openff-bespokefit

Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.

https://github.com/openforcefield/openff-bespokefit

Science Score: 67.0%

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

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 4 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
4 of 12 committers (33.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary

Keywords from Contributors

chemistry computational-chemistry quantum-chemistry standards codata nist periodic-table physical-constant

Last synced: 6 months ago · JSON representation ·

Repository

Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.

Basic Info

Host: GitHub
Owner: openforcefield
License: mit
Language: Python
Default Branch: main
Homepage: https://docs.openforcefield.org/bespokefit
Size: 1.73 MB

Statistics

Stars: 70
Watchers: 20
Forks: 10
Open Issues: 58
Releases: 14

Created about 6 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Codeowners

BespokeFit

The BespokeFit framework aims to offer a completely automated workflow for creating bespoke, highly accurate, SMIRNOFF format parameters for individual molecules up to entire lead series.

**Warning: This code is currently experimental and under active development. If you are using this it, please be aware that it is not guaranteed to provide correct results, the documentation and testing may be incomplete, and the API can change without notice.

Getting Started

To start using this framework we recommend looking over the documentation. If you'd like to run some basic examples immediately, see the quick start guide, or if you plan to explore the functionality in more depth, begin with the installation guide. For information on developing and contributing to BespokeFit, see CONTRIBUTING.md.

How to cite

In any publications using BespokeFit, please cite:

Joshua T. Horton, Simon Boothroyd, Jeffrey Wagner, Joshua A. Mitchell, Trevor Gokey, David L. Dotson, Pavan Kumar Behara, Venkata Krishnan Ramaswamy, Mark Mackey, John D. Chodera, Jamshed Anwar, David L. Mobley, and Daniel J. Cole "Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale" J. Chem. Inf. Model. 2022, 62, 22, 5622–5633

A pre-print of this paper is freely available from ChemRxiv.

License

OpenFF BespokeFit is released under the MIT license.

Copyright

Owner

Name: Open Force Field Initiative
Login: openforcefield
Kind: organization

Website: http://openforcefield.org
Repositories: 61
Profile: https://github.com/openforcefield

An open source, open science, and open data approach to better force fields

Citation (CITATION.cff)

cff-version: 1.2.0
title: OpenFF BespokeFit
message: >-
  In any publications using force fields produced by
  BespokeFit, please cite:
type: software
authors:
  - given-names: The BespokeFit Contributors
identifiers:
  - type: doi
    value: 10.1021/acs.jcim.2c01153
  - type: url
    value: 'https://doi.org/10.26434/chemrxiv-2022-6h628'
    description: ChemRxiv
repository-code: 'https://github.com/openforcefield/openff-bespokefit'
url: 'https://docs.openforcefield.org/bespokefit'
abstract: >-
  The development of accurate transferable force fields is
  key to realizing the full potential of atomistic modeling
  in the study of biological processes such as
  protein–ligand binding for drug discovery.
  State-of-the-art transferable force fields, such as those
  produced by the Open Force Field Initiative, use modern
  software engineering and automation techniques to yield
  accuracy improvements. However, force field torsion
  parameters, which must account for many stereoelectronic
  and steric effects, are considered to be less transferable
  than other force field parameters and are therefore often
  targets for bespoke parametrization. Here, we present the
  Open Force Field QCSubmit and BespokeFit software packages
  that, when combined, facilitate the fitting of torsion
  parameters to quantum mechanical reference data at scale.
  We demonstrate the use of QCSubmit for simplifying the
  process of creating and archiving large numbers of quantum
  chemical calculations, by generating a dataset of 671
  torsion scans for druglike fragments. We use BespokeFit to
  derive individual torsion parameters for each of these
  molecules, thereby reducing the root-mean-square error in
  the potential energy surface from 1.1 kcal/mol, using the
  original transferable force field, to 0.4 kcal/mol using
  the bespoke version. Furthermore, we employ the bespoke
  force fields to compute the relative binding free energies
  of a congeneric series of inhibitors of the TYK2 protein,
  and demonstrate further improvements in accuracy, compared
  to the base force field (MUE reduced from
  0.56_{0.39}^{0.77} to 0.42_{0.28}^{0.59} kcal/mol and R2
  correlation improved from 0.72_{0.35}^{0.87} to
  0.93_{0.84}^{0.97}).
keywords:
  - force field
  - free energy
  - molecular mechanics
  - forcebalance
  - openff
  - smirnoff
  - qcsubmit
  - qcengine
license: MIT

preferred-citation:
  type: article
  title: >-
    Open Force Field BespokeFit: Automating Bespoke Torsion
    Parametrization at Scale
  authors:
    - given-names: Joshua T.
      family-names: Horton
      orcid: 'https://orcid.org/0000-0001-8694-7200'
      affiliation: >-
        School of Natural and Environmental Sciences,
        Newcastle University
    - given-names: Simon
      family-names: Boothroyd
      affiliation: Boothroyd Scientific Consulting Ltd.
      orcid: 'https://orcid.org/0000-0002-3456-1872'
    - given-names: Jeffrey
      family-names: Wagner
      affiliation: The Open Force Field Initiative
      orcid: 'https://orcid.org/0000-0001-6448-0873'
    - given-names: Joshua A.
      family-names: Mitchell
      affiliation: The Open Force Field Initiative
      orcid: 'https://orcid.org/0000-0002-8246-5113'
      email: josh.mitchell@openforcefield.org
    - given-names: Trevor
      family-names: Gokey
      affiliation: 'Dept. Chemistry, UC Irvine'
      orcid: 'https://orcid.org/0000-0001-7856-1156'
    - given-names: David L.
      family-names: Dotson
      orcid: 'https://orcid.org/0000-0001-5879-2942'
      affiliation: The Open Force Field Initiative
    - given-names: Pavan Kumar
      family-names: Behara
      orcid: 'https://orcid.org/0000-0001-6583-2148'
      affiliation: 'Dept. Pharmaceutical Sciences, UC Irvine'
    - given-names: Venkata Krishnan
      family-names: Ramaswamy
      affiliation: Cresset BioMolecular Discovery Ltd.
      orcid: 'https://orcid.org/0000-0002-5804-8483'
    - given-names: Mark
      family-names: Mackey
      affiliation: Cresset BioMolecular Discovery Ltd.
      orcid: 'https://orcid.org/0000-0001-5131-7583'
    - orcid: 'https://orcid.org/0000-0003-0542-119X'
      given-names: John D.
      family-names: Chodera
      affiliation: >-
        Computational & Systems Biology Program, Sloan
        Kettering Institute
    - given-names: Jamshed
      family-names: Anwar
      affiliation: 'Dept. Chemistry, Lancaster University'
      orcid: 'https://orcid.org/0000-0003-1721-0330'
    - given-names: David L.
      family-names: Mobley
      affiliation: 'Dept. Chemistry, UC Irvine'
      orcid: 'https://orcid.org/0000-0002-1083-5533'
    - given-names: Daniel J.
      family-names: Cole
      affiliation: >-
        School of Natural and Environmental Sciences,
        Newcastle University
      orcid: 'https://orcid.org/0000-0003-2933-0719'
      email: daniel.cole@ncl.ac.uk
  identifiers:
    - type: doi
      value: 10.1021/acs.jcim.2c01153
    - type: url
      value: 'https://doi.org/10.26434/chemrxiv-2022-6h628'
      description: ChemRxiv Pre-Print
  doi: "10.1021/acs.jcim.2c01153"
  journal: "J. Chem. Inf. Model."
  month: 11
  start: 5622 # First page number
  end: 5633 # Last page number
  issue: 22
  volume: 62
  year: 2022

GitHub Events

Total

Create event: 17
Release event: 2
Issues event: 33
Watch event: 8
Delete event: 8
Issue comment event: 90
Push event: 78
Pull request review comment event: 8
Pull request review event: 25
Pull request event: 39
Fork event: 1

Last Year

Create event: 17
Release event: 2
Issues event: 33
Watch event: 8
Delete event: 8
Issue comment event: 90
Push event: 78
Pull request review comment event: 8
Pull request review event: 25
Pull request event: 39
Fork event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 222
Total Committers: 12
Avg Commits per committer: 18.5
Development Distribution Score (DDS): 0.671

Past Year

Commits: 68
Committers: 9
Avg Commits per committer: 7.556
Development Distribution Score (DDS): 0.426

Top Committers

Name	Email	Commits
SimonBoothroyd	s**d@h**m	73
Josh Mitchell	y**i@g**m	52
Josh Horton	J**n@n**k	24
dependabot[bot]	4**]@u**m	17
jthorton	j**1@g**m	16
jthorton	j**2@n**k	15
Matt Thompson	m**n@p**m	10
j-wags	j**l@g**m	10
Josh Horton	J**2@n**k	2
Matt Thompson	m**n@o**g	1
Xavier Linn	x**n@b**u	1
pre-commit-ci[bot]	6**]@u**m	1

Committer Domains (Top 20 + Academic)

newcastle.ac.uk: 3 berkeley.edu: 1 openforcefield.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 76
Total pull requests: 80
Average time to close issues: 18 days
Average time to close pull requests: about 1 month
Total issue authors: 24
Total pull request authors: 8
Average comments per issue: 2.7
Average comments per pull request: 3.09
Merged pull requests: 52
Bot issues: 0
Bot pull requests: 11

Past Year

Issues: 20
Pull requests: 15
Average time to close issues: 13 days
Average time to close pull requests: 21 days
Issue authors: 8
Pull request authors: 4
Average comments per issue: 1.0
Average comments per pull request: 1.0
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 2

View more stats

Top Authors

Issue Authors

mattwthompson (16)
j-wags (16)
xiki-tempula (13)
Yoshanuikabundi (9)
jthorton (5)
simonlichtinger (4)
ognjenperisic (3)
okbckim (2)
jgninterline (2)
orionarcher (2)
lilyminium (2)
hmacdope (2)
kexul (1)
yongfengye (1)
simonaxelrod (1)

Pull Request Authors

mattwthompson (46)
Yoshanuikabundi (18)
j-wags (15)
jthorton (11)
dependabot[bot] (9)
pre-commit-ci[bot] (6)
SimonBoothroyd (3)
xperrylinn (1)
mikemhenry (1)
hmacdope (1)
ntBre (1)

Top Labels

Issue Labels

documentation (11) dependencies (7) enhancement (4) external-dependencies (3) bug (3) question (1) proton-transfer (1) help wanted (1)

Pull Request Labels

dependencies (9)

Packages

Total packages: 1
Total downloads: unknown

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 3

conda-forge.org: openff-bespokefit

Homepage: https://openforcefield.org/
License: MIT
Latest release: 0.1.2
published almost 4 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 1

Rankings

Dependent repos count: 24.3%

Average: 42.2%

Stargazers count: 44.1%

Forks count: 48.9%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

.github/workflows/CI.yaml actions

actions/checkout v3 composite
codecov/codecov-action v3.1.1 composite
mamba-org/provision-with-micromamba main composite

.github/workflows/installer.yml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
mamba-org/provision-with-micromamba main composite

setup.py pypi

openff-bespokefit

Science Score: 67.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

BespokeFit

Getting Started

How to cite

License

Copyright

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

conda-forge.org: openff-bespokefit

Rankings

Dependencies