make-zigzag-subsamples.py doesn't output the union, rips-consistency-zigzag.cpp fixed show_progress
% 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>