cycless

Algorithms for cycles in a graph

https://github.com/vitroid/cycless

Science Score: 39.0%

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Found 4 DOI reference(s) in README
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Low similarity (4.7%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Algorithms for cycles in a graph

Basic Info

Host: GitHub
Owner: vitroid
Language: Jupyter Notebook
Default Branch: main
Size: 2.67 MB

Statistics

Stars: 6
Watchers: 2
Forks: 1
Open Issues: 1
Releases: 0

Created over 5 years ago · Last pushed over 1 year ago

Metadata Files

Readme Citation

README.md

cycless

A collection of algorithms to analyze a graph as a set of cycles.

Some codes come from https://github.com/vitroid/Polyhed and https://github.com/vitroid/countrings are integrated and improved.

Version 0.5

API

API manual is here.

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]

The surface of the hull is made of irreducible cycles.
Two or three cycles shares a vertex of the hull.
Two cycles shares an edge of the hull.
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.cyclesiter(g, maxsize=6)] for polyhed in ph.polyhedraiter(cycles): print(polyhed) ```

simplex.py

Enumerate triangle, tetrahedral, and octahedral subgraphs found in the given graph.

References

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
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

Owner

Name: Masakazu Matsumoto
Login: vitroid
Kind: user
Location: Okayama, Japan
Company: Okayama University

Repositories: 56
Profile: https://github.com/vitroid

Citation (CITATION.cff)

GitHub Events

Total

Issues event: 1
Watch event: 1
Push event: 8
Fork event: 1

Last Year

Issues event: 1
Watch event: 1
Push event: 8
Fork event: 1

Committers

Last synced: over 3 years ago

All Time

Total Commits: 13
Total Committers: 1
Avg Commits per committer: 13.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Masakazu Matsumoto	v**d@g**m	13

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 2
Total pull requests: 0
Average time to close issues: about 1 hour
Average time to close pull requests: N/A
Total issue authors: 2
Total pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

abhigyanh (1)
vitroid (1)

Pull Request Authors

Top Labels

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Packages

Total packages: 1
Total downloads:
- pypi 351 last-month

Total dependent packages: 3
Total dependent repositories: 5
Total versions: 13
Total maintainers: 1

pypi.org: cycless

A collection of algorithms for cycles in a graph.

Documentation: https://cycless.readthedocs.io/
License: MIT
Latest release: 0.6.3
published over 1 year ago

Versions: 13
Dependent Packages: 3
Dependent Repositories: 5
Downloads: 351 Last month

Rankings

Dependent packages count: 3.2%

Dependent repos count: 6.6%

Average: 7.5%

Downloads: 12.7%

Maintainers (1)

vitroid

Last synced: 11 months ago

Dependencies

setup.py pypi

methodtools *
networkx >=2.0.dev20160901144005
numpy *
wheel *

Pipfile pypi

cycless * develop
genice2 * develop
jinja2 * develop
jupyter * develop
mdanalysis * develop
networkx * develop
pairlist * develop
pdoc3 * develop
py3dmol * develop
toml * develop
twine * develop
networkx *
numpy *

pyproject.toml pypi