relax SVN archive

Removed a debugging print out.

Fixes for the looping over non-protein/RNA/DNA residues.

Removed an empty line.

Modified the 'nucleus' variable to its new designations as part of the move to the new design.

Modified the 'nucleus' variable to its new designation.

Aliased the current data pipe and removed the run arguments.

Created the __residue_loop() method and have it called from atom_loop().

atom_loop() now calls __molecule_loop().

Created the private __molecule_loop() method.

This is for looping over the individual molecules of the scientific data structures.

A few fixes for the atom_loop() structural API method (for Scientific).