> hi Miguel,
> attached are the two files that I modified, in a zip archive. let me
> know if this is acceptable mode of transfer (i.e., do you want the
> entire JMol-HEAD?).
> what I did:
> added residue ids for a small number of modified nucleotides.
> added residue ids for mono, di, and tri-nucleotides.
> added atomids for nucleic acid backbone atoms.
> added defined set for 'base'.
> updated defined set for backbone to include nucleic acids.
> updated defined sets for various nucleotides (a, t, c, g, u, etc.).
> compiled and tested changes in app.
Your code modifications are checked in!
Very well done ... you did a great job.
Unfortunately, because of problems at sourceforge, you probably need to
wait until tomorrow for your changes to be replicated from the 'real' cvs
to the 'backup/anonymous' cvs.
But tomorrow, when you do your cvs update, your changes will be be included.
CVS is going to do something interesting. It knows that your files have
been modified locally. It is then going to see that someone (me) modified
the files on the server. It will then try to merge the differences
But, there are no differences ... so there should be no conflicts ... so I
think everything will be fine. (If cvs complains, just delete those two
files from your sandbox and run cvs update again.)
When reviewing the code I saw a couple of things that we may want to fix
at some point. Some of them are yours and some of them are mine.
These are just optimizations that really do not *need* to be done, but
we'll keep them in mind. (We know that we will have to be working on this
'atom expression' code again).
These strings all get included in the executable and downloaded.
Therefore, it is a good idea for us to keep them short and small, makes
the .jar smaller.
* we are using _resid in all these comparisions. We may want to change
that _g (for group) That will save 8 bytes per use (4 characters * 2
bytes per unicode caracter).
* rather than using " or " we can just use ","
* the comparisons for a,t,c,g are now somewhat more complicated. We may
want to reorder the groupIDs (note new terminology :-) so that these
comparisons can be reduced to: