Re: [Jmol-developers] Symmetry.java questions

[Bob H. <ha...@st...>]

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