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‎.binder/environment.yml‎

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name: openfe-notebooks
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channels:
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- jaimergp/label/unsupported-cudatoolkit-shim
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- conda-forge
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dependencies:
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- MDAnalysis
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- pytest-cov
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- pytest-xdist
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- pydantic
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- python==3.11.*
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- python
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- rdkit
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- typing_extensions
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- gufe>=0.9.4
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- openfe>=0.13.0
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- gufe>=1.7.0
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- openfe>=1.7.0
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- py3dmol

‎.github/workflows/CI.yml‎

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push:
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branches:
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- main
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- master
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pull_request:
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branches:
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- main
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- master
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schedule:
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# nightly tests, 2 am
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- cron: "0 2 * * *"
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defaults:
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run:
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shell: bash -l {0}
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shell: bash -leo pipefail {0}
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.11",]
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os: ["ubuntu-latest", "macos-latest"]
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python-version: ["3.12"]
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steps:
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- uses: actions/checkout@v2.4.0
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- name: Get current date
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id: date
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run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
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- uses: conda-incubator/setup-miniconda@v2.1.1
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- uses: mamba-org/setup-micromamba@v1
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with:
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python-version: "${{ matrix.python-version }}"
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environment-file: .binder/environment.yml
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activate-environment: test
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auto-activate-base: false
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mamba-version: "*"
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miniforge-version: latest
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miniforge-variant: Mambaforge
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use-mamba: true
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channel-priority: true
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cache-environment: true
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cache-downloads: true
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cache-environment-key: environment-${{ steps.date.outputs.date }}
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cache-downloads-key: downloads-${{ steps.date.outputs.date }}
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create-args: >-
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python=${{ matrix.python-version }}
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init-shell: bash
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- name: Additional info about the build
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run: |
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- name: Environment Information
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run: |
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conda info
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conda list
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micromamba info
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micromamba list
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- name: Run example notebooks
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run: |
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python -m pytest -v setup/ openmm_rbfe/ networks/ --nbval-lax -n auto --dist loadscope
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python -m pytest -v --nbval-lax --nbval-cell-timeout=3000 -n auto --dist loadscope

‎.github/workflows/build-image.yml‎

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This file was deleted.

.github/workflows/binder-badge.yaml renamed to .github/workflows/colab-badge.yaml

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#./.github/workflows/binder-badge.yaml
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name: Binder Badge
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#./.github/workflows/colab-badge.yaml
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name: Colab Badge
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on:
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pull_request_target:
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types: [opened]
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jobs:
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binder:
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colab:
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runs-on: ubuntu-latest
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permissions:
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pull-requests: write
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steps:
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- name: comment on PR with Binder link
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uses: actions/github-script@v3
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- name: comment on PR with Colab link
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uses: actions/github-script@v8
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with:
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github-token: ${{secrets.GITHUB_TOKEN}}
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script: |
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var PR_HEAD_USERREPO = process.env.PR_HEAD_USERREPO;
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var PR_HEAD_REF = process.env.PR_HEAD_REF;
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github.issues.createComment({
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github.rest.issues.createComment({
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issue_number: context.issue.number,
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owner: context.repo.owner,
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repo: context.repo.repo,
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body: `[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/${PR_HEAD_USERREPO}/${PR_HEAD_REF}) :point_left: Launch a binder notebook on branch _${PR_HEAD_USERREPO}/${PR_HEAD_REF}_`
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body: `[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/${PR_HEAD_REF}/showcase) :point_left: Launch a Colab session on branch _${PR_HEAD_REF}_`
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})
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env:
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PR_HEAD_REF: ${{ github.event.pull_request.head.ref }}

‎.github/workflows/openfe-doc-build.yaml‎

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name: Test openfe doc build
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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schedule:
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# nightly tests, 2 am
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- cron: "0 2 * * *"
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concurrency:
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group: "${{ github.workflow }}-${{ github.ref }}"
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cancel-in-progress: true
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defaults:
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run:
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shell: bash -leo pipefail {0}
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jobs:
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test-openfe-docs-build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout openfe
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uses: actions/checkout@v4
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with:
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repository: OpenFreeEnergy/openfe
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path: openfe
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- name: Checkout ExampleNotebooks repository
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uses: actions/checkout@v4
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with:
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path: openfe/docs/ExampleNotebooks
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- name: Get current date
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id: date
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run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
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- name: Install doc environment
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: openfe/docs/environment.yaml
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cache-environment: true
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cache-downloads: true
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cache-environment-key: environment-${{ steps.date.outputs.date }}
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cache-downloads-key: downloads-${{ steps.date.outputs.date }}
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init-shell: bash
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- name: Build the docs
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run: |
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cd openfe
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# install so that we can get a version metadata we use in docs
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pip install . --no-deps
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cd docs
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make html

‎.pre-commit-config.yaml‎

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files: (^notebooks)
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repos:
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- repo: https://github.com/psf/black
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rev: 22.3.0
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 25.9.0
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hooks:
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- id: black
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- repo: https://github.com/psf/black
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rev: 22.3.0
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 25.9.0
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hooks:
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- id: black-jupyter

‎README.md‎

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[![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/)
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[![full_tests](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml)
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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/ExampleNotebooks/master.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/ExampleNotebooks/main)
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[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb)
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[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/showcase/openfe_showcase.ipynb)
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# OpenFE Notebooks
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Collection of notebooks for the Open FreeEnergy project.
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These can be ran in the browser via the Binder links.
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These can be run in the browser via the Colab links.
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| Binder link | Description |
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| Colab link | Description |
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| --- | --- |
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| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb) | Start here. This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the `openfe` package. |
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| [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OpenFreeEnergy/ExampleNotebooks/HEAD?labpath=openmm-rbfe%2FApplyingProtocolToNetworkQuickrunDemo.ipynb) | Demonstrating how to plan a free energy network and apply a protocol Note: This notebook might not load if Binder is experiencing heavy usage. |
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| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/showcase/openfe_showcase.ipynb) | Start here. This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the `openfe` package. |
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## Running these notebooks locally
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To run these notebooks locally you will need to install the `openfe` package,
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this is best done using [miniconda](https://docs.conda.io/en/latest/miniconda.html)
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Once miniconda is installed, from a terminal run:
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- `conda create -n openfe -c conda-forge openfe jupyter MDAnalysis nglview`
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- `conda activate openfe`
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this is best done using [the instuctions here](https://docs.openfree.energy/en/stable/installation.html)
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Then you can download a copy of the notebooks:
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- https://github.com/OpenFreeEnergy/ExampleNotebooks/archive/refs/tags/nov-2022.tar.gz
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Or via the command line as:
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- `wget -O OpenFEExampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/master`
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- `wget -O OpenFEExampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/main`
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- or (depending on your platform)
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- `curl -L -k -o OpenFEEXampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/master`
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- `curl -L -k -o OpenFEExampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/main`
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Unpack, then navigate to the downloaded notebooks:
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‎abfe_tutorial/abfe-cycle.png‎

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