Thank you Tim, works fine now. Best regards, Dmitry.
On 09/24/2010 04:58 PM, Tim Vandermeersch wrote: > 2010/9/24 Dmitry Osolodkin <[email protected]>: >> 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: [email protected] >> Phone: +7-495-9393557 >> Fax: +7-495-9390290 >> -- Dmitry Osolodkin Researcher Group of Computational Molecular Design Department of Chemistry Moscow State University Moscow 119991 Russia e-mail: [email protected] Phone: +7-495-9393557 Fax: 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