It is a header-only library. You need to ensure that
include directory is in your include path
when compiling your program. For example:
git clone https://github.com/project-gemmi/gemmi.git c++ -std=c++11 -Igemmi/include -O2 my_program.cpp
If you want Gemmi to uncompress gzipped files on the fly
(i.e. if you
you will also need to link your program with the zlib library.
If a file name is passed to Gemmi (through
it is assumed to be in ASCII or UTF-8.
Python 2.7/3.x module¶
To install the gemmi module you need pip, git and not too old C++ compiler (GCC 4.8+, Clang 3.4+, MSVC 2015+, ICC 17+):
pip install gemmi
(We have binary wheels for some Python versions on Windows, so the command above may actually download binaries).
Alternatively, to install the latest version directly from the repository:
pip install git+https://github.com/project-gemmi/gemmi.git
or clone the project (or download a zip file) and from the top-level directory do:
pip install .
If gemmi is already installed, uninstall the old version first
pip uninstall) or add option
On Windows Python 3.5+ should automatically find an appropriate compiler (MSVC 2015+) . If the compiler is not installed, pip shows a message with a download link. For Python 2.7 pip prefers MSVC 2008, which is too old to compile gemmi. You may still use MSVC 2015, 2017 or 2019, but before invoking pip you need to set the compiler environment with one of these commands:
"%VS140COMNTOOLS%\..\..\VC\vcvarsall.bat" x64 "%VS140COMNTOOLS%\..\..\VC\vcvarsall.bat"
If you’d like to use PyPy instead of CPython – PyPy2.7 >= 5.7 is supported (although only occasionally tested – open an issue if it doesn’t work).
Fortran and C bindings¶
The Fortran bindings are in early stage and are not documented yet.
They use the ISO_C_BINDING module introduced in Fortran 2003.
You may see the
fortran/ directory to know what to expect.
The bindings and usage examples can be compiled with CMake:
cmake -D USE_FORTRAN=1 . make
The C bindings are used only for making Fortan bindings,
but they should be usable on their own.
If you use cmake to build the project
you get a static library
libcgemmi.a that can be used from C,
together with the
The library comes with a command-line program. To build it from source,
first make sure you have git, cmake and C++ compiler installed
sudo apt install git cmake make g++), then:
git clone https://github.com/project-gemmi/gemmi.git cd gemmi cmake . make
Binaries are distributed with the CCP4 suite and with Global Phasing software. They are also included in conda-forge packages. Additionally, the very latest Windows builds (as well as older ones) can be downloaded from AppVeyor CI: click the first (green) job, then in the Artifacts tab you should find gemmi.exe.
This project is using code from a number of third-party open-source projects.
Projects used in the C++ library and included under
- PEGTL – library for creating PEG parsers. License: MIT.
- sajson – high-performance JSON parser. License: MIT.
- PocketFFT – FFT library. License: 3-clause BSD.
- stb_sprintf – locale-independent snprintf() implementation. License: Public Domain.
- tinydir – directory (filesystem) reader. License: 2-clause BSD.
Code derived from the following projects is used in the library:
- ksw2 – sequence alignment in
seqalign.hppis based on the ksw_gg function from ksw2. License: MIT.
- QCProt – superposition method
qcp.hppis taken from QCProt and adapted to our project. License: BSD.
- Larch – calculation of f’ and f”
fprime.hppis based on CromerLiberman code from Larch. License: 2-clause BSD.
Projects included under
third_party/, not used in the library itself,
but used in command-line utilities, python bindings or tests:
- The Lean Mean C++ Option Parser – command-line option parser. License: MIT.
- doctest – testing framework. License: MIT.
- linalg.h – linear algebra library. License: Public Domain.
- zlib – a subset of the zlib library for uncompressing gz files, used as a fallback when the zlib library is not found in the system. License: zlib.
Not distributed with Gemmi:
- pybind11 – used for creating Python bindings. License: 3-clause BSD.
- cctbx – used in tests and in scripts that generated space group data. License: 3-clause BSD.
Email me if I forgot about something.