Hi, I am using CDK 1.0 to visualize SMILES structures. I have noticed that SMILES parsing can be very slow, (it can take close one minute) when big structures are concerned. This is the call to IMolecule im = sp.parseSmiles(smilesString); which is time consuming. Here are a few examples of SMILES structures that take about 20 seconds each to be parsed:
1/ NC(=[NH2+])c1ccc(O)c(\C=C\CN(C(=O)CCC(=O)O)c2ccc(OC3CCN(CC(=O)O)CC3)c(c2)C(F)(F)F)c1 2/ COc1ccc(NS(=O)(=O)C(F)(F)F)cc1Oc2c(F)c(Oc3cccc(c3)C4=NCCN4C)nc(Oc5cc(ccc5O)C(=[NH2+])N)c2F 3/ COC(=O)[EMAIL PROTECTED](Cc1cccc(c1)C(=[NH2+])N)[C@@H](CC(C)C)NC(=O)c2ccc(cc2)c3cccc(CN)c3 4/ CCOC(=O)c1cc(Oc2c(F)c(Oc3cccc(c3)C4=NCCN4C)nc(Oc5cc(ccc5O)C(=[NH2+])N)c2F)cc(c1)C(=O)O 5/ CN(C)C(=O)c1cccc(Oc2nc(Oc3cc(ccc3O)C(=[NH2+])N)c4nc(C)n(Cc5ccccc5)c4n2)c1 6/ Cc1cc(C(=O)Nc2ccc(cc2)c3ccccc3F)n(n1)c4cccc(c4)C(=[NH2+])N Is that a known issue?Is it possible to set like a timeout when parsing is too long? here are other informations that can be useful : Hardware configuration : Windows Vista Intel core 2CPU 2Ghz 3000Mo RAM (same pb with XP) JDK 1.5.0_11 CDK 1.0 thanks a lot for your help. Miriame ALLOUCHE _________________________________________________________________ Gagnez des pc Windows Vista avec Live.com http://www.image-addict.fr/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
