acellera-lomap2 3.3.0__tar.gz

acellera_lomap2-3.3.0/.git-blame-ignore-revs

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+# https://github.com/OpenFreeEnergy/Lomap/pull/130 -- ruff auto-formatting
+23ea8b4a6019b3c83da278696ddeb38e27cf57bb

acellera_lomap2-3.3.0/.gitattributes

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+Lomap/_version.py export-subst
+lomap/_version.py export-subst

acellera_lomap2-3.3.0/.github/pull_request_template.md

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+<!--
+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/ ):
+-->
+
+<!--
+see https://regro.github.io/rever-docs/news.html for details on how to add news entry (you do not need to run the rever command)
+-->
+
+Checklist
+* [ ] All new code is appropriately documented (user-facing code _must_ have complete docstrings).
+* [ ] Added a ``news`` entry, or the changes are not user-facing.
+* [ ] Ran pre-commit: you can run [pre-commit](https://pre-commit.com) locally or comment on this PR with `pre-commit.ci autofix`.
+* [ ] Add yourself to the AUTHORS.md list.
+
+## 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/>.

acellera_lomap2-3.3.0/.github/workflows/ci.yaml

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+name: CI
+
+on:
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # At 07:00 UTC on Monday and Thursday
+    - cron: "0 7 * * *"
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+concurrency:
+  # Probably overly cautious group naming.
+  # Commits to develop/master will cancel each other, but PRs will only cancel
+  # commits within the same PR
+  group: "${{ github.ref }}-${{ github.head_ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, Gufe ${{ matrix.gufe }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, macos-15-intel, macos-latest]
+        gufe: ["yes"]
+        include:
+          - os: "ubuntu-latest"
+            python-version: "3.12"
+            gufe: "no"
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Additional info about the build
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
+
+      - uses: mamba-org/setup-micromamba@v3
+        with:
+          micromamba-binary-path: ~/.local/bin/micromamba
+          environment-file: environment.yaml
+          environment-name: lomap-env
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install optional gufe"
+        if: ${{ matrix.gufe == 'yes' }}
+        run: |
+          micromamba install -c conda-forge "gufe>=1.6.1"
+
+      - name: Install package
+        run: python -m pip install --no-deps -v -e .
+
+      - name: Test imports
+        run: |
+          python -Ic "import lomap; print(lomap.__version__)"
+
+      - name: Environment Information
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: Test the package
+        env:
+          DUECREDIT_ENABLE: 'yes'
+        run: pytest -n auto -vv
+
+      - name: Codecov
+        uses: codecov/codecov-action@v5
+        if: ${{ github.repository == 'OpenFreeEnergy/Lomap'
+                && github.event_name == 'pull_request' }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          fail_ci_if_error: False
+          verbose: True

acellera_lomap2-3.3.0/.github/workflows/clean_cache.yaml

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+# from https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows#force-deleting-cache-entries
+name: cleanup caches by a branch
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ github.repository }}
+          BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
+
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH | cut -f 1 )
+
+          ## Setting this to not fail the workflow while deleting cache keys.
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

acellera_lomap2-3.3.0/.github/workflows/mypy.yaml

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+name: "mypy static type checking"
+on:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "**.py"
+  push:
+    branches:
+      - main
+    paths:
+      - "**.py"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+    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:
+          micromamba-binary-path: ~/.local/bin/micromamba
+          environment-file: environment.yaml
+          environment-name: lomap-env
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=3.12
+            mypy
+            types-networkx
+            gufe>=1.6.1
+          init-shell: bash
+
+      - name: "Install steps"
+        run: |
+          python -m pip install --no-deps -e .
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: "Lint with mypy"
+        run: mypy

acellera_lomap2-3.3.0/.github/workflows/pull_request_template.md

@@ -0,0 +1,20 @@
+<!--
+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/ ):
+-->
+
+<!--
+see https://regro.github.io/rever-docs/news.html for details on how to add news entry (you do not need to run the rever command)
+-->
+
+Checklist
+* [ ] All new code is appropriately documented (user-facing code _must_ have complete docstrings).
+* [ ] Added a ``news`` entry, or the changes are not user-facing.
+* [ ] Ran pre-commit: you can run [pre-commit](https://pre-commit.com) locally or comment on this PR with `pre-commit.ci autofix`.
+
+## 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/>.

acellera_lomap2-3.3.0/.gitignore

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+.duecredit.p
+
+# 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/
+*.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
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# 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
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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
+
+# Rever
+rever/

acellera_lomap2-3.3.0/.pre-commit-config.yaml

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+# 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|gpickle)$'
+    - id: check-added-large-files
+      args: ["--maxkb=4000"]
+    - id: check-case-conflict
+    - id: check-symlinks
+    - id: check-toml
+    - id: check-yaml
+    - id: debug-statements
+    - id: destroyed-symlinks
+    - id: end-of-file-fixer
+      exclude: '\.(graphml|gpickle|pickle)$'
+
+- 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_lomap2-3.3.0/.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: "ubuntu-24.04"
+  tools:
+    python: "mambaforge-4.10"
+
+sphinx:
+   configuration: docs/conf.py
+   fail_on_warning: true
+
+conda:
+  environment: docs/environment.yaml
+
+python:
+  # Install our python package before building the docs
+  install:
+    - method: pip
+      path: .

acellera_lomap2-3.3.0/AUTHORS.md

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+Lomap is developed by:
+
+- Gaetano Calabro' gcalabro@uci.edu
+- David Mobley dmobley@uci.edu
+- Mark Mackey
+- Lester Hedges
+- Antonia S J S Mey
+- Jenke Scheen
+- Mike M Henry
+- Richard J Gowers
+- Irfan Alibay
+- David Swenson
+- Nigel Palmer
+- Shuai Liu
+- Alyssa Travitz
+- Hannah Baumann
+- Shaochen Shi
+- Ashley Mitchell
+- Tom Ginsberg
+- Josh Horton

acellera_lomap2-3.3.0/CITATION.bib

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+%% Citations for LOMAP
+
+@article{liu2013lead,
+  title={Lead optimization mapper: automating free energy calculations for lead optimization},
+  abstract={Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger’s and OpenEye’s APIs, has been made available freely under the BSD license.},
+  author={Liu, Shuai and Wu, Yujie and Lin, Teng and Abel, Robert and Redmann, Jonathan P and Summa, Christopher M and Jaber, Vivian R and Lim, Nathan M and Mobley, David L},
+  journal={Journal of computer-aided molecular design},
+  volume={27},
+  number={9},
+  pages={755--770},
+  year={2013},
+  publisher={Springer}
+}

acellera_lomap2-3.3.0/LICENSE.txt

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+Copyright (c) 2016-2017, Mobley Lab at UC Irvine.
+
+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_lomap2-3.3.0/MANIFEST.in

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+graft src/lomap
+recursive-include src/lomap/tests  *sdf
+recursive-include src/lomap/tests  *mol2
+recursive-include src/lomap/tests  *gpickle
+recursive-include src/lomap/tests  *pickle
+recursive-include src/lomap/tests  *txt
+
+
+include MANIFEST.in
+include README.md
+include LICENSE.txt
+include examples/example.py
+include versioneer.py
+include src/lomap/_version.py

acellera_lomap2-3.3.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: acellera-lomap2
+Version: 3.3.0
+Summary: Lead Optimization Mapper 2
+Author: Gaetano Calabro and David Mobley
+Maintainer-email: The Open Free Energy developers <openfreeenergy@omsf.io>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/OpenFreeEnergy/Lomap
+Keywords: alchemical free energy,network,perturbation,setup
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: matplotlib
+Requires-Dist: networkx
+Requires-Dist: numpy
+Requires-Dist: rdkit
+Provides-Extra: credits
+Requires-Dist: duecredit; extra == "credits"
+Provides-Extra: graphviz
+Requires-Dist: pygraphviz; extra == "graphviz"
+Provides-Extra: test
+Requires-Dist: codecov; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+[![CI](https://github.com/OpenFreeEnergy/Lomap/actions/workflows/CI.yaml/badge.svg)](https://github.com/OpenFreeEnergy/Lomap/actions/workflows/CI.yaml)
+[![Documentation Status](https://readthedocs.org/projects/lomap/badge/?version=latest)](https://lomap.readthedocs.io/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16898468.svg)](https://doi.org/10.5281/zenodo.16898468)
+# Lomap
+The Lead Optimization Mapper (LOMAP) is an automated algorithm for planning
+efficient relative free energy calculation networks across a set of ligands,
+built on freely available tools such as RDKit.
+With the optional [`gufe`](https://github.com/OpenFreeEnergy/gufe) dependency installed,
+it also integrates with the [Open Free Energy](https://openfree.energy) ecosystem.
+The method is described in the original
+[LOMAP publication](https://doi.org/10.1007/s10822-013-9678-y).
+
+## Installation
+
+`lomap` is available on conda-forge as the `lomap2` package. See the
+[installation documentation](https://lomap.readthedocs.io/en/latest/installation.html)
+for install instructions, including the development install and optional
+dependencies (`gufe` and `pygraphviz`).
+
+## Quickstart
+
+This example uses LOMAP's optional `gufe` bindings to load two example ligands
+bundled with the package and plan a perturbation network between them with the
+default atom mapper and scorer.
+
+```python
+# requires the optional `gufe` dependency (see Installation)
+import importlib.resources
+
+import lomap
+from gufe import SmallMoleculeComponent
+
+# Two example ligands ship with the package under lomap.tests.data
+data = importlib.resources.files("lomap.tests.data")
+ligands = [
+    SmallMoleculeComponent.from_sdf_file(data / name)
+    for name in ["lig_41.sdf", "lig_74.sdf"]
+]
+
+# Build a LigandNetwork using LOMAP's scoring and network-construction rules
+network = lomap.generate_lomap_network(
+    ligands=ligands,
+    mappers=lomap.LomapAtomMapper(),
+    scorer=lomap.default_lomap_score,
+)
+print(f"{len(network.nodes)} ligands, {len(network.edges)} edges")
+```
+
+For proposing individual mappings, customising edge scores, and the full set of
+network options, see the [documentation](https://lomap.readthedocs.io).
+
+## Authors
+
+See [AUTHORS.md](https://github.com/OpenFreeEnergy/Lomap/blob/main/AUTHORS.md).
+
+## History
+
+Open Free Energy took over maintenance of LOMAP in 2022. The original
+development repository has since been archived, but can be found at
+https://github.com/MobleyLab/Lomap.

acellera_lomap2-3.3.0/README.md

@@ -0,0 +1,60 @@
+[![CI](https://github.com/OpenFreeEnergy/Lomap/actions/workflows/CI.yaml/badge.svg)](https://github.com/OpenFreeEnergy/Lomap/actions/workflows/CI.yaml)
+[![Documentation Status](https://readthedocs.org/projects/lomap/badge/?version=latest)](https://lomap.readthedocs.io/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16898468.svg)](https://doi.org/10.5281/zenodo.16898468)
+# Lomap
+The Lead Optimization Mapper (LOMAP) is an automated algorithm for planning
+efficient relative free energy calculation networks across a set of ligands,
+built on freely available tools such as RDKit.
+With the optional [`gufe`](https://github.com/OpenFreeEnergy/gufe) dependency installed,
+it also integrates with the [Open Free Energy](https://openfree.energy) ecosystem.
+The method is described in the original
+[LOMAP publication](https://doi.org/10.1007/s10822-013-9678-y).
+
+## Installation
+
+`lomap` is available on conda-forge as the `lomap2` package. See the
+[installation documentation](https://lomap.readthedocs.io/en/latest/installation.html)
+for install instructions, including the development install and optional
+dependencies (`gufe` and `pygraphviz`).
+
+## Quickstart
+
+This example uses LOMAP's optional `gufe` bindings to load two example ligands
+bundled with the package and plan a perturbation network between them with the
+default atom mapper and scorer.
+
+```python
+# requires the optional `gufe` dependency (see Installation)
+import importlib.resources
+
+import lomap
+from gufe import SmallMoleculeComponent
+
+# Two example ligands ship with the package under lomap.tests.data
+data = importlib.resources.files("lomap.tests.data")
+ligands = [
+    SmallMoleculeComponent.from_sdf_file(data / name)
+    for name in ["lig_41.sdf", "lig_74.sdf"]
+]
+
+# Build a LigandNetwork using LOMAP's scoring and network-construction rules
+network = lomap.generate_lomap_network(
+    ligands=ligands,
+    mappers=lomap.LomapAtomMapper(),
+    scorer=lomap.default_lomap_score,
+)
+print(f"{len(network.nodes)} ligands, {len(network.edges)} edges")
+```
+
+For proposing individual mappings, customising edge scores, and the full set of
+network options, see the [documentation](https://lomap.readthedocs.io).
+
+## Authors
+
+See [AUTHORS.md](https://github.com/OpenFreeEnergy/Lomap/blob/main/AUTHORS.md).
+
+## History
+
+Open Free Energy took over maintenance of LOMAP in 2022. The original
+development repository has since been archived, but can be found at
+https://github.com/MobleyLab/Lomap.