IUPAC name generator

Since version 4.1.7, Marvin contains a IUPAC name generator.

Purpose

This module enables to compute the IUPAC names of any compound. The snapshot below shows a molecule taken from the IUPAC specification, with its name computed by Marvin.

The next snapshot below shows a functionality that is available from version 5.0: the IUPAC name can be inserted into the sketch, and it changes with the structure dinamically. This functionality is available from the Insert menu under by selecting the IUPAC Name option.

When possible, the generated name conforms to the IUPAC Provisional Recommendations for the Nomenclature of Organic Chemistry published in 2004. However, we do not claim full conformance with that document. Our current goal is to generate chemically correct names for as many cases as possible.

Importing IUPAC names (i.e. generating the chemical structure from it) is not supported yet, but it is under development.

Current limitations

Molecules containing multiple radicals (e.g. ethane-1,2-diyl) are not supported yet.
Stereo descriptors (r) and (s) are not supported (as in the whole of marvin).
Amino-acids and peptides are supported only when the amino-acids are represented as groups.
Some aspects of nomenclature are only partially implemented, in particular complex cases of fused systems and multiplicative nomenclature. In those cases, a less straightforward but chemically correct name will be generated.

Usage

Individual molecules

A molecule displayed in MarvinView or MarvinSketch can be named by using the Tools/IUPAC Name menu entry.

In MarvinSketch, the name can be added to the canvas by using the "IUPAC Name" entry in the "Insert" menu. The name will be displayed below the molecule, and updated in real-time when the molecule is modified.

Batch naming

Naming of a large number of molecules contained in a file can be achieved in two ways: with MarvinView, and on the command line, with molconvert. In both cases, all formats supported by Marvin are acceptable as input.

With MarvinView, open the file containing the structures to be names. Then select the menu File/Save As, and choose "IUPAC Name files" in the "Files of type" drop-down box. Choose a name for the file, and click on the Save button. The file will contain the names of the structures, one per line.

Alternatively, on the command line, you can use the following command:

molconvert name inputs.mol -o names.txt

The file names.txt will contain the names of the molecules in the input file, with one name per line.

It is possible to use a format option to chose a nomenclature style:

i (default) uses the IUPAC rules for prefered names;
t uses a more traditional style.

For instance, to generate traditional names, use the following:

molconvert name:t inputs.mol -o names.txt

Adding names as an additional field to a SDfile can be achieved with the cxcalc tool.

cxcalc -S name input.sdf -o named.sdf

API

For information about how names can be generated from Java programs, see the developer documentation.