2010/9/24 Dmitry Osolodkin <divan...@rambler.ru>: > On 09/24/2010 04:08 PM, Tim Vandermeersch wrote: >>>> babel --canonical somefile.mol2 somefile_can.mol2 >>> >>> It doesn't work. Atom order remains the same as in input files. Using >>> the latest development version or stable 2.2.3 -- no difference. >> >> Make sure to run make install or use ./bin/babel, otherwise you are >> just using the older installed version. It works on your example files >> here. > > I have checked everything, but atom order is still different even for > these files (see attachment). Development version:
Sorry, I forgot to commit the changes to the build system. It's in svn now. You can verify that the --canonical option is present by running "babel -H", it should be in the list now. Tim >> which babel > /usr/local/openbabel/bin/babel > >> echo $LD_LIBRARY_PATH > /usr/lib/mpi/gcc/openmpi/lib:/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32::/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32:/usr/local/openbabel/lib > > >> babel --canonical 1UV5_extract.mol2 1UV5_extract_can.mol2 ---errorlevel 5 > ============================== > *** Open Babel Audit Log in ReadChemObjectImpl > OpenBabel::Read molecule Sybyl Mol2 format > ============================== > *** Open Babel Audit Log in Clear > Ran OpenBabel::Clear Molecule > ============================== > *** Open Babel Audit Log in Kekulize > Ran OpenBabel::Kekulize > ============================== > *** Open Babel Audit Log in FindSSSR > Ran OpenBabel::FindSSSR > ============================== > *** Open Babel Audit Log in FindRingAtomsAndBonds > Ran OpenBabel::FindRingAtomsAndBonds > ============================== > *** Open Babel Audit Log in IsClosure > Ran OpenBabel::PerceiveClosureBonds > ============================== > *** Open Babel Audit Log in FindLSSR > Ran OpenBabel::FindLSSR > ============================== > *** Open Babel Audit Log in ReadChemObjectImpl > OpenBabel::Read molecule Sybyl Mol2 format > ============================== > *** Open Babel Audit Log in Clear > Ran OpenBabel::Clear Molecule > ============================== > *** Open Babel Audit Log in WriteChemObjectImpl > OpenBabel::Write molecule Sybyl Mol2 format > ============================== > *** Open Babel Audit Log in AssignTypes > Ran OpenBabel::AssignTypes > ============================== > *** Open Babel Audit Log in AssignAromaticFlags > Ran OpenBabel::AssignAromaticFlags > ============================== > *** Open Babel Audit Log in AssignImplicitValence > Ran OpenBabel::AssignImplicitValence > ============================== > *** Open Babel Audit Log in AssignHyb > Ran OpenBabel::AssignHybridization > ============================== > *** Open Babel Audit Log in AssignHyb > Ran OpenBabel::AssignHybridization > 1 molecule converted > 15 audit log messages > > >> babel --canonical 1UV5_docked.mol2 1UV5_docked_can.mol2 ---errorlevel 5 > ============================== > *** Open Babel Audit Log in ReadChemObjectImpl > OpenBabel::Read molecule Sybyl Mol2 format > ============================== > *** Open Babel Audit Log in Clear > Ran OpenBabel::Clear Molecule > ============================== > *** Open Babel Audit Log in Kekulize > Ran OpenBabel::Kekulize > ============================== > *** Open Babel Audit Log in FindSSSR > Ran OpenBabel::FindSSSR > ============================== > *** Open Babel Audit Log in FindRingAtomsAndBonds > Ran OpenBabel::FindRingAtomsAndBonds > ============================== > *** Open Babel Audit Log in IsClosure > Ran OpenBabel::PerceiveClosureBonds > ============================== > *** Open Babel Audit Log in FindLSSR > Ran OpenBabel::FindLSSR > ============================== > *** Open Babel Audit Log in ReadChemObjectImpl > OpenBabel::Read molecule Sybyl Mol2 format > ============================== > *** Open Babel Audit Log in Clear > Ran OpenBabel::Clear Molecule > ============================== > *** Open Babel Audit Log in WriteChemObjectImpl > OpenBabel::Write molecule Sybyl Mol2 format > ============================== > *** Open Babel Audit Log in AssignTypes > Ran OpenBabel::AssignTypes > ============================== > *** Open Babel Audit Log in AssignAromaticFlags > Ran OpenBabel::AssignAromaticFlags > ============================== > *** Open Babel Audit Log in AssignImplicitValence > Ran OpenBabel::AssignImplicitValence > ============================== > *** Open Babel Audit Log in AssignHyb > Ran OpenBabel::AssignHybridization > ============================== > *** Open Babel Audit Log in AssignHyb > Ran OpenBabel::AssignHybridization > ============================== > *** Open Babel Audit Log in PerceiveChains > Ran OpenBabel::PerceiveChains > ============================== > *** Open Babel Information in ParseLine > Could not parse line in phmodel table from phmodel.txt > ============================== > *** Open Babel Audit Log in AssignPartialCharges > Ran OpenBabel::AssignPartialCharges > 1 molecule converted > 1 info messages 17 audit log messages > > > > -- > Dmitry Osolodkin > Researcher > Group of Computational Molecular Design > Department of Chemistry > Moscow State University > Moscow 119991 Russia > e-mail: dmitr...@qsar.chem.msu.ru > Phone: +7-495-9393557 > Fax: +7-495-9390290 > ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - 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