12. Examples

• 12.1. Basics, Graphs, and Rules
  • 12.1.1. Hello World
  • 12.1.2. Graph Loading
  • 12.1.3. Printing Graphs/Molecules
  • 12.1.4. Graph Interface
  • 12.1.5. Graph Morphisms
  • 12.1.6. Rule Loading
  • 12.1.7. Rule Morphisms
  • 12.1.8. Formose Grammar
  • 12.1.9. Including Files
• 12.2. Rule Composition
  • 12.2.1. Unary Operators
  • 12.2.2. Parallel Composition
  • 12.2.3. Supergraph Composition
  • 12.2.4. Overall Formose Reaction
• 12.3. Derivations and Reaction Networks
  • 12.3.1. Rule Application
  • 12.3.2. Repetition
  • 12.3.3. Application Constraints
  • 12.3.4. Advanced Printing
  • 12.3.5. Double Pushout Printing
• 12.4. Local Geometry and Stereochemistry
  • 12.4.1. Stereospecific Aconitase
  • 12.4.2. Stereoisomers of Tartaric Acid
  • 12.4.3. Non-trivial Stereoisomers
• 12.5. Integer Hyperflows and Pathways
  • 12.5.1. A Specific Pathway
  • 12.5.2. Extra Constraints
  • 12.5.3. Multiple Solutions
  • 12.5.4. Finding Autocatalytic Cycles
• 12.6. EpiM
  • 12.6.1. A Basic Process Encoding
  • 12.6.2. A Process Encoding with Restrictions
  • 12.6.3. A Recursive Encoding
  • 12.6.4. Config for Visualization of Encodings
  • 12.6.5. Compute Execution Spaces
  • 12.6.6. Process Execution Spaces with Recursive Processes
  • 12.6.7. Hospital