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JChem Table Format
(JTF)

The JChem Table Format is a simple text format that primarily useful for two purposes:

• Using this format one can export a chemical database and import it again without any data loss (including additional fields). Although this can also be done with SDF files, the JTF format consumes less space.
• The format is compatible with most spreadsheet software like Excel or StarOffice, therefore it is possible to make charts or use the data for calculations.

Details

Each row of the JTF file represents a a record in the database. The fields are enclosed in one of the following characters : quotation mark (") or apostrophe ('). The fields are separated with one of the following characters (delimiters):

• semicolon (;)
• colon (:)
• comma (,)
• tabulator
• space

Two delimiters following each other denote an empty field, as well as a delimiter in the beginning of a line. There is no field delimiter at the end of the lines.
The first row of JTF is special. It contains the names of the database columns in the same manner as described above.

The chemical structure

The chemical structure represents the last column in the format, it must have the name "CD_STRUCTURE", and it contains a (compressed) MOLFILE.
Note: In JChemManager, you can choose to exclude the structure information at export. In this case the file will not be valid for import by JChem.

Since the MOL format consists of several lines, end of line characters are represented as a character pair : "\n". Therefore if the original molfile contains the following string: "\n" (backslash followed by the letter n) in the comment line, it will be converted to "\N", to distinguish it from the end of line character.

There is another minor issue with quotation marks and apostrophes. If the enclosing characters are quotation marks ("), all quotation marks in the fields will be converted to apostrophes(') on export. If the user chooses apostrophes as enclosing characters, then all apostrophes in the fields are converted to quotation marks.
Although JChem uses uniform field enclosing characters at export, it is allowed to have fields enclosed with different types of characters in the same row.

An example for a correct row:

"123";;'type "TH" chiral';"John's molecule";"Chemistry 447\n  Accord  1116011748\n\n 36 40  0  0  0  0  0  0  0  0  1 V2000\nfiFWY ... "

This row contains 5 columns:

1. A number: 123
2. Empty field (means null in the database)
3. A string : type "TH" chiral
4. Another string: John's molecule
5. Finally, the structure as a converted molfile

In the example above semicolons(;) are used as delimiter characters, but it is also allowed to use different delimiters within the same line (selected from the five characters mentioned previously).

 

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