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?