Miscellaneous improvements to 'makestructure', 'dssp', 'change', and 'bonds'; small DSSP fix.

[drroe]

• Add [refvalsout <file>] and [founddihout <file>] keywords to makestructure ref; makes for easier debugging.
• Add namesg <S name> keyword to dssp to identify potential disulfide bridges. DSSP will skip these when looking for next/previous residue by bonding.
• In dssp, residues that have none of the DSSP atoms selected (C, CA, N, O, H) are now skipped. This avoids nonsense assignments. FtuFabI assignment test output updated (properly ignoring the TCS and NDP residues).
• Add change removebonds to allow removal of bonds from an atom, or removal of bonds between specific atoms. Can also write which bonds are removed to a file.

change removebonds <mask1> [<mask2>] [out <file>]

• Add nointrares keyword to bonds command to skip intra-residue bonds; useful when all you want to know is connectivity.
• Charmm histidine residue naming now recognized when converting to single-character residue names.