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.
Use Log4J logging instead.
Added Log4J configurations.
Oops. Shouldn't have pushed. Fix "org.biojava.structure" -->
"org.biojava.bio.structure".
Made AstralSet.getId() and AstralSet.getUrl() public.
1. Made RCSBLigandsFactory handle describeHet queries. 2. Wrote helper
methods for using ligandInfo and describeHet queries with multiple PDB
Ids. 3. Made a backwards-incompatible change: renamed RCSBLigands.get()
to RCSBLigands.getFromPdbId(). This shouldn't be a problem because the
class is so new and has not yet been included in any stable release; if
it is this commit can be reverted. 4. Fixed example usage in header
comment.
Ran cleanup and fixed comments.
Added a getStructureForDomain that takes a ScopDatabase.
Added methods that take SCOP Ids rather than SCOPDomains.
1. Added support for chain Ids of more than 1 character. This deprecates
the method ResidueRange.getChain() in favor of the new
ResidueRange.getChainId(). 2. Changed interface of parseMultiple(String,
AtomPositionMap) so that if the range is the whole chain, it returns a
ResidueRange with null start and end rather than a null ResidueRange. 3.
Fixed issue where A_1-100_ was considered a valid range (underscores
were being allowed). 4. Added a new method parseMultiple(List<String>).
5. Added a new method looksLikeRange(String).
Made AtomPositionMap work with chain Ids of more than 1 character.
Don't allow a period (.) as a range specifier. Really we should reserve
periods as chain specifiers, and allow either _ or : as range
specifiers.
Added a match(String) method, and added some argument checks.
Made AtomPositionMap constructor take a GroupMatcher, which is a new
callback inner interface.