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Add CoC and Contribution guide, update readme (#241)
* Add CoC and Contribution guide, update readme * Fix CoC links * CoC typos * Add link to pre-print * Simplify links * Update CONTRIBUTING.md Co-authored-by: Matt Thompson <[email protected]> * More info on pre-commit from Matt * Remove slightly redundant pre-commit badge * Add CITATION.cff * Update CONTRIBUTING.md --------- Co-authored-by: Matt Thompson <[email protected]>
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| 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: [email protected] | ||
| - 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: [email protected] | ||
| 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 |
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| # Code of conduct | ||
|
|
||
| The OpenFF BespokeFit *Code of Conduct* sets the rules for the behavior of | ||
| every member in the OpenFF BespokeFit community so that everyone can | ||
| experience a welcoming, supportive, and productive environment that is | ||
| free from harassment. | ||
|
|
||
| **Table of Contents** | ||
|
|
||
| - [Code of conduct](#code-of-conduct) | ||
| - [Code of Conduct and Community Guidelines](#code-of-conduct-and-community-guidelines) | ||
| - [Scope](#scope) | ||
| - [Enforcement](#enforcement) | ||
| - [Acknowledgments](#acknowledgments) | ||
|
|
||
| ## Code of Conduct and Community Guidelines | ||
|
|
||
| OpenFF BespokeFit is part of an engaged and respectful community made up of | ||
| people from all over the world. Your involvement helps us to further our | ||
| mission and to create an open platform that serves a broad range of | ||
| communities, from research and education to industry and beyond. This diversity | ||
| is one of our biggest strengths, but it can also lead to communication issues | ||
| and conflicts. Therefore, we have a few ground rules we ask that our community | ||
| members adhere to. | ||
|
|
||
| Fundamentally, we are committed to providing a productive, | ||
| harassment-free environment for everyone. Rather than considering this | ||
| code an exhaustive list of things that you can't do, take it in the | ||
| spirit it is intended - a guide to make it easier to enrich all of us | ||
| and the communities in which we participate. | ||
|
|
||
| Importantly: as a member of our community, you are also a steward of these | ||
| values. Not all problems need to be resolved via formal processes, and often a | ||
| quick, friendly but clear word on an online forum or in person can help resolve | ||
| a misunderstanding and de-escalate things. | ||
|
|
||
| By embracing the following principles, guidelines and actions to follow or | ||
| avoid, you will help us make OpenFF BespokeFit a welcoming and productive | ||
| community. | ||
|
|
||
| 1. **Be friendly and patient**. | ||
|
|
||
| 2. **Be welcoming**. We strive to be a community that welcomes and supports | ||
| people of all backgrounds and identities. This includes, but is not limited | ||
| to, members of any race, ethnicity, culture, national origin, color, | ||
| immigration status, social and economic class, educational level, sex, | ||
| sexual orientation, gender identity and expression, age, physical | ||
| appearance, family status, political belief, technological or professional | ||
| choices, academic discipline, religion, mental ability, and physical | ||
| ability. | ||
|
|
||
| 3. **Be considerate**. Your work will be used by other people, and you in turn | ||
| will depend on the work of others. Any decision you take will affect users | ||
| and colleagues, and you should take those consequences into account when | ||
| making decisions. Remember that we're a world-wide community. You may be | ||
| communicating with someone with a different primary language or cultural | ||
| background. | ||
|
|
||
| 4. **Be respectful**. Not all of us will agree all the time, but disagreement | ||
| is no excuse for poor behavior or poor manners. We might all experience some | ||
| frustration now and then, but we cannot allow that frustration to turn into | ||
| a personal attack. It's important to remember that a community where people | ||
| feel uncomfortable or threatened is not a productive one. | ||
|
|
||
| 5. **Be careful in the words that you choose**. Be kind to others. Do not | ||
| insult or put down other community members. Harassment and other | ||
| exclusionary behaviors are not acceptable. This includes, but is not | ||
| limited to: | ||
| * threats or violent language directed against another person | ||
| * discriminatory jokes and language | ||
| * posting sexually explicit or violent material | ||
| * posting (or threatening to post) other people's personally identifying | ||
| information ("doxing") | ||
| * personal insults, especially those using racist or sexist terms | ||
| * unwelcome sexual attention, even if believed to be welcome | ||
| * advocating for, or encouraging, any of the above behavior | ||
| * repeated harassment of others. In general, if someone asks you to stop, | ||
| then stop | ||
|
|
||
| 6. **Moderate your expectations**. Many in our community volunteer their time. | ||
| They are probably not purposefully ignoring issues, refusing to engage in | ||
| discussion, avoiding features, etc. but often just unavailable. | ||
|
|
||
| 7. **When we disagree, try to understand why**. Disagreements, both social and | ||
| technical, happen all the time and OpenFF BespokeFit is no exception. It is | ||
| important that we resolve disagreements and differing views constructively. | ||
| Remember that we're different. The strength of OpenFF BespokeFit comes from | ||
| its varied community that includes people from a wide range of backgrounds. | ||
| Different people have different perspectives on issues. Being unable to | ||
| understand why someone holds a viewpoint doesn't mean they're wrong. Don't | ||
| forget that it is human to err and blaming each other doesn't get us | ||
| anywhere. Instead, focus on helping to resolve issues and learning from | ||
| mistakes. | ||
|
|
||
| 8. **A simple apology can go a long way**. It can often de-escalate a | ||
| situation, and telling someone that you are sorry is act of empathy that | ||
| doesn't automatically imply an admission of guilt. | ||
|
|
||
|
|
||
| ## Scope | ||
|
|
||
| This Code of Conduct applies both within project spaces and in public spaces | ||
| when an individual is representing the project or its community. Examples of | ||
| representing a project or community include using an official project e-mail | ||
| address, posting via an official social media account, or acting as an | ||
| appointed representative at an online or offline event. Representation of a | ||
| project may be further defined and clarified by project maintainers. | ||
|
|
||
| ## Enforcement | ||
|
|
||
| Instances of abusive, harassing, or otherwise unacceptable behavior may be | ||
| reported by contacting the project team at [email protected]. | ||
| The project team will review and investigate all complaints, and will respond | ||
| in a way that it deems appropriate to the circumstances. The project team is | ||
| obligated to maintain confidentiality with regard to the reporter of an | ||
| incident. Further details of specific enforcement policies may be posted | ||
| separately. | ||
|
|
||
| Project maintainers who do not follow or enforce the Code of Conduct in good | ||
| faith may face temporary or permanent repercussions as determined by other | ||
| members of the project's leadership. | ||
|
|
||
|
|
||
| ## Acknowledgments | ||
|
|
||
| This code of conduct is adapted from the [OpenFF NAGL code of conduct]. | ||
| Original text was adapted from the [*Speak Up!*], [*Django*], | ||
| [*Contributor Covenant*], [*Jupyter*], [*MolSSI*], and [*MDAnalysis*] | ||
| projects. We are grateful to those projects for contributing these materials | ||
| under open licensing terms for us to easily reuse. | ||
|
|
||
| All content on this page is licensed under a [*Creative Commons Attribution*] | ||
| license. | ||
|
|
||
| [OpenFF NAGL code of conduct]: https://github.com/openforcefield/openff-nagl/blob/main/CODE_OF_CONDUCT.md | ||
| [*Speak Up!*]: http://web.archive.org/web/20141109123859/http://speakup.io/coc.html | ||
| [*Django*]: https://www.djangoproject.com/conduct | ||
| [*Contributor Covenant*]: http://contributor-covenant.org/ | ||
| [*Jupyter*]: https://github.com/jupyter/governance/blob/master/conduct/code_of_conduct.md | ||
| [*MolSSI*]: https://github.com/MolSSI/cookiecutter-cms/blob/master/%7B%7Bcookiecutter.repo_name%7D%7D/CODE_OF_CONDUCT.md | ||
| [*MDAnalysis*]: https://github.com/MDAnalysis/mdanalysis/blob/develop/CODE_OF_CONDUCT.md | ||
| [*Creative Commons Attribution*]: http://creativecommons.org/licenses/by/3.0/ |
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| # Contributing to BespokeFit | ||
|
|
||
| OpenFF BespokeFit developers follow a [code of conduct]. Please familiarize yourself with the code. | ||
|
|
||
| Despite being developed primarily by UK and Australian developers, BespokeFit uses US English in all documentation. | ||
|
|
||
| BespokeFit is developed in the open at [GitHub]. We welcome PRs and issues from the general public! Please consider raising an issue there to discuss changes or additions to the code before you commit time to a PR! | ||
|
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| A development environment for BespokeFit can be created using [Mamba], which is a faster implementation of the [Conda] package manager: | ||
|
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| ```shell | ||
| git clone https://github.com/openforcefield/openff-bespokefit.git | ||
| cd openff-bespokefit | ||
| mamba env create --file devtools/conda-envs/test-env.yaml --name bespokefit-dev | ||
| mamba env update --file devtools/conda-envs/docs-env.yaml --name bespokefit-dev | ||
| conda activate bespokefit-dev | ||
| pip install -e . | ||
| ``` | ||
|
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| With this environment, tests can be run locally with [PyTest]: | ||
|
|
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| ```shell | ||
| pytest openff/bespokefit/tests | ||
| ``` | ||
|
|
||
| And documentation can be built with [Sphinx] and viewed in a web browser: | ||
|
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| ```shell | ||
| sphinx-build -j auto docs docs/_build/html | ||
| firefox docs/_build/html/index.html | ||
| ``` | ||
|
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||
| Finally, BespokeFit uses a number of lints and code formatters to help maintain code quality. These will be run automatically on any PRs by [pre-commit.ci], so be aware that there's a bot potentially committing to your feature branch. You can run the lints and formatters yourself automatically on each local commit by installing the pre-commit hook: | ||
|
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||
| ```shell | ||
| mamba install pre-commit -c conda-forge | ||
| pre-commit install | ||
| ``` | ||
|
|
||
| These hooks are installed in isolated virtual environments, separate from the `conda` environment you created for development (though pre-commit itself will be installed in the current environment). Installing `pre-commit` and hooks locally may help avoid frustration associated with the remote branch coming out of sync when multiple commits are pushed in sequence without pulling the automated changes. | ||
|
|
||
| [code of conduct]: CODE_OF_CONDUCT.md | ||
| [GitHub]: https://github.com/openforcefield/openff-bespokefit | ||
| [Mamba]: https://mamba.readthedocs.io/ | ||
| [Conda]: https://docs.conda.io/ | ||
| [PyTest]: https://pytest.org/ | ||
| [Sphinx]: https://www.sphinx-doc.org/ | ||
| [pre-commit.ci]: https://results.pre-commit.ci/latest/github/openforcefield/openff-bespokefit/main |
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