Cannot initialize database is fixed by setting the environment variable BABEL_DATADIR to point to the Open Babel data files, typically installed in C:\Users\noel\AppData\Roaming\OpenBabel-2.3.2\data. Setting this correctly should sort out the problem.
- Noel On 16 January 2013 22:31, Gaudreault, Francis <francis.gaudrea...@usherbrooke.ca> wrote: > I am unable to convert adequately (using the OpenBabel::OBConversion method > in my own-program) the following standard PDB ligand to the MOL2 format on my > Win32 machine. > > REMARK THIS IS THE LIGAND FROM 1stp.pdb > HETATM 903 C11 BTN A 300 9.051 4.576 -14.459 1.00 21.57 C > HETATM 904 O11 BTN A 300 8.147 5.373 -14.172 1.00 21.65 O > HETATM 905 O12 BTN A 300 8.697 3.498 -15.132 1.00 22.67 O > HETATM 906 C10 BTN A 300 10.321 4.413 -13.702 1.00 20.77 C > HETATM 907 C9 BTN A 300 10.215 3.247 -12.658 1.00 20.09 C > HETATM 908 C8 BTN A 300 11.487 2.972 -11.964 1.00 19.24 C > HETATM 909 C7 BTN A 300 11.627 1.558 -11.402 1.00 18.33 C > HETATM 910 C2 BTN A 300 10.923 1.086 -10.195 1.00 17.74 C > HETATM 911 S1 BTN A 300 10.884 2.103 -8.662 1.00 16.59 S > HETATM 912 C6 BTN A 300 10.299 0.620 -7.760 1.00 17.06 C > HETATM 913 C5 BTN A 300 11.142 -0.543 -8.274 1.00 17.47 C > HETATM 914 N1 BTN A 300 12.443 -0.631 -7.613 1.00 17.73 N > HETATM 915 C3 BTN A 300 13.467 -0.443 -8.453 1.00 17.95 C > HETATM 916 O3 BTN A 300 14.692 -0.446 -8.205 1.00 17.93 O > HETATM 917 N2 BTN A 300 12.974 -0.237 -9.695 1.00 17.92 N > HETATM 918 C4 BTN A 300 11.513 -0.265 -9.727 1.00 17.65 C > CONECT 903 904 905 906 > CONECT 904 903 > CONECT 905 903 > CONECT 906 903 907 > CONECT 907 906 908 > CONECT 908 907 909 > CONECT 909 908 910 > CONECT 910 909 911 918 > CONECT 911 910 912 > CONECT 912 911 913 > CONECT 913 912 914 918 > CONECT 914 913 915 > CONECT 915 914 916 917 > CONECT 916 915 > CONECT 917 915 918 > CONECT 918 910 913 917 > END > > Here are the errors in the output that comes out of it: > =========================== > *** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init > Error 1. > Cannot initialize database > =========================== > *** Open Babel Warning in OpenBabel::OBTypeTable::Translate > Error 2. > Cannot perform atom type translation: table cannot find requested types. > =========================== > OpenBabel :: converted 1 molecule > > The error 2 comes out multiple times. > > The PDB file is indeed converted. > I am also able to do the same conversion using the same sources on my Linux > or MacOSX machines. > > However there are some odd SYBYL atom types in the MOL2 format in the Win32 > version: > C3, Cac, Nam, C2... where all of those do appear as C.3, ?? Cac ??, N.am, C.2 > on my Linux/MacOS machines. > > I updated the latest sources using svn (revision 5061) and recompiled the > whole Visual Studio solution using VS10. > The solution was generated using the default_build.bat file in the > windows-vc2008 folder. > So, I do have the latest openbabel-2.dll version. > > When compiliing my application, I did link to openbabel-2.lib (the latest). > I copied all required files (more than I needed I suppose) in the same folder > as my application: > openbabel-2.dll > formats_*.obf files > plugin_*.obf files > > and the following libraries: > zlib1.dll (version 1.2.3.0) > xdr-0.dll > libxml2.dll > libinchi.dll (version 1.0.4.1) > libpng14-14.dll > libfontconfig-1.dll > libexpat-1.dll > iconv.dll (version 1.9.0.0) > libcairo-2.dll > freetype6.dll > > Thank you all for your answers. > > Francis Gaudreault > ------------------------------------------------------------------------------ > Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery > and much more. Keep your Java skills current with LearnJavaNow - > 200+ hours of step-by-step video tutorials by Java experts. > SALE $49.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122612 > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
