[Open Babel] query about marking or identifying specific atoms
Hello, Here I explain a task I am trying to do using openbabel in python. But, I am facing some difficulties. I want to break a molecule in small molecules by breaking a bond from predefined groups and want to mark those two atoms (atoms which were at the two ends of broken bond). *And that marking should be preserved after breaking or joining molecules And I can save the molecule file with marking data (sdf or other format).* for example A molecule containing amide(R1-C(=O)-N-R2) group. If I break the C-N bond in amide group, I wish to mark these two atoms C and N. After braking the molecule in two parts, In both parts these atoms should preserve the mark. And I can write the molecule file including this data. And If I join these two parts again, still those markings on the atoms should be preserved. *What I tried:* I tried to enter data (mark) on OBAtom object by OBPairData. But, I can't save the file with OBPairData on atoms. If we have data on OBMol Object, then It saves in sdf file, but not from OBAtom object. So, If I write a molecule file, I lose the information. Is there any solution?? Even if something different then this approach (OBPairData), I would like to try. *One more option:* Does the idea of marking the positions with some unusual atoms [Replacing with unusual atoms] sounds terribly wrong? At least i could save it then in any format even in SMILES? I would appreciative your suggestions. Thanks.. Regards, -Hitesh Patel -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer generation using openbabel - take two
On 31 May 2012 03:56, Geoff Hutchison wrote: > > On May 29, 2012, at 11:23 AM, JP wrote: > > > This value of 1A in the steric filter is not available from the command > line, correct? > > No, there isn't (yet) a way to set that. The current SVN trunk now has an > improved filter. It considers hydrogens, and will also filter based on VdW > radii for each element. > > I'm considering adding a "slop," since a near-clash might be less > important after an energy minimization. Consider also that some conformer > might suddenly place a hydrogen bond… So I think I might want something > like: > >// check distance >if (distanceSquared < m_cutoff // defaults to 1.0A -- filter bad > clashes >|| distanceSquared < vdwCutoff - 0.1A // OK if atoms are *just* > touching > > What do you think? > > I think the steric filter default (1A) is an internal parameter and should not be exposed in the command line. Anyway -- this value is now less important since you have implemented an improved steric filter. When is the next obabel release aimed for? Is energy minimization a recommended step after GA conformer generation? If I understand correctly there is no energy minimization for the GA RMSD score. I am not sure I understand the benefit of adding the "slop", If there is no energy minimization (see question above) atoms will simply be allowed to be slightly closer. If there is energy minimization 0.1A will not make such a big difference, and the minimizer should be able to push the atom out of the way. I think detecting and handling intra molecule H bonds will require something a little bit more sophisticated (as it is not just a question of allowable distances, but also of angles). Also is it not the case that (vdwCutoff - 0.1A) is always greater than m_cutoff ? I guess my question is does distanceSquared < vdwCutoff - 0.1A always imply distanceSquared < m_cutoff. I have been through just a few conformer ensembles, my initial impression is that --score energy produces better geometries. I will try to prove this to you in a more quantitative manner rather than "gut feeling". Thanks for your help in this Geoff. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Perl bindings in current SVN
Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] query about marking or identifying specific atoms
Just save the atom data in a field of the SDF file, e.g. mol.data["marks"] = "atom 6, atom 9". - Noel On 31 May 2012 10:27, Hitesh Patel wrote: > Hello, > Here I explain a task I am trying to do using openbabel in python. But, I am > facing some difficulties. > I want to break a molecule in small molecules by breaking a bond > from predefined groups and want to mark those two atoms (atoms which were at > the two ends of broken bond). And that marking should be preserved after > breaking or joining molecules And I can save the molecule file with marking > data (sdf or other format). for example A molecule containing > amide(R1-C(=O)-N-R2) group. If I break the C-N bond in amide group, I wish > to mark these two atoms C and N. After braking the molecule in two parts, In > both parts these atoms should preserve the mark. And I can write the > molecule file including this data. And If I join these two parts again, > still those markings on the atoms should be preserved. > What I tried: > I tried to enter data (mark) on OBAtom object by OBPairData. But, I can't > save the file with OBPairData on atoms. If we have data on OBMol Object, > then It saves in sdf file, but not from OBAtom object. So, If I write a > molecule file, I lose the information. > Is there any solution?? Even if something different then this approach > (OBPairData), I would like to try. > One more option: > Does the idea of marking the positions with some unusual atoms [Replacing > with unusual atoms] sounds terribly wrong? At least i could save it then in > any format even in SMILES? > > I would appreciative your suggestions. > Thanks.. > > Regards, > -Hitesh Patel > > > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] query about marking or identifying specific atoms
Hello Noel, Thanks..But, If we join two molecules, then atom Index will be changed from second molecule. Regards, -Hitesh Patel On Thu, May 31, 2012 at 11:35 AM, Noel O'Boyle wrote: > Just save the atom data in a field of the SDF file, e.g. > mol.data["marks"] = "atom 6, atom 9". > > - Noel > > On 31 May 2012 10:27, Hitesh Patel wrote: > > Hello, > > Here I explain a task I am trying to do using openbabel in python. But, > I am > > facing some difficulties. > > I want to break a molecule in small molecules by breaking a bond > > from predefined groups and want to mark those two atoms (atoms which > were at > > the two ends of broken bond). And that marking should be preserved after > > breaking or joining molecules And I can save the molecule file with > marking > > data (sdf or other format). for example A molecule containing > > amide(R1-C(=O)-N-R2) group. If I break the C-N bond in amide group, I > wish > > to mark these two atoms C and N. After braking the molecule in two > parts, In > > both parts these atoms should preserve the mark. And I can write the > > molecule file including this data. And If I join these two parts again, > > still those markings on the atoms should be preserved. > > What I tried: > > I tried to enter data (mark) on OBAtom object by OBPairData. But, I can't > > save the file with OBPairData on atoms. If we have data on OBMol Object, > > then It saves in sdf file, but not from OBAtom object. So, If I write a > > molecule file, I lose the information. > > Is there any solution?? Even if something different then this approach > > (OBPairData), I would like to try. > > One more option: > > Does the idea of marking the positions with some unusual atoms [Replacing > > with unusual atoms] sounds terribly wrong? At least i could save it then > in > > any format even in SMILES? > > > > I would appreciative your suggestions. > > Thanks.. > > > > Regards, > > -Hitesh Patel > > > > > > > > > -- > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] query about marking or identifying specific atoms
Hi, Can't you can just read in the data on the marked atoms, join the molecules, correct the atom index, and write it out again? - Noel On 31 May 2012 10:48, Hitesh Patel wrote: > Hello Noel, > > Thanks..But, If we join two molecules, then atom Index will be changed from > second molecule. > > Regards, > -Hitesh Patel > > > On Thu, May 31, 2012 at 11:35 AM, Noel O'Boyle wrote: >> >> Just save the atom data in a field of the SDF file, e.g. >> mol.data["marks"] = "atom 6, atom 9". >> >> - Noel >> >> On 31 May 2012 10:27, Hitesh Patel wrote: >> > Hello, >> > Here I explain a task I am trying to do using openbabel in python. But, >> > I am >> > facing some difficulties. >> > I want to break a molecule in small molecules by breaking a bond >> > from predefined groups and want to mark those two atoms (atoms which >> > were at >> > the two ends of broken bond). And that marking should be preserved after >> > breaking or joining molecules And I can save the molecule file with >> > marking >> > data (sdf or other format). for example A molecule containing >> > amide(R1-C(=O)-N-R2) group. If I break the C-N bond in amide group, I >> > wish >> > to mark these two atoms C and N. After braking the molecule in two >> > parts, In >> > both parts these atoms should preserve the mark. And I can write the >> > molecule file including this data. And If I join these two parts again, >> > still those markings on the atoms should be preserved. >> > What I tried: >> > I tried to enter data (mark) on OBAtom object by OBPairData. But, I >> > can't >> > save the file with OBPairData on atoms. If we have data on OBMol Object, >> > then It saves in sdf file, but not from OBAtom object. So, If I write a >> > molecule file, I lose the information. >> > Is there any solution?? Even if something different then this approach >> > (OBPairData), I would like to try. >> > One more option: >> > Does the idea of marking the positions with some unusual atoms >> > [Replacing >> > with unusual atoms] sounds terribly wrong? At least i could save it then >> > in >> > any format even in SMILES? >> > >> > I would appreciative your suggestions. >> > Thanks.. >> > >> > Regards, >> > -Hitesh Patel >> > >> > >> > >> > >> > -- >> > Live Security Virtual Conference >> > Exclusive live event will cover all the ways today's security and >> > threat landscape has changed and how IT managers can respond. >> > Discussions >> > will include endpoint security, mobile security and the latest in >> > malware >> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> > ___ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try "VERBOSE=1 make" to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski wrote: > Hi, > > I have trouble building Perl bindings in openbabel SVN branch. My system is > running 64bit CentOS 6. > > To compile i use following command: > > cmake ../openbabel \ > -DRUN_SWIG=ON \ > -DPERL_BINDINGS=ON \ > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ > -DPERL_PREFIX=/usr/lib64/perl5/ \ > -DPYTHON_BINDINGS=ON \ > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ > > Which leads to error: > Linking CXX shared module ../lib/OpenBabel.so > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_resdat_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_chainsparser_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_atomtyper_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_aromtyper_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_isotab_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: > more undefined references to `pthread_getspecific' follow > collect2: ld returned 1 exit status > make[2]: *** [lib/OpenBabel.so] Błąd 1 > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 > > To clarify, given cmake command build 2.3.1 version without problem. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle > We changed to compiling the bindings directly rather than use Perl's > build system. It seems to work fine on some Linux OSes but not on > others. I haven't tracked down the problem but you could try > "VERBOSE=1 make" to see the command that we are using to compile, and > repeating it manually but adding -lpthread to see what happens. > > - Noel > > On 31 May 2012 09:56, Maciek Wójcikowski wrote: > > Hi, > > > > I have trouble building Perl bindings in openbabel SVN branch. My system > is > > running 64bit CentOS 6. > > > > To compile i use following command: > > > > cmake ../openbabel \ > > -DRUN_SWIG=ON \ > > -DPERL_BINDINGS=ON \ > > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ > > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ > > -DPERL_PREFIX=/usr/lib64/perl5/ \ > > -DPYTHON_BINDINGS=ON \ > > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ > > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ > > > > Which leads to error: > > Linking CXX shared module ../lib/OpenBabel.so > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_resdat_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_chainsparser_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_atomtyper_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_aromtyper_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_isotab_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: > > undefined reference to `pthread_getspecific' > > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: > > more undefined references to `pthread_getspecific' follow > > collect2: ld returned 1 exit status > > make[2]: *** [lib/OpenBabel.so] Błąd 1 > > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 > > > > To clarify, given cmake command build 2.3.1 version without problem. > > > > > > Pozdrawiam, | Best regards, > > Maciek Wójcikowski > > mac...@wojcikowski.pl > > > > > -- > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
For the record, on the Linux Mint 12 (64-bit) system I have tested, the compile works fine. But the command line contains -pthread (if this is removed, I get the same error message as reported). I don't quite understand where this comes from or why it's set on this OS but not on CentOS. On 31 May 2012 12:27, Maciek Wójcikowski wrote: > It worked. > > The failing line was: > /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags > -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared > -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o > -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz > -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib > > Adding -lpthread leads to succesful compilation. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2012/5/31 Noel O'Boyle >> >> We changed to compiling the bindings directly rather than use Perl's >> build system. It seems to work fine on some Linux OSes but not on >> others. I haven't tracked down the problem but you could try >> "VERBOSE=1 make" to see the command that we are using to compile, and >> repeating it manually but adding -lpthread to see what happens. >> >> - Noel >> >> On 31 May 2012 09:56, Maciek Wójcikowski wrote: >> > Hi, >> > >> > I have trouble building Perl bindings in openbabel SVN branch. My system >> > is >> > running 64bit CentOS 6. >> > >> > To compile i use following command: >> > >> > cmake ../openbabel \ >> > -DRUN_SWIG=ON \ >> > -DPERL_BINDINGS=ON \ >> > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ >> > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ >> > -DPERL_PREFIX=/usr/lib64/perl5/ \ >> > -DPYTHON_BINDINGS=ON \ >> > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ >> > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ >> > >> > Which leads to error: >> > Linking CXX shared module ../lib/OpenBabel.so >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_resdat_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_chainsparser_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_atomtyper_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_aromtyper_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_isotab_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: >> > undefined reference to `pthread_getspecific' >> > >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: >> > more undefined references to `pthread_getspecific' follow >> > collect2: ld returned 1 exit status >> > make[2]: *** [lib/OpenBabel.so] Błąd 1 >> > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 >> > >> > To clarify, given cmake command build 2.3.1 version without problem. >> > >> > >> > Pozdrawiam, | Best regards, >> > Maciek Wójcikowski >> > mac...@wojcikowski.pl >> > >> > >> > -- >> > Live Security Virtual Conference >> > Exclusive live event will cover all the ways today's security and >> > threat landscape has changed and how IT managers can respond. >> > Discussions >> > will include endpoint security, mobile security and the latest in >> > malware >> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> > ___ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about that in wiki, since that could potentially lead to some other undiscovered errors. Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski > It worked. > > The failing line was: > /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags > -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared > -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o > -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz > -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib > > Adding -lpthread leads to succesful compilation. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2012/5/31 Noel O'Boyle > >> We changed to compiling the bindings directly rather than use Perl's >> build system. It seems to work fine on some Linux OSes but not on >> others. I haven't tracked down the problem but you could try >> "VERBOSE=1 make" to see the command that we are using to compile, and >> repeating it manually but adding -lpthread to see what happens. >> >> - Noel >> >> On 31 May 2012 09:56, Maciek Wójcikowski wrote: >> > Hi, >> > >> > I have trouble building Perl bindings in openbabel SVN branch. My >> system is >> > running 64bit CentOS 6. >> > >> > To compile i use following command: >> > >> > cmake ../openbabel \ >> > -DRUN_SWIG=ON \ >> > -DPERL_BINDINGS=ON \ >> > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ >> > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ >> > -DPERL_PREFIX=/usr/lib64/perl5/ \ >> > -DPYTHON_BINDINGS=ON \ >> > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ >> > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ >> > >> > Which leads to error: >> > Linking CXX shared module ../lib/OpenBabel.so >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_resdat_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_chainsparser_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_atomtyper_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_aromtyper_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_isotab_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: >> > undefined reference to `pthread_getspecific' >> > >> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: >> > more undefined references to `pthread_getspecific' follow >> > collect2: ld returned 1 exit status >> > make[2]: *** [lib/OpenBabel.so] Błąd 1 >> > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 >> > >> > To clarify, given cmake command build 2.3.1 version without problem. >> > >> > >> > Pozdrawiam, | Best regards, >> > Maciek Wójcikowski >> > mac...@wojcikowski.pl >> > >> > >> -- >> > Live Security Virtual Conference >> > Exclusive live event will cover all the ways today's security and >> > threat landscape has changed and how IT managers can respond. >> Discussions >> > will include endpoint security, mobile security and the latest in >> malware >> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> > ___ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > >> > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
I was wrong. something went wrong and SWIG wasnt recognized at all. I'm looking for another problem. Do you have any Idea where first to look? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski > Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. > Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about > that in wiki, since that could potentially lead to some other undiscovered > errors. > > Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2012/5/31 Maciek Wójcikowski > >> It worked. >> >> The failing line was: >> /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags >> -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared >> -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so >> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o >> -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz >> -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib >> >> Adding -lpthread leads to succesful compilation. >> >> >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl >> >> >> 2012/5/31 Noel O'Boyle >> >>> We changed to compiling the bindings directly rather than use Perl's >>> build system. It seems to work fine on some Linux OSes but not on >>> others. I haven't tracked down the problem but you could try >>> "VERBOSE=1 make" to see the command that we are using to compile, and >>> repeating it manually but adding -lpthread to see what happens. >>> >>> - Noel >>> >>> On 31 May 2012 09:56, Maciek Wójcikowski wrote: >>> > Hi, >>> > >>> > I have trouble building Perl bindings in openbabel SVN branch. My >>> system is >>> > running 64bit CentOS 6. >>> > >>> > To compile i use following command: >>> > >>> > cmake ../openbabel \ >>> > -DRUN_SWIG=ON \ >>> > -DPERL_BINDINGS=ON \ >>> > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ >>> > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ >>> > -DPERL_PREFIX=/usr/lib64/perl5/ \ >>> > -DPYTHON_BINDINGS=ON \ >>> > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ >>> > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ >>> > >>> > Which leads to error: >>> > Linking CXX shared module ../lib/OpenBabel.so >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_resdat_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_chainsparser_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_atomtyper_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_aromtyper_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_isotab_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: >>> > undefined reference to `pthread_getspecific' >>> > >>> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: >>> > more undefined references to `pthread_getspecific' follow >>> > collect2: ld returned 1 exit status >>> > make[2]: *** [lib/OpenBabel.so] Błąd 1 >>> > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 >>> > >>> > To clarify, given cmake command build 2.3.1 version without problem. >>> > >>> > >>> > Pozdrawiam, | Best regards, >>> > Maciek Wójcikowski >>> > mac...@wojcikowski.pl >>> > >>> > >>> -- >>> > Live Security Virtual Conference >>> > Exclusive live event will cover all the ways today's security and >>> > threat landscape has changed and how IT managers can respond. >>> Discussions >>> > will include endpoint security, mobile security and the latest in >>> malware >>> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> > ___ >>> > OpenBabel-discuss mailing list >>> > OpenBabel-discuss@lists.sourceforge.net >>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> > >>> >> >> > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoin
Re: [Open Babel] Perl bindings in current SVN
Yes - I doublechecked. The latest SWIG still fails. What I can do is add in the output of perl -V:perllibs. This solves the problem at the moment. I still don't understand the underlying problem though. - Noel On 31 May 2012 13:43, Maciek Wójcikowski wrote: > I was wrong. something went wrong and SWIG wasnt recognized at all. I'm > looking for another problem. Do you have any Idea where first to look? > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2012/5/31 Maciek Wójcikowski >> >> Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. >> Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about >> that in wiki, since that could potentially lead to some other undiscovered >> errors. >> >> Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. >> >> >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl >> >> >> 2012/5/31 Maciek Wójcikowski >>> >>> It worked. >>> >>> The failing line was: >>> /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags >>> -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared >>> -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so >>> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o >>> -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz >>> -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib >>> >>> Adding -lpthread leads to succesful compilation. >>> >>> >>> Pozdrawiam, | Best regards, >>> Maciek Wójcikowski >>> mac...@wojcikowski.pl >>> >>> >>> 2012/5/31 Noel O'Boyle We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try "VERBOSE=1 make" to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski wrote: > Hi, > > I have trouble building Perl bindings in openbabel SVN branch. My > system is > running 64bit CentOS 6. > > To compile i use following command: > > cmake ../openbabel \ > -DRUN_SWIG=ON \ > -DPERL_BINDINGS=ON \ > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ > -DPERL_PREFIX=/usr/lib64/perl5/ \ > -DPYTHON_BINDINGS=ON \ > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ > > Which leads to error: > Linking CXX shared module ../lib/OpenBabel.so > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_resdat_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_chainsparser_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_atomtyper_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_aromtyper_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: > undefined reference to `pthread_getspecific' > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > `_wrap_isotab_get': > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: > more undefined references to `pthread_getspecific' follow > collect2: ld returned 1 exit status > make[2]: *** [lib/OpenBabel.so] Błąd 1 > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 > > To clarify, given cmake command build 2.3.1 version without problem. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > OpenBabel-discuss mailing list
Re: [Open Babel] Perl bindings in current SVN
Tried newest cmake, no success either. Actually it is not even looking for ptherad.h. I also found out in CMake file in tools/ directory that the check is made while you build OB staticly, Have you tried build_shared=off and on? Which variable exactly should contain -lpthreads? My perllibs='-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc'; Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle > Yes - I doublechecked. The latest SWIG still fails. > > What I can do is add in the output of perl -V:perllibs. This solves > the problem at the moment. I still don't understand the underlying > problem though. > > - Noel > > On 31 May 2012 13:43, Maciek Wójcikowski wrote: > > I was wrong. something went wrong and SWIG wasnt recognized at all. I'm > > looking for another problem. Do you have any Idea where first to look? > > > > > > Pozdrawiam, | Best regards, > > Maciek Wójcikowski > > mac...@wojcikowski.pl > > > > > > 2012/5/31 Maciek Wójcikowski > >> > >> Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. > >> Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note > about > >> that in wiki, since that could potentially lead to some other > undiscovered > >> errors. > >> > >> Curiously cmake calls for SWIG in version 2.0 and > loads successfully 1.x. > >> > >> > >> Pozdrawiam, | Best regards, > >> Maciek Wójcikowski > >> mac...@wojcikowski.pl > >> > >> > >> 2012/5/31 Maciek Wójcikowski > >>> > >>> It worked. > >>> > >>> The failing line was: > >>> /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags > >>> -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc > -shared > >>> -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so > >>> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o > >>> -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl > -lz > >>> -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib > >>> > >>> Adding -lpthread leads to succesful compilation. > >>> > >>> > >>> Pozdrawiam, | Best regards, > >>> Maciek Wójcikowski > >>> mac...@wojcikowski.pl > >>> > >>> > >>> 2012/5/31 Noel O'Boyle > > We changed to compiling the bindings directly rather than use Perl's > build system. It seems to work fine on some Linux OSes but not on > others. I haven't tracked down the problem but you could try > "VERBOSE=1 make" to see the command that we are using to compile, and > repeating it manually but adding -lpthread to see what happens. > > - Noel > > On 31 May 2012 09:56, Maciek Wójcikowski > wrote: > > Hi, > > > > I have trouble building Perl bindings in openbabel SVN branch. My > > system is > > running 64bit CentOS 6. > > > > To compile i use following command: > > > > cmake ../openbabel \ > > -DRUN_SWIG=ON \ > > -DPERL_BINDINGS=ON \ > > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ > > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ > > -DPERL_PREFIX=/usr/lib64/perl5/ \ > > -DPYTHON_BINDINGS=ON \ > > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ > > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ > > > > Which leads to error: > > Linking CXX shared module ../lib/OpenBabel.so > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_resdat_get': > > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_chainsparser_get': > > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_atomtyper_get': > > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_aromtyper_get': > > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_isotab_get': > > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: > > undefined reference to `pthread_getspecific' > > > > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: > > more undefined references to `pthread_getspecific' follow > > collect2: ld returned 1 exit status > > make[2]: *** [lib/OpenBabel.so] Błąd 1 > > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 > > > > To clarify, given cmake command build 2.3.
[Open Babel] openbabel-2.3.1.tar.gz : false trojan alert?
I decided to try compiling OB for Cygwin but found that openbabel-2.3.1.tar.gz makes the firewall unhappy: "This request is blocked by the SonicWALL Gateway Anti-Virus Service. Name: FraudLoad.ZKTH_2 (Trojan)" A couple of years ago TJ found an alert that was deemed likely false (http://forums.openbabel.org/possible-trojan-td2755841.html). Any ideas about this event? KerryFowler -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel-2.3.1.tar.gz : false trojan alert?
> I decided to try compiling OB for Cygwin but found that > openbabel-2.3.1.tar.gz makes the firewall unhappy: "This request is blocked > by the SonicWALL Gateway Anti-Virus Service. Name: FraudLoad.ZKTH_2 (Trojan)" I can vouch that the md5sum matches that which I uploaded. The tar contains source code (text), a DLL for C# bindings, and a Jar for Java bindings. There is no executable code, save a few easily-inspected shell and other scripts. A search on this "FraudLoad" turns up another false positive from an open source project: http://grokbase.com/t/gg/selenium-users/125emgktdh/trojan-in-the-seleium-server-download If you're concerned, you may always get the source: http://openbabel.org/wiki/Subversion http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/branches/openbabel-2-3-x/ Hope that helps, -Geoff-- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
