ADCGAL <cutoff> <prune> <file prefix>
cutoff = maximum limit on perturbation (in the same units as the coordinates, i.e. 
         Angstrom for proteins).  This is the parameter epsilon in my definition 
	 of AD(epsilon).  To try it out, a typical default value is 1.0 Angstrom,
         though values from 0.01 to 2.0 Angstrom are useful for capturing different 
	 ranges of perturbation in proteins.
prune = maximum edge length allowed in a simplex.  This gets rid of long edges on the
        convex hull and within interior pockets and cavities.  A typical default
	value in proteins is 10 (Angstrom), though values from 6.0 to 15.0 Angstrom
	may be useful.  "SHORT" edges, triangles and tetrahedra are those with all 
	edges below the prune in length.
file prefix = 1xyz if your 3D coordinates are stored as rows of three coordinates 
              in a file "1xyz.out".  This parameter can include a full path if the 
	      .out file lies elsewhere.  If this parameter is missing, input comes
	      from the standard input, and te prefix "points" is made up for purposes 
	      of writing output (hence you can use AD as an input pipe, though
	      minor changes are required to use it as an output pipe).  

Output: If the file prefix for input was "1xyz", output is written to files as follows:
	      1xyz.del: short Delaunay edges, written as rows of SORTED point index 
			pairs starting at 0; example row "0 4" 
	      1xyz.AD: short AD edges with threshold>0, written as rows of sorted edge 
		       index pairs and a threshold. Example row: 5 6 0.7773 
	      The files below are generated only by the version of ADCGAL that calculates
	      simplices, and not by the edge version (the symbol ADSIMP_CGAL has to be
	      defined during compilation.  
	      1xyz.del3: Delaunay triangles with short edges, rows of 3 sorted indices
	      1xyz.AD3: AD triangles, rows of 3 sorted indices and a threshold
	      1xyz.del4: Delaunay tetrahedra, 4 indices
	      1xyz.AD4: AD tetrahedra, 4 indices and a threshold

Visualizing AD edges, triangles and tetrahedra:

Please refer to the README.ADMATLAB.txt, where there is some spiffy code (plotAD.m, plotAD4.m, 
plotADspheres.m, and the kinemage converters) to visualize these AD tetrahedra, triangles or 
edges on top of the set of points.  It is not too hard to write your own visualizer also, 
in MATLAB, C++ or anything else, remembering to index the points from 1xyz.out and treating 
the indices in *.del*,*.AD* files as a C-style index starting at 0 (hence adding 1 if you are 
in MATLAB).