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Automating tasks in protein structure determination with the clipper python module.

Stuart McNicholas1, Tristan Croll2, Tom Burnley3

  • 1Department of Chemistry, York Structural Biology Laboratory, The University of York, York, YO10 5DD, United Kingdom.

Protein Science : a Publication of the Protein Society
|September 14, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a Python module that integrates the Clipper C++ crystallographic library for enhanced scientific computing. This approach boosts efficiency and maintainability in crystallography and cryo-electron microscopy research.

Keywords:
ClipperNumPyPythonSWIGautomationcrystallographyelectron cryo-microscopylibrariespipelinesscripting

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Area of Science:

  • Computational crystallography
  • Structural biology
  • Scientific software development

Background:

  • Scripting languages offer rapid prototyping and improved code maintainability.
  • Integrating high-performance libraries with scripting languages can overcome traditional efficiency limitations.
  • Crystallography and cryo-electron microscopy (cryo-EM) require efficient computational tools.

Purpose of the Study:

  • To describe the development and application of a Python module for crystallographic computations.
  • To demonstrate the adaptation and generalization of the Clipper C++ library for Python scripting.
  • To highlight best practices in automating scientific workflows using this new module.

Main Methods:

  • Wrapping the efficient C++ crystallographic library, Clipper, for Python.
  • Adapting and generalizing the library for diverse scientific applications.
  • Implementing best practices for automation in scientific software.

Main Results:

  • A generalized Python module enabling efficient scripting of crystallographic and cryo-EM tasks.
  • Demonstration of seamless integration between a C++ library and a high-level scripting language.
  • Improved automation capabilities for complex scientific data analysis.

Conclusions:

  • The developed Python module enhances the usability and efficiency of the Clipper library.
  • This approach facilitates advanced research in crystallography and cryo-electron microscopy.
  • The module promotes best practices in scientific software development and automation.