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from-smiles-step

A SEAMM plug-in for creating structures from a SMILES string.

https://github.com/molssi-seamm/from_smiles_step

Science Score: 49.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
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    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords

computational-chemistry computational-materials-science molssi molssi-seamm
Last synced: 7 months ago · JSON representation

Repository

A SEAMM plug-in for creating structures from a SMILES string.

Basic Info
  • Host: GitHub
  • Owner: molssi-seamm
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 5.31 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 1
  • Releases: 25
Topics
computational-chemistry computational-materials-science molssi molssi-seamm
Created about 8 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Authors Zenodo

README.rst 

.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/from_smiles_step
   :target: https://github.com/molssi-seamm/from_smiles_step/pulls
   :alt: GitHub pull requests

.. image:: https://github.com/molssi-seamm/from_smiles_step/workflows/CI/badge.svg
   :target: https://github.com/molssi-seamm/from_smiles_step/actions
   :alt: Build Status

.. image:: https://codecov.io/gh/molssi-seamm/from_smiles_step/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/molssi-seamm/from_smiles_step
   :alt: Code Coverage

.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/from_smiles_step.svg?logo=lgtm&logoWidth=18
   :target: https://lgtm.com/projects/g/molssi-seamm/from_smiles_step/context:python
   :alt: Code Quality

.. image:: https://github.com/molssi-seamm/from_smiles_step/workflows/Documentation/badge.svg
   :target: https://molssi-seamm.github.io/from_smiles_step/index.html
   :alt: Documentation Status

.. image:: https://pyup.io/repos/github/molssi-seamm/from_smiles_step/shield.svg
   :target: https://pyup.io/repos/github/molssi-seamm/from_smiles_step/
   :alt: Updates for Dependencies

.. image:: https://img.shields.io/pypi/v/from_smiles_step.svg
   :target: https://pypi.python.org/pypi/from_smiles_step
   :alt: PyPi VERSION

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5159800.svg
   :target: https://doi.org/10.5281/zenodo.5159800
   :alt: DOI

=========================
SEAMM From SMILES plug-in
=========================

A SEAMM plug-in for creating structures from a SMILES string.

This plug-in accepts SMILES_ (Simplified Molecular-Input Line Entry
System) string representing a structure, and creates the structure if
the current system/conformation in SEAMM. It uses the implementation
in `Open Babel`_ which has an extension for handling radicals_.

* Free software: BSD license
* Documentation: https://from-smiles-step.readthedocs.io.

.. _SMILES: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
.. _`Open Babel`: http://openbabel.org/wiki/Main_Page
.. _radicals: http://openbabel.org/wiki/Radicals_and_SMILES_extensions

Features
--------

* Accepts with a SMILES string directly or from a variable.
* The generated structure can optionally be optimized using one of
  several forcefields.

Acknowledgements
----------------

This package was created with Cookiecutter_ and the `molssi-seamm/cookiecutter-seamm-plugin`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin

Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the `National Science Foundation`_ under
award OAC-1547580 and CHE-2136142.

.. _MolSSI: https://www.molssi.org
.. _`National Science Foundation`: https://www.nsf.gov

Owner

  • Name: MolSSI SEAMM
  • Login: molssi-seamm
  • Kind: organization
  • Email: seamm@molssi.org

Simulation Environment for Atomistic and Molecular Modeling

GitHub Events

Total
  • Release event: 4
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 16
  • Pull request review event: 5
  • Pull request event: 7
  • Create event: 4
Last Year
  • Release event: 4
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 16
  • Pull request review event: 5
  • Pull request event: 7
  • Create event: 4

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 95
  • Total Committers: 3
  • Avg Commits per committer: 31.667
  • Development Distribution Score (DDS): 0.147
Top Committers
Name Email Commits
Paul Saxe p****l@t****t 81
Paul Saxe p****e@t****t 13
dependabot[bot] 4****]@u****m 1
Committer Domains (Top 20 + Academic)
thesaxes.net: 2

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 3
  • Total pull requests: 26
  • Average time to close issues: 11 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 2
  • Total pull request authors: 4
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.42
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 25 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.17
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • seamm (2)
  • pyup-bot (1)
Pull Request Authors
  • paulsaxe (19)
  • seamm (6)
  • doaa-altarawy (1)
  • dependabot[bot] (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
bug (6) enhancement (5) Documentation (1) dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 300 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 27
  • Total maintainers: 1
pypi.org: from-smiles-step

A SEAMM plug-in for creating structures from a SMILES string.

  • Versions: 27
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 300 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 11.5%
Downloads: 15.3%
Average: 21.1%
Forks count: 29.8%
Stargazers count: 38.8%
Maintainers (1)
seamm
Last synced: 8 months ago

Dependencies

requirements.txt pypi
  • seamm ==2021.2.2
requirements_dev.txt pypi
  • black * development
  • coverage * development
  • flake8 * development
  • pytest * development
  • pytest-runner * development
  • sphinx * development
  • tox * development
  • twine * development
requirements_install.txt pypi
  • seamm *
.github/workflows/BranchCI.yaml actions
  • actions/checkout v1 composite
  • codecov/codecov-action v2 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/CI.yaml actions
  • actions/checkout v1 composite
  • codecov/codecov-action v2 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/Docs.yaml actions
  • actions/checkout v1 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/Release.yaml actions
  • actions/checkout v1 composite
  • actions/setup-python v1 composite
  • codecov/codecov-action v2 composite
  • conda-incubator/setup-miniconda v2 composite
  • pypa/gh-action-pypi-publish master composite
setup.py pypi