A while back I got this question
”I’m about to hit the tedious part of writing my chemistry PhD thesis in Microsoft Word: having all mentioned compounds numbered in text and in the chemdraw imported files. My question: is there any automated option for this task or do I have to insert every number manually? In particular renumbering after adding a new compound in the middle of the text”
There are a couple of ways to do this in LaTex (http://www.jkwchui.com/2010/03/writing-chemistry-with-latex-33/) and (http://piti.exroot.org/konwerter/) but in my experience LaTex is not particularly popular among chemists. However help is at hand, I’ve just been sent details of a brilliant applescript that works with ChemBioDraw and Word.
The process is described in detail here (http://www.martinp23.com/blog/2013/03/chemdraw-and-word-compound-numbering-on-mac/) so I won’t give anymore details just to add that one thing I’ve been using in recent Chemdraw scripts is
tell application id "com.cambridgesoft.ChemDraw"
It avoids the problems with application naming with different versions of Chem(Bio)Draw Std/Pro/Ultra.
There are many more applescripts here.
A while back I posted a script that copied a file to a users MobilMe Public folder and created an email link to that file. With the imminent demise of MobileMe a couple of people have asked me for a script that does the same but uses Dropbox.
This script shows how to copy a file to your Dropbox Public folder and then email a link to it.
A reader commented that they often emailed ChemBioDraw .cdx structures to colleagues who it turned out did not have a copy of ChemBioDraw to view them, whilst it is possible to convert the cdx file to other formats using OpenBabel they usually just ended up exchanging an image. They asked if there was a better solution and this is an ideal task for Applescript. This script assumes the structure you want to email is open in ChemBioDraw, it will create an email using Apple Mail containing the structure as a SMILES string, and embed the .cdx file together with an image in PNG format.
The name to structure feature in ChemBioDraw is very useful but is pretty much limited to systematic names and certainly does not support other chemical identifiers like CAS Numbers. There are a number of online services that do support these sort of functions but you end up having to cut and paste from different web sites. This is where the Chemical Identifier Resolver script comes into play.
Unfortunately I don’t have ChemBiodraw 11 (or earlier versions) so I can’t explore the problem but perhaps it might be possible to offer a work around using Applescript. Read More...