MDAnalysis project
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This page contains the details of a technical writing project accepted for
Google Season of Docs.
Project summary
- Open source organization:
- MDAnalysis
- Technical writer:
- lilyminium
- Project name:
- A user guide structured by topic
- Project length:
- Long running (5 months)
Project description
A guide to the MDAnalysis library, separate from the API reference, that includes:
A detailed guide to the data structures used in MDAnalysis. This page will introduce the Atom, AtomGroup, and Universe classes; include I/O options; and contain information on manipulating Atoms and combining AtomGroups.
A page on the Analysis building blocks. The AnalysisBase class, AnalysisFromFunction class, and analysis_class functions form the basis of any user-defined analysis. What each class does under the hood is worthwhile knowing, e.g. if it’s analogous to numpy.vectorize.
A page on selecting groups of atoms using Universe.select_atoms. Both the technical details and the molecular dynamics knowledge behind the way that this is implemented.
A page on topologies. Users should understand the data structure, usage, manipulation and framework for building systems.
A page on available visualization methods, both for the trajectory and for current analyses that return data for visualization.
Except as otherwise noted, the content of this page is licensed under the Creative Commons Attribution 4.0 License. For details, see the Google Developers Site Policies. Java is a registered trademark of Oracle and/or its affiliates.
Last updated 2024-11-08 UTC.
[[["Easy to understand","easyToUnderstand","thumb-up"],["Solved my problem","solvedMyProblem","thumb-up"],["Other","otherUp","thumb-up"]],[["Missing the information I need","missingTheInformationINeed","thumb-down"],["Too complicated / too many steps","tooComplicatedTooManySteps","thumb-down"],["Out of date","outOfDate","thumb-down"],["Samples / code issue","samplesCodeIssue","thumb-down"],["Other","otherDown","thumb-down"]],["Last updated 2024-11-08 UTC."],[[["This project aims to create a comprehensive user guide for the MDAnalysis library, focusing on topics like data structures, analysis tools, atom selection, topologies, and visualization methods."],["The guide will provide detailed explanations of key MDAnalysis classes such as Atom, AtomGroup, Universe, and AnalysisBase, along with practical examples of their usage."],["This long-running project will complement the existing API reference by offering a more user-friendly and topic-oriented approach to understanding MDAnalysis."],["It will empower users to effectively utilize the library for molecular dynamics analysis by providing clear guidance on data manipulation, analysis customization, and visualization techniques."]]],["The core of this project involves creating a user guide for the MDAnalysis library. This guide will include detailed explanations of MDAnalysis data structures like Atom, AtomGroup, and Universe, covering I/O and manipulation. It will detail the underlying AnalysisBase and AnalysisFromFunction classes, alongside `Universe.select_atoms` functionality. The project also covers topologies, focusing on structure, usage, and system construction. Lastly, it will detail trajectory and analysis data visualization methods.\n"]]
