relax SVN archive

The index_flag argument to the ScientificPython structural object atom_loop() method is now used.

Fix for the structure.write_pdb user function for the internal structural object.

Helix and sheet PDB record creation is now skipped if no helices or sheets are defined.

Lots of fixes for the change to the structural API atom_loop() method.

This method when returning a single item now returns a single item rather than a tuple of length 1.

Modified the ScientificPython structural object atom_loop() method to match the internal object.

If only one element is returned from the atom_loop(), then this is returned as a single item rather
than a tuple of length 1.

Implemented the Internal._trim_sheet() internal structural object method.

This is also now used by the structure.delete user function to remove sheet metadata for residues
which no longer exist.

Created 13 unit tests of the Internal._trim_sheet() internal structural object method.

These are mirror the 13 unit tests of Internal._trim_helix().

Fixes for the helix metadata deletion for the internal structural object.

This affects the structure.delete user function.

Fix for the internal structural object _trim_helix() method for the helix metadata format.

Modified all of the unit tests of the internal structural object _trim_helix() method.

The structure of the helix metadata in the internal structural object was not correctly mimicked.

Implemented the internal structural object _trim_helix() method.

This is used when the structure.delete user function is called to trim and remove the helix
metadata. For this to work, the additional method _residue_data() was written to create a
dictionary with residue numbers as keys and the residue names as numbers. This dictionary is used
by _trim_helix() to change the residue names in the helix metadata.