On 16/12/2011 08:00, Jochen Schreiber wrote: > Hello guys, > > i think i have a problem with my syntax. > > I have an sdf-File then i make an mol-File with: babel input.sdf -omol > query.mol > > and then i want to search with the query-File against one fs-File: > > babel Compound_000000001_000025000.fs babelresult.sdf -sbabelsearch.mol > -at0.85 >
The following worked for me (v2.3.1): babel chembl_02.fs result.sdf -squery.mol -at0.75 22 molecules converted 402 audit log messages The query.mol was taken (luckily) from the one you pasted. It would be safer to use obabel, rather than babel, to reduce the possibility of misinterpretion of a mistyped command line. So the above would be better as: obabel chembl_02.fs -O result.sdf -s query.mol -at 0.75 The error you received is because openbabel thinks the parameter on the -s option is a SMILES string. The possibility of it being a file was introduced in 2.3.0. Try obabel -L ops s to check that the version you are using is sufficiently new and that the plugin code which provides the functionality has got loaded. Chris > But i became he following error: > > ============================== > *** Open Babel Warning in ParseSimple > Illegal aromatic element b > ============================== > *** Open Babel Error in ObtainTarget > Could not make a molecule from babelsearch.mol > This needs to be valid SMILES when using fastsearch.You can use the more > versatile SMARTS in a normal substructure search. > 0 molecules converted > 1 errors 1 warnings 5 audit log messages > > What is my Problem? > > The query.mol looks like this: > > 1 > OpenBabel12161108573D > > 31 30 0 0 0 0 0 0 0 0999 V2000 > 0.3387 0.9262 0.4600 O 0 0 0 0 0 > 3.4786 -1.7069 -0.3119 O 0 0 0 0 0 > 1.8428 -1.4073 1.2523 O 0 0 0 0 0 > 0.4166 2.5213 -1.2091 O 0 0 0 0 0 > -2.2359 -0.7251 0.0270 N 0 0 0 0 0 > -0.7783 -1.1579 0.0914 C 0 0 0 0 0 > 0.1368 -0.0961 -0.5161 C 0 0 0 0 0 > -3.1119 -1.7972 0.6590 C 0 0 0 0 0 > -2.4103 0.5837 0.7840 C 0 0 0 0 0 > -2.6433 -0.5289 -1.4260 C 0 0 0 0 0 > 1.4879 -0.6438 -0.9795 C 0 0 0 0 0 > 2.3478 -1.3163 0.1002 C 0 0 0 0 0 > 0.4627 2.1935 -0.0312 C 0 0 0 0 0 > 0.6678 3.1549 1.1001 C 0 0 0 0 0 > -0.7073 -2.1051 -0.4563 H 0 0 0 0 0 > -0.5669 -1.3392 1.1503 H 0 0 0 0 0 > -0.3089 0.3239 -1.4193 H 0 0 0 0 0 > -2.9705 -2.7295 0.1044 H 0 0 0 0 0 > -2.8083 -1.9210 1.7028 H 0 0 0 0 0 > -4.1563 -1.4762 0.6031 H 0 0 0 0 0 > -2.0398 1.4170 0.1863 H 0 0 0 0 0 > -3.4837 0.7378 0.9384 H 0 0 0 0 0 > -1.9129 0.5071 1.7551 H 0 0 0 0 0 > -2.2450 0.4089 -1.8190 H 0 0 0 0 0 > -2.3000 -1.3879 -2.0100 H 0 0 0 0 0 > -3.7365 -0.4723 -1.4630 H 0 0 0 0 0 > 1.3299 -1.3744 -1.7823 H 0 0 0 0 0 > 2.0900 0.1756 -1.3923 H 0 0 0 0 0 > -0.1953 3.1280 1.7699 H 0 0 0 0 0 > 0.7681 4.1684 0.7012 H 0 0 0 0 0 > 1.5832 2.9010 1.6404 H 0 0 0 0 0 > 1 7 1 0 0 0 > 1 13 1 0 0 0 > 2 12 1 0 0 0 > 3 12 2 0 0 0 > 4 13 2 0 0 0 > 5 6 1 0 0 0 > 5 8 1 0 0 0 > 5 9 1 0 0 0 > 5 10 1 0 0 0 > 6 7 1 0 0 0 > 6 15 1 0 0 0 > 6 16 1 0 0 0 > 7 11 1 0 0 0 > 7 17 1 0 0 0 > 8 18 1 0 0 0 > 8 19 1 0 0 0 > 8 20 1 0 0 0 > 9 21 1 0 0 0 > 9 22 1 0 0 0 > 9 23 1 0 0 0 > 10 24 1 0 0 0 > 10 25 1 0 0 0 > 10 26 1 0 0 0 > 11 12 1 0 0 0 > 11 27 1 0 0 0 > 11 28 1 0 0 0 > 13 14 1 0 0 0 > 14 29 1 0 0 0 > 14 30 1 0 0 0 > 14 31 1 0 0 0 > M CHG 2 2 -1 5 1 > M END > > > > Regards, > Jochen > > > ------------------------------------------------------------------------------ > Learn Windows Azure Live! Tuesday, Dec 13, 2011 > Microsoft is holding a special Learn Windows Azure training event for > developers. It will provide a great way to learn Windows Azure and what it > provides. You can attend the event by watching it streamed LIVE online. > Learn more at http://p.sf.net/sfu/ms-windowsazure > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
