Python API can now also split PDB-files into chains

Also fixed bug in freesasa_structure_array() that caused seg-faults when invalid structures were loaded.

More PDB options

Lots of minor additions to interface, mainly for dealing with PDB files. Can include hydrogens in input. Can split PDB file into chains and/or models for separate analyses. Update to CLI with new options and improved help messages. ACE and NH2 capping groups recognized if HETATM activated.

Minor bug fixes

Added tests for CLI that revealed a few bugs, which have been fixed.

Also some code cleanup, with better variable names and some extra comments where deemed helpful.

Extended Python interface

• More functionality added to the Python interface, and it is now part of the general build (if enabled with ./configure --enable-python-binding). Classification of atoms in Python can now be done without directly using C-functions, allowing the user to extend the Classifier class to create custom classifiers, without having to deal with any C extensions. The Python bindings should still be considered experimental, there might still be major changes here. Input is welcome.
• Minor bug fixes and missing dist-targets added (to allow building extra features from dist).
• Simplification of the L&R calculation, which leaves performance unchanged, but reduces code complexity of the innermost loop significantly (which calculates overlap of arcs on the circle, now without recursion).

Expanded API

Added more of the Structure API to the public API. Improved documentation both for C and Python interfaces.

Python bindings

This release adds updated Python bindings. The Python interface should still be considered experimental, but it gives correct results for the standard test cases.

Stateless API

Refactored API to not keep track of any state (except for the global verbosity setting). This added a few more lines to simple cases (such as example.c), but the reduced book-keeping should make it much more maintainable and closer to bug-free.

From this release onwards distribution tarballs of releases (maybe not all patches) will be available for download on the GitHub-pages. This is to provide an autotools-independent version (#9).

This breaks the Python bindings, anyone in need of those can use 0.2.1.4 for now.

0.2.1.4

Fixed configuration and dependency issues discussed in #6.