FIRECODE - Filtering Refiner and Embedder for Conformationally Dense Ensembles

• Introduction
• Installation
  • Optional dependencies
    • CREST
    • AIMNET2 models
    • UMA models
    • XTB
    • TBLITE (prefer over xTB)
    • ORCA
• Usage
  • Command Line Program
  • Standalone Optimizer
• Environment Variables
• Operators and keywords
  • Operators
    • Deprecated operators (legacy)
  • General keywords
    • Legacy: Embedding-specific keywords
• Legacy: Embedding runs
  • Pairings
  • Embeddings: good practice and suggested options
  • Legacy: example embeddings
    • 1. Trimolecular input
    • 2. Peptide-substrate binding mode
    • 3. Complex embedding with internal and external constraints
• Input formatting and examples
  • Constraints
  • Operators
  • Input examples
    • 1. Conformational search and refinement
    • 2. Complex transition state search routine
    • 3. Constrained conformational search, partial optimization, saddle optimization
    • 4. Atropisomer rotation
• License