A few weeks ago Shinsaku Fujita submitted a new update of XyMTeX to CTAN. Why is this worth mentioning? Because of two (or three) reasons:
Both has changed: the new version v5.01 from 2013 is on CTAN and part of TeX Live again. It came in with today’s update on my machine. More importantly for me at least: it got a huge manual. Shinsaku Fujita wrote a 780 pages long (1) book (you have to call it so). I haven’t done more than to glance through it but it seems very comprehensive and has lots and lots of examples. What I’m missing is an index and PDF bookmarks but this is minor compared to the situation before this update.
- The last update to CTAN has been quite some while ago (years?) so only v4.06 (new in 2009) was available when the current version had long stepped to 5.00 (new in 2010).
had therefore been moved to the obsolete branch on CTAN and wasn’t part of TeX Live - had always had a rather tedious to use manual which was the main reason why I had never used it.
Both has changed: the new version v5.01 from 2013 is on CTAN and part of TeX Live again. It came in with today’s update on my machine. More importantly for me at least: it got a huge manual. Shinsaku Fujita wrote a 780 pages long (1) book (you have to call it so). I haven’t done more than to glance through it but it seems very comprehensive and has lots and lots of examples. What I’m missing is an index and PDF bookmarks but this is minor compared to the situation before this update. 
This is indeed good news since I have many structures in Xymtex and hopefully they will be useful any further. Mostly about structures that are derived from cholesterol and steran. I could make them available somewhere for general use.
Bernhard
Myself I’m not a $\XyMTeX$ user but I’m quite sure there are people who’d be interested.