GESAMT-based protein distance computation library

Distance is computed as 1 - Q-Score. If computation fails (structures are too dissimilar), distance is set to 1.

Requirements

Cmake, C++17 compiler (for <filesystem>), pthreads, zlib, Java JDK.

Directory with mmCIF files

All the mmCIF files must have a name in the following format:

<pdbid>_updated.cif

where <pdbid> is a PDBID in lowercase letters.

List of structures to preload

When the first distance computation is issued, structures specified in this file will be preloaded. Each line of the file has the format: <PDBID>:<CHAINID>. For example:

12AS:A
13PK:B
153L:A
15C8:H  

Building the library:

$ mkdir build && cd build
$ cmake ..
$ make

Output binaries are located in build/distance directory.

Testing the library

LD_LIBRARY_PATH must be set correctly for Java to find the shared library libProteinDistance.so.

$ LD_LIBRARY_PATH=. java -jar java_distance.jar