MØD
0.11.1
Index
Site
1. Installation
2. libMØD
3. PyMØD
4. PostMØD (
mod_post
)
5. The Wrapper Script (
mod
)
6. EpiM
7. Data Formats
8. Derivation Graph Strategies
9. Hyperflow Model
10. Examples
11. Known Issues
12. Changes
13. References
Page
10. Examples
« 9. Hyperflow Model
10.1. Basics,... »
10.
Examples
¶
10.1. Basics, Graphs, and Rules
10.1.1. Hello World
10.1.2. Graph Loading
10.1.3. Printing Graphs/Molecules
10.1.4. Graph Interface
10.1.5. Graph Morphisms
10.1.6. Rule Loading
10.1.7. Rule Morphisms
10.1.8. Formose Grammar
10.1.9. Including Files
10.2. Rule Composition
10.2.1. Unary Operators
10.2.2. Parallel Composition
10.2.3. Supergraph Composition
10.2.4. Overall Formose Reaction
10.3. Derivations and Reaction Networks
10.3.1. Rule Application
10.3.2. Repetition
10.3.3. Application Constraints
10.3.4. Advanced Printing
10.3.5. Double Pushout Printing
10.4. Local Geometry and Stereochemistry
10.4.1. Stereospecific Aconitase
10.4.2. Stereoisomers of Tartaric Acid
10.4.3. Non-trivial Stereoisomers
10.5. Integer Hyperflows and Pathways
10.5.1. A Specific Pathway
10.5.2. Extra Constraints
10.5.3. Multiple Solutions
10.5.4. Finding Autocatalytic Cycles
10.6. EpiM
10.6.1. A Basic Process Encoding
10.6.2. A Process Encoding with Restrictions
10.6.3. A Recursive Encoding
10.6.4. Config for Visualization of Encodings
10.6.5. Compute Execution Spaces
10.6.6. Process Execution Spaces with Recursive Processes
10.6.7. Hospital