Thursday, 21 May 2009

Have your hamburger and eat it - Edit molecules in PDFs II

In Part I, I showed how to hack some code together that allowed you to paste images directly from the clipboard (e.g. from a PDF) into Beda's BKChem, a 2D drawing program. The magic conversion from image to chemical was done by Igor's OSRA.

Well, Igor has taken this idea and run with it. The latest version of OSRA now includes plugins for BKChem, Symyx Draw, MolSketch and Pipeline Pilot.

If you use the Windows installer, the Symyx Draw plugin is automatically installed and adds an "Import Structures from OSRA" option to the File menu. The first time you choose it, you will need to change the path to something like "C:\Program Files\osra\osra.exe" under "Settings...". Here's the plugin in action:
Note that the other plugins appear to be only available from the Windows .zip release.


ChemSpiderman said...

Thanks for the info Noel. This area of image conversion is really starting to hit mainstream now and OSRA connectivity to tools like Symyx Draw is definitely going to increase usage. With that will come feedback, then the loop of the benefit of us all.

Unknown said...

Noel, thank you for the kind words!
To give credit where credit is due Symyx Draw plugin was written by James Jack of Symyx.
I did not include the other plugins in the installer because I'm not sure how to automatically do all the steps required for BKChem plugin for example (and whether it would be desired to have it automated). All the plugins with the short instructions on the installation and attribution where appropriate are available with the .zip archive.

ChemSpiderman said...

That James Jack is a clever guy! He wrote the ChemMobi application integrated to DiscoveryGate and ChemSPider: