Absolute solvation free energy calculations with OpenFF and OpenMM

Related tags

Miscellaneous absolv
Overview

ABsolute SOLVantion Free Energy Calculations

Test Status Language grade: Python codecov License: MIT

The absolv framework aims to offer a simple API for computing the change in free energy when transferring a solute from one solvent to another, or to vacuum in the case of solvation free energy calculations.

It offers two routes to this end: standard equilibrium calculations and non-equilibrium switching type calculations, where the latter is the main focus of this framework.

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 is incomplete, and the API can change without notice.

Installation

The core dependencies can be installed using the conda package manager:

conda env create --name absolv --file devtools/conda-envs/test-env.yaml
python setup.py develop

Getting Started

To begin with we define a schema that will, for all intents and purposes, encode the entirety of the absolute free energy calculation that we will be running.

In particular, we must specify:

i) the solutes and the two solvents that they will be transferred between ii) the state, i.e. temperature and optionally pressure, to perform the calculation at iii) and finally, the type of free energy calculation to perform as well as the protocol to follow while perform it

This can be compactly done by creating a new TransferFreeEnergySchema object:

from absolv.models import EquilibriumProtocol, State, System, TransferFreeEnergySchema

schema = TransferFreeEnergySchema(
    # Define the solutes in the system. There may be multiple in the case of,
    # e.g., ion pairs like Na+ + Cl-. Here we use `None` to specify that the solute 
    # will be transferred into a vacuum.
    system=System(solutes={"CCO": 1}, solvent_a={"O": 895}, solvent_b=None),
    # Define the state that the calculation will be performed at.
    state=State(temperature=298.15, pressure=1.0),
    # Define the alchemical pathway to transform the solute along in the first
    # and second (i.e. vacuum) solvent respectively.
    alchemical_protocol_a=EquilibriumProtocol(
        lambda_sterics=[  # fmt: off
            1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40,
            0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00,
        ],
        lambda_electrostatics=[  # fmt: off
            1.00, 0.75, 0.50, 0.25, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
            0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
        ],
    ),
    alchemical_protocol_b=EquilibriumProtocol(
        lambda_sterics=[1.0, 1.0, 1.0, 1.0, 1.0],
        lambda_electrostatics=[1.0, 0.75, 0.5, 0.25, 0.0],
    ),
)

Here we have specified that we will be computing the solvation free energy of one ethanol molecule in 895 water molecules at a temperature and pressure of 298.15 K and 1 atm.

We have also specified that we will be performing a standard 'equilibrium' free energy calculation according to the paper described by Mobley et al [1].

We can then trivially set up,

from openff.toolkit.typing.engines.smirnoff import ForceField
force_field = ForceField("openff-2.0.0.offxml")

from absolv.runners.equilibrium import EquilibriumRunner
EquilibriumRunner.setup(schema, force_field)

run,

EquilibriumRunner.run(schema, platform="CUDA")

and analyze the calculations

free_energies = EquilibriumRunner.analyze(schema)
print(free_energies)

Theory

...

Equilibrium Calculations

...

Non-equilibrium Calculations

...

Alchemical Transformations

...

Electrostatics

...

LJ Soft Core

...

Custom vdW Forms

...

References

[1] Mobley, David L., et al. "Escaping atom types in force fields using direct chemical perception." Journal of chemical theory and computation 14.11 (2018): 6076-6092.

License

The main package is release under the MIT license.

Copyright

Copyright (c) 2021, Simon Boothroyd

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    • #689 Bump to node16 and small fixes

    Features

    • #688 Incorporate gcov arguments for the Codecov uploader

    Dependencies

    • #548 build(deps-dev): bump jest-junit from 12.2.0 to 13.0.0
    • #603 [Snyk] Upgrade @‚Äčactions/core from 1.5.0 to 1.6.0
    • #628 build(deps): bump node-fetch from 2.6.1 to 3.1.1
    • #634 build(deps): bump node-fetch from 3.1.1 to 3.2.0
    • #636 build(deps): bump openpgp from 5.0.1 to 5.1.0
    • #652 build(deps-dev): bump @‚Äčvercel/ncc from 0.30.0 to 0.33.3
    • #653 build(deps-dev): bump @‚Äčtypes/node from 16.11.21 to 17.0.18
    • #659 build(deps-dev): bump @‚Äčtypes/jest from 27.4.0 to 27.4.1
    • #667 build(deps): bump actions/checkout from 2 to 3
    • #673 build(deps): bump node-fetch from 3.2.0 to 3.2.3
    • #683 build(deps): bump minimist from 1.2.5 to 1.2.6
    • #685 build(deps): bump @‚Äčactions/github from 5.0.0 to 5.0.1
    • #681 build(deps-dev): bump @‚Äčtypes/node from 17.0.18 to 17.0.23
    • #682 build(deps-dev): bump typescript from 4.5.5 to 4.6.3
    • #676 build(deps): bump @‚Äčactions/exec from 1.1.0 to 1.1.1
    • #675 build(deps): bump openpgp from 5.1.0 to 5.2.1
    Changelog

    Sourced from codecov/codecov-action's changelog.

    3.0.0

    Breaking Changes

    • #689 Bump to node16 and small fixes

    Features

    • #688 Incorporate gcov arguments for the Codecov uploader

    Dependencies

    • #548 build(deps-dev): bump jest-junit from 12.2.0 to 13.0.0
    • #603 [Snyk] Upgrade @‚Äčactions/core from 1.5.0 to 1.6.0
    • #628 build(deps): bump node-fetch from 2.6.1 to 3.1.1
    • #634 build(deps): bump node-fetch from 3.1.1 to 3.2.0
    • #636 build(deps): bump openpgp from 5.0.1 to 5.1.0
    • #652 build(deps-dev): bump @‚Äčvercel/ncc from 0.30.0 to 0.33.3
    • #653 build(deps-dev): bump @‚Äčtypes/node from 16.11.21 to 17.0.18
    • #659 build(deps-dev): bump @‚Äčtypes/jest from 27.4.0 to 27.4.1
    • #667 build(deps): bump actions/checkout from 2 to 3
    • #673 build(deps): bump node-fetch from 3.2.0 to 3.2.3
    • #683 build(deps): bump minimist from 1.2.5 to 1.2.6
    • #685 build(deps): bump @‚Äčactions/github from 5.0.0 to 5.0.1
    • #681 build(deps-dev): bump @‚Äčtypes/node from 17.0.18 to 17.0.23
    • #682 build(deps-dev): bump typescript from 4.5.5 to 4.6.3
    • #676 build(deps): bump @‚Äčactions/exec from 1.1.0 to 1.1.1
    • #675 build(deps): bump openpgp from 5.1.0 to 5.2.1
    Commits
    • e3c5604 Merge pull request #689 from codecov/feat/gcov
    • 174efc5 Update package-lock.json
    • 6243a75 bump to 3.0.0
    • 0d6466f Bump to node16
    • d4729ee fetch.default
    • 351baf6 fix: bash
    • d8cf680 Merge pull request #675 from codecov/dependabot/npm_and_yarn/openpgp-5.2.1
    • b775e90 Merge pull request #676 from codecov/dependabot/npm_and_yarn/actions/exec-1.1.1
    • 2ebc2f0 Merge pull request #682 from codecov/dependabot/npm_and_yarn/typescript-4.6.3
    • 8e2ef2b Merge pull request #681 from codecov/dependabot/npm_and_yarn/types/node-17.0.23
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    dependencies 
    opened by dependabot[bot] 2
  • Bump JamesIves/github-pages-deploy-action from 4.1.8 to 4.3.0

    Bump JamesIves/github-pages-deploy-action from 4.1.8 to 4.3.0

    Bumps JamesIves/github-pages-deploy-action from 4.1.8 to 4.3.0.

    Release notes

    Sourced from JamesIves/github-pages-deploy-action's releases.

    v4.3.0

    Changes

    • Implements a new option available behind a flag, force. If set to false the action will no longer force push, instead attempting 3 times to resolve rejected commits when making parallel/subsequent deployments. In a future version false will be set as the default. Massive thanks to @‚Äčrossjrw for this feature addition.
    • Modified the Node version which the action is developed/tested against from 14 to 16.

    Minor Changes

    • Third-party dependency updates.
    • Test coverage improvements.

    v4.2.5

    Minor Changes

    • Corrects an issue in the publishing pipeline that was causing workflow failures.

    v4.2.4

    Minor Changes

    v4.2.3

    Minor Changes

    • Improved action logging. This is part 1 or 2 updates that will make the logs easier to traverse. Warnings and notices are now provided so you don't need to expand the logs to get the termination message.
    • Dependency bumps across the board.

    v4.2.2

    Minor Changes

    • Introduces major version tags. You can now point your workflow to JamesIves/[email protected] if you'd like to always have the most cutting edge changes outside of using the release branch directly.
    • The version tags for this project now include a v to be consistent with other officially provided actions by GitHub. You can use JamesIves/[email protected] for instance. Dependabot should pick up this change automatically.

    4.2.1

    Minor Changes

    • Resolves an issue where the operating system warning was showing incorrectly.

    4.2.0

    Happy New Year 2022!

    London

    Minor Changes

    • Implements a warning if you're using an unsupported operating system. This will occur if the workflow runs within MacOS or Windows. The workflow will not be cancelled.
    • The action is now case insensitive, allowing you to make casing changes to files so long as you commit them using the git mv command prior to the workflow running. (#895)
    • Fixes an issue that was causing single-commit to fail when using repository-name if the branch name was equal from the origin to destination. (#665)
    • Enabled Dependabot updates for the GitHub Actions that are used as part of the projects integration tests.

    ... (truncated)

    Commits
    • 360c8e7 Merge branch 'dev' into releases/v4
    • 6ae2891 Update integration.yml
    • e6c302f Update README.md
    • cf0ab8f Deploy Production Code for Commit 7598e9b3fc39a35565f529abe095d4dfe75d52e4 ūüöÄ
    • 7598e9b Merge branch 'dev' into releases/v4
    • 36e9415 Improe coverage
    • e71f256 Bump prettier from 2.6.1 to 2.6.2 (#1068)
    • 95f8a2c Resolve simultaneous deployments with rebase (#1054)
    • cd846de Bump @‚Äčactions/github from 5.0.0 to 5.0.1 (#1067)
    • 7117b56 Bump prettier from 2.6.0 to 2.6.1 (#1065)
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 2
  • Bump actions/setup-python from 2.3.1 to 3.1.0

    Bump actions/setup-python from 2.3.1 to 3.1.0

    Bumps actions/setup-python from 2.3.1 to 3.1.0.

    Release notes

    Sourced from actions/setup-python's releases.

    Support caching poetry dependencies and caching on GHES 3.5

    steps:
    - uses: actions/[email protected]
    - name: Install poetry
      run: pipx install poetry
    - uses: actions/[email protected]
      with:
        python-version: '3.9'
        cache: 'poetry'
    - run: poetry install
    - run: poetry run pytest
    

    v3.0.0

    What's Changed

    Breaking Changes

    With the update to Node 16, all scripts will now be run with Node 16 rather than Node 12.

    This new major release removes support of legacy pypy2 and pypy3 keywords. Please use more specific and flexible syntax to specify a PyPy version:

    jobs:
      build:
        runs-on: ubuntu-latest
        strategy:
          matrix:
            python-version:
            - 'pypy-2.7' # the latest available version of PyPy that supports Python 2.7
            - 'pypy-3.8' # the latest available version of PyPy that supports Python 3.8
            - 'pypy-3.8-v7.3.8' # Python 3.8 and PyPy 7.3.8
        steps:
        - uses: actions/[email protected]
        - uses: actions/[email protected]
          with:
            python-version: ${{ matrix.python-version }}
    

    See more usage examples in the documentation

    Update primary and restore keys for pip

    In scope of this release we include a version of python in restore and primary cache keys for pip. Besides, we add temporary fix for Windows caching issue, that the pip cache dir command returns non zero exit code or writes to stderr. Moreover we updated node-fetch dependency.

    Commits

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    dependencies 
    opened by dependabot[bot] 2
  • Bump actions/checkout from 2.4.0 to 3

    Bump actions/checkout from 2.4.0 to 3

    Bumps actions/checkout from 2.4.0 to 3.

    Release notes

    Sourced from actions/checkout's releases.

    v3.0.0

    • Update default runtime to node16
    Changelog

    Sourced from actions/checkout's changelog.

    Changelog

    v2.3.1

    v2.3.0

    v2.2.0

    v2.1.1

    • Changes to support GHES (here and here)

    v2.1.0

    v2.0.0

    v2 (beta)

    • Improved fetch performance
      • The default behavior now fetches only the SHA being checked-out
    • Script authenticated git commands
      • Persists with.token in the local git config
      • Enables your scripts to run authenticated git commands
      • Post-job cleanup removes the token
      • Coming soon: Opt out by setting with.persist-credentials to false
    • Creates a local branch
      • No longer detached HEAD when checking out a branch
      • A local branch is created with the corresponding upstream branch set
    • Improved layout

    ... (truncated)

    Commits

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    dependencies 
    opened by dependabot[bot] 2
  • Bump codecov/codecov-action from 2.1.0 to 3.1.1

    Bump codecov/codecov-action from 2.1.0 to 3.1.1

    Bumps codecov/codecov-action from 2.1.0 to 3.1.1.

    Release notes

    Sourced from codecov/codecov-action's releases.

    3.1.1

    What's Changed

    New Contributors

    Full Changelog: https://github.com/codecov/codecov-action/compare/v3.1.0...v3.1.1

    v3.1.0

    3.1.0

    Features

    ... (truncated)

    Changelog

    Sourced from codecov/codecov-action's changelog.

    3.1.1

    Fixes

    • #661 Update deprecation warning
    • #593 Create codeql-analysis.yml
    • #712 README: fix typo
    • #725 fix: Remove a blank row
    • #726 Update README.md with correct badge version
    • #633 Create scorecards-analysis.yml
    • #747 fix: add more verbosity to validation
    • #750 Regenerate scorecards-analysis.yml
    • #774 Switch to v3
    • #783 Fix network entry in table
    • #791 Trim arguments after splitting them
    • #769 Plumb failCi into verification function.

    Dependencies

    • #713 build(deps-dev): bump typescript from 4.6.3 to 4.6.4
    • #714 build(deps): bump node-fetch from 3.2.3 to 3.2.4
    • #724 build(deps): bump github/codeql-action from 1 to 2
    • #717 build(deps-dev): bump @‚Äčtypes/jest from 27.4.1 to 27.5.0
    • #729 build(deps-dev): bump @‚Äčtypes/node from 17.0.25 to 17.0.33
    • #734 build(deps-dev): downgrade @‚Äčtypes/node to 16.11.35
    • #723 build(deps): bump actions/checkout from 2 to 3
    • #733 build(deps): bump @‚Äčactions/github from 5.0.1 to 5.0.3
    • #732 build(deps): bump @‚Äčactions/core from 1.6.0 to 1.8.2
    • #737 build(deps-dev): bump @‚Äčtypes/node from 16.11.35 to 16.11.36
    • #749 build(deps): bump ossf/scorecard-action from 1.0.1 to 1.1.0
    • #755 build(deps-dev): bump typescript from 4.6.4 to 4.7.3
    • #759 build(deps-dev): bump @‚Äčtypes/node from 16.11.36 to 16.11.39
    • #762 build(deps-dev): bump @‚Äčtypes/node from 16.11.39 to 16.11.40
    • #746 build(deps-dev): bump @‚Äčvercel/ncc from 0.33.4 to 0.34.0
    • #757 build(deps): bump ossf/scorecard-action from 1.1.0 to 1.1.1
    • #760 build(deps): bump openpgp from 5.2.1 to 5.3.0
    • #748 build(deps): bump actions/upload-artifact from 2.3.1 to 3.1.0
    • #766 build(deps-dev): bump typescript from 4.7.3 to 4.7.4
    • #799 build(deps): bump openpgp from 5.3.0 to 5.4.0
    • #798 build(deps): bump @‚Äčactions/core from 1.8.2 to 1.9.1

    3.1.0

    Features

    • #699 Incorporate xcode arguments for the Codecov uploader

    Dependencies

    • #694 build(deps-dev): bump @‚Äčvercel/ncc from 0.33.3 to 0.33.4
    • #696 build(deps-dev): bump @‚Äčtypes/node from 17.0.23 to 17.0.25
    • #698 build(deps-dev): bump jest-junit from 13.0.0 to 13.2.0

    3.0.0

    Breaking Changes

    • #689 Bump to node16 and small fixes

    ... (truncated)

    Commits
    • d9f34f8 release: update changelog and version to 3.1.1 (#828)
    • 0e9e7b4 Plumb failCi into verification function. (#769)
    • 7f20bd4 build(deps): bump @‚Äčactions/core from 1.8.2 to 1.9.1 (#798)
    • 13bc253 build(deps): bump openpgp from 5.3.0 to 5.4.0 (#799)
    • 5c0da1b Trim arguments after splitting them (#791)
    • 68d5f6d Fix network entry in table (#783)
    • 2a829b9 Switch to v3 (#774)
    • 8e09eaf build(deps-dev): bump typescript from 4.7.3 to 4.7.4 (#766)
    • 39e2229 build(deps): bump actions/upload-artifact from 2.3.1 to 3.1.0 (#748)
    • b2b7703 build(deps): bump openpgp from 5.2.1 to 5.3.0 (#760)
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    dependencies 
    opened by dependabot[bot] 0
  • Bump actions/setup-python from 2.3.1 to 4.2.0

    Bump actions/setup-python from 2.3.1 to 4.2.0

    Bumps actions/setup-python from 2.3.1 to 4.2.0.

    Release notes

    Sourced from actions/setup-python's releases.

    Add check-latest input and bug fixes

    In scope of this release we add the check-latest input. If check-latest is set to true, the action first checks if the cached version is the latest one. If the locally cached version is not the most up-to-date, the version will then be downloaded from python-versions repository. By default check-latest is set to false. For PyPy it will to try to reach https://downloads.python.org/pypy/versions.json

    Example of usage:

    steps:
      - uses: actions/[email protected]
      - uses: actions/[email protected]
        with:
          python-version: '3.9'
          check-latest: true
      - run: python --version
    

    Besides, it includes such changes as

    v4.1.0

    In scope of this pull request we updated actions/cache package as the new version contains fixes for caching error handling. Moreover, we added a new input update-environment. This option allows to specify if the action shall update environment variables (default) or not.

    Update-environment input

        - name: setup-python 3.9
          uses: actions/[email protected]
          with:
            python-version: 3.9
            update-environment: false
    

    Besides, we added such changes as:

    v4.0.0

    What's Changed

    • Support for python-version-file input: #336

    Example of usage:

    - uses: actions/[email protected]
      with:
        python-version-file: '.python-version' # Read python version from a file
    - run: python my_script.py
    </tr></table> 
    

    ... (truncated)

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    dependencies 
    opened by dependabot[bot] 0
  • Bump JamesIves/github-pages-deploy-action from 4.1.8 to 4.4.0

    Bump JamesIves/github-pages-deploy-action from 4.1.8 to 4.4.0

    Bumps JamesIves/github-pages-deploy-action from 4.1.8 to 4.4.0.

    Release notes

    Sourced from JamesIves/github-pages-deploy-action's releases.

    v4.4.0

    What's Changed

    New Contributors

    Sponsors ‚̧ԳŹ

      

    Full Changelog: https://github.com/JamesIves/github-pages-deploy-action/compare/v4...v4.4.0

    v4.3.4

    Minor Changes

    • The branch parameter is no longer required. It now defaults to gh-pages.
    • Linting scripts have been updated to ensure that everything across the repo gets picked up.
    • Numerous dependency updates.

    New Contributors

    Sponsors ‚̧ԳŹ

      

    Full Changelog: https://github.com/JamesIves/github-pages-deploy-action/compare/v4...v4.3.4

    v4.3.3

    Changes

    • Resolves an issue in some workflows that were caused by a recent change to permission handling.

    v4.3.2

    Changes

    • Resolves an issue with folder permissions that causes an issue in container workflows when rsync attempts to run.

    v4.3.1

    Changes

    • Resolves an issue caused by Git 2.36 when running the action within a container.
      • The working directory is now added to the safe.directory global directory.
      • Integration tests have been updated so one of the samples run in a Docker container so this gets picked up by integration tests in the future.

    ... (truncated)

    Commits
    • 13046b6 Deploy Production Code for Commit f0e6e506b4860acdb0c7a8db5ffd3de19af76596 ūüöÄ
    • f0e6e50 Merge branch 'dev' into releases/v4
    • ccec059 fix: Trims
    • 331dd26 fix: :bug: Fixes an issue where informational messages are throwing errors (#...
    • 1dfbc4c Bump @‚Äčtypes/node from 18.0.0 to 18.0.6 (#1169)
    • 21fb2a4 Bump eslint-plugin-prettier from 4.0.0 to 4.2.1 (#1159)
    • 976c0c8 Deploying to dev from @ JamesIves/[email protected]
    • 6a0cc4d chore: Format
    • 73a6bac test: Fixes test case
    • f08f40f chore: Fix spelling
    • Additional commits viewable in compare view

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  • Bump actions/checkout from 2.4.0 to 3.0.2

    Bump actions/checkout from 2.4.0 to 3.0.2

    Bumps actions/checkout from 2.4.0 to 3.0.2.

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    v3.0.2

    What's Changed

    Full Changelog: https://github.com/actions/checkout/compare/v3...v3.0.2

    v3.0.1

    v3.0.0

    • Updated to the node16 runtime by default
      • This requires a minimum Actions Runner version of v2.285.0 to run, which is by default available in GHES 3.4 or later.

    v2.4.2

    What's Changed

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    v2.4.1

    • Fixed an issue where checkout failed to run in container jobs due to the new git setting safe.directory
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    v3.0.2

    v3.0.1

    v3.0.0

    v2.3.1

    v2.3.0

    v2.2.0

    v2.1.1

    • Changes to support GHES (here and here)

    v2.1.0

    v2.0.0

    v2 (beta)

    • Improved fetch performance
      • The default behavior now fetches only the SHA being checked-out
    • Script authenticated git commands

    ... (truncated)

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