This pull request contains all the methods and data structures implemented to support secondary structure assignment and prediction for proteins #112. To summarize in points, the new features are:

• DSSP implementation: predicts "the novo" the secondary structure of a BioJava Structure object and assigns the SS types accordingly to each Group.
• DSSP file format Parser: is able to read a DSSP output format file and convert it to the BioJava DS, from where it can be assigned to the corresponding Structure. The parser can also fetch the DSSP files from the PDB webpage automatically, or it can read files providing a file path. All the DS in BioJava that store SS information are able to write the results in the DSSP file format, so that they can be stored as a DSSP file and parsed again later.
• Secondary Structure Elements: the SSE can be retrieved from a structure with a simple method, once the Structure has been assigned the SS types. This is useful for counting the number of SSE, or defining the overall structure, for example.
• SS storage: the secondary structure was only possible in AminoAcids. From this pull request on, the SS is stored in the Group's properties, so that modified aminoacids (that are Hetatoms) can also be assigned a SS type. The storage of SS information is done in two layers: a cheap version, that only stores the type of SS of the residue, and an optional extensive version, that stores all the information about hydrogen bonds, bridge partners, energies, etc.
• Assignment of SS: there are three types of assignments of SS. Authors assignment (coming from the PDB or mmCIF file), DSSP assignment (coming from a DSSP output file) and BioJava assignment, when the SS was assigned with the BioJava implementation. Although there are no differences in the output between DSSP and BioJava assignments, the BioJava implementation could include some parameters in the future to customize the SS assignment with the user needs, so it is worth making a distinction.