[Open Babel] Residue support in Pybel
Hi, I've added few lines to pybel to make life easier while working with files containing proteins, f.e. PDB structures. With this capability you could do something like that: for residue in protein.residues: print residue.name for atom in residue: print atom.name If you think it's a good idea would it be possible to add it to trunk? PS. How is github/git integration going? Github repo seams to be forgotten since initial sync somewhere in October 2012... Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.plhttps://mail.google.com/mail/u/0/?view=cmfs=1tf=1to=mac...@wojcikowski.pl pybel.diff Description: Binary data -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] install on Centos 64 bits
Hi Peter, in case you really didn't want to use the python version originally provided by your distribution, make sure that the version you are using was configured at build time with --enable-shared (I think this is the likely reason for the error you reported). You might also want to consider the python26 package that is available from the EPEL repositories. Best regards, Riccardo On 19 February 2013 16:16, Peter Maas peter.m...@specs.net wrote: Hi Noel, ** ** Then I did the right thing. I also checked whether the files python files exists. Hell, I even reinstalled python which is kind of tricky because a lot of tools are depending on it. Anyway, I’m getting the same results. It feels like a defeat but if you would be so kind to take a look at the file I appreciate it very much. Please find it attached. ** ** Thanks, ** ** Peter ** ** *From:* Noel O'Boyle [mailto:baoille...@gmail.com] *Sent:* Tuesday, February 19, 2013 3:21 PM *To:* Peter Maas *Cc:* openbabel-discuss@lists.sourceforge.net *Subject:* Re: [Open Babel] install on Centos 64 bits ** ** By define at the command-line, I meant -DPYTHON_LIBRARY=wherever when running cmake. Don't worry about the eigen3 warning. If Eigen3 is found, it uses that in preference to Eigen2. Just a note, to force a Python rebuild, use touch src/scripts/openbabel-python.i. ** ** If you use VERBOSE=1 make you will see the command-line used to compile the Python bindings. If you still can't figure it out, please attach your CMakeCache.txt. ** ** - Noel ** ** ** ** On 19 February 2013 13:38, Peter Maas peter.m...@specs.net wrote: Hi Noel, Thanks for your suggestion. I checked the variables in CMakeCache.txt and all are pointing to the right (system) Python. If set the parameters as environmental setting and redid everything but the same error comes up. I’m not sure what you mean by “define them at the command-line” Do you mean at the cmake command line or the make command line. Something else I noticed. The documentation says you need to install eigen2. CMake give this warning (while I’ve eigen2 in the command line):* *** Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)** ** So should I install Eigen3 as well? Thanks, Peter *From:* Noel O'Boyle [mailto:baoille...@gmail.com] *Sent:* Monday, February 18, 2013 12:26 PM *To:* Peter Maas *Cc:* openbabel-discuss@lists.sourceforge.net *Subject:* Re: [Open Babel] install on Centos 64 bits I've seen this before. You should compile against the system Python. Your locally-compiled version was not compiled in a way consistent with linking against it (I don't know what options you should have used, but I recognise the symptoms). To compile against the system Python, check your CMakeCache.txt for various Python related variables and define them at the command-line (something like PYTHON_INCLUDE, PYTHON_LIBRARY, PYTHON_EXECUTABLE). - Noel On 18 February 2013 10:52, Peter Maas peter.m...@specs.net wrote: Dear All, I’m trying to install openbabel with python bindings on a 64 bits CentOS release 5.9 (kernel 2.6.18-348.1.1.el5). I performed the following steps: (I also downloaded and unzipped the eigen2 package as shown in the cmake line) tar zxf openbabel-2.3.2.tar.gz mkdir build cd build cmake ../openbabel-2.3.2 -DEIGEN2_INCLUDE_DIR=/home/peter/lib/eigen-eigen-b23437e61a07 -DPYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=/home/peter/tools/openbabel -DCMAKE_BUILD_TYPE=DEBUG make Now I’m getting an error which I can’t seem to fix: Linking CXX shared module ../lib/_openbabel.so /usr/bin/ld: /usr/local/lib/python2.6/config/libpython2.6.a(abstract.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/python2.6/config/libpython2.6.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [lib/_openbabel.so] Error 1 make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 make: *** [all] Error 2 Any suggestion would be appreciated. Thanks, Peter Maas [image: Specs] http://www.specs.net/ -- Kluyverweg 6, 2629 HT Delft, The Netherlands *p* +31 15 2518139 *f* +31 15 2518181 peter.m...@specs.net This message may contain privileged/confidential information and may be subject to legal privilege. Access to this e-mail by anyone other than the intended is unauthorised. If you have received this message in
[Open Babel] Installation error due to zlib
I am trying to do a NON-root installation on RHEL Server release 5.4. The first step (cmake) works (fine i.e. -- The C compiler identification is GNU 4.1.2 -- The CXX compiler identification is GNU 4.1.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Using included inchi library. -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR) (found version 2.6.26) CMake Warning at CMakeLists.txt:152 (message): libxml2 not found - disabling CML support! -- Found ZLIB: /usr/lib64/libz.so (found version 1.2.3) -- Could NOT find wxWidgets (missing: wxWidgets_FOUND) -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - not found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Found Eigen3: /home/XXX/bin/eigen3 (Required is at least version 2.91.0) -- Found PkgConfig: /usr/bin/pkg-config (found version 0.21) -- checking for module 'cairo' -- found cairo, version 1.2.4 -- Could NOT find Cairo (missing: CAIRO_LIBRARIES CAIRO_INCLUDE_DIRS) -- Could NOT find Cairo. PNG output will NOT be supported. -- Looking for getopt -- Looking for getopt - found -- Attempting to build the GUI --wxWidgets not found = GUI will not be built -- Found PythonInterp: /usr/bin/python (found version 2.4.3) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: EIGEN2_INCLUDE_DIR -- Build files have been written to: /home/XXX/bin/openbabel/obbuild However the second step i.e. make throws error at [ 21%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.o make[2]: *** No rule to make target `/usr/lib64/libz.so', needed by `lib/libopenbabel.so.4.0.2'. Stop. make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2 make: *** [all] Error 2 I checked for libz.so and a soft link is present lrwxrwxrwx 1 root root 19 Sep 27 11:57 /usr/lib64/libz.so - ../../lib64/libz.so I did install a local copy of libz and specified during cmake -DZLIB_INCLUDE_DIR=/home/XXX/bin/zlib-1.2.7/ and -DZLIB_LIBRARY=/home/XXX/bin/zlib-1.2.7/ But it gave warning as Targets may link only to libraries. CMake is dropping the item. and then again during make it throw-ed an error. Thanks. -- View this message in context: http://forums.openbabel.org/Installation-error-due-to-zlib-tp4655989.html Sent from the General discussion mailing list archive at Nabble.com. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
