[Open Babel] Problem when a fasta file was converted into PDB file
Dear Madam or Sir, When I used Openbabel to convert a fasta file into PDB format, I met a problem. My fasta file is like >protein A It is a protein, but the retrieved PDB was DNA structure. How could I restrain the input parameters to output a protein structure? Thank you very much!! your sincerely, yookeee-- 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] Anyone using the parallel implementation of MMFF94 forcefield (via OpenMP)
Hi list, In the ChangeLog I found Tim wrote about the GCC compilation options to be used in order to enable MMFF94 parallelization. His entry reads as follows. 2008-04-28 Tim Vandermeersch * src/forcefields/forcefieldmmff94.cpp: OpenMP version of MMFF94. Does not affect normal compilation. Only used with GCC options "-lgomp -fopenmp". This is from the time before OpenBabel moved to CMake. I look at the CMakeLists.txt and there is no OpenMP flags there (-fopenmp, -lgomp). Which is the preferred way to do it. Should I create a custom CMakeLists.txt or should I opt for the custom static binary approach as suggested in the project Wiki. http://openbabel.org/wiki/CMake Thanks & regards, -- Omar V.M. ovale...@ichec.ie -- 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] OpenBabel compilation/use with OpenMP
Hi list, In a previous version of OpenBabel (OpenBabel-2.2) it was possible to instruct the build to make use of OpenMP to parallelize the forcefields routines in OpenBabel. The way it was done was using compiler flags read by the configure command inside babel source directory: $tar zxvf openbabel-2.2.tar.gz $cd openbabel-2.2 $./configure CXXFLAGS="-g -fopenmp -lgomp" Now that OpenBabel uses CMake to build itself, I found no longer reference about OpenMP, whether in the current documentation, library optional dependencies, CMakeLists.txt. The OpenMP preprocessor directives are however still there in the forcefield source fields. I am not familiar with CMake but I have been looking around and I think adding an extra flags to the build on condition that OpenMP support is found shouldn't be a problem. Or is there a better approach I am willing to hear what are your suggestions. Also I couldn't find any mention of OpenMP support in the latest OpenBabel documentation and I was wondering why this is the case. Regards, -- Omar V.M. ovale...@ichec.ie -- 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] Anyone using the parallel implementation of MMFF94 forcefield (via OpenMP)
> This is from the time before OpenBabel moved to CMake. I look at the > CMakeLists.txt and there is no OpenMP flags there (-fopenmp, -lgomp). > Which is the preferred way to do it. Either edit you CMakeCache.txt (e.g., "ccmake .") after setting up the cmake build directory, or declare these as CXX_FLAGS, e.g., CXXFLAGS="-fopenmp -lgomp" cmake /path/to/source/dir 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
Re: [Open Babel] Problem when a fasta file was converted into PDB file
> It is a protein, but the retrieved PDB was DNA structure. You don't say what version of Open Babel you're using. Looking at the current code for fastaformat.cpp, it should accept: >protein >peptide >Protein >Peptide -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
