Difference between revisions of "Python Macromolecular Library"
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| − | The '''Python Macromolecular Library''' ('''mmLib''') is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the [[Python]] programming language.<ref name="Painter2004">Painter J, Merritt EA (2004). "[http://www.bmsc.washington.edu/parvati/mmLib.pdf mmLib Python toolkit for manipulating annotated structural models of biological macromolecules]". ''J Appl Cryst 37(1):174-178''. {{doi|10.1107/S0021889803025639}}</ref> 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.<ref name="Painter2005">Painter J, Merritt EA (2005). "[http://www.bmsc.washington.edu/parvati/TLSview.pdf mmLib A molecular viewer for the analysis of TLS rigid-body motion in macromolecules]". ''Acta Cryst D61(4):465-471''. {{doi|10.1107/S0907444905001897}}</ref> 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. | + | 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.<ref name="Painter2004">Painter J, Merritt EA (2004). "[http://www.bmsc.washington.edu/parvati/mmLib.pdf mmLib Python toolkit for manipulating annotated structural models of biological macromolecules]". ''J Appl Cryst 37(1):174-178''. {{doi|10.1107/S0021889803025639}}</ref> 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.<ref name="Painter2005">Painter J, Merritt EA (2005). "[http://www.bmsc.washington.edu/parvati/TLSview.pdf mmLib A molecular viewer for the analysis of TLS rigid-body motion in macromolecules]". ''Acta Cryst D61(4):465-471''. {{doi|10.1107/S0907444905001897}}</ref> 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. |
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| + | I was the lead developer and maintainer of the Python Macromolecular Library from 2006 to 2010. I contributed [http://www.ohloh.net/p/12891/contributors/55366423429103 20,590] lines of code to pymmlib (27.8% in [[Python]] and 25.5% in Fortran). I added hundreds of new features, including [[Skittles]],<ref>Zucker F, [[Christoph Champ|Champ PC]], Merritt EA (2010). "[https://docs.google.com/file/d/0B7cFvC52gEb9MTRmNDQyNmYtZDVhNS00OTViLTkxZGItODk3ZmU2ZjdjYzM5/edit Validation of crystallographic models containing TLS or other descriptions of anisotropy]". ''Acta Cryst.'' D'''66''', 889-900. {{doi|10.1107/S0907444910020421}}</ref> which was added to the [[:Category:Ccp4|CCP4]] codebase. | ||
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| + | Version 1.2.0 was released (with tarball) in June 2011. | ||
==Keywords== | ==Keywords== | ||
| − | macromolecular crystallography; computer programs; Python; mmCIF; PDB; TLSView; TLS models | + | macromolecular crystallography; computer programs; Python; mmCIF; PDB; TLSView; TLS models; pymmlib |
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| − | |||
==See also== | ==See also== | ||
*[[TLSMD]] | *[[TLSMD]] | ||
| + | *[[Skittles]] | ||
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| + | ==References== | ||
| + | <references/> | ||
==External links== | ==External links== | ||
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[[Category:Crystallography]] | [[Category:Crystallography]] | ||
| + | [[Category:Portfolio]] | ||
Latest revision as of 20:58, 2 March 2015
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.[1] 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.[2] 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,[3] which was added to the CCP4 codebase.
Version 1.2.0 was released (with tarball) in June 2011.
Contents
Keywords
macromolecular crystallography; computer programs; Python; mmCIF; PDB; TLSView; TLS models; pymmlib
See also
References
- ↑ 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
