biojava/biojava — pull request #175 by josemduarte (2014-09-20 11:20:12+00:00)
Title: Removing padding spaces in internal atom name representation

This should fix the issue of dealing with padding spaces in atom names internally with all its associated problems (see #148 ).

There are some API changes here (for the 4.0 release):
- removed `Atom.getFullName/setFullName`
- removed already deprecated `Atom.getParent/setParent`, had been replaced by `getGroup/setGroup`
- `Group.getAtom(String)` and `Group.hasAtom(String)` will now only work with trimmed atom names, searching for " CA " will return null.

Ambiguities in atom names (especially the CA=C-alpha/Calcium) will happen if using the atom name alone, one needs to resort to `Atom.getElement()` if C-alphas are required for instance:
- the methods for getting CA and backbone atom arrays in `StructureTools` have been rewritten accordingly
- the generic method `StructureTools.getAtomArray(Structure,String[])` will have the ambiguity problem because it will only be checking atom names and not elements
- `FileParsingParameters.getAcceptedAtomNames()` will also have the ambiguity problem
- `FileParsingParameters.isParseCAonly()` should work properly

`Group.hasAminoAtoms` now checks for backbone only (no CB), this is more consistent for the cases where it was used.