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PDB-REDO / alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://alphafill.eu
BSD 2-Clause "Simplified" License
89 stars 16 forks source link

Installing issue on CentOS 7 system #24

Closed syx2017-bot closed 1 year ago

syx2017-bot commented 1 year ago

Hi,

I really like this AlphafFill work, and would like to apply it to a large protein dataset. However, I am not so familiar with how to install it using camke. I just followed the instructions and try to install it on a HPC with CentOS system. However, I encountered a problem when running the cmake --build . command under the build folder:

[ 6%] Built target webpack Scanning dependencies of target alphafill [ 13%] Building CXX object CMakeFiles/alphafill.dir/src/alphafill.cpp.o [ 20%] Building CXX object CMakeFiles/alphafill.dir/src/main.cpp.o [ 26%] Building CXX object CMakeFiles/alphafill.dir/src/utilities.cpp.o [ 33%] Building CXX object CMakeFiles/alphafill.dir/src/data-service.cpp.o /home/alphafill/src/data-service.cpp:42:10: fatal error: mrsrc.hpp: No such file or directory 42 | #include "mrsrc.hpp" | ^~~ compilation terminated. gmake[2]: [CMakeFiles/alphafill.dir/build.make:186: CMakeFiles/alphafill.dir/src/data-service.cpp.o] Error 1 gmake[1]: [CMakeFiles/Makefile2:124: CMakeFiles/alphafill.dir/all] Error 2 gmake: *** [Makefile:114: all] Error 2

I believe the error was pointing to the mrc package, but I have already installed it, and it seems the camke didn't find it, since I installed it in a non-default path:

-- Could NOT find Mrc (missing: MRC_EXECUTABLE) CMake Warning at CMakeLists.txt:86 (find_package): Found package configuration file: /home/package/make/usr/local/share/mrc/cmake/mrc-config.cmake but it set Mrc_FOUND to FALSE so package "Mrc" is considered to be NOT FOUND. Using resources compiled with MRC_EXECUTABLE-NOTFOUND -- Configuring done -- Generating done -- Build files have been written to: /home/alphafill/build

Any ideas on how to fix it would be appreciated! Thanks!

mhekkel commented 1 year ago

You can tell cmake to search for the required files by adding -DCMAKE_PREFIX_PATH=/home/package/make/usr/local/ to the cmake configure step for alphafill.

diao-347 commented 1 year ago

I have come across a similar issue when running the cmake --build . command under the build folder:

[ 66%] Built target webpack [ 66%] Building CXX object CMakeFiles/alphafill.dir/src/data-service.cpp.o /mnt/home/runjie/software/alphafill/src/data-service.cpp:42:10: fatal error: mrsrc.hpp: No such file or directory 42 | #include "mrsrc.hpp" | ^~~ compilation terminated. make[2]: [CMakeFiles/alphafill.dir/build.make:167: CMakeFiles/alphafill.dir/src/data-service.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:105: CMakeFiles/alphafill.dir/all] Error 2 make: *** [Makefile:95: all] Error 2

I am still a beginner in software compilation. It appears that there are numerous header files in the alphafill/src/ directory, but the mrsrc.hpp file is missing. I would greatly appreciate it if you could kindly guide me on where I can obtain the mrsrc.hpp file. Thank you sincerely for your assistance.

mhekkel commented 1 year ago

The mrsrc.hpp file is generated by cmake if mrc can be found. It is obviously an error in the code to try to include that file if mrc is not installed, will have to fix that.

For now, what you should do is install mrc and then reconfigure alphafill and build it.

diao-347 commented 1 year ago

I am pleased to inform you that the software has been installed successfully at this time. Thank you for your kind assistance.