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Open Source Science

https://github.com/cmelab/grits

A toolkit for working with coarse-grain systems

https://github.com/cmelab/grits

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 5 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords

backmapping coarse-grain-mappings coarse-grained coarse-graining coarse-to-fine smarts smiles

Keywords from Contributors

molecular-dynamics molecular-simulation
Last synced: 6 months ago · JSON representation

Repository

A toolkit for working with coarse-grain systems

Basic Info
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 10
  • Open Issues: 10
  • Releases: 9
Topics
backmapping coarse-grain-mappings coarse-grained coarse-graining coarse-to-fine smarts smiles
Created almost 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License

README.md

GRiTS : Grits Reduces/Restores Topology with SMILES

Anaconda-Server Badge pytest codecov Documentation Status Docker build

GRiTS workflow

GRiTS is a toolkit for working with coarse-grain systems. It uses mBuild to build up molecules and SMILES chemical grammar to facilitate the mapping from fine-to-coarse and coarse-to-fine.

Installation

Using a container

To use GRiTS in a prebuilt container (using Apptainer), run: bash apptainer pull docker://ghcr.io/cmelab/grits:latest apptainer run grits_latest.sif python

Or using Docker, run: bash docker pull ghcr.io/cmelab/grits:latest docker run -it cmelab/grits:latest

Micromamba install

To create a local environment with micromamba, run: bash micromamba create grits -f environment.yml micromamba activate grits

Owner

  • Name: Computational Materials Engineering Laboratory
  • Login: cmelab
  • Kind: organization
  • Location: Boise, ID

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 2
  • Issue comment event: 7
  • Push event: 30
  • Pull request review comment event: 3
  • Pull request review event: 6
  • Pull request event: 27
  • Fork event: 1
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 2
  • Issue comment event: 7
  • Push event: 30
  • Pull request review comment event: 3
  • Pull request review event: 6
  • Pull request event: 27
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 306
  • Total Committers: 5
  • Avg Commits per committer: 61.2
  • Development Distribution Score (DDS): 0.173
Past Year
  • Commits: 15
  • Committers: 4
  • Avg Commits per committer: 3.75
  • Development Distribution Score (DDS): 0.667
Top Committers
Name Email Commits
Jenny Fothergill j****l@u****u 253
Jenny 3****l@u****m 24
pre-commit-ci[bot] 6****]@u****m 23
chrisjonesBSU c****4@u****u 5
chrisjonesBSU c****4@b****u 1
Committer Domains (Top 20 + Academic)
u.boisestate.edu: 2 boisestate.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 20
  • Total pull requests: 66
  • Average time to close issues: 3 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 5
  • Total pull request authors: 5
  • Average comments per issue: 0.9
  • Average comments per pull request: 0.52
  • Merged pull requests: 56
  • Bot issues: 0
  • Bot pull requests: 40
Past Year
  • Issues: 3
  • Pull requests: 16
  • Average time to close issues: N/A
  • Average time to close pull requests: about 22 hours
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.19
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 14
View more stats
Top Authors
Issue Authors
  • jennyfothergill (13)
  • chrisjonesBSU (4)
  • erjank (1)
  • eridanirojas (1)
  • StephMcCallum (1)
Pull Request Authors
  • pre-commit-ci[bot] (40)
  • jennyfothergill (16)
  • chrisjonesBSU (9)
  • StephMcCallum (1)
  • marjanAlbouye (1)
Top Labels
Issue Labels
bug (1) good first issue (1) maintenance (1)
Pull Request Labels
WIP (1) bug (1) maintenance (1)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
conda-forge.org: grits

GRiTS is a toolkit for working with coarse-grain systems. It uses mBuild <https://mbuild.mosdef.org> to build up molecules and SMILES <https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html> chemical grammar to facilitate the mapping from fine-to-coarse and coarse-to-fine.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 48.3%
Forks count: 49.6%
Dependent packages count: 51.2%
Stargazers count: 58.4%
Last synced: 6 months ago

Dependencies

.github/workflows/pytest.yml actions
  • actions/checkout v2 composite
  • codecov/codecov-action v1 composite
  • conda-incubator/setup-miniconda v2 composite
pyproject.toml pypi
setup.py pypi
environment.yml conda
  • cmeutils >=1.2.0
  • ele
  • freud 2.13.2.*
  • freud
  • gsd >=3.0
  • jupyterlab
  • mbuild
  • numpy
  • openbabel
  • pip
  • pre-commit
  • py3dmol
  • pytest
  • pytest-cov
  • python 3.10.*
  • rdkit