 0 0
6 5 2 0 0 0 0
M END
$$$$
| Lines | Section | Description |
|---|---|---|
| 1-3 | Header | |
| 1 | Molecule name ("benzene") | |
| 2 | User/Program/Date/etc information | |
| 3 | Comment (blank) | |
| 4-17 | Connection table (Ctab) | |
| 4 | Counts line: 6 atoms, 6 bonds, ..., V2000 standard | |
| 5-10 | Atom block (1 line for each atom): x, y, z (in angstroms), element, etc. | |
| 11-16 | Bond block (1 line for each bond): 1st atom, 2nd atom, type, etc. | |
| 17 | Properties block (empty) | |
| 18 | $$$$ | See note |
SDF
| Filename extension |
.sd, .sdf |
|---|---|
| Internet media type |
chemical/x-mdl-sdfile |
| Type of format | chemical file format |
SDF is one of a family of chemical-data file formats developed by MDL; it is intended especially for structural information. "SDF" stands for structure-data file, and SDF files actually wrap the molfile (MDL Molfile) format. Multiple compounds are delimited by lines consisting of four dollar signs ($$$$). A feature of the SDF format is its ability to include associated data.
Associated data items are denoted as follows:
> <Unique_ID>
XCA3464366
> <ClogP>
5.825
> <Vendor>
Sigma
> <Molecular Weight>
499.611
Multiple-lines data items are also supported. The MDL SDF-format specification requires that a hard-carriage-return character be inserted if a single line of any text field exceeds 200 characters. This requirement is frequently violated in practice, as many SMILES and InChI strings exceed that length.
Other formats of the family
There are other, less commonly used formats of the family:
- RXNFile - for representing a single chemical reaction;
- RDFile - for representing a list of chemical reactions with associated data, as well as tabular data;
- RGFile - for representing the Markush structures (deprecated, Molfile V3000 can represent Markush structures);
- XDFile - for representing chemical information in XML format.
See also
References
- ↑ Dalby, A.; Nourse, J. G.; Hounshell, W. D.; Gushurst, A. K. I.; Grier, D. L.; Leland, B. A.; Laufer, J. (1992). "Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited". Journal of Chemical Information and Modeling. 32 (3): 244. doi:10.1021/ci00007a012.
- ↑ Biovia (June 2014), CT File Formats, Biovia. CTFile format definitions available on request (registration required).
- ↑ Chemical table file specification is available at http://download.accelrys.com/freeware/ctfile-formats/ctfile-formats.zip (December 2011)
External links
- SDF Toolkit free software to process SD files (SDF).
- NCI/CADD Chemical Identifier Resolver generates SD files (SDF) from chemical names, CAS Registry Numbers, SMILES, InChI, InChIKey, ....
- KNIME free software to manipulate data and do datamining, can also read and write SD files (SDF).
- Comparative Toxicology Dashboard service provided by the Environmental Protection Agency (EPA) which generates SD files (SDF) from chemical names, CAS Registry Numbers, SMILES, InChI, InChIKey, ...