MØD
1.0.0
Index
Site
1. Installation
2. Compiling from Source
3. libMØD
4. PyMØD
5. PostMØD
6. The Wrapper Script
7. Graph, Rule, and Molecule Model
8. Data Formats
9. Derivation Graph Strategies
10. Hyperflow Model
11. Examples
12. Known Issues
13. Changes
14. References
Page
11. Examples
« 10. Hyperflow Model
11.1. Basics,... »
11.
Examples
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11.1. Basics, Graphs, and Rules
11.1.1. Hello World
11.1.2. Graph Loading
11.1.3. Printing Graphs/Molecules
11.1.4. Graph Interface
11.1.5. Graph Morphisms
11.1.6. Rule Loading
11.1.7. Rule Morphisms
11.1.8. Formose Grammar
11.1.9. Including Files
11.2. Rule Composition
11.2.1. Unary Operators
11.2.2. Parallel Composition
11.2.3. Supergraph Composition
11.2.4. Overall Formose Reaction
11.3. Derivations and Reaction Networks
11.3.1. Rule Application
11.3.2. Repetition
11.3.3. Application Constraints
11.3.4. Advanced Printing
11.3.5. Double Pushout Printing
11.4. Local Geometry and Stereochemistry
11.4.1. Stereospecific Aconitase
11.4.2. Stereoisomers of Tartaric Acid
11.4.3. Non-trivial Stereoisomers
11.5. Integer Hyperflows and Pathways
11.5.1. A Specific Pathway
11.5.2. Extra Constraints
11.5.3. Multiple Solutions
11.5.4. Finding Autocatalytic Cycles