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

  libcwd -      for debugging 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:int=3 would set

  optimization to -O3. All of this can be set using a text user interface by

  running ccmake instead of cmake.

Author

  Dmitriy Morozov <morozov@cs.duke.edu>