GenerateMD killer molecule (boran hairnet)

Hi, usually GenerateMD has a throughput of 1000 molecules per


second on a Pentium M 1.7 GHz but this killer boran hairnet will


get stuck for 21 minutes in GenerateMD. Its known since 99 in the


NCI99 DB. This is the beauty:











This will also affect, Jcman, cxcalc and Instant-JChem.





The SMILES code is:


[H]1B234[H]B256B378B149B%10%11%12[H]B%10%13%14%15%16[H]B%13%17%18B%19%20%21[H]B%19%22%23[H]B%22%24%25B%20%23%26B%17%21%27B%24%26%28B%14%18%27B5%15%25%28%29B67%30B89%11B%12%16%29%30


The command is:


generatemd c killer-boran.smi -k CF >garstiges-haarnetz-boran-fp.txt





The output is:


chemaxon.descriptors.ChemicalFingerprint


<?xml version="1.0" encoding="UTF-8"?>\n<ChemicalFingerprintConfiguration Version="0.3" schemaLocation="cfp.xsd">\n<Parameters Length="1024" BondCount="7" BitCount="3"/>\n<ScreeningConfiguration>\n <ParametrizedMetrics>\n <ParametrizedMetric Name="Tanimoto" ActiveFamily="Generic" Metric="Tanimoto" Threshold="0.2"/>\n <ParametrizedMetric Name="Euclidean" ActiveFamily="Generic" Metric="Euclidean" Threshold="10"/>\n </ParametrizedMetrics>\n</ScreeningConfiguration>\n<StandardizerConfiguration Version="0.1"><Actions><Action ID="dehydrogenize" Act="dehydrogenize"/><Action ID="aromatize" Act="aromatize"/></Actions></StandardizerConfiguration></ChemicalFingerprintConfiguration>


1 -2141187584 8456328 1073807552 134365699 67649536 16777728 50397184 135270416 2097159 2048 -1610603512 4196356 -2130702336 3163136 -2143269887 2629632 16785472 1346375680 2425920 -1073479103 0 69206050 16384 2097156 -1609023488 1074020352 109051924 285212676 1091567616 23330820 4286464 1090556928








(I know, its not a bug, its a feature :-)


Tobias

Hi Tobias,





thank you for the "feature-report"! ;-)





See discussion at http://www.chemaxon.com/forum/viewpost9235.html#9235





I have an idea how to make Fp generation faster for such monster structures even for extreme fp parameter values (such as path length = 19), I will discuss it with the developer of fp generaration and I'll get back to you afterwards.





Best regards, Miklos





Ps: Keep experimenting, it's very useful for us to see how our systems behave at such extreme conditions.

Hi Miklos,


this looks like the travelling salesman when he was visiting Königsberg.


Looking at this nasty/beauty molecule (depending on the point of view - developer/user) -


maybe a genetic algorithm with simulated annealing can help. Or maybe using Bayesian Networks


and the Max-Min Hill-Climbing Algorithm [PDF]. But now I am happy, I am just a user .-)


Tobias