Added a convenience getScop(String) method.
Added getTMScoreAlternate().
Made updateSuperposition() set block rotation matrices and shift
vectors.
Added a demo for using FastaAFPChainConverter for display.
Added an extra CP test, and fixed a test to work with change in
updateSuperposition().
Merge branch 'master' of https://github.com/dmyersturnbull/biojava.git
Merge branch 'master' of https://github.com/biojava/biojava
adding cleaner logging and new option to disable domain based alignments
Added another CP factory method.
Merge branch 'master' of https://github.com/biojava/biojava
Added support for SCOP com files. ScopDatabase now has a getComments()
method.
Created tests for ScopInstallation and BerkeleyScopInstallation.
Return an empty list when sunId is not listed, rather than null.
Added Log4J to POM.
Added support for Astral sets.
Comments.
Moved general XML utilities to a new class ReadUtils.
Created classes for RCSB ligands (should have committed this a while
ago).
Fixed demo: can't use same structure.
Set ScopFactory to 1.75B to prevent test failure.