Bugs item #2955101, was opened at 2010-02-19 13:26 Message generated for change (Tracker Item Submitted) made by makio323 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2955101&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: 2.2.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: makio (makio323) Assigned to: Nobody/Anonymous (nobody) Summary: difficulty reading from fastsearch index Initial Comment: This problem was originally posted on openbabel-discuss forum by David Rose-9 on Nov. 15, 2007. However, I still have exactly the same problem using version 2.2.3, which is the last one on Feb. 19, 2010, on my x86 64 bit RedHat Linux and it is better to notice the problem here. --------------------------- I have had several instances where I build a fast search index without any apparent trouble but then can't search it without an error. I finally have a small example of this problem that I can post, using a 10 molecule smi file (ten.smi) as input: $ cat ten.smi C12(C(N(C(=O)C)c3c2cccc3)=O)Nc2c(ccc(c2N1)OCCCC)OCCCC n1c([nH]c(cc1c1ccccc1)=O)c1ccc(cc1)Br n1c(nc2c(c1N(C)C)cccc2)c1c(O)cccc1 C1(/[CH]2[CH]3\C(=C4/CC(C)(C)NC(C4)(C)C)C=C[CH]3[CH]1C=C2)=C1/CC(C)(C)NC(C1)(C)C n1c(c2ccc(C(=O)O)cc2)ccc(c1)CCCCC N1(C(CN(CC1=O)C(=O)C1CCCCC1)=O)CCc1ccccc1 S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O c12c(c(OC)c3c(c1OC)occ3)ccc(o2)=O c12c(O[CH](C1=O)C(C)C)cc1c(c2)ccc(=O)o1 c12[C]3([...@h]4([N@@](CCc1c1ccccc1[nH]2)c...@h](C=C4CC)C3))C(=O)OC # file looks OK...build index: $ babel ten.smi -ofs This will prepare an index of ten.smi and may take some time... It took 0 seconds 10 molecules converted 37 audit log messages $ ls -lt ten.fs -rw-r--r-- 1 rose staff 1564 Nov 15 12:51 ten.fs # looks OK, no errors, fs file exists and has stuff in it. Try a search: $ babel ten.fs -ifs -s'Nc2nc(c1ccccc1)nc3ccccc23' out.smi ============================== *** Open Babel Error in ReadChemObject Difficulty reading from index ten.fs 0 molecules converted 1 errors 1 audit log messages >From this past post ---Problem using fs index file--- >(http://n4.nabble.com/Problem-using-fs-index-file-td958832.html#a958832), >problem may be caused by incompatible binary operation on 64 bit machine but I >cannot figure out the cause. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2955101&group_id=40728 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
