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