Re: [Open Babel] Issues Maintaining Bond Order Through Conversion
On 6/27/2018 3:39 PM, Geoffrey Hutchison wrote: OB includes an algorithm to perceive bond orders, but it's hardly foolproof. So if you want to ensure bond orders are preserved, don't use those formats. With PDB, you could convert to mmCIF using either pdb-extract online or download maxit from RCSB. That will calculate the bonds from 3D coordinates and put them in _chem_comp_bond table. Of course doing that that would be a bit back-asswards if you're starting from a format that has correct bond information in the first place. Dima -- 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] Installation of Python Binding ubuntu
Hello All, I have been struggling to install the python bindings under ubuntu for several weeks now. I am compiling from source as per the wiki instructions. Could anyone please advise on the meaning of " Install FILES given no DESTINATION" Here is my command and the resulting error output. bilal@ubuntu ~/openbabel/build :( $ cmake ../ -DPYTHON_BINDINGS=ON -DBUILD_GUI=ON -DRUN_SWIG=ON -DPYTHON_EXECUTABLE=/home/bilal/envs/minconda3/envs/babel/bin/python3.5 -DPYTHON_LIBRARY=/home/bilal/env/miniconda3/envs/babel/lib/libpython.so -DPYTHON_INCLUDE_DIRS=/home/bilal/env/miniconda3/envs/babel/include -DPYTHON_INSTDIR=/home/bilal/env/miniconda3/envs/bable/lib/python3.5/site-packages/obabel/ CMake Deprecation Warning at CMakeLists.txt:11 (cmake_policy): The OLD behavior for policy CMP0005 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Using included inchi library. -- Checking available shared pointer... -- Use std::shared_ptr in memory -- Could NOT find RapidJSON (missing: RAPIDJSON_INCLUDE_DIRS) (Required is at least version "1.1.0") -- JSON formats will be supported. Using RapidJSON 1.1.0 at /home/bilal/openbabel/external/rapidjson-1.1.0/include -- Cairo found. PNG output will be supported. -- Attempting to build the GUI --wxWidgets found => GUI will be built -- Found SWIG: /usr/bin/swig3.0 (found version "3.0.12") -- Found SWIG: /usr/bin/swig3.0 (found suitable version "3.0.12", minimum required is "2.0") -- Python bindings will be compiled CMake Error at scripts/CMakeLists.txt:122 (install): install TARGETS given no LIBRARY DESTINATION for module target "bindings_python". CMake Error at scripts/CMakeLists.txt:125 (install): install FILES given no DESTINATION! CMake Error at scripts/CMakeLists.txt:128 (install): install FILES given no DESTINATION! -- Configuring incomplete, errors occurred! See also "/home/bilal/openbabel/build/CMakeFiles/CMakeOutput.log". See also "/home/bilal/openbabel/build/CMakeFiles/CMakeError.log". -- Sent from: http://forums.openbabel.org/General-discussion-f3090658.html -- 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
