Applescript to export ChemBioDraw as a mol file

Rempel Jody

• May 29, 2022 02:48
• Edited

I recently wrote an Applescript to export a ChemBioDraw selection as a mol file. One of the difficulties I'm seeing is that the mol file has the erroneous file name in the first line. It should be the same as the conversation. I'm not sure how to set this attribute with applescript. I also believe there is a flaw in the ChemBiodraw algorithms used to generate a mole file. This has been filed to support; however, I'm wondering how one might modify the file's properties or remove the first line of the text file and replace it with the file's name.

The molfile format is a well-established format with the benefit of being a human-readable text format, which means you can open and read them with any text editor. See Chris Swain's Macs in Chemistry site on the Applescript I made (using previous examples he had uploaded) for additional information and access to the Applescript: http://www.macinchem.org/applescript/exportAsmol.php krunker

0

• Official comment

  

  Juan Ortega

  • May 31, 2022 17:17
  • Edited

  Hi,

  In order to request assistance with your Applescript code, you will need to reach out to the manufacturer of that software, as it is beyond the scope of support for ChemDraw/ChemOffice.

  Any mol file created in ChemDraw can be edited in Notepad.  Since version 18, the MolFile and SDF files are consistent with the CTfile format.  If you are using an older version of the software, we recommend that you update to the latest version available.

  You can also adjust the format for the mol file to be V3000 and not to be defaulted to v2000.  There is in ChemDraw a specific file format for V3000

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