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.
9-481: 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 . The CT file is an open format . BIOVIA publishes its specification. BIOVIA requires users to register to download the CT file format specifications. An MDL Molfile
18-400: A file timestamp) (1 line for each atom): x, y, z (in angstroms ), element, etc. (1 line for each bond): 1st atom, 2nd atom, type, etc. (NOTE: some programs don't like a blank line before M END) 0 = not chiral additional properties 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
27-485: 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. There are other, less commonly used formats of the family: MDL Information Systems Too Many Requests If you report this error to the Wikimedia System Administrators, please include
36-476: 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
45-450: Is intended especially for structural information. "SDF" stands for structure-data format, and SDF files actually wrap the molfile ( MDL Molfile ) format. Multiple records are delimited by lines consisting of four dollar signs ($ $ $ $ ). A key feature of this format is its ability to include associated data. Associated data items are denoted as follows: Multiple-line data items are also supported. The MDL SDF-format specification requires that
54-465: 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: SDF is one of a family of chemical-data file formats developed by MDL; it
63-532: 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 extended Rgroup molfile has the same header format as a non-Rgroup molfile. A counts line
72-423: The following table: 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 12 = 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
81-401: 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. (3 lines) (Name of source program and
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