% Dionysus README
% Dmitriy Morozov

## Dependencies

  * [CGAL]-3.3 ---  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/

## Configuration
  The path to CGAL's Makefile is expected to be set in `$CGAL_MAKEFILE`, the rest
  is just the usual CMake configuration

## 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>