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CHANGELOG.md

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Changelog

FreeSASA uses semantic versioning. Changelog added for versions 2.x

Upcoming release

  • Breaking: Support 3-letter chain labels (auth_sym_id) in CIF-files. Default and RSA output formats have changes in whitespace as a consequence, to give space to the larger labels.

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.

2.0.3

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.

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()

2.0.1

  • 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

2.0

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