acellera-konnektor 0.4.0__tar.gz

acellera_konnektor-0.4.0/.coveragerc

@@ -0,0 +1,12 @@
+[run]
+omit =
+    */_version.py
+    */tests/dev/*py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    pragma: no-cover
+    -no-cov
+    raise NotImplementedError
+    \.\.\.

acellera_konnektor-0.4.0/.git-blame-ignore-revs

@@ -0,0 +1,5 @@
+# applying ruff formatting by atravitz in https://github.com/OpenFreeEnergy/konnektor/pull/109
+52f9e1018ebc66c3f624e2a89f772f3aa7edd11f
+
+# black formatting by riesben in https://github.com/OpenFreeEnergy/konnektor/pull/62
+e18c6abf5297a44cba65c88131b73f813a93dc42

acellera_konnektor-0.4.0/.github/pull_request_template.md

@@ -0,0 +1,25 @@
+<!--
+Thank you for pull request.
+Below are a few things we ask you kindly to self-check before getting a review. Remove checks that are not relevant.
+-->
+
+<!--
+Please note any issues this fixes using [closing keywords]( https://help.github.com/articles/closing-issues-using-keywords/ ):
+-->
+
+## PR Author Checklist
+- [ ] added news item, or changes are not user-facing
+- [ ] pre-commit CI passes (comment `pre-commit.ci autofix` to auto-format your PR).
+
+## Tips
+* Comment `pre-commit.ci autofix` to have pre-commit.ci auto-format your PR.
+  Since this will create a commit, it is best to make this comment when you are finished with your work.
+
+## Developers certificate of origin
+- [ ] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the **Developer Certificate of Origin** at <https://developercertificate.org/>.
+
+
+## Reviewer Checklist
+- [ ] news entry has been added if necessary
+- [ ] pre-commit auto fix has been run
+- [ ] any API breaks have been documented

acellera_konnektor-0.4.0/.github/workflows/ci.yaml

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+name: "CI"
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+    # Skip CI if changed files only affect the following folders
+    # See here for more details: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-excluding-paths
+    paths-ignore:
+      - "docs/*"
+  push:
+    branches:
+      - main
+  schedule:
+    # Run a cron job once daily
+    - cron: "0 0 * * *"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.OS }}-latest
+    name: "tests"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu',]
+        python-version:
+          - "3.11"
+          - "3.12"
+          - "3.13"
+        include:
+          - os: 'macos'
+            python-version: "3.12"
+
+    steps:
+      - uses: actions/checkout@v6
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
+      - uses: mamba-org/setup-micromamba@v3
+        with:
+          environment-file: environment.yaml
+          environment-name: konnektor
+          cache-environment: true
+          cache-downloads: true
+          cache-environment-key: environment-${{ steps.date.outputs.date }}
+          cache-downloads-key: downloads-${{ steps.date.outputs.date }}
+          create-args: >-
+            python=${{ matrix.python-version }}
+
+      - name: "Install"
+        run: pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import konnektor"
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+      - name: "Run tests"
+        run: |
+          pytest -n auto -v --cov=konnektor --cov-report=xml
+      - name: "Test Notebooks"
+        run: |
+          # another dep I don't want to include in the env
+          pip install --no-deps git+https://github.com/OpenFreeEnergy/kartograf.git
+          # Only need to test the notebook(s) in tutorials/
+          pytest -v --nbval-lax docs/tutorials/
+
+      - name: codecov
+        if: ${{ github.repository == 'OpenFreeEnergy/konnektor' && github.event != 'schedule'}}
+        uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          env_vars: OS,PYTHON
+          fail_ci_if_error: True
+          verbose: True

acellera_konnektor-0.4.0/.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
+.env
+.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/
+
+#version
+_version.py
+
+#IDE
+.idea
+.vscode
+
+# rever
+rever/

acellera_konnektor-0.4.0/.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+# comment / label "pre-commit.ci autofix" to a pull request to manually trigger auto-fixing
+ci:
+    autofix_prs: false
+    autoupdate_schedule: monthly
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    - id: trailing-whitespace
+      exclude: '\.(pdb|gro|top|sdf|xml|cif|graphml)$'
+    - id: check-added-large-files
+      args: ["--maxkb=4000"]
+    - id: check-case-conflict
+    - id: check-symlinks
+    - id: check-toml
+    - id: check-yaml
+    - id: debug-statements
+    - id: destroyed-symlinks
+    - id: end-of-file-fixer
+      exclude: '\.(graphml)$'
+
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: "v2.23.0"
+  hooks:
+    - id: pyproject-fmt
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.15
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [--fix ]
+    # Run the formatter.
+    - id: ruff-format

acellera_konnektor-0.4.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "miniconda3-3.12-24.9"
+
+sphinx:
+   configuration: docs/conf.py
+   fail_on_warning: true
+
+conda:
+  environment: docs/environment.yaml
+
+python:
+  # Install our python package before building the docs so setuptools-scm generates the version for RTD to find.
+  install:
+    - method: pip
+      path: .

acellera_konnektor-0.4.0/CITATION.cff

@@ -0,0 +1,31 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Ries"
+  given-names: "Benjamin"
+  orcid: "https://orcid.org/0000-0002-0945-8304"
+- family-names: "Gowers"
+  given-names: "Richard J."
+  orcid: "https://orcid.org/0000-0002-3241-1846"
+- family-names: "Baumann"
+  given-names: "Hannah M."
+  orcid: "https://orcid.org/0000-0002-1736-7744"
+- family-names: "Swenson"
+  given-names: "David W.H."
+  orcid: "https://orcid.org/0000-0001-9922-7923"
+- family-names: "Alibay"
+  given-names: "Irfan"
+  orcid: "https://orcid.org/0000-0001-5787-9130"
+- family-names: "Henry"
+  given-names: "Michael M."
+  orcid: "https://orcid.org/0000-0002-3870-9993"
+- family-names: "Eastwood"
+  given-names: "James R. B."
+  orcid: "https://orcid.org/0000-0003-3895-5227"
+- family-names: "Travitz"
+  given-names: "Alyssa"
+  orcid: "https://orcid.org/0000-0001-5953-8807"
+title: "Konnektor: A Tool for Planning Free Energy Networks"
+url: "https://openfree.energy/"
+repository-code: "https://github.com/OpenFreeEnergy/konnektor"
+# doi: -

acellera_konnektor-0.4.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Open Free Energy
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

acellera_konnektor-0.4.0/MANIFEST.in

@@ -0,0 +1,3 @@
+include src/konnektor/tests/data/*.sdf
+include src/konnektor/tests/data/*.mol2
+include src/konnektor/data/*.sdf

acellera_konnektor-0.4.0/PKG-INFO

@@ -0,0 +1,130 @@
+Metadata-Version: 2.4
+Name: acellera-konnektor
+Version: 0.4.0
+Summary: Konnektor is a package for calculating networks.
+Author-email: Alyssa Travitz <alyssa.travitz@omsf.io>, Benjamin Ries <benjamin-ries@outlook.com>, David Swenson <dwhswenson@gmail.com>, Hannah Baumann <hannah.baumann@omsf.io>, Irfan Alibay <irfan.alibay@gmail.com>, Mike Henry <mike.henry@choderalab.org>, Richard J Gowers <richardjgowers@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/OpenFreeEnergy/konnektor
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: <3.14,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ipycytoscape
+Requires-Dist: networkx
+Requires-Dist: numpy
+Requires-Dist: rdkit
+Requires-Dist: scikit-learn
+Requires-Dist: scikit-mol
+Requires-Dist: tqdm
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov[all]; extra == "test"
+Dynamic: license-file
+
+[//]: # (Badges)
+[![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/)
+[![build](https://github.com/OpenFreeEnergy/konnektor/actions/workflows/ci.yaml/badge.svg)](https://github.com/OpenFreeEnergy/konnektor/actions/workflows/ci.yaml)
+[![coverage](https://codecov.io/gh/OpenFreeEnergy/konnektor/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenFreeEnergy/konnektor)
+[![Documentation Status](https://readthedocs.org/projects/konnektor/badge/?version=latest)](https://konnektor.readthedocs.io/en/latest/?badge=latest)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/konnektor/main.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/konnektor/main)
+[![DOI](https://zenodo.org/badge/614010709.svg)](https://doi.org/10.5281/zenodo.18868798)
+
+<p align="center">
+    <picture align="center">
+      <source media="(prefers-color-scheme: dark)" srcset="https://github.com/OpenFreeEnergy/konnektor/blob/2e52eadb32a4a2813bc81fc3d0499f7563c8b4e6/.img/konnektor_logo_5.png">
+      <source media="(prefers-color-scheme: light)" srcset="https://github.com/OpenFreeEnergy/konnektor/blob/2e52eadb32a4a2813bc81fc3d0499f7563c8b4e6/.img/konnektor_logo_4.png">
+      <img alt="Konnektor`s fancy logo" src="https://github.com/OpenFreeEnergy/konnektor/blob/2e52eadb32a4a2813bc81fc3d0499f7563c8b4e6/.img/konnektor_logo_4.png" width=35% >
+    </picture>
+</p>
+
+Konnektor: A library for planning networks for use in free energy calculations
+==============================================================================
+
+Check out our article on Konnektor in the Journal of Chemical Information and Modeling: [Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations - Benjamin Ries*, Richard J. Gowers, Hannah M. Baumann, David W. H. Swenson,  Michael M. Henry, James R. B. Eastwood, Irfan Alibay, and David Mobley](https://pubs.acs.org/doi/10.1021/acs.jcim.4c01710).
+
+You can also find our pre-print on [ChemRxiv](https://chemrxiv.org/engage/chemrxiv/article-details/66d9b574cec5d6c1423643e4).
+
+
+## Content
+### Implemented Network Layouts
+Several Network layout generating algorithms are implemented in Konnektor, with different advantages and disadvantages.
+From an algorithmic perspective most of the algorithms are actually a reduction method of the Maximal Network.
+To speed-up the Maximal Network Algorithm we implemented an parallelization scheme to it. Below you can find some of our layouts:
+
+![image](docs/_static/img/network_layouts.png)
+
+### Tools for handling Networks
+Konnektor implements tools, that allow for example to merge (if a node is shared in the networks) or concatenate (if no node is shared) networks,
+append single molecules (nodes) to a network or delete transformations/molecules from a network.
+
+![image](docs/_static/img/network_operations_small.png)
+
+### Enable More Complex Higher Order Networks
+Another goal of Konnektor is to go beyond the standard network layout algorihtms and allow easy implementation of more complex network algorithms.
+This is achieved by combining the Tools and Network Generator Algorithms, to build up to more advanced workflows.
+
+![image](docs/_static/img/advanced_networking.png)
+
+## Code Example
+
+```python3
+# Here we generate some input data.
+from konnektor.data import get_benzene_ligands
+
+compounds = list(filter(lambda x: not x.name in ["lig_2", "lig_3", "lig_4", "lig_7"],
+                        get_benzene_ligands()))
+
+# Pick your Favourite Network layout with favourite AtomMapper and Scorer
+from openfe.setup import KartografAtomMapper, lomap_scorers
+from konnektor.network_planners import CyclicNetworkGenerator
+
+networker = CyclicNetworkGenerator(mappers=KartografAtomMapper(),
+                                   scorer=lomap_scorers.default_lomap_score)
+
+# Generate Network
+network = networker.generate_ligand_network(compounds)
+network.name = "Cyclic Network"
+
+# Visualize the generated network
+from konnektor.visualization import draw_ligand_network
+fig = draw_ligand_network(network=network, title=network.name)
+
+fig.show()
+```
+![example fig](.img/example_out.png)
+
+
+## Installation
+
+See our [installation guide](https://konnektor.openfree.energy/en/latest/install.html) for full details, or see below for developer install instructions.
+
+### Developer Install
+The development version of **konnektor** can be install directly from this repo:
+
+```shell
+git clone https://github.com/OpenFreeEnergy/konnektor.git
+
+cd konnektor
+micromamba env create -f environment.yaml
+
+micromamba activate konnektor
+pip install -e .
+
+```
+
+## License
+This library is made available under the MIT open source license.
+
+## Authors
+
+The OpenFE development team.
+
+## Acknowledgments
+Thanks to Enrico Ruijsenaars, Jenke Scheen, and Josh Horton for great discussions!

acellera_konnektor-0.4.0/README.md

@@ -0,0 +1,100 @@
+[//]: # (Badges)
+[![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/)
+[![build](https://github.com/OpenFreeEnergy/konnektor/actions/workflows/ci.yaml/badge.svg)](https://github.com/OpenFreeEnergy/konnektor/actions/workflows/ci.yaml)
+[![coverage](https://codecov.io/gh/OpenFreeEnergy/konnektor/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenFreeEnergy/konnektor)
+[![Documentation Status](https://readthedocs.org/projects/konnektor/badge/?version=latest)](https://konnektor.readthedocs.io/en/latest/?badge=latest)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/konnektor/main.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/konnektor/main)
+[![DOI](https://zenodo.org/badge/614010709.svg)](https://doi.org/10.5281/zenodo.18868798)
+
+<p align="center">
+    <picture align="center">
+      <source media="(prefers-color-scheme: dark)" srcset="https://github.com/OpenFreeEnergy/konnektor/blob/2e52eadb32a4a2813bc81fc3d0499f7563c8b4e6/.img/konnektor_logo_5.png">
+      <source media="(prefers-color-scheme: light)" srcset="https://github.com/OpenFreeEnergy/konnektor/blob/2e52eadb32a4a2813bc81fc3d0499f7563c8b4e6/.img/konnektor_logo_4.png">
+      <img alt="Konnektor`s fancy logo" src="https://github.com/OpenFreeEnergy/konnektor/blob/2e52eadb32a4a2813bc81fc3d0499f7563c8b4e6/.img/konnektor_logo_4.png" width=35% >
+    </picture>
+</p>
+
+Konnektor: A library for planning networks for use in free energy calculations
+==============================================================================
+
+Check out our article on Konnektor in the Journal of Chemical Information and Modeling: [Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations - Benjamin Ries*, Richard J. Gowers, Hannah M. Baumann, David W. H. Swenson,  Michael M. Henry, James R. B. Eastwood, Irfan Alibay, and David Mobley](https://pubs.acs.org/doi/10.1021/acs.jcim.4c01710).
+
+You can also find our pre-print on [ChemRxiv](https://chemrxiv.org/engage/chemrxiv/article-details/66d9b574cec5d6c1423643e4).
+
+
+## Content
+### Implemented Network Layouts
+Several Network layout generating algorithms are implemented in Konnektor, with different advantages and disadvantages.
+From an algorithmic perspective most of the algorithms are actually a reduction method of the Maximal Network.
+To speed-up the Maximal Network Algorithm we implemented an parallelization scheme to it. Below you can find some of our layouts:
+
+![image](docs/_static/img/network_layouts.png)
+
+### Tools for handling Networks
+Konnektor implements tools, that allow for example to merge (if a node is shared in the networks) or concatenate (if no node is shared) networks,
+append single molecules (nodes) to a network or delete transformations/molecules from a network.
+
+![image](docs/_static/img/network_operations_small.png)
+
+### Enable More Complex Higher Order Networks
+Another goal of Konnektor is to go beyond the standard network layout algorihtms and allow easy implementation of more complex network algorithms.
+This is achieved by combining the Tools and Network Generator Algorithms, to build up to more advanced workflows.
+
+![image](docs/_static/img/advanced_networking.png)
+
+## Code Example
+
+```python3
+# Here we generate some input data.
+from konnektor.data import get_benzene_ligands
+
+compounds = list(filter(lambda x: not x.name in ["lig_2", "lig_3", "lig_4", "lig_7"],
+                        get_benzene_ligands()))
+
+# Pick your Favourite Network layout with favourite AtomMapper and Scorer
+from openfe.setup import KartografAtomMapper, lomap_scorers
+from konnektor.network_planners import CyclicNetworkGenerator
+
+networker = CyclicNetworkGenerator(mappers=KartografAtomMapper(),
+                                   scorer=lomap_scorers.default_lomap_score)
+
+# Generate Network
+network = networker.generate_ligand_network(compounds)
+network.name = "Cyclic Network"
+
+# Visualize the generated network
+from konnektor.visualization import draw_ligand_network
+fig = draw_ligand_network(network=network, title=network.name)
+
+fig.show()
+```
+![example fig](.img/example_out.png)
+
+
+## Installation
+
+See our [installation guide](https://konnektor.openfree.energy/en/latest/install.html) for full details, or see below for developer install instructions.
+
+### Developer Install
+The development version of **konnektor** can be install directly from this repo:
+
+```shell
+git clone https://github.com/OpenFreeEnergy/konnektor.git
+
+cd konnektor
+micromamba env create -f environment.yaml
+
+micromamba activate konnektor
+pip install -e .
+
+```
+
+## License
+This library is made available under the MIT open source license.
+
+## Authors
+
+The OpenFE development team.
+
+## Acknowledgments
+Thanks to Enrico Ruijsenaars, Jenke Scheen, and Josh Horton for great discussions!