beginning to break out caching functionality from pdbfilereader

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8830 7c6358e6-4a41-0410-a743-a5b2a554c398
demo how to show a structure in jmol

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8831 7c6358e6-4a41-0410-a743-a5b2a554c398
AtomCache can now fetch Biological unit files and cache them locally.

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8832 7c6358e6-4a41-0410-a743-a5b2a554c398
setting path now system wide

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8833 7c6358e6-4a41-0410-a743-a5b2a554c398
Fixed a few warnings (deprecation, improper use of generics).
Improved reporting when guessing scop domains.

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8834 7c6358e6-4a41-0410-a743-a5b2a554c398
fixing some minor issues and docu improvements for biological units.

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8835 7c6358e6-4a41-0410-a743-a5b2a554c398
new utility method that allows to access all atoms in all models

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8836 7c6358e6-4a41-0410-a743-a5b2a554c398
Bug fix for dealing with X amino acids during translation. Submitted by Brad Chapman. Patch available at https://gist.github.com/864088. Many thanks.

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8837 7c6358e6-4a41-0410-a743-a5b2a554c398
Bugzilla 3180 applied. Frame parameter was ignored by code

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8838 7c6358e6-4a41-0410-a743-a5b2a554c398
Equality now added to backing stores & compounds. SequenceMixin now has a method for assessing sequence equality

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8839 7c6358e6-4a41-0410-a743-a5b2a554c398
small speedup

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8840 7c6358e6-4a41-0410-a743-a5b2a554c398
this is now a Comparable class

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8841 7c6358e6-4a41-0410-a743-a5b2a554c398
if a line causes a crash, print that line now.

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8842 7c6358e6-4a41-0410-a743-a5b2a554c398
catching linking of SITE records to groups

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8845 7c6358e6-4a41-0410-a743-a5b2a554c398
adding check to make sure that map of sites is not null

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8846 7c6358e6-4a41-0410-a743-a5b2a554c398
ignoring if a group can't be found...

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8847 7c6358e6-4a41-0410-a743-a5b2a554c398
more transparent warning message

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8848 7c6358e6-4a41-0410-a743-a5b2a554c398
small speedup in Element class

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8849 7c6358e6-4a41-0410-a743-a5b2a554c398
disabling Hill order for now, since it seems wrong.

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8850 7c6358e6-4a41-0410-a743-a5b2a554c398
making sure we can lookup in allElements in O(1);

git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8851 7c6358e6-4a41-0410-a743-a5b2a554c398