[Open Babel] Java bindings undefined symbol: _ZTVN9OpenBabel30OBMinimizingRMSDConformerScoreE
Dear OPenBabel Users
I am using OpenBabel in my (Java) application and want to pack this
application and use it in different operating systems like Windows, Linux,
and MacOs.
I have compiled JAVA bindings for OpenBabel using the command
*sudo cmake
/home/vin/openbabel2.4-DCMAKE_INSTALL_PREFIX=~/Tools-DCMAKE_BUILD_TYPE=DEBUG-DJAVA_BINDINGS=ON-DEIGEN3_INCLUDE_DIR=/home/vin/Eigen3-DSWIG_EXECUTABLE=/usr/bin/swig-DRUN_SWIG=ONsudo
make*
The compilation went well and took the libopenbabel_java.so and
libopenbabel.so from the build directory and packed it along with my
application in the directory (app/rescources) and specified the path to the
app/resources directory in the source code
(system.load("/home/vin/app/resources/libopenbabel_java.so")) of my
application for performing an openbabel task.
When I run my application jar file (app.jar) and perform an openbabel task
(generate conformers) I am getting the below error
Exception in thread "AWT-EventQueue-0" java.lang.UnsatisfiedLinkError:
/home/praktikant/OPAS_ALPHA_1.0/resources/libopenbabel_java.so:
*/home/vin/app_ALPHA_1.0/resources/libopenbabel_java.so:
undefined symbol: _ZTVN9OpenBabel30OBMinimizingRMSDConformerScoreE*
By the way, my application runs perfectly fine where OpenBabel is already
installed (like in my development environment). Any hints in the right
direction is highly appreciated. Thank you.
--
Regards
Vinothkumar Mohanakrishnan
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[Open Babel] Open a large .rsmi (443 MB)
Hello, I am trying to open a large .rsmi file (443 MB) with Python (open babel library), but every time I try the script freezes. I have tried also to split the file through Open Babel software for Windows, but I could not do that. I need to go through the reactions contained in the file to select the reactions related to a certain group of compounds. Thanks in advance for your help. Best regards, Mirko Hu -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Open a large .rsmi (443 MB)
Unfortunately, neither the current release nor development code can handle rsmi from Python. If you wish to do this, you should check out the branch referred to in the following pull request: https://github.com/openbabel/openbabel/pull/1836 Regards, - Noel On 16 July 2018 at 15:28, Mirko Hu wrote: > Hello, > > > I am trying to open a large .rsmi file (443 MB) with Python (open babel > library), but every time I try the script freezes. I have tried also to > split the file through Open Babel software for Windows, but I could not do > that. > > > I need to go through the reactions contained in the file to select the > reactions related to a certain group of compounds. > > > Thanks in advance for your help. > > > Best regards, > > Mirko Hu > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Confab conformer search for hydrogen
Hi everyone, The confab conformer search has been a life saver for me. There is only a small but Important issue. Any help would be greatly appreciated. When I do conformer search on ethanol it finds no conformer for it simply because it ignores the CCOH as a rotatable bond. However, this becomes important when dealing with alcohols, amines, carboxylic acids, or other molecules having dihedrals involving atoms that only have hydrogens and one substituent. This means the exhaustive conformer search does not actually examine all the conformers for these cases. Is there any option that I am missing? Here my command: obabel ethanol.sdf -O ethanol.xyz —confab —nconf 10 —original —writeconformers -Tayeb Tayeb Kakeshpour Graduate Research Assistant Jackson Research Group Michigan State University Department of Chemistry 578 S. Shaw Lane, room 535 East Lansing, MI 48824 kakes...@msu.edu -Tayeb Tayeb Kakeshpour Graduate Research Assistant Jackson Research Group Michigan State University Department of Chemistry 578 S. Shaw Lane, room 535 East Lansing, MI 48824 kakes...@msu.edu -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
