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To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent - a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data. Extensible Python modules have been developed, which provide object-oriented abstractions (based on a hierarchical representation of macromolecules), efficient data structures (e.g. kD-trees), fast implementations of common algorithms (e.g. surface-area calculations), read/write support for Protein Data Bank-related file formats and wrappers for external command-line applications (e.g. Stride). Integration of this code into PyCogent is symbiotic, allowing sequence-based work to benefit from structure-derived data and, reciprocally, enabling structural studies to leverage PyCogent's versatile tools for phylogenetic and evolutionary analyses.

Supporting information

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Portable Document Format (PDF) file https://doi.org/10.1107/S0021889811004481/kk5078sup1.pdf
Supplementary information

exe

Executable (exe) file https://doi.org/10.1107/S0021889811004481/kk5078sup2.exe
Python code use-case_1.py

exe

Executable (exe) file https://doi.org/10.1107/S0021889811004481/kk5078sup3.exe
Python code use-case_2.py


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