I would like to use to export the surface data and to use it outside
jmol. For that I exported the surface with "write mesh isosurface
<path.xjvxl>", but now I have a few more questions:
1. Is it true that "write mesh" should put enough information for my
needs in the xjvxl file, and that "write isosurface" is not necessary
for my goals?
2. x = getProperty("isosurfaceInfo"); print x["polygons"] seems to
show that the polygons have 5 vertices each (i.e., they are
pentagons). However in the mesh xjvxl file there is triangle data. Is
each pentagon split into 3 triangles to create the triangle data?
3. What is the difference between jvxlTriangleData and jvxlTriangleEdgeData?
4. Is the vertex data from jvxlVertexData represented in Angstroms?
The same also holds for the "min" and "max" attributes? Is the vertex
data represented by any chance relative to the "min" position?
5. Why is the number of triangles exactly twice the number of vertices
in the xjvxl file?
6. I would like to use the Jmol Reader API to read the .xjvxl files in
Java, but I need some help to figure out how to do that. I tried the
following:
SurfaceGenerator sg = new SurfaceGenerator();
sg.setParameter("readFile", br);
JvxlData jvxlData = sg.getJvxlData();
System.out.println(jvxlData);
but I'm able to find neither the triangle data nor the vertex data. In
particular, JvxlXmlReader.jvxlDecodeTriangleData (latest svn version)
executes on line 704 the statement "int[][] triangles = null;" and
later on line 773 it executes "return triangles", without changing the
mentioned local variable in between. However it does pass further the
triangle data using "addTriangleCheck". Any hints about how to get
hold of the triangle and vertex data through the Reader API, perhaps
transformed into Angstroms, would be highly appreciated.
7. If I could save the x["vertices"], x["polygons"] and
x["vertexValues"] to something like a .csv file, or a Java serialized
file, or some other simple format, that would work for me. How can I
do that?
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