Dependencies
  CGAL-3.3 -    for alpha-shapes and kinetic data structures
  DSR-PDB -     for reading in PDB files
  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

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.  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.

Author
  Dmitriy Morozov <morozov@cs.duke.edu>