First, be sure you are looking at bob200603, not the preliminary stuff I
put in the trunk. I presume that's true with everything I've done, but I
thought I'd make sure that is your reference point. The Symmetry.java
in the trunk was just a placeholder. In any case, I've removed it from
the trunk because there's no point in anyone looking at that now.
They are definitely used. The symmetry operations utilize
rotation/translation 4x4 matrices that these points are multiplied by to
give the final point3f. If you haven't downloaded bob200603 recently,
you should synchronize now.
Miguel wrote:
Bob,
I have some questions about src/org/jmol/adapter/smarter/Symmetry.java ...
You are allocating some objects of type Point4f. As far as I can tell, the
4th parameter is set to 1 and is never used ... so, it seems to me that
Point3f would be sufficient. Point4f objects are not used anywhere else in
Jmol.
Q: Is there any reason why you used Point4f objects in Symmetry.java?
Regarding the method isUnityOperation ...
It is not called from anyplace. There is a comment that says:
// unused -- it's best to leave x,y,z in there.
I have doubts as to whether or not this routine would even work as
intended, given the general problems of doing equality comparisons with
floating point numbers. That is, in the general case I believe that there
will be situations in which
please just leave that. The unity operations described in CIF files are
1 1 1 -- very clean. It works, trust me. I just didn't need it in the
end. But I want to leave it in there.
temp.equals(temp2)
will return 'false' when the actual (symbolic) answer is 'true'.
Q: Can we remove this routine?
no
The method setMatrixFromXYZ is parsing a string.
Q: Is there a URL reference that we can introduce that documents the
syntax for this string?
The URL is at the top of Symmetry.java
And you can look in any CIF file.
Basically you can have any readable linear expression in x, y, and z:,
including unary operators and simple fractions, each separated by a
comma from the next:
x + 0.5, 1/3 + y, -z - 1/2
Bob
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