Re: [Open Babel] Shortest path between 2 atoms
Hi, >>> I would to know the number of bonds between two atoms within a molecule >>> (i.e. the shortest path). >> You're looking for a breadth-first search (BFS) >> You just need to start the BFS at atom1, and stop it when it comes to >> atom2. The value of depth will give you the answer. Ok, I have now the number of bonds between 2 atoms. Is there an easy way to know the type of each bond for the path between the 2 atoms? (I'm especially interested in counting the non-ring bong). Thanks, Regards, Pascal -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. Connect with experts. Get tools for creating Super Apps. See the latest technologies. Sessions, hands-on labs, demos & much more. Register early & save! http://p.sf.net/sfu/rim-blackberry-1 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] OBChemTsfm in Python
> I am trying to use OBChemTsfm in Python 3.1 with OpenBabel 2.3 . I can access > the basic parts of openbabel (OBMol) but not OBChemTsfm. My code is as > follows: The scripting bindings must "wrap" each class from C++. So we have a very large subset in the Python bindings, but not OBChemTsfm. We can certainly add that. Cheers, -Geoff -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. Connect with experts. Get tools for creating Super Apps. See the latest technologies. Sessions, hands-on labs, demos & much more. Register early & save! http://p.sf.net/sfu/rim-blackberry-1 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obabel PNG depiction speedup and make test failures
If you're going to run "make test", you may have to set up the environment a bit as it uses the files from the build directory (rather than from "make install"). Try setting BABEL_DATADIR to ob-source-dir/data. You may also need to set BABEL_FORMATDIR (to build-dir/lib) or LD_LIBRARY_PATH (to build-dir/lib). On BSD, I've found that the forcefield tests fail when run through "make test" but run fine from the command-line, so there's some Cmake magic messing things up there somehow. (FYI, our test dashboard is at http://my.cdash.org/index.php?project=Open+Babel) - Noel On 2 August 2011 15:22, Vedrin Jeliazkov wrote: > Hi Noel, > > We've upgraded successfully both our development and production system > to use the latest svn trunk (rev. 4534) version of obabel. PNG > depiction of SMILES works fine on both systems and is much faster than > with the older obabel versions that we've tried -- that's great! > > We've also noticed that some of the tests that are executed by 'make > test' are failing. Some of these failures are specific to the > development server (Linux 2.6.26-2-amd64, gcc 4.3.2: > inchiSamples.sdf_Test, logp_psa_Test), others to the production server > (FreeBSD 8.2-STABLE, amd64, gcc 4.2.2: charge-gasteiger_Test), while > the remaining failures are exhibited on both servers (builder_Test, > charge-mmff94_Test, ffgaff_Test, ffghemical_Test, ffuff_Test). The > cmake options we've used in both cases are: > > -DCMAKE_INSTALL_PREFIX=/usr/local/openbabel -DPYTHON_BINDINGS=OFF > -DBUILD_GUI=OFF > > Kind regards, > Vedrin > > PS: I'm attaching a list of these make test failures in case that you > would like to have a closer look at them: > > 1) Development server > > ambit:/home/vedrin/obabel/svn/openbabel/build# make test > Running tests... > Start processing tests > Test project /home/vedrin/obabel/svn/openbabel/build > 1/ 57 Testing automorphism_Test Passed > 2/ 57 Testing builder_Test ***Failed Error regular > expression found in output. Regex=[FAIL] > 3/ 57 Testing canonconsistent_Test Passed > 4/ 57 Testing canonstable_Test Passed > 5/ 57 Testing cistrans_Test Passed > 6/ 57 Testing graphsym_Test Passed > 7/ 57 Testing implicitH_Test Passed > 8/ 57 Testing lssr_Test Passed > 9/ 57 Testing isomorphism_Test Passed > 10/ 57 Testing rotor_Test Passed > 11/ 57 Testing shuffle_Test Passed > 12/ 57 Testing smiles_Test Passed > 13/ 57 Testing spectrophore_Test Passed > 14/ 57 Testing squareplanar_Test Passed > 15/ 57 Testing stereo_Test Passed > 16/ 57 Testing stereoperception_Test Passed > 17/ 57 Testing tetrahedral_Test Passed > 18/ 57 Testing tetranonplanar_Test Passed > 19/ 57 Testing tetraplanar_Test Passed > 20/ 57 Testing uniqueid_Test Passed > 21/ 57 Testing inchiSamples.sdf_Test ***Failed > 22/ 57 Testing inchiSamplesTechMan.sdf_Test Passed > 23/ 57 Testing inchiSteffen_PubChem.smi_Test Passed > 24/ 57 Testing aromatest_Test Passed > 25/ 57 Testing atom_Test Passed > 26/ 57 Testing bond_Test Passed > 27/ 57 Testing cansmi_Test Passed > 28/ 57 Testing charge-mmff94_Test ***Failed > 29/ 57 Testing charge-gasteiger_Test Passed > 30/ 57 Testing conversion_Test Passed > 31/ 57 Testing datatest_Test Passed > 32/ 57 Testing ffgaff_Test ***Failed > 33/ 57 Testing ffghemical_Test ***Failed > 34/ 57 Testing ffmmff94_Test Passed > 35/ 57 Testing ffuff_Test ***Failed > 36/ 57 Testing formalcharge_Test Passed > 37/ 57 Testing format_Test Passed > 38/ 57 Testing formula_Test Passed > 39/ 57 Testing internalcoord_Test Passed > 40/ 57 Testing invalidsmarts_Test Passed > 41/ 57 Testing invalidsmiles_Test Passed > 42/ 57 Testing iterators_Test Passed > 43/ 57 Testing logp_psa_Test ***Failed Error regular > expression found in output. Regex=[not ok] > 44/ 57 Testing math_Test Passed > 45/ 57 Testing mol_Test Passed > 46/ 57 Testing phmodel_Test Passed > 47/ 57 Testing residue_Test Passed > 48/ 57 Testing ringtest_Test Passed > 49/ 57 Testing smartstest_Test Passed > 50/ 57 Testing smartsparse_Test Passed > 51/ 57 Testing smilesmatch_Test Passed > 52/ 57 Testing unitcell_Test Passed > 53/ 57 Testing p
Re: [Open Babel] OBChemTsfm in Python
On Aug 2, 2011, at 2:36 PM, Tom Lamar wrote: > So for now if I want to access OBChemTsfm I should just code in C++? It depends upon how fast you need a revised binding. We can try out adding phmodel.h to the openbabel-python.i SWIG file and re-run. I won't have time to try that today, but it's usually pretty easy to add new classes for the "trunk" development code. As long as you're happy to compile from the SVN repository, there's not much problem. Best regards, -Geoff -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. Connect with experts. Get tools for creating Super Apps. See the latest technologies. Sessions, hands-on labs, demos & much more. Register early & save! http://p.sf.net/sfu/rim-blackberry-1 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Shortest path between 2 atoms
On 2 August 2011 14:08, Pascal Muller wrote: > Hi, > I would to know the number of bonds between two atoms within a molecule (i.e. the shortest path). > >>> You're looking for a breadth-first search (BFS) >>> You just need to start the BFS at atom1, and stop it when it comes to >>> atom2. The value of depth will give you the answer. > > Ok, I have now the number of bonds between 2 atoms. > Is there an easy way to know the type of each bond for the path > between the 2 atoms? (I'm especially interested in counting the > non-ring bong). You'll need to implement a BFS yourself, and keep track of the atoms in the path. See http://baoilleach.blogspot.com/2008/02/calculate-circular-fingerprints-with.html for some ideas (it's a different link that my previous email). > Thanks, > Regards, > Pascal > > -- > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. Connect with experts. Get tools for creating Super Apps. See the latest technologies. Sessions, hands-on labs, demos & much more. Register early & save! http://p.sf.net/sfu/rim-blackberry-1 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
