Welcome to goose’s documentation!

Contents:

• What is GOOSE?
  • Why was GOOSE made?
  • How can I use GOOSE?
• Installation - GOOSE takes flight!
• Important limitations
  • Allowed error in sequence properties
  • Speed, specified properties, and stochasticity
  • Failed sequence generation
  • Limits on specifying sequence properties
  • Best practices when using GOOSE
• Leaving the nest - how to use GOOSE in Python
• Generating sequences with specified properties
  • Examples of sequence generation by properties
• Generating Sequences specifying Fractions of Amino Acids
  • Examples of Sequence Generation by Fractions
• Generating Sequences specifying Ensemble Dimensions
  • Examples of generating sequences by specifying Rg or Re
• Creating Sequence Variants in Python
  • Types of sequence variants
  • The constant_class_var()
  • The new_seq_constant_class_var()
  • The constant_properties_var()
  • The constant_residue_var()
  • The region_shuffle_var()
  • The excluded_shuffle_var()
  • The targeted_shuffle_var()
  • The asymmetry_var()
  • The hydro_class_var()
  • The fcr_class_var()
  • The ncpr_class_var()
  • The kappa_var()
  • The all_props_class_var()
  • The re_var() and rg_var
• Sequence analysis in GOOSE
  • Using the analyze module in GOOSE
• Generating sequence libraries in GOOSE
  • Generating sequence libraries by properties
  • Generating sequence libraries by fractions
• How to cite GOOSE
• Acknowledgements
  • Funding
  • Development
  • Cookiecutter
• Python Module Documentation
  • Recommended usage
  • GOOSE functions
• Recent changes

Indices and tables

• Index