% Dionysus README

% Dmitriy Morozov

## Dependencies

  * [CGAL]-3.4 ---  for alpha-shapes and kinetic data structures

  * [DSR-PDB] ---   for reading in PDB files (if use_dsrpdb is turned on in cmake)

  * [CMake] ---     for controlling the build process

  * [boost] ---     great set of C++ libraries

  * [Doxygen] ---   for building documentation

  * [rlog] ---      for logging only (is not needed by default)

  * [SYNAPS] ---    for solving polynomials (for kinetic kernel), which in turn requires GMP

[CGAL]:         http://www.cgal.org

[DSR-PDB]:      http://www.salilab.org/~drussel/pdb/

[CMake]:        http://www.cmake.org

[boost]:        http://www.boost.org

[Doxygen]:      http://www.stack.nl/~dimitri/doxygen/

[rlog]:         http://www.arg0.net/rlog

[SYNAPS]:       http://www-sop.inria.fr/galaad/synaps/

## Building

  To build examples, create a directory build (to keep everything in one place),

  go to that directory and run cmake and make:

    mkdir build

    cd build

    cmake ..   (or "ccmake .." if you want a curses interface)

    make

  In the cmake line you can provide `-Ddebug:bool=on` to turn on debugging,

  `-Dcounters:bool=on` to turn on counters, `-Doptimize:bool=on` to turn on

  optimization, `-Duse_dsrpdb:bool=on` to turn on reading PDB files.  Depending on

  the combination of debugging and optimization, a particular `CMAKE_CXX_FLAGS*`

  is chosen.  All of this can be set using a text user interface by running

  `ccmake` instead of `cmake`.

  When compiling on a 64 bit platform (with Boost 1.34) add

  `-DBOOST_NO_INTRINSIC_INT64_T` to `CMAKE_CXX_FLAGS`.

## Author

  Dmitriy Morozov <dmitriy@mrzv.org>