Fingerprinter hangs for larger molecule

[WolframT]

BitSet bs = fingerprinter.getFingerprint(molecule);

Hangs and doesn't react anymore for me when applied to some large molecules (exp. >80 bonds).
I'll post some example below.

[WolframT]

(Deleted, formatting made post unusable)

WolframT, could you post your molfile as a Gist and add the link to this thread? The whitespace formatting has made a mess of the molfile and I'd like to test your file.

[WolframT]

Of course. I can try the smiles as well - a simple porphyrin derivative

CCN(CC)c4nc3cc2c1nc%12nc(nc%10[nH]c(nc7[nH]c(nc(n1)c2cc3nc4N(CC)CC)c6cc5nc(N(CC)CC)c(N(CC)CC)nc5cc67)c9cc8nc(N(CC)CC)c(N(CC)CC)nc8cc9%10)c%13cc%11nc(N(CC)CC)c(N(CC)CC)nc%11cc%12%13

[WolframT]

https://gist.github.com/1511307

[WolframT]

I tried again and started the task 20 minutes ago, now it successfully finished.

Unfortunately, I've got a few hundred such molecules... but good to see it works in the end.

Your molecule contains a huge number of rings and very long paths, which would require a lot of resources to fully enumerate. Fortunately, exhaustive enumeration isn't the goal of the fingerprinter, so there are two settings you could try:

1. PathFingerprinter#setMaximumPathDepth - try a number like 8

2. PathFingerprinter#setMaximumRingSize - try a number like 10

You can likely bring these numbers down a bit more and still get a good fingerprint screen. Please feel free to post again if this doesn't work.

[WolframT]

Thank you. I didn't check the fingerprint performance yet, but these settings make the whole process 100'000x faster and solve the issue.

"contains a huge number of rings and very long paths" - True - but there are very many such molecules of interest.... e.g.

CC(=O)N[C@@h]1CCC[C@H]1C(=O)N[C@@h]2CCC[C@H]2C(=O)N[C@@h]3CNC[C@H]3C(=O)N[C@@h]4CCC[C@H]4C(=O)N[C@@h]5CNC[C@H]5C(=O)N[C@@h]6CCC[C@H]6C(=O)N[C@@h]7CCC[C@H]7C(=O)N[C@@h]8CNC[C@H]8C(=O)N[C@@h]9CCC[C@H]9C(=O)N[C@@h]%10CNC[C@H]%10C(=O)N[C@@h]%11CCC[C@H]%11C(=O)N[C@@h]%12CCC[C@H]%12C(=O)N[C@@h]%13CNC[C@H]%13C(=O)N[C@@h]%14CCC[C@H]%14C(=O)N[C@@h]%15CNC[C@H]%15C(=O)N[C@@h]%16CCC[C@H]%16C(=O)N[C@@h]%17CCC[C@H]%17C(N)=O

Takes even much longer using the standard settings.