Chemical table file

Chemical table files are files that contain information about chemicals.

File formats
Chemical table files come in various formats. In addition to the formats discussed below, other formats include RGfiles, Rxnfiles, RDfiles, XDfiles and Clipboard.

Molfiles
A MDL Molfile is a file format created (and owned) by Elsevier 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.

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

Following are the contents of a Molfile of benzene created in ChemSketch, as seen in a text editor:

1: header

2: comment

3: general information: 6 atoms, 6 bonds, ..., V2000 standard

4-9: x, y, z, element, extra information

10-15: bonding information (each bond listed): 1st atom, 2nd atom, type, extra information

SDF
SDF is one of a family of file formats from MDL holding chemical data, especially structure information. "SDF" stands for structure-data file and SDF files actually wrap 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.