Make initial commit

.github/PULL_REQUEST_TEMPLATE.md

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+## What does this PR do?
+
+<!--
+Please include a summary of the change and which issue is fixed.
+Please also include relevant motivation and context.
+List any dependencies that are required for this change.
+List all the breaking changes introduced by this pull request.
+-->
+
+Fixes #\<issue_number>
+
+## Before submitting
+
+- [ ] Did you make sure **title is self-explanatory** and **the description concisely explains the PR**?
+- [ ] Did you make sure your **PR does only one thing**, instead of bundling different changes together?
+- [ ] Did you list all the **breaking changes** introduced by this pull request?
+- [ ] Did you **run pre-commit hooks** with `pre-commit run -a` command?
+
+## Did you have fun?
+
+Make sure you had fun coding 🙃

.github/codecov.yml

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+coverage:
+  status:
+    # measures overall project coverage
+    project:
+      default:
+        threshold: 100% # how much decrease in coverage is needed to not consider success
+
+    # measures PR or single commit coverage
+    patch:
+      default:
+        threshold: 100% # how much decrease in coverage is needed to not consider success
+
+
+    # project: off
+    # patch: off

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+    ignore:
+      - dependency-name: "pytorch-lightning"
+        update-types: ["version-update:semver-patch"]
+      - dependency-name: "torchmetrics"
+        update-types: ["version-update:semver-patch"]

.github/release-drafter.yml

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+name-template: "v$RESOLVED_VERSION"
+tag-template: "v$RESOLVED_VERSION"
+
+categories:
+  - title: "🚀 Features"
+    labels:
+      - "feature"
+      - "enhancement"
+  - title: "🐛 Bug Fixes"
+    labels:
+      - "fix"
+      - "bugfix"
+      - "bug"
+  - title: "🧹 Maintenance"
+    labels:
+      - "maintenance"
+      - "dependencies"
+      - "refactoring"
+      - "cosmetic"
+      - "chore"
+  - title: "📝️ Documentation"
+    labels:
+      - "documentation"
+      - "docs"
+
+change-template: "- $TITLE @$AUTHOR (#$NUMBER)"
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions
+
+version-resolver:
+  major:
+    labels:
+      - "major"
+  minor:
+    labels:
+      - "minor"
+  patch:
+    labels:
+      - "patch"
+  default: patch
+
+template: |
+  ## Changes
+
+  $CHANGES

.github/workflows/changelog-enforcer.yaml

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+name: Changelog Enforcer
+
+on: # yamllint disable-line rule:truthy
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  changelog:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: dangoslen/changelog-enforcer@v3
+        with:
+          skipLabels: "skip-changelog"

.github/workflows/code-quality-main.yaml

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+# Same as `code-quality-pr.yaml` but triggered on commit to main branch
+# and runs on all files (instead of only the changed ones)
+
+name: Code Quality Main
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v2.0.3

.github/workflows/code-quality-pr.yaml

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+# This workflow finds which files were changed, prints them,
+# and runs `pre-commit` on those files.
+
+# Inspired by the sktime library:
+# https://github.com/alan-turing-institute/sktime/blob/main/.github/workflows/test.yml
+
+name: Code Quality PR
+
+on:
+  pull_request:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Find modified files
+        id: file_changes
+        uses: trilom/file-changes-action@v1.2.4
+        with:
+          output: " "
+
+      - name: List modified files
+        run: echo '${{ steps.file_changes.outputs.files}}'
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v2.0.3
+        with:
+          extra_args: --files ${{ steps.file_changes.outputs.files}}

.github/workflows/release-drafter.yml

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+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: write
+
+    runs-on: ubuntu-latest
+
+    steps:
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### VisualStudioCode
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+*.code-workspace
+**/.vscode
+
+# JetBrains
+.idea/
+
+# Data & Models
+*.h5
+*.tar
+*.tar.gz
+
+# PoseBench
+configs/local/default.yaml
+/*cache_dir/
+/casp15_ligand_scoring/
+/data/
+/ensemble_generation_scripts/
+/logs/
+/outputs/
+/PoseBench/
+/results/
+.env
+*.npy
+*.pdb
+
+# Aim logging
+.aim
+
+# Forks
+/workdir/
+/forks/DiffDock1.0/
+/forks/DiffDock/DiffDock/
+/forks/DynamicBind/*.npy
+/forks/DynamicBind/DynamicBind/
+/forks/DynamicBind/esm_models/
+/forks/DynamicBind/workdir/
+/forks/FABind/ckpt/best_model.bin
+/forks/FABind/FABind/
+/forks/NeuralPLexer/NeuralPLexer/
+/forks/NeuralPLexer/**/neuralplexermodels*
+/forks/*/inference*/
+/forks/RoseTTAFold-All-Atom/blast-2.2.26
+/forks/RoseTTAFold-All-Atom/rf2aa/config/inference/*_rfaa_inference.yaml
+/forks/RoseTTAFold-All-Atom/csblast-2.2.3
+/forks/RoseTTAFold-All-Atom/ensemble_generation_scripts/
+/forks/RoseTTAFold-All-Atom/outputs/
+/forks/RoseTTAFold-All-Atom/pdb100_2021Mar03/
+/forks/RoseTTAFold-All-Atom/prediction_inputs/
+/forks/RoseTTAFold-All-Atom/prediction_outputs/
+/forks/RoseTTAFold-All-Atom/RFAA/
+/forks/RoseTTAFold-All-Atom/RFAA_paper_weights.pt
+/forks/RoseTTAFold-All-Atom/SE3nv-20240131.sif
+/forks/RoseTTAFold-All-Atom/psipred/
+/forks/TULIP/outputs/
+/forks/Vina/ADFR/