FreeSASA 0.6.0: Final round of pre-releases

FreeSASA is an open source library and command line tool to calculate the solvent accessible surface areas of protein molecules. This is the first release submitted to Zenodo. See GitHub for the change-log up to this date. The library is as fast and accurate as existing tools, with the advantage of being open source and available as both a library, a command line tool and it has Python bindings.

Until there is a formal publication for this project use of FreeSASA can be cited using this DOI or that of later versions.

Versions 0.6.* marks the final round of pre-releases. No new features will be added, focus will be on bug-fixing, optimization and adding documentation.

Interface changes:

• The output of the CLI has been updated. It should now be slightly clearer, and more consistent between options. The changes may however break tools relying on the output from older versions.
• Atomic radii are now determined using the definitions by Tsai et al. ((JMB 1999, 290: 253). The old classifier is still available as the variable freesasa_oons_classifier.
• Atomic radii are determined when a structure is read and stored with the structure. This means that they do not have to be calculated explicitly as before. It also means that the signature of a few of the central functions have changed. The default behavior is to guess the radius of unrecognized atoms, but the user can pass an option to specify that they should be skipped or that reading should halt when this happens.
• When memory allocation fails, the library attempts to clean up as much memory as possible. When emulating this error in the file tests/broken_malloc.c Valgrind detects no memory leaks from within the library.
• Two scripts have been added to facilitate generating classifiers, see the files for explanations of what they do.

Internal changes:

• The default classifier is stored the same way as the classifiers generated from config-files. This reduces code size slightly, and makes configuring easier. The default classifier is stored statically in src/protor.c. This code has been generated automatically using the scripts added in this release.