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.
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 Systèmes of Dassault Group.[1]
The CT file is an open format. BIOVIA publishes its specification.[2] BIOVIA requires users to register to download the CT file format specifications.[3]
| ctab | |
| Mime: | chemical/x-mdl-molfile |
| Genre: | 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.
| Title line (can be blank but line must exist) | Header Block(3 lines) | ||
|---|---|---|---|
ABCDEFGH09071717442D | Program / file timestamp lineName of source program, a sequence number (often a timestamp), and a 2D or 3D specifier (often meaningless, examining the "Z" coordinates is more reliable) | ||
Exported | Comment line (can be blank but line must exist) | ||
6 5 0 0 1 0 3 V2000 | Counts line | Connection table | |
-0.6622 0.5342 0.0000 C 0 0 2 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 -0.7207 2.0817 0.0000 C 1 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0 | Atom block (1 line for each atom): x, y, z (in angstroms), element, etc. | ||
1 2 1 0 0 0 0 1 3 1 0 1 0 0 1 4 1 0 0 0 0 2 5 2 0 0 0 0 2 6 1 0 0 0 0 | Bond block(1 line for each bond): 1st atom, 2nd atom, type, etc. | ||
M CHG 2 4 1 6 -1 M ISO 1 3 13 | Properties block | ||
| M END | END line(NOTE: some programs don't like a blank line before M END) | END |
| Description | number of atoms | number of bonds | number of atom list | Chiral flag, 1 = chiral;0 = not chiral | number of stext entries | number of lines of additional properties | mol version | |
| Type | [Generic] | [Generic] | [Query] | [Generic] | [ISIS/Desktop] | [Generic] |
The Bond Block is made up of bond lines, one line per bond, with the following format:
111 222 ttt sss xxx rrr ccc
where the values are described in the following table:
| 111 | first atom number | ||
| 222 | second atom number | ||
| ttt | bond type | 1= Single, 2 = Double, 3 = Triple, 4 = Aromatic,5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = Any | |
| sss | bond stereo | For single bonds:0 = not stereo; 1= up; 4=either, 6= down For double bonds: 0= Use x-, y-, z-coords from atom block to determine cis or trans; 3=Cis or trans (either) double bond | |
| xxx | not used | ||
| rrr | bond topology | 0 = Either, 1 = Ring, 2 = Chain | |
| ccc | reacting center status | 0 = unmarked, 1 = a center, -1 = not a center, Additional: 2 = no change, 4 = bond made/broken, 8 = bond order changes12 = 4+8 (both made/broken and changes); 5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1) are also possible |
The extended (V3000) molfile consists of a regular molfile “no structure” followed by a single molfile appendix that contains the body of the connection table (Ctab). The following figure shows both an alanine structure and the extended molfile corresponding to it.
Note that the “no structure” is flagged with the “V3000” instead of the “V2000” version stamp. There are two other changes to the header in addition to the version:
Unlike the V2000 molfile, the V3000 Rgroup molfile has the same header format as a non-Rgroup molfile. V3000 format can represent the following things that are out of reach for V2000:[4]
| Header block | ||
| GSMACCS-II07189510252D 1 0.00366 0.00000 0 | Header with timestamp | |
|---|---|---|
| Figure 1, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992 | Comment line | |
| 0 0 0 0 0 999 V3000 | V2000-compatibility line | |
| M V30 BEGIN CTAB | Connection table | |
| M V30 COUNTS 6 5 0 0 1 | Counts line | |
M V30 BEGIN ATOM M V30 1 C -0.6622 0.5342 0 0 CFG=2 M V30 2 C 0.6622 -0.3 0 0 M V30 3 C -0.7207 2.0817 0 0 MASS=13 M V30 4 N -1.8622 -0.3695 0 0 CHG=1 M V30 5 O 0.622 -1.8037 0 0 M V30 6 O 1.9464 0.4244 0 0 CHG=-1 M V30 END ATOM | Atom block | |
M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 3 CFG=1 M V30 3 1 1 4 M V30 4 2 2 5 M V30 5 1 2 6 M V30 END BOND | Bond block | |
| M V30 END CTAB M END |
A counts line is required, and must be first. It specifies the number of atoms, bonds, 3D objects, and Sgroups. It also specifies whether or not the CHIRAL flag is set. Optionally, the counts line can specify molregno. This is only used when the regno exceeds 999999 (the limit of the format in the molfile header line). The format of the counts line is:
| M V30 COUNTS | na | nb | nsg | n3d | chiral | [REGNO=regno] | |
| M V30 COUNTS | 6 | 5 | 0 | 0 | 1 | ||
| ctab | |
| Extension: | , |
| Mime: | chemical/x-mdl-sdfile |
| Genre: | chemical file format |
SDF (structure-data format, also known as "SD file") is developed by MDL for representing structural information. An SDF file consists of several records delimited by a line consisting of four dollar signs ($$$$). Each record starts like a normal molfile, but includes associated data items after the M END line.
SDF can be built on top of either a V2000 or V3000 molfile. As a result there are two separate formats, V2000 SDF and V3000 SDF.
Associated data items are denoted as follows:
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There are other, less commonly used formats of the family.
There are also alternative encodings derived from the formats:
