2.1.2

• Fix error where CLI options weren't parsed properly on ARM processors.
• Fix error in man pages.

2.1.1

• Fix error where compiling without multithread support still set the default number of threads to 2.
• Fix issue when stripping quotes from atom names in CIF-files, which sometimes caused memory errors.

2.1.0

The new features in this release were created on initiative by and in collaboration
with Danny Diaz.

Added

• Support for mmCIF input with the CLI option --cif.
  • The CLI was ported to C++ to allow using Gemmi for CIF import.
  • Gemmi is imported as a git submodule, see README for details.
  • A test runner was added to verify that CIF and PDB input files
    give the same result.
  • The C API does not support CIF for now (this would require conversion to C++).
• Add output option --format=cif that can be used when input is mmCIF.
  See documentation for an example.
• Added VdW-radii for all elements.
  • Using values from Gemmi when missing in paper by Mantina et al.
  • Correct Mg radius from 1.74 to 1.73 Å.

Fixed

• Fix bug in JSON output where relative SASA for amino acids without sidechan
  were written as NaN, which is not valid JSON. These values are now
  simply skipped.
• Fix bug where elements with H or D as second letter, such as CD, were classified
  as hydrogens.
• Change some type definitions to be more C++ friendly.

2.1.0-beta

This is a beta release for the new version with mmCIF support. It should be relatively stable, but
any feedback is welcome on unexpected behavior or missing features.

Changes

• Support for mmCIF input with the CLI option --cif.
  • The CLI was ported to C++ to allow using Gemmi for CIF import.
  • Gemmi is imported as a git submodule, see README for details.
  • A test runner was added to verify that CIF and PDB input files
    give the same result.
  • The C API does not support CIF for now (this would require conversion to C++).
• Add output option --format=cif that can be used when input is mmCIF.
  See documentation for an example.

Bug-fixes

• Fix bug in JSON output where relative SASA for amino acids without sidechan
  were written as NaN, which is not valid JSON. These values are now
  simply skipped.
• Fix bug where elements with H or D as second element, such as CD, were classified
  as hydrogens.

Version 2.0.3

This version separates the Python bindings into a separate module. To be able to release Windows binaries of the Python module, the code has been changed to be C89 compatible where necessary, with a few macros to allow using restrict and inline when compiled with a C99 compiler. There are no changes to the behavior of the CLI or C API in this release.

FreeSASA 2.0.2

• Relative SASA values are now calculated using the same reference
  configurations as NACCESS. This means relative SASA values will
  differ slightly from those of previous versions.
• Python bindings compatible with Python 3.
• Man page added
• Bugs fixed:
  • CLI option --separate-models now outputs all models in PDB output.
  • On some platforms compilation failed when libxml and/or json-c was
    not present. Now fixed.
  • Some memory allocations were not checked for failure in S&R
    calculations. These are now properly checked, and done more
    seldomly, which should improve performance slightly.
• Residue numbers now include the iCode field for insterted residues
• Compatibility with Microsoft C Compiler:
  • No variable length arrays
  • Some macros and keywords are redefined when necessary
  • Lexer does not depend on header unistd.h
  • GNU getline not used, replaced by fgets()

FreeSASA 2.0.1

Changes

• Add function calcCoord() to Python interface, wraps C function
  freesasa_calc_coord().
• Expand selection syntax:
  • Allow negative residue numbers resi \-10 (escaped with
    backslash), and expression such as resi \-10-\-5+\-3-5
  • Allow open-ended residue ranges resi -10, resi 10- and
    combined as resi -10+15-20+30-
  • Allow primes in atom names (i.e. O5')
  • Allow selection names to be numbers or start with a number

FreeSASA 2.0

Version 2.0 involves a large number of minor changes, mainly to the C API. The two most siginificant new featueres is a new tree interface for navigating the results, and the ability to export results to XML and JSON.

Changed

General

• Classifier configuration files now have new name field

C API

• Classifier interface changed.
  • Pointer is now opaque and classification done via
    freesasa_classifier_class() instead of
    classifier->sasa_class().
  • Classifiers only classify polar/apolar/unknown. Arbitrary classes
    no longer allowed.
  • The static classifiers in freesasa.h have reference values for
    all residue types, allowing calculation of relative SASA for for
    example RSA output. At the moment no support for defining these
    values in classifier configuration file (TODO?).
  • Interface for classifying using string-value pairs has been
    removed (type freesasa_strvp and functions
    freesasa_result_classifiy() and freesasa_strvp_free()). The
    new tree-interface should be used instead.
• Structure interface changed: A structure is initialized with a
  classifier and the relevant classifier values are stored directly in
  the structure. This assures that the structure and results are
  always analyzed with consistent parameters. One effect is that the
  function freesasa_calc_structure() no longer takes the atomic
  radii as an explicit parameters.
• The logging functions freesasa_log(), freesasa_write_result(),
  freesasa_write_parameters(), freesasa_write_rsa(),
  freesasa_write_pdb(), freesasa_per_residue(),
  freesasa_per_residue_type() and freesasa_per_chain() have been
  removed from the interface. The same functionality can be achieved
  using freesasa_tree_export().

CLI

• CLI output format is controlled by the option -f or
  --format. Options specifying files for specific outpt types have
  been removed, and the separate options controlling output format
  have been deprecated (see below). An option --deprecated can be
  used to list these. This has also made the option -l or --no-log
  obsolete.

Added

General

• New output formats
  • XML using libmxl2 (optional)
  • JSON using JSON-C (optional)
  • RSA (was present already in 1.1, but interface now consolidated)
• To build FreeSASA 2.0 the libraries libxml2 and JSON-C need to be
  installed. These can be disabled by ./configure --disable-json --disable-xml to build a dependency-free version of the library.

C API

• New node interface. Results in tree form can be generated using
  freesasa_calc_tree() or freesasa_tree_init(). The feature was
  added to facilitate generation of XML and JSON output, but can be
  used directly to analyze results as well. The results of a
  calculation are to now best exported using freesasa_tree_export().

Fixed

• structure.c was refactored, hopefully code is slightly more
  transparent now
• general bug cleaning, some minor memory leaks removed.
• Memory error mocking is now more sophisticated: uses dlsym instead
  of macros, allowing more uniform test structure.

Deprecated

CLI

• options -B, -r, -R, --rsa and -l are deprecated (use
  -f or --format instead)

C API

• Logging using structure and results now deprecated in favor of
  using tree interface
• Function freesasa_select_area() is deprecated

Add RSA output

Changes:

• CLI options --rsa and --rsa-file can be used to output RSA files similar to those of NACCESS. RSA is mainly intended to be useful as a CLI setting, the RSA API is still to be considered experimental. Since there might be need for more functionality before it stabilizes. A file format for RSA reference values might be added in the future, for example.
• The library ships with AXA tripeptides that can be used to calculate new RSA reference SASA values, and a simple Perl script that performs this calculation and outputs C code for the combined reference values for all 20 residues.
• Options -O and --radius-from-occupancy were added to allow using the occupancy values in the input file as atomic radii. This can be useful for on the fly changes, or if individual atoms need special treatment.
• An NACCESS configuration is now also stored statically in the library, this allows the CLI to produce RSA output with verified consistency between atomic radii and SASA reference values. This is access through the option --radii=naccess (or --radii=protor).
• Travis and Coveralls testing have been added to the configuration

Moving to MIT license

• Changed to MIT license (as per request in #11).
• Added experimental Bio.PDB interface in Python bindings.
• Some internal rewriting to make code more readable.