https://github.com/ale94mleon/toff

TOFF (Topologies from OpenFF) is a python package to get topologies from the OpenFF initiative for MD simulations

Science Score: 26.0%

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
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DOI references
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary

Keywords

drug-design molecular-dynamics openff topology

Last synced: 10 months ago · JSON representation

Repository

TOFF (Topologies from OpenFF) is a python package to get topologies from the OpenFF initiative for MD simulations

Basic Info

Host: GitHub
Owner: ale94mleon
License: apache-2.0
Language: Jupyter Notebook
Default Branch: main
Homepage: https://toff.rtfd.io
Size: 2.59 MB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 5

Topics

drug-design molecular-dynamics openff topology

Created over 3 years ago · Last pushed 10 months ago

Metadata Files

Readme License Code of conduct

README.rst

TOFF
=======
|logo|

.. list-table::
    :widths: 12 35

    * - **Documentation**
      - |docs|
    * - **Tutorials**
      - |binder|
    * - **CI/CD**
      - |tests| |codecov| |codacy|
    * - **Build**
      - |pypi-version|
    * - **Source Code**
      - |github|
    * - **Python Versions**
      - |pyversions|
    * - **Dependencies**
      - |rdkit| |OpenMM| |OpenFF| |ParmEd|
    * - **License**
      - |license|
    * - **Downloads**
      - |downloads|

Description
-----------

**TOFF** (Topologies from Open Force Fields) is a Python package initially developed to get topologies from the OpenFF initiative. Now it is possible to get GAFF and Espaloma topological parameters as well. It was strongly inspired in this `Aniket's script `__.

Since version **0.1.0** it is also possible to get `GAFF `__ and
`Espaloma `__.

You can try it out prior to any installation on `Binder `__.

Documentation
-------------

The installation instructions, documentation and tutorials can be found online on `ReadTheDocs `_.

Issues
------

If you have found a bug, please open an issue on the `GitHub Issues `_.

Discussion
----------

If you have questions on how to use **TOFF**, or if you want to give feedback or share ideas and new features, please head to the `GitHub Discussions `_.

Citing **TOFF**
------------------

Please refer to the `citation page `__ on the documentation.

Funding
-------

This project received funding from `Marie Skłodowska-Curie Actions `__. It was developed in the 
`Computational Biophysics Group `__ of `Saarland University `__.

..  |logo|  image:: https://github.com/ale94mleon/toff/blob/main/docs/source/_static/logo.png?raw=true
    :target: https://github.com/ale94mleon/toff/
    :alt: logo

..  |docs|  image:: https://readthedocs.org/projects/toff/badge/?version=latest
    :target: https://toff.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation

..  |binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/ale94mleon/TOFF/HEAD?labpath=%2Fdocs%2Fnotebooks%2F
    :alt: binder

..  |tests| image:: https://github.com/ale94mleon/TOFF/actions/workflows/tests.yml/badge.svg
    :target: https://github.com/ale94mleon/TOFF/actions/workflows/tests.yml
    :alt: tests

..  |codecov| image::  https://app.codacy.com/project/badge/Coverage/53c53c810b3c4767ab76f5d622ec6aef
    :target: hhttps://app.codacy.com/gh/ale94mleon/TOFF/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage
    :alt: codecov

..  |codacy| image:: https://app.codacy.com/project/badge/Grade/53c53c810b3c4767ab76f5d622ec6aef
    :target: https://app.codacy.com/gh/ale94mleon/TOFF/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
    :alt: codacy

..  |pypi-version|  image:: https://img.shields.io/pypi/v/TOFF.svg
    :target: https://pypi.python.org/pypi/TOFF/
    :alt: pypi-version

..  |conda|  image:: https://anaconda.org/ale94mleon/TOFF/badges/version.svg
    :target: https://anaconda.org/ale94mleon/TOFF
    :alt: conda

..  |github|    image:: https://badgen.net/badge/icon/github?icon=github&label
    :target: https://github.com/ale94mleon/TOFF
    :alt: GitHub-TOFF

..  |pyversions|    image:: https://img.shields.io/pypi/pyversions/toff.svg
    :target: https://pypi.python.org/pypi/toff/

..  |rdkit| image:: https://img.shields.io/static/v1?label=Powered%20by&message=RDKit&color=3838ff&style=flat&logo=data:image/x-icon;base64,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
    :target: https://www.rdkit.org/docs/index.html
    :alt: rdkit

..  |OpenMM| image:: https://img.shields.io/static/v1?label=Powered%20by&message=OpenMM&color=6858ff&style=flat
    :target: http://docs.openmm.org/latest/userguide/
    :alt: OpenMM

..  |OpenFF| image:: https://img.shields.io/static/v1?label=Powered%20by&message=OpenFF&color=9438ff&style=flat
    :target: https://docs.openforcefield.org/projects/toolkit/en/latest/
    :alt: OpenFF

..  |ParmEd| image:: https://img.shields.io/static/v1?label=Powered%20by&message=ParmEd&color=2038ff&style=flat
    :target: https://parmed.github.io/ParmEd/html/'
    :alt: ParmEd

..  |license| image:: https://badgen.net/pypi/license/toff/
    :target: https://pypi.python.org/pypi/toff/
    :alt: license

..  |downloads| image:: https://static.pepy.tech/personalized-badge/toff?period=total&units=international_system&left_color=grey&right_color=brightgreen&left_text=Downloads
    :target: https://pepy.tech/project/toff
    :alt: download

Owner

Name: Alejandro Martínez-León
Login: ale94mleon
Kind: user
Location: Germany
Company: Universität des Saarlandes

Website: https://alejandro.netlify.app/
Repositories: 26
Profile: https://github.com/ale94mleon

GitHub Events

Total

Release event: 2
Delete event: 4
Push event: 13
Create event: 4

Last Year

Release event: 2
Delete event: 4
Push event: 13
Create event: 4

Committers

Last synced: over 2 years ago

All Time

Total Commits: 59
Total Committers: 1
Avg Commits per committer: 59.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 27
Committers: 1
Avg Commits per committer: 27.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
ale94mleon	a**n@g**m	59

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 0
Total pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 26 minutes
Total issue authors: 0
Total pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 2.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

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

View more stats

Top Authors

Issue Authors

Pull Request Authors

ale94mleon (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 57 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 6
Total maintainers: 1

pypi.org: toff

toff is a python package to get topologies from the OpenFF initiative.

Documentation: https://toff.readthedocs.io/en/latest/
License: Apache Software License
Latest release: 0.2.0
published about 1 year ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 57 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 29.8%

Average: 38.6%

Stargazers count: 38.8%

Downloads: 47.3%

Dependent repos count: 67.1%

Maintainers (1)

ale94mleon

Last synced: 10 months ago

Dependencies

.github/workflows/codeql-analysis.yml actions

actions/checkout v3 composite
github/codeql-action/analyze v2 composite
github/codeql-action/autobuild v2 composite
github/codeql-action/init v2 composite

.github/workflows/pypi-publish.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/tests.yml actions

actions/checkout v3 composite
codecov/codecov-action v3 composite
s-weigand/setup-conda v1 composite

.binder/environment.yml pypi

matplotlib *
requests *
toff *

.conda_create_env/environment.yml pypi

myst_nb *
parmed *
pyyaml *
recommonmark *
sphinx_book_theme *
sphinx_copybutton *

pyproject.toml pypi

parmed *
pyyaml *
rdkit *

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/ale94mleon/toff

Science Score: 26.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.rst

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

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Top Labels

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Packages

pypi.org: toff

Rankings

Maintainers (1)

Dependencies