freesasa for Mac

FreeSASA is a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) of biomolecules. It is designed to be simple to use with defaults, but allows customization of all parameters of the calculation and provides a few different tools to analyze the results. Python bindings are provided separately (see below).

By default Lee & Richards' algorithm is used, but Shrake & Rupley's is also available. Both can be parameterized to arbitrary precision, and for high resolution versions of the algorithms, the calculations give identical results.

FreeSASA assigns a radius and a class to each atom. The atomic radii are by default the _ProtOr_ radii defined by Tsai et al. (JMB 1999, 290: 253) for standard amino acids and nucleic acids, and the van der Waals radius of the element for other atoms. Each atom is also classified as either polar or apolar.

Users can provide their own atomic radii and classifications via configuration files. The input format for configuration files is described in the online documentation, and the share/ directory contains some sample configurations, including one for the NACCESS parameters (Hubbard & Thornton 1993).

Version 2.0 adds some new features and breaks a few parts of the interface from 1.x (mainly the API), see CHANGELOG.md for detailed information.

Building and installing

FreeSASA can be compiled and installed using the following

autoreconf -i # only necessary if you're cloning git repo ./configure make && make install

NB: If the source is downloaded from the git repository the configure-script needs to be set up first using autoreconf -i. Users who don't have autotools installed, can download a tarball that includes the autogenerated scripts from http://freesasa.github.io/ or from the latest GitHub-release.

If you are upgrading from a pre 2.1.0 build you might need to call make clean before building.

The above commands build and install the command line tool freesasa (built in src/), the commands

freesasa -h

and, if installed,

man freesasa

give an overview of options. To run a calculation from PDB-file input using the defaults, simply type

freesasa

In addition, make install installs the header freesasa.h and the library libfreesasa.

The configuration can be changed with these options: --disable-json build without support for JSON output. --disable-xml build without support for XML output. --disable-threads build without multithreaded calculations --enable-doxygen activates building of Doxygen documentation

For developers: --enable-check enables unit-testing using the Check framework --enable-gcov adds compiler flags for measuring coverage of tests using gcov --enable-parser-generator rebuild parser/lexer source from Flex/Bison sources (the autogenerated code is included in the repository, so no need to do this if you are not going to change the parser).

Installing using package managers

You can install binaries that have already been built using the package managers.