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rgrow

The rgrow kinetic tile assembly simulator

https://github.com/cgevans/rgrow

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

The rgrow kinetic tile assembly simulator

Basic Info
  • Host: GitHub
  • Owner: cgevans
  • License: mit
  • Language: Rust
  • Default Branch: main
  • Homepage:
  • Size: 2.59 MB
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 0
  • Open Issues: 6
  • Releases: 9
Created about 2 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation Zenodo

README.md

Introduction

rgrow (which may change name in the future) is a fast, extensible simulator for Tile Assembly Models, primarily focused on kinetic models that require fast simulations of attachment and detachment events. It is inspired by Xgrow, but seeks to be more extensible and easier and faster to use programmably. It has Rust and Python interfaces, and a command line and UI interface similar to Xgrow. It includes an implementation of forward flux sampling for nucleation rate calculations.

Python documentation is available at https://rgrow.readthedocs.io/en/latest/.

Rust documentation is available at https://docs.rs/rgrow/.

For FFS examples, see the examples/ffs folder.

Installation

Python library

Releases are pushed, in both source and a variety of binary forms, to PyPI. To install the latest release, use:

bash pip install rgrow

To install directly from git using Pip:

bash pip install "git+https://github.com/cgevans/rgrow.git"

For backwards compatibility, you can also use:

bash pip install "git+https://github.com/cgevans/rgrow.git#subdirectory=py-rgrow"

or check out the repository, and use

bash cd py-rgrow maturin develop --release -- -C target-cpu=native

The FLTK-based UI is usable within Python if you have the correct dependencies, and activate the "ui" feature:

bash cd py-rgrow maturin develop --release -F ui -- -C target-cpu=native

Rust / CLI

Note that the rust version currently requires Rust nightly. This should change soon.

bash cargo install rgrow

Owner

  • Name: Constantine Evans
  • Login: cgevans
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Evans"
    given-names: "Constantine"
    orcid: "https://orcid.org/0000-0002-7053-1670"
  - family-names: "Cervera Roldan"
    given-names: "Angel"
    orcid: "https://orcid.org/0009-0006-9183-5303"
title: "Rgrow tile self-assembly simulator"
license: MIT
doi: 10.5281/zenodo.15270474
url: "https://doi.org/10.5281/zenodo.15270474"
version: "0.19.4"

GitHub Events

Total
  • Create event: 13
  • Release event: 3
  • Issues event: 2
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 3
  • Push event: 133
  • Pull request review comment event: 2
  • Pull request review event: 5
  • Pull request event: 13
Last Year
  • Create event: 13
  • Release event: 3
  • Issues event: 2
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 3
  • Push event: 133
  • Pull request review comment event: 2
  • Pull request review event: 5
  • Pull request event: 13

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 6
  • Total pull requests: 15
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: 11 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.6
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.75
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cgevans (6)
Pull Request Authors
  • cgevans (15)
  • angelcerveraroldan (6)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cargo 10,842 total
    • pypi 165 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 32
  • Total maintainers: 2
pypi.org: rgrow

Python interface to rgrow.

  • Versions: 18
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 165 Last month
Rankings
Dependent packages count: 6.6%
Forks count: 30.5%
Dependent repos count: 30.6%
Average: 35.2%
Stargazers count: 39.1%
Downloads: 69.1%
Maintainers (1)
cevans
Last synced: 6 months ago
crates.io: rgrow

A modular Tile Assembly Model simulator, inspired by Xgrow.

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 10,842 Total
Rankings
Dependent repos count: 29.3%
Dependent packages count: 33.8%
Forks count: 37.5%
Average: 48.0%
Stargazers count: 50.6%
Downloads: 88.6%
Maintainers (1)
cgevans
Last synced: 7 months ago