foyer

A package for atom-typing as well as applying and disseminating forcefields

https://github.com/mosdef-hub/foyer

Science Score: 77.0%

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
Found 1 DOI reference(s) in README
✓
Academic publication links
Links to: arxiv.org, sciencedirect.com, zenodo.org
✓
Committers with academic emails
20 of 47 committers (42.6%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary

Keywords

atom-typing disseminating-forcefields force-field foyer molecular-dynamics molecular-simulation python

Keywords from Contributors

chemistry computational-chemistry quantum-chemistry standards data-management reproducibility

Last synced: 6 months ago · JSON representation ·

Repository

A package for atom-typing as well as applying and disseminating forcefields

Basic Info

Host: GitHub
Owner: mosdef-hub
License: mit
Language: Python
Default Branch: main
Homepage: https://foyer.mosdef.org
Size: 31.6 MB

Statistics

Stars: 133
Watchers: 20
Forks: 77
Open Issues: 63
Releases: 39

Topics

atom-typing disseminating-forcefields force-field foyer molecular-dynamics molecular-simulation python

Created almost 11 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Citation

Foyer: A package for atom-typing as well as applying and disseminating forcefields

Overview

Foyer is an open-source Python tool for defining and applying force field atom-typing rules in a format that is both human- and machine-readable. It parametrizes chemical topologies, generating, syntactically correct input files for various simulation engines. Foyer provides a framework for force field dissemination, helping to eliminate ambiguity in atom-typing and improving reproducibility (for more information, see our paper or its corresponding pre-print).

About the name: foyer was inspired by the antechamber tool in the Amber ecosystem. Foyer plays a similar role to antechamber, hence the tongue-in-cheek, shared vestibular reference.

Foyer within the MoSDeF Ecosystem

Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type and “overrides” are used to set rule precedence, rather than a rigid hierarchical scheme. Foyer builds upon the OpenMM .xml force field file, annotated with SMARTS-based atomtypes, e.g.:

xml <ForceField> <AtomTypes> <Type name="opls_135" class="CT" element="C" mass="12.01100" def="[C;X4](C)(H)(H)H" desc="alkane CH3"/> <Type name="opls_140" class="HC" element="H" mass="1.00800" def="H[C;X4]" desc="alkane H"/> </AtomTypes> </ForceField>

Foyer can apply the forcefield to arbitrary chemical topologies. We currently support:

Application of a force field can be as simple as: ```python from foyer import Forcefield import parmed as pmd

untypedethane = pmd.loadfile('ethane.mol2', structure=True) oplsaa = Forcefield(forcefieldfiles='oplsaa.xml') ethane = oplsaa.apply(untypedethane)

Save to any format supported by ParmEd

ethane.save('ethane.top') ethane.save('ethane.gro') ```

The Foyer package is part of the Molecular Simulation Design Framework (MoSDeF) project. Libraries in the MoSDeF ecosystem are designed to provide utilities necessary to streamline a researcher's simulation workflow. When setting up simulation studies, we also recommend users to follow the TRUE (Transparent, Reproducible, Usable-by-others, and Extensible) standard, which is a set of common practices meant to improve the reproducibility of computational simulation research.

Getting started

Quick Start with Docker

To use foyer in a jupyter-notebook that runs from a docker container with all the dependencies installed use the following command:

sh $ docker pull mosdef/foyer:latest $ docker run -it --name foyer -p 8888:8888 mosdef/foyer:latest\ /opt/conda/envs/foyer-docker/bin/jupyter notebook --ip="*"

Alternatively, you can also start a Bourne shell directly: sh $ docker run -it --name foyer mosdef/foyer:latest

To learn more about using foyer with docker, please refer to the documentation here .

Getting started with SMARTS-based atom-typing

Defining force fields:

Example foyer force field files:

Foyer currently includes a subset of the OPLS AA and TraPPE forcefields, currently part of the source distribution: * https://github.com/mosdef-hub/foyer/tree/master/foyer/forcefields

Additional example force field XML files: * https://github.com/chrisiacovella/OPLSaaperfluoroalkanes * https://github.com/mosdef-hub/forcefieldperfluoroethers * https://github.com/summeraz/OPLSaa_alkylsilanes

Example template for disseminating force fields: * https://github.com/mosdef-hub/forcefield_template

Using Foyer to perform atom typing:

Documentation:

Documentation website: http://foyer.mosdef.org

Installation instructions

Installation instructions

Citing Foyer:

If you use this package, please cite our paper published in Computational Materials Science.
This manuscript is also available in its pre-print form on arxiv
The paper and examples in this work were developed for tag paperCOMMAT2019
Please also cite the github repository, https://github.com/mosdef-hub/foyer

Various sub-portions of this library may be independently distributed under different licenses. See those files for their specific terms.

This material is based upon work supported by the National Science Foundation under grants NSF ACI-1047828 and NSF ACI-1535150. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Owner

Name: MoSDeF - the Molecular Simulation Design Framework
Login: mosdef-hub
Kind: organization

Website: https://mosdef.org
Repositories: 26
Profile: https://github.com/mosdef-hub

MoSDeF builds, atom types, and parametrizes arbitrary chemical systems for molecular simulation in an engine agnostic manner.

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  Foyer: A package for atom-typing as well as
  applying and disseminating forcefields
message: >-
  If you use this software, please cite it using the
  metadata from this file and the preferred citation.
type: software
authors:
  - given-names: Christoph
    family-names: Klein
    affiliation: "Vanderbilt University"
  - given-names: "Andrew Z."
    family-names: Summers
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0001-8477-3059'
  - given-names: "Matthew W."
    family-names: Thompson
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-1460-3983'
  - given-names: "Justin B."
    family-names: Gilmer
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-6915-5591'
  - given-names: "Co D."
    family-names: Quach
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-1255-4161'
  - given-names: Umesh
    family-names: Timalsina
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-5430-3993'
  - given-names: Peter
    family-names: Volgyesi
    orcid: 'https://orcid.org/0000-0002-7478-4317'
    affiliation: "Vanderbilt University"
  - given-names: Janos
    family-names: Sallai
    affiliation: "Vanderbilt University"
  - given-names: "Chris R."
    family-names: Iacovella
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0003-0557-0427'
  - given-names: Clare
    family-names: McCabe
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-8552-9135'
  - given-names: "Peter T."
    family-names: Cummings
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-9766-2216'
identifiers:
  - type: doi
    value: 10.5281/zenodo.6229092
    description: Zenodo Doi
repository-code: 'https://github.com/mosdef-hub/foyer'
url: 'https://foyer.mosdef.org'
repository: 'https://github.com/mosdef-hub/foyer'
repository-artifact: 'https://github.com/mosdef-hub/foyer/releases'
abstract: >-
  Foyer is an open-source Python tool for defining
  and applying force field atom-typing rules in a
  format that is both human- and machine-readable. It
  parametrizes chemical topologies, generating,
  syntactically correct input files for various
  simulation engines. Foyer provides a framework for
  force field dissemination, helping to eliminate
  ambiguity in atom-typing and improving
  reproducibility.
keywords:
  - atom-typing
  - reproducibility
  - 'TRUE'
  - mosdef
  - python
license: MIT
preferred-citation:
  type: article
  authors:
    - given-names: Christoph
      family-names: Klein
      affiliation: "Vanderbilt University"
    - given-names: "Andrew Z."
      family-names: Summers
      affiliation: "Vanderbilt University"
      orcid: 'https://orcid.org/0000-0001-8477-3059'
    - given-names: "Matthew W."
      family-names: Thompson
      affiliation: "Vanderbilt University"
      orcid: 'https://orcid.org/0000-0002-1460-3983'
    - given-names: "Justin B."
      family-names: Gilmer
      affiliation: "Vanderbilt University"
      orcid: 'https://orcid.org/0000-0002-6915-5591'
    - given-names: Clare
      family-names: McCabe
      affiliation: "Vanderbilt University"
      orcid: 'https://orcid.org/0000-0002-8552-9135'
    - given-names: "Peter T."
      family-names: Cummings
      affiliation: "Vanderbilt University"
      orcid: 'https://orcid.org/0000-0002-9766-2216'
    - given-names: Janos
      family-names: Sallai
      affiliation: "Vanderbilt University"
    - given-names: "Chris R."
      family-names: Iacovella
      affiliation: "Vanderbilt University"
      orcid: 'https://orcid.org/0000-0003-0557-0427'
  title: "Formalizing atom-typing and the dissemination of force fields with foyer"
  journal: "Comput. Mater. Sci."
  volume: "167"
  pages: "12"
  year: "2019"
  doi: "10.1016/j.commatsci.2019.05.026"

GitHub Events

Total

Issues event: 8
Watch event: 13
Issue comment event: 32
Push event: 60
Pull request review comment event: 24
Pull request review event: 19
Pull request event: 58
Create event: 1

Last Year

Issues event: 8
Watch event: 13
Issue comment event: 32
Push event: 60
Pull request review comment event: 24
Pull request review event: 19
Pull request event: 58
Create event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 681
Total Committers: 47
Avg Commits per committer: 14.489
Development Distribution Score (DDS): 0.767

Past Year

Commits: 28
Committers: 10
Avg Commits per committer: 2.8
Development Distribution Score (DDS): 0.607

Top Committers

Name	Email	Commits
Christoph Klein	c**n@m**m	159
Matthew W. Thompson	m**n@v**u	136
Andrew Summers	a**s@g**m	66
Co Quach	d**7@g**m	38
Alex Yang	a**z@v**u	37
Umesh Timalsina	u**a@v**u	34
pre-commit-ci[bot]	6**]@u**m	27
Co Quach	4**7@u**m	22
Ray A. Matsumoto	r**o@v**u	20
Justin Gilmer	j**r@g**u	17
Justin Gilmer	j**r@v**u	14
Arjun Bansal	a**l@v**u	10
ahy3nz	a**g@v**u	10
sallai	j**i@g**m	8
AndrewPuente	a**e@v**u	7
Jenny	3**l@u**m	7
Arjun Bansal	5**9@u**m	6
Mike Henry	m**y@b**u	5
matt.thompson@vanderbilt.edu	m**p@g**m	5
Justin	j**r@g**m	4
Peter Volgyesi	p**i@v**u	4
Janos Sallai	j**i@v**u	4
Parashara Shamaprasad	p**a@v**u	4
Matt Thompson	m**n@p**m	3
Ray Matsumoto	r**o@M**l	3
Ryan S. DeFever	r**r@g**m	3
chrisiacovella	c**a@v**u	3
sallai	s**s@v**u	2
Eisuke Kawashima	e**m@u**m	2
CalCraven	5**n@u**m	2
and 17 more...

Committer Domains (Top 20 + Academic)

vanderbilt.edu: 12 ioe.edu.np: 1 dh-129-59-37-231.vuse.vanderbilt.edu: 1 nd.edu: 1 bradleydice.com: 1 uci.edu: 1 master.cl.vanderbilt.edu: 1 boisestate.edu: 1 g.clemson.edu: 1 virginia.edu: 1 me.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 69
Total pull requests: 167
Average time to close issues: over 1 year
Average time to close pull requests: 15 days
Total issue authors: 31
Total pull request authors: 21
Average comments per issue: 1.99
Average comments per pull request: 1.19
Merged pull requests: 142
Bot issues: 0
Bot pull requests: 94

Past Year

Issues: 8
Pull requests: 61
Average time to close issues: 2 months
Average time to close pull requests: 3 days
Issue authors: 3
Pull request authors: 4
Average comments per issue: 1.0
Average comments per pull request: 0.16
Merged pull requests: 50
Bot issues: 0
Bot pull requests: 51

View more stats

Top Authors

Issue Authors

iGulitch (11)
daico007 (7)
mattwthompson (6)
CalCraven (4)
bc118 (4)
rsdefever (3)
umesh-timalsina (3)
chrisjonesBSU (2)
jennyfothergill (2)
ctk3b (2)
mikemhenry (2)
chrisiacovella (2)
InnocentBug (2)
mattiafelice-palermo (1)
bkpgh (1)

Pull Request Authors

pre-commit-ci[bot] (103)
daico007 (21)
chrisjonesBSU (15)
mattwthompson (8)
jennyfothergill (5)
umesh-timalsina (5)
justinGilmer (3)
CalCraven (2)
e-kwsm (2)
jaclark5 (2)
XiaoboLinlin (2)
rsdefever (1)
dyukovsm (1)
ctk3b (1)
bc118 (1)

Top Labels

Issue Labels

feature (7) question (3) bug (2) maintenance (2) documentation (2) atomtyping (1)

Pull Request Labels

maintenance (11) documentation (2) bug (1)

Packages

Total packages: 2
Total downloads:
- pypi 122 last-month
Total docker downloads: 100

Total dependent packages: 4
(may contain duplicates)
Total dependent repositories: 28
(may contain duplicates)
Total versions: 33
Total maintainers: 2

pypi.org: foyer

Foyer: Atomtyping and forcefield applying.

Homepage: https://github.com/mosdef-hub/foyer
Documentation: https://foyer.readthedocs.io/
License: MIT
Latest release: 0.7.6
published over 5 years ago

Versions: 20
Dependent Packages: 0
Dependent Repositories: 10
Downloads: 122 Last month
Docker Downloads: 100

Rankings

Docker downloads count: 2.2%

Dependent repos count: 4.6%

Forks count: 5.2%

Stargazers count: 7.0%

Average: 8.3%

Dependent packages count: 10.0%

Downloads: 20.9%

Maintainers (2)

mosdef sallai

Last synced: 6 months ago

conda-forge.org: foyer

Foyer is an open-source Python tool that enables users to define and apply force field atom-typing rules in a format that is both human- and machine-readable and provides a framework for force field dissemination, thus eliminating ambiguity in atom-typing and improving reproducibility. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type and "overrides" are used to set rule precedence, rather than a rigid hierarchical scheme.

Homepage: https://github.com/mosdef-hub/foyer
License: MIT
Latest release: 0.11.3
published over 3 years ago

Versions: 13
Dependent Packages: 4
Dependent Repositories: 18

Rankings

Dependent repos count: 8.4%

Dependent packages count: 12.5%

Average: 19.4%

Forks count: 21.8%

Stargazers count: 35.0%

Last synced: 6 months ago

Dependencies

.github/workflows/CI.yaml actions

actions/checkout v2 composite
codecov/codecov-action v2 composite
docker/build-push-action v2 composite
docker/login-action v1 composite
docker/setup-buildx-action v1 composite
mamba-org/provision-with-micromamba main composite

.github/workflows/codeql.yml actions

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

Dockerfile docker

continuumio/miniconda3 4.10.3-alpine build

setup.py pypi

environment.yml conda

ele
gmso
lark-parser
lxml
networkx >=2.5
openmm
parmed >=3.4.3
python >=3.8
requests

foyer

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Foyer: A package for atom-typing as well as applying and disseminating forcefields

Overview

Foyer within the MoSDeF Ecosystem

Save to any format supported by ParmEd

Getting started

Quick Start with Docker

Getting started with SMARTS-based atom-typing

Defining force fields:

Example foyer force field files:

Using Foyer to perform atom typing:

Documentation:

Installation instructions

Citing Foyer:

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: foyer

Rankings

Maintainers (2)

conda-forge.org: foyer

Rankings

Dependencies