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
After cloning the repository, add git submodules
git submodule init git submodule update
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 <pdb-file>
In addition, make install installs the header freesasa.h and the library libfreesasa.
The configuration can be changed with these options:
--disable-jsonbuild without support for JSON output.--disable-xmlbuild without support for XML output.--disable-threadsbuild without multithreaded calculations--enable-doxygenactivates building of Doxygen documentation
For developers:
--enable-checkenables unit-testing using the Check framework--enable-gcovadds compiler flags for measuring coverage of tests using gcov--enable-parser-generatorrebuild 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).
Python module
The Python bindings are available from PyPi and can be installed using
pip install freesasa
This module is found in a separate repository https://github.com/freesasa/freesasa-python The PyPi module has binaries for Mac OS X and Windows, for a number of Python versions and separate documentation.
Documentation
Enabling Doxygen builds a full reference manual, documenting both CLI and API in the folder doc/html/doxygen/, also available on the web at http://freesasa.github.io/.
After building the package, calling
freesasa -h
explains how the commandline tool can be used.
Compatibility and dependencies
The library has been tested successfully with several versions of GNU C/C++ Compiler and Clang/LLVM. It can be built using only standard C and GNU libraries, in addition to Gemmi (as a git submodule). The standard build depends on json-c and libxml2. These can be disabled by configuring with --disable-json and --disable-xml respectively.
Developers who want to do testing need to install the Check unit testing framework. Building the full reference manual requires Doxygen (version > 1.8.8). Changing the selection parser and lexer requires Flex and Bison. These build options, which add extra dependencies, are disabled by default to simplify installation for users only interested in the command line tool and and/or C Library.
The C API can be built using MSVC, see: https://github.com/mittinatten/freesasa/issues/22#issuecomment-374661526 (no project files provided though), but probably not the command line tool. It should be relatively straightforwad to build the command line tool for Windows using MinGW or Cygwin, but this hasn't been tested (let me know if you've got it to work).
Prerequisites for Ubuntu
The following command will install all dependencies needed, some of which most users will already have, for a minimal build of FreeSASA in Ubuntu (verified for version 16, 18 and 20).
apt-get update apt-get install git build-essential autoconf libc++-dev libc++abi-dev
For a fully featured build, with ability to run unit tests, these additional packages are needed
apt-get install check libjson-c-dev libxml2-dev libxml2-utils
Prerequisites for RHEL / CentOS
Thanks to @jvlehtonen for providing the following:
GNU Build System and git install on RHEL 7 and 8 -based systems (including CentOS 7, AlmaLinux, Rocky Linux, etc) as "yum group":
sudo yum install @development
The additional dependencies can be installed on RHEL-based systems with:
sudo yum install json-c-devel libxml2-devel
The system GCC in RHEL 7 (and hence CentOS 7) does not support required C++ standard.Later version of GCC are available via Software Collections (SCL). RHEL 7 has its method to enable SCL. CentOS 7 enables SCL repo with:
sudo yum install centos-release-scl-rh
"Toolchain" from Developer Toolset is sufficient for building with GCC. For example:
sudo yum install devtoolset-9-toolchain
In order to use programs from SCL one has to enable environment:
scl enable devtoolset-9 bash
The bash that starts above does have gcc version 9 on PATH. The built freesasa binary does not require the environment.
Citing FreeSASA
FreeSASA can be cited using the following publication
- Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:189. (doi: 10.12688/f1000research.7931.1)
The DOI numbers from Zenodo can be used to cite a specific version of FreeSASA.