New class: High scoring patches of contiguous residues on the surface a protein.
Added new methods for patch building.
New class: Commandline access to building patches.
1st check in
Update map conservation scores / res annot to structure
Fix null exception for parentDir
account for possibility that jmol may load more atoms than PdbStructure
save file location of pdb structure
Updates to PdbStructureTools.java found in com.neogenesis.pfaat.pdb.
