cxcalc stereo plugin -vtrue timeout problem

User 90a49d1eda

28-10-2015 15:25:05



I am trying to compute all of the stereoisomers of a large set of compounds from inchi strings. When I use the -vf command I get a consistent number of isomers, but some of them are redundant, especially with respect to substituents at bridgehead positions (which get placed as "up" or "down," when they really can only be straight out), so unique stereo inchis are generated which do not represent unique compounds

For example:

Cxcalc C2-7Ox.Adenine.inchi stereoisomers -v false -f inchi > C:\Inchis10.7.15\C2-7Ox.Adenine.stereo.vf.aux2.inchi

But when I try to use the verify= true command:

Cxcalc C2-7Ox.Adenine.inchi stereoisomers -v true -f inchi > C:\Inchis10.7.15\C2-7Ox.Adenine.stereo.vf.aux2.inchi

I get a lot of log errors including timeouts and a variable number of output structures each time I run the calculation.

I am guessing this is because the program gets hung up on some structures and then times out and movves on to the next one, but it does not seem that the time limit can be extended for this calculation.

Can anyone help with this?

Many thanks!

ChemAxon d51151248d

30-10-2015 12:10:24


Thank you for reporting this. However, we would need some test molecules so that we can exactly reproduce the problem. 

Thank you, 


ChemAxon d51151248d

04-11-2015 10:35:00

Hi Jim, 

Thank you for the input file. We have managed to re-produce this issue. The problem lies not in the stereoisomer generation but in the underlying 3D coordinate generation process. 

We will work on this issue and fix it as soon as our priorities allow us. 

Thank you for your patience, 


User 90a49d1eda

26-11-2015 05:00:34

Dear Dr. Szisz,

How are you? I just wanted to
follow up with you regarding our issue with the cxcalc stereoisomer
generation. I appreciate you and your colleaguues may not have a lot of
time to dedicate to every small technical problem that comes your way,
so I sincerely hope we are not pestering you.

However, we are deep into a
project we hoped could be solved using your software and we're stuck at
the moment. If you think this is trivial issue which might be solved on
your end in the next few weeks, we would certainly wait too see what you
come up with. We hope our issue is of use for improving your software.
But, if you think it is a "deep" issue which may take a long time to
address, perhaps simply because it doesn't come up very often, we will
probably explore other avenues. Could you please advise us whether we
should wait to hear from you soon or move on to other solutions?

Otherwise, thank you very much, we have really found your software very helpful!

All the best,


ChemAxon d51151248d

26-11-2015 09:24:11

Hi Jim, 

All I can say to you about the 3D coordinate generation issue is that currently it is not in our scope to provide a fix for this issue. We have many other developmental directions right now and our priorities don't allow us to focus our efforts on further developing the conformer generation module. Unfortunately we can't even give you an estimate when this issue would be settled in the future. This is totally up to our priorities. The issue is already put in our backlog as something we know we should work in the future. 

Thank you for your understanding.