On May 7, 2009, at 3:07 PM, Loren Lenzen wrote: > 1) The daylight spec for SMARTS queries implies that the dot is > used as an AND. However, the SQT is either just taking the first > fragment or is using the dot as an OR (I can't tell yet). ([CH3]Br). > ([OH,O-,$([OX2]([#6])[#6])][CH]1([CH]=[CH][CH]5([CH]4(N([CH3])[CH2] > [CH2]C25(c3c(O[CH]12)c(O[CH3])[cH][cH]c3[CH2]4))))) returns every > listing that contains BrC. in its SMILES.
I don't remember exactly, but I think the dot is related to component level grouping which is not supported by the CDK SMARTS parser > 2) What is the most efficient way to multithread the SQT? Does a > new instance of the SQT have to be created for each thread? Hmm, good question. I know that some others are looking at multi- threading issues across the API. I'm not much of an expert in Java multithreading, but I'd venture that the SQT is not multi-threaded, mainly due to the underlying UIT code not being thread safe. Thus it's probably safest ot have multiple instances of the SQT (which is not very efficient) > 3) It appears that the SMILES parser doesn't recognize the heavier > metals (e.g. Eu). How much of the periodic table is left out? Is > there a way to capture these atoms without them returning a > CDKexception. Hmm, the time is coming for a JJTree parser ... ------------------------------------------------------------------- Rajarshi Guha <rg...@indiana.edu> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. ------------------------------------------------------------------------------ The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
