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.

Prerequisites for using MMTF in C++

You need the headers of the MessagePack C++ library (version 2.1.1 or newer). If you do not have them on your machine already, you can download the "include" directory from the MessagePack GitHub repository.

How to use MMTF

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.exe

Here, <MSGPACK_INCLUDE_PATH> and <MMTF_INCLUDE_PATH> are the paths to the "include" directories of MessagePack and this library respectively.

Examples and tests

The examples folder contains tests and examples for you to run. To test the library on your machine, you can run:

./test_compile_and_traverse.sh <MSGPACK_INCLUDE_PATH>

If it concludes stating that the test has passed, it is all good.

Example codes:

• demo.cpp: Loads an MMTF file and checks internal consistency using mmtf::StructureData::hasConsistentData.
• traverse.cpp: Loads an MMTF file and dumps it in human-readable forms. The json-like output is used in test_compile_and_traverse.sh.

Furthermore, we have:

• data folder: MMTF test set
• out_json_ref.tar.gz: Reference output generated using the mmtf-c library. This is used in test_compile_and_traverse.sh.
• compile_and_run.sh: Convenience script to compile and run an executable with a single argument. E.g. with demo.cpp:

./compile_and_run.sh <MSGPACK_INCLUDE_PATH> demo.cpp "./data/173D.mmtf"

• compile_and_run_all.sh: Similar to compile_and_run.sh, but processing all .mmtf files in the data folder. E.g. with demo.cpp:

./compile_and_run_all.sh <MSGPACK_INCLUDE_PATH> demo.cpp

Code documentation

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.