Table of Contents

Import and conversion of Markush DARC files

Thomson Reuters Markush DARC (*.vmn) files contain Markush structures extracted from patents. This is the "Merged Markush Service database", now owned and distributed by Thomson Reuters. These files are particularly useful when imported into a JChem table of type Markush libraries as you can search the table of Markush structures using substructure or exact structure searches. For more information about Markush DARC file format support in Marvin see the Marvin documentation.

The Markush DARC files are available from Thomson Reuters through ChemAxon for evaluation purposes. Please contact sales at chemaxon dot com for more information.

Single file import

Each VMN file contains a single Markush structure. Import of a VMN file can be done in one of two ways:

File import

Use the standard file import wizard to import the file into a new or an existing Markush structure table. See the Using File Import page for more information.

Insert row

An existing JChem table can have additional structures added to it just be adding a new row to the table. See the Adding and Deleting Rows page for more information. When the new row dialog opens use the File->Open functionality of MarvinSketch to locate the file to import and then add this structure as a new row.

Converting multiple VMN files to MRV format

If you have a large number of VMN files to import then loading them individually can become tedious. To solve this we provide a utility that can convert the files to a single MRV file that contains all the structures and can be imported in a single step.

The files are typically organised into a hierarchy using directories. The name of each directory encodes the patent number. As an example, files might be found in a common root directory as paths like this:

            usa1/2003/15/82/26mrk001.vmn
            usa1/2004/12/67/02mrk001.vmn
            usa1/2004/12/67/02mrk002.vmn
        

The convertor utility will search a directory for *.vmn files in any subdirectory (and subdirectories of the subdirectory etc.) and generate a single MRV format file with the structures of all the VMN files that are found. It will also write the directory path information as properties of the structure so that when the MRV file is imported these properties are also imported into the database table allowing you to see some information about the patent the structure came from.

To run this convertor:

1. Open the convertor using File->Convert VMN files to MRV
2. Specify the root directory containing the files. The lowest directory containing all the files.
3. Change the output name of the file (optional)
4. Press the Run button and conversion will start. Message are displayed showing the progress. This will take some seconds or minutes depending on the number of files.
5. Press Close when finished.

The converted file will be found in the root directory of the converted files, unless you specified a different location.

To import the converted files:

Use the standard file import wizard to import the converted file. See Using File Import page for more information.

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