adam

re-wrote association code to use the Sequence pdb chain association method

updated for allAtomsResidueDistance and timing with writeSubclassesAndQuit

added support for associating a pdb chain with sequence

// Code for associating a pdbFIle with the specifeid sequence in a given alignment.

made change to residue propensity adjumentment: all score are multipled by 1 over highest score to extend range from 0 to 1.

made small change for cases where pdb structure include Hydrogens

updated GetResidueProperties

added forceAssociateSequenceWithPDBFile, which associates pdb to specified sequence in an alignment without prompting the user via dialog boxes about potential mismatches.