README
author Christos Mantoulidis <cmad@stanford.edu>
Tue, 04 Aug 2009 13:23:16 -0700
branchdev
changeset 156 f75fb57d2831
parent 115 a3410b6ba79c
child 235 07b3070cea74
permissions -rw-r--r--
Changed implementation of WeightedRips to store simplex values (max distance between simplices' vertices) as an invisible layer on top of each simplex object, so that the data() field of WeightedRips has been freed for use by the users again.

% 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>