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−% Dionysus README
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−% Dmitriy Morozov
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−
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−## Dependencies
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−
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−  * [CGAL]-3.3 ---  for alpha-shapes and kinetic data structures
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−  * [DSR-PDB] ---   for reading in PDB files (if use_dsrpdb is turned on in cmake)
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−  * [CMake] ---     for controlling the build process
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−  * [boost] ---     great set of C++ libraries
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−  * [Doxygen] ---   for building documentation
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−  * [rlog] ---      for logging only (is not needed by default)
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−  * [SYNAPS] ---    for solving polynomials (for kinetic kernel), which in turn requires GMP
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−
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−[CGAL]:         http://www.cgal.org
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−[DSR-PDB]:      http://www.salilab.org/~drussel/pdb/
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−[CMake]:        http://www.cmake.org
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−[boost]:        http://www.boost.org
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−[Doxygen]:      http://www.stack.nl/~dimitri/doxygen/
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−[rlog]:         http://www.arg0.net/rlog
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−[SYNAPS]:       http://www-sop.inria.fr/galaad/synaps/
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−
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−## Configuration
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−  The path to CGAL's Makefile is expected to be set in `$CGAL_MAKEFILE`, the rest
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−  is just the usual CMake configuration
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−
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−## Building
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−  To build examples, create a directory build (to keep everything in one place),
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−  go to that directory and run cmake and make:
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−
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−    mkdir build
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−    cd build
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−    cmake ..   (or "ccmake .." if you want a curses interface)
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−    make
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−  
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−  In the cmake line you can provide `-Ddebug:bool=on` to turn on debugging,
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−  `-Dcounters:bool=on` to turn on counters, `-Doptimize:bool=on` to turn on
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−  optimization, `-Duse_dsrpdb:bool=on` to turn on reading PDB files.  Depending on
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−  the combination of debugging and optimization, a particular `CMAKE_CXX_FLAGS*`
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−  is chosen.  All of this can be set using a text user interface by running
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−  `ccmake` instead of `cmake`.
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−
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−  When compiling on a 64 bit platform (with Boost 1.34) add
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−  `-DBOOST_NO_INTRINSIC_INT64_T` to `CMAKE_CXX_FLAGS`.
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−
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−## Author
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−  Dmitriy Morozov <dmitriy@mrzv.org>