molify 0.0.1a0__tar.gz

molify-0.0.1a0/.claude/settings.local.json

@@ -0,0 +1,16 @@
+{
+  "permissions": {
+    "allow": [
+      "WebFetch(domain:luthaf.fr)",
+      "Bash(uvx pre-commit run:*)",
+      "Bash(uv run pytest:*)",
+      "WebFetch(domain:github.com)",
+      "Bash(python -m pytest tests/test_substructure.py::test_select_carbons -v)",
+      "Bash(uv run:*)",
+      "Bash(git checkout:*)",
+      "Bash(git add:*)",
+      "Bash(git commit:*)"
+    ],
+    "deny": []
+  }
+}

molify-0.0.1a0/.github/workflows/pages.yaml

@@ -0,0 +1,61 @@
+name: docs
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.12"
+        os:
+          - ubuntu-latest
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: julia-actions/setup-julia@v2
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev --all-groups
+
+      - name: Install packmol.jl
+        run: julia -e 'import Pkg; Pkg.add("Packmol")'
+
+      - name: Install pandoc
+        run: |
+          sudo apt update
+          sudo apt install -y pandoc
+
+      - name: Build documentation
+        run: |
+          cd docs
+          uv run make html
+
+      - name: Upload GitHub Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+      - name: Deploy GitHub Pages site
+        id: deployment
+        uses: actions/deploy-pages@v4

molify-0.0.1a0/.github/workflows/publish.yaml

@@ -0,0 +1,19 @@
+name: Release
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Publish
+        env:
+          PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          uv build
+          uv publish --token $PYPI_TOKEN

molify-0.0.1a0/.github/workflows/pytest.yaml

@@ -0,0 +1,62 @@
+# This workflow will install Python dependencies, run tests
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+  schedule:
+    - cron: '14 3 * * 1'  # at 03:14 on Monday.
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.13"
+          - "3.12"
+          - "3.11"
+          - "3.10"
+        os:
+          - ubuntu-latest
+        packmol-version:
+          - "20.15.1"
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v2
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install the project
+        run: uv sync --all-extras --dev
+      - name: Install packmol
+        run: |
+          wget https://github.com/m3g/packmol/archive/refs/tags/v${{ matrix.packmol-version}}.tar.gz
+          tar -xvf v${{ matrix.packmol-version}}.tar.gz
+          cd packmol-${{ matrix.packmol-version}}
+          make
+      - name: Install packmol.jl
+        run: |
+          julia -e 'import Pkg; Pkg.add("Packmol")'
+      - name: Pytest
+        run: |
+          # add packmol to path
+          export PATH=$PATH:$(pwd)/packmol-${{ matrix.packmol-version}}
+
+          uv run python --version
+          uv run pytest --cov --junitxml=junit.xml -o junit_family=legacy
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

molify-0.0.1a0/.gitignore

@@ -0,0 +1,162 @@
+# 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/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+tmp/
+.DS_Store

molify-0.0.1a0/.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+default_language_version:
+  python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-merge-conflict
+        args: ['--assume-in-merge']
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: ['--fix=lf']
+      - id: sort-simple-yaml
+      - id: trailing-whitespace
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        additional_dependencies: ["tomli"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.12.12
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.22
+    hooks:
+    - id: mdformat
+      args: ["--wrap=80"]

molify-0.0.1a0/.python-version

@@ -0,0 +1 @@
+3.11

molify-0.0.1a0/CONTRIBUTING.md

@@ -0,0 +1,15 @@
+# Contribution Guidelines
+
+All contributions are welcome!
+
+Ideally, please open an issue first to discuss the feature or bugfix you plan to
+work on. Create a dedicated branch from `main` for your changes and open a pull
+request.
+
+To be accepted, your contribution should include tests for any new functionality
+and pass all existing tests in the `/tests` directory. We use
+`.pre-commit-config.yaml` to ensure consistent code quality - please make sure
+all checks pass.
+
+For any further questions, feel free to use the issue tracker to start a
+discussion.

molify-0.0.1a0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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molify-0.0.1a0/PKG-INFO

@@ -0,0 +1,75 @@
+Metadata-Version: 2.4
+Name: molify
+Version: 0.0.1a0
+Summary: Interface between rdkit and ASE
+Author-email: Fabian Zills <fzills@icp.uni-stuttgart.de>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: ase>=3.25.0
+Requires-Dist: matplotlib>=3.10.1
+Requires-Dist: networkx>=3.4.2
+Requires-Dist: rdkit>=2024
+Provides-Extra: vesin
+Requires-Dist: vesin>=0.3.7; extra == 'vesin'
+Description-Content-Type: text/markdown
+
+[![zincware](https://img.shields.io/badge/Powered%20by-zincware-darkcyan)](https://github.com/zincware)
+[![codecov](https://codecov.io/gh/zincware/rdkit2ase/graph/badge.svg?token=Q0VIN03185)](https://codecov.io/gh/zincware/rdkit2ase)
+[![PyPI version](https://badge.fury.io/py/rdkit2ase.svg)](https://badge.fury.io/py/rdkit2ase)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15423477.svg)](https://doi.org/10.5281/zenodo.15423477)
+[![Docs](https://github.com/zincware/rdkit2ase/actions/workflows/pages.yaml/badge.svg)](https://zincware.github.io/rdkit2ase/)
+[![status](https://joss.theoj.org/papers/4c1ec2a0b66ed6baaf3fe93066696d5f/status.svg)](https://joss.theoj.org/papers/4c1ec2a0b66ed6baaf3fe93066696d5f)
+
+# rdkit2ase - Interface between the rdkit and ASE package.
+
+Installation via `pip install rdkit2ase`. For more information please visit the
+[documentation](https://zincware.github.io/rdkit2ase/).
+
+A common use case is to create 3D structures from SMILES strings. This can be
+achieved using the `rdkit2ase.rdkit2ase` function.
+
+```py
+import ase
+from rdkit import Chem
+from rdkit2ase import rdkit2ase, ase2rdkit
+
+mol = Chem.MolFromSmiles("O")
+atoms: ase.Atoms = rdkit2ase(mol)
+mol = ase2rdkit(atoms)
+```
+
+Because this is such a common use case, there is a convenience function
+`rdkit2ase.smiles2atoms` that combines the two steps.
+
+```py
+import ase
+from rdkit2ase import smiles2atoms
+
+atoms: ase.Atoms = smiles2atoms("O")
+
+print(atoms)
+>>> Atoms(symbols='OH2', pbc=False)
+```
+
+## Packmol Interface
+
+Given the molecular units, you can build periodic boxes with a given density
+using the `rdkit2ase.pack` function.
+
+If you have [packmol](https://github.com/m3g/packmol) (at least `v20.15.0`) you
+can use the rdkit2ase interface as follows:
+
+```py
+from rdkit2ase import pack, smiles2conformers
+
+water = smiles2conformers("O", 2)
+ethanol = smiles2conformers("CCO", 5)
+density = 1000  # kg/m^3
+box = pack([water, ethanol], [7, 5], density)
+print(box)
+>>> Atoms(symbols='C10H44O12', pbc=True, cell=[8.4, 8.4, 8.4])
+```
+
+Many additional features are described in the
+[documentation](https://zincware.github.io/rdkit2ase/).