The macromolecular transmission format (MMTF) is a binary encoding of biological structures.
This repository holds the C++-03 compatible API, encoding and decoding libraries. The MMTF specification can be found here.
You need the headers of the MessagePack C++ library (version 2.1.5 or newer). If you do not have them on your machine already, you can download the "include" directory from the MessagePack GitHub repository.
You only need to include the mmtf.hpp header in your code to use MMTF. For instance a minimal example to load an MMTF file looks as follows:
#include <mmtf.hpp>
int main(int argc, char** argv) {
mmtf::StructureData data;
mmtf::decodeFromFile(data, "test.mmtf");
return 0;
}The C++ MMTF library is header only so you do not need to compile it. If you
have a source file named demo.cpp (e.g. including the code above), you can
generate an executable demo.exe as follows:
g++ -I<MSGPACK_INCLUDE_PATH> -I<MMTF_INCLUDE_PATH> demo.cpp -o demo.exeHere, <MSGPACK_INCLUDE_PATH> and <MMTF_INCLUDE_PATH> are the paths to the
"include" directories of MessagePack and this library respectively.
For your more complicated projects, a CMakeLists.txt is included for you.
You can also perform a system wide installation with cmake and ninja (or make).
To do so:
mkdir build
cd build
cmake -G Ninja ..
sudo ninja installcmake automatically sets the installation directory to /usr/local/include, if you want to install it to another *include/ directory
run cmake with the command:
cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/home/me/local ..Be aware that /include is added to the end of DCMAKE_INSTALL_PREFIX and that is where your files are installed (i.e. the above would install at /home/me/local/include/).
To build the tests + examples we recommend using the following lines:
# download Catch2 testing framework, msgpack-c, and the mmtf-spec test-dataset
git submodule update --init --recursive
mkdir build
cd build
cmake -G Ninja -DBUILD_TESTS=ON -Dmmtf_build_local=ON -Dmmtf_build_examples=ON ..
ninja
chmod +x ./tests/mmtf_tests
./tests/mmtf_testsExample codes:
- mmtf_demo.cpp: Loads an MMTF file and checks internal consistency using mmtf::StructureData::hasConsistentData.
./examples/mmtf_demo ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf- traverse.cpp: Loads an MMTF file and dumps it in human-readable forms.
./examples/traverse ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf
./examples/traverse ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf json
./examples/traverse ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf print- print_as_pdb.cpp: Loads an MMTF file and prints it in pdb format.
./examples/print_as_pdb ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtfUsing the following simple code:
#include <mmtf.hpp>
int main(int argc, char** argv)
{
for (int i=1; i<argc; ++i) {
mmtf::StructureData sd;
mmtf::decodeFromFile(sd, argv[i]);
}
}compiled via:
g++ -Ofast -Immtf/include -Imsgpack/include decode_all_mmtf.cpp
We are able to load 153,987 mmtf files (current size of the pdb) or 14.3GB from an SSD in 211.3 seconds (averaged over 4 runs with minimal differences between the runs).
You can generate a doxygen based documentation of the
library by calling doxygen in the docs folder. You will need doxygen 1.8.11 or
later for that. Open docs/html/index.html to see the generated documentation.
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