Python Macromolecular Library
The Python Macromolecular Library (mmLib/pymmlib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer. The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization. This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.
I was the lead developer and maintainer of the Python Macromolecular Library from 2006 to 2010. I contributed 20,590 lines of code to pymmlib (27.8% in Python and 25.5% in Fortran). I added hundreds of new features, including Skittles, which was added to the CCP4 codebase.
Version 1.2.0 was released (with tarball) in June 2011.
macromolecular crystallography; computer programs; Python; mmCIF; PDB; TLSView; TLS models; pymmlib
- Painter J, Merritt EA (2004). "mmLib Python toolkit for manipulating annotated structural models of biological macromolecules". J Appl Cryst 37(1):174-178. DOI:10.1107/S0021889803025639
- Painter J, Merritt EA (2005). "mmLib A molecular viewer for the analysis of TLS rigid-body motion in macromolecules". Acta Cryst D61(4):465-471. DOI:10.1107/S0907444905001897
- Zucker F, Champ PC, Merritt EA (2010). "Validation of crystallographic models containing TLS or other descriptions of anisotropy". Acta Cryst. D66, 889-900. DOI:10.1107/S0907444910020421