GEMMI - library for structural biology

Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with:

• macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),

• refinement restraints (CIF files),

• reflection data (MTZ and mmCIF formats),

• data on a 3D grid (electron density maps, masks, MRC/CCP4 format)

• crystallographic symmetry.

Parts of this library can be useful in structural bioinformatics (for symmetry-aware analysis of protein models), and in other molecular-structure sciences that use CIF files (we have the fastest open-source CIF parser).

Gemmi is open-source (MPL) and portable – it runs on Linux, Windows, MacOS and even inside a web browser if compiled to WebAssembly. It is written in C++11, with Python (2 and 3) bindings, and with partial C and Fortran 2003 interface.

Occasionally, the project gets sidetracked into visualization of the PDB data.

Gemmi is a joint project of Global Phasing Ltd and CCP4.

The project is named after Gemmi Pass. The name can also be expanded as GEneral MacroMolecular I/o.

Source code repository: https://github.com/project-gemmi/gemmi

Important

As of 2020 the library is under intensive development and not everything is documented yet. Just ask questions.

Contents

• Installation
  • C++ library
  • Python 2.7/3.x module
  • Fortran and C bindings
  • Gemmi program
  • Credits
• CIF Parser
  • What are STAR, CIF, DDL, mmCIF?
  • What is parsed?
  • Getting started
  • DOM and SAX
  • Reading a file
  • Writing a file
  • Document
  • Block
  • Frame
  • Pairs and Loops
  • Column
  • Table
  • JSON
  • Design choices
  • Performance
  • Directory walking
  • Examples
• Symmetry
  • Space group table
  • Operations
  • Groups of Operations
  • C++ Example
• Molecular models
  • Elements
  • Small Molecules
  • Chemical Components
  • Coordinates and matrices
  • Unit Cell
  • Reading coordinate files
  • PDB format
  • PDBx/mmCIF format
  • mmJSON format
  • Hierarchy
  • Structure
  • Sequence
  • Model
  • Chain
  • ResidueSpan, ResidueGroup
  • Residue
  • AtomGroup
  • Atom
  • AtomAddress and CRA
  • Examples
• Structure analysis
  • Neighbor search
  • Contact search
  • Selections
  • Graph analysis
  • Torsion Angles
  • Local copy of the PDB archive
• Grids and maps
  • Volumetric grid
  • MRC/CCP4 maps
• Reciprocal space
  • MTZ format
  • SF mmCIF
  • hkl CIF
  • Data on 3D grid
  • FFT
  • Scattering factors
• Gemmi program
  • validate
  • grep
  • cif2json
  • json2cif
  • convert
  • tags
  • map
  • mask
  • mtz
  • mtz2cif
  • cif2mtz
  • sf2map
  • map2sf
  • sfcalc
  • fprime
  • residues
  • align
  • sg
  • contents
  • contact
  • blobs
  • h
  • mondiff
  • wcn
• Python API
• C++ API