https://github.com/vitroid/cycless
Algorithms for cycles in a graph
https://github.com/vitroid/cycless
Last synced: 12 months ago
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Algorithms for cycles in a graph
- Host: GitHub
- URL: https://github.com/vitroid/cycless
- Owner: vitroid
- Created: 2020-12-12T02:09:18.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2024-03-27T03:57:36.000Z (over 2 years ago)
- Last Synced: 2024-11-10T02:28:56.458Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 2.65 MB
- Stars: 4
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Citation: CITATION.cff
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README
# cycless
A collection of algorithms to analyze a graph as a set of cycles.
Some codes come from [https://github.com/vitroid/Polyhed](vitroid/Polyhed) and [https://github.com/vitroid/countrings](vitroid/countrings) are integrated and improved.
Version 0.5
## API
API manual is [here](https://vitroid.github.io/cycless).
## cycles.py
A simple algorithm to enumerate all irreducible cycles of n-members and smaller in an undirected graph. [Matsumoto 2007]
```python
import cycless.cycles as cy
import networkx as nx
g = nx.cubical_graph()
for cycle in cy.cycles_iter(g, maxsize=6):
print(cycle)
```
## dicycles.py
An algorithm to enumerate the directed cycles of a size in a dircted graph. [Matsumoto 2021]
```python
from genice2.genice import GenIce
from genice2.plugin import Lattice, Format, Molecule
import cycless.dicycles as dc
# Generate an ice I structure as a directed graph
lattice = Lattice("1h")
formatter = Format("raw", stage=(3,))
raw = GenIce(lattice, signature="ice 1h", rep=[2, 2, 2]).generate_ice(formatter)
for cycle in dc.dicycles_iter(raw["digraph"], size=6):
print(cycle)
```
## polyhed.py
An algorithm to enumerate the quasi-polyhedral hull made of cycles in an undirected graph. A quasi-polyhedral hull (vitrite) obeys the following conditions: [Matsumoto 2007]
1. The surface of the hull is made of irreducible cycles.
2. Two or three cycles shares a vertex of the hull.
3. Two cycles shares an edge of the hull.
4. Its Euler index (F-E+V) is two.
```python
import cycless.cycles as cy
import cycless.polyhed as ph
import networkx as nx
g = nx.dodecahedral_graph()
cycles = [cycle for cycle in cy.cycles_iter(g, maxsize=6)]
for polyhed in ph.polyhedra_iter(cycles):
print(polyhed)
```
## simplex.py
Enumerate triangle, tetrahedral, and octahedral subgraphs found in the given graph.
## References
1. M. Matsumoto, A. Baba, and I. Ohmine, Topological building blocks of hydrogen bond network in water, J. Chem. Phys. 127, 134504 (2007). http://doi.org/10.1063/1.2772627
2. Matsumoto, M., Yagasaki, T. & Tanaka, H. On the anomalous homogeneity of hydrogen-disordered ice and its origin. J. Chem. Phys. 155, 164502 (2021). https://doi.org/10.1063/5.0065215