Hello, i have joined all sdf in one (join.sdf).
Now i want to search: babel join.sdf resultadawd.sdf -s"B(C1=CC(=CC=C1)N2C(=O)C3CC=C4C(C3C2=O)CC5=C(C4C6=C(C(=CC=C6)F)O)C(=O)C=C(C5=O)Br)(O)O" But i became the following output: ============================== *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Cannot read atom and bond count Expected standard 6 character atom and bond count 0 molecules converted 1 warnings 9 audit log messages And the executing time is only about 1 second. I think this doesn't work. But why? I also couldn't create an fs from the join.sdf (babel join.sdf -ofs). There i became the following output: *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Cannot read atom and bond count Expected standard 6 character atom and bond count This will prepare an index of join.sdf and may take some time... It took 0 seconds 1 molecule converted 1 warnings 10 audit log messages I have created join.sdf with: cat *.sdf > tmp.txt and then mv tmp.txt join.sdf Am 05.12.2011 um 15:30 schrieb Noel O'Boyle: > I don't know if Open Babel supports joining fs files, so joining the > sdf may be your only choice. Chris? > > On 5 December 2011 15:20, Jochen Schreiber <joc...@googlemail.com> wrote: >> One question: Sholud i join the fs Files or the sdf Files and create the fs >> File on the joined sdf Files? >> >> What is better? >> >> Am 05.12.2011 um 14:50 schrieb Noel O'Boyle: >> >>> If I would you, I would join the sdf files, and then convert that to a >>> single fs file. >>> >>> To join: >>> cat *.sdf tmp.txt >>> mv tmp.txt joined.sdf >>> >>> - Noel >>> >>> On 3 December 2011 11:53, Jochen Schreiber <joc...@googlemail.com> wrote: >>>> Hello to everybody, >>>> >>>> first i want to say hello. My first post in this mailinglist. >>>> >>>> I have a question. I have downloaded the full pubchem compound database >>>> and convert all the sdf files to fs Files. >>>> >>>> Now i have 2138 fs-Files and i have a query.mol and i want to search the >>>> top 5 similarity molecules in all fs-Files. My usage: >>>> >>>> sh: babel Compound_000025001_000050000.fs results2.sdf -query.mol >>>> >>>> Now i want to put in all fs-Files in this command. How does it work? >>>> >>>> I found solutions for that problem in java but i need to do this over the >>>> commandline. >>>> >>>> So i hope you could help me. >>>> >>>> With best, >>>> >>>> Jochen Schreiber >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> All the data continuously generated in your IT infrastructure >>>> contains a definitive record of customers, application performance, >>>> security threats, fraudulent activity, and more. Splunk takes this >>>> data and makes sense of it. IT sense. And common sense. >>>> http://p.sf.net/sfu/splunk-novd2d >>>> _______________________________________________ >>>> OpenBabel-discuss mailing list >>>> OpenBabel-discuss@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> ------------------------------------------------------------------------------ Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
