Welcome to goose’s documentation!

Contents:

• What is GOOSE?
  • What can GOOSE do?
  • What is new in V0.2.2 through V0.2.5?
  • How can I use GOOSE?
  • Python Requirements
• Installation - GOOSE takes flight!
• Important Limitations
  • GOOSE makes sequences predicted to be disordered
  • Allowed error in sequence properties
  • Specified properties and speed
  • Failed sequence generation
  • Limits on specifying sequence properties
  • Best practices when using GOOSE
• Creating Sequences
  • Getting Started
  • Generating sequences with specified properties
  • Generating Sequences specifying Fractions of Amino Acids
  • Generating Sequences specifying Amino Acid Classes
  • Generating Sequences specifying Ensemble Dimensions
  • Function Selection Guide
• Creating Sequence Variants
  • Overview of the variant() function
  • Types of sequence variants
  • Common parameters
  • Shuffling variants
  • Property-based variants
  • Property modification variants
  • Asymmetry variants
  • Dimensional variants
  • Error handling and troubleshooting
  • Function selection guide
  • Backward compatibility notes
• Using the SequenceOptimizer
  • Key Features of the New SequenceOptimizer
  • Critical Differences between SequenceOptimizer and Create Functionality
  • Quick Start Example
  • Property Classes Overview
  • Optimizer Initialization and Basic Parameters
  • Hard Composition Constraints During Optimization
  • Multiple Properties, Weights, and Tolerances
  • Custom Properties
  • Advanced Optimizer Configuration
  • Troubleshooting and Optimization Tips
  • Examples and Demo Notebooks
  • API Reference
  • See Also
• Sequence Libraries (deprecated)
• Sequence analysis in GOOSE
  • Using the analyze module in GOOSE
• How to cite GOOSE
• Acknowledgements
  • Funding
  • Development
  • Cookiecutter
• Python Module Documentation
  • Recommended usage
  • GOOSE functions
• Recent changes

Indices and tables

• Index