[Cdk-devel] SMILES parsing takes forever

[Nina J. <ni...@ac...>]

Hello all,

Is it be possible to set a timeout for SMILESparser? 

The problem is that it takes too long to parse the following SMILES 

"n(c(c(c(Nc(c(c(nc(c(c(Nc(c1c(cccc2)c2)c3)c3)c(cccc4)c4)c5)c5)c(cccc6)c6)c7)c7)c(cccc8)c8)cc9)c19"

(don't know exactly how long, I've interrupted it after 10 minutes, which IMHO
is already too much)

I was thinking that aromaticity detector timeout will manage it, but it turns
out valencyChecker.saturate(molecule) is what hangs forever.
Has anybody experienced something similar?

Best regards,
Nina 

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			      Dr. Nina Nikolova-Jeliazkova
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