Bugs item #3434544, was opened at 2011-11-07 07:42 Message generated for change (Tracker Item Submitted) made by jlaszlo You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3434544&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: Command-line Tools Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Laszlo Jicsinszky (jlaszlo) Assigned to: Nobody/Anonymous (nobody) Summary: error in similarity search Initial Comment: OS: Windows 7, 64 bit, OB 2.3.1 a) Minor, and affect the help file and the extraction of first file. The ChEMBLdb current version (11) is > 2 GB, and the extraction method for Windows in not working anymore (a shortcut might be using the type command, output to file and break immediately, then the output file can be opened by even notepad) b) Major, affect the usage. Testing the similarity search, and followed the suggested way in help, I have encountered the following problems: b.1.) using command babel: L:\pgm\openbabel>babel chembl_11.sdf mostsim.sdf -s firstmol.sdf -at5 ============================== *** Open Babel Error in OpenBabel::VF2Mapper::MapGeneric time limit exceeded... output file length=0, and babel seems to hang up working, prompt has not been back b.2) It is recommended to use obabel instead of babel. typing obabel (recommended) instead of babel I got the following message L:\pgm\openbabel>obabel chembl_11.sdf mostsim.sdf -s firstmol.sdf -at5 Missing or unknown output file or format spec or possibly a misplaced option. Options, other than -i -o -O -m, must come after the input files. Open Babel 2.3.1 -- Oct 9 2011 -- 17:57:01 Usage: obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options] Try -H option for more information. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3434544&group_id=40728 ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
