ms-contactmap 0.1.0__tar.gz

ms_contactmap-0.1.0/.github/workflows/docs.yml

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+name: Documentation
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+concurrency:
+  group: documentation
+  cancel-in-progress: false
+
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - uses: actions/configure-pages@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.x
+      - run: pip install zensical "mkdocstrings[python]" "mike @ git+https://github.com/squidfunk/mike.git"
+      - name: Configure Git author
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+      - name: Deploy development documentation
+        if: github.ref == 'refs/heads/main'
+        run: |
+          mike deploy --push dev
+          if ! mike list latest >/dev/null 2>&1; then
+            mike set-default --push dev
+          fi
+      - name: Deploy release documentation
+        if: startsWith(github.ref, 'refs/tags/v')
+        run: |
+          mike deploy --push --update-aliases --alias-type redirect "$GITHUB_REF_NAME" latest
+          mike set-default --push latest
+      - name: Export versioned site
+        run: |
+          mkdir -p site
+          git archive gh-pages | tar -x -C site
+      - uses: actions/upload-pages-artifact@v5
+        with:
+          path: site
+      - uses: actions/deploy-pages@v5
+        id: deployment

ms_contactmap-0.1.0/.github/workflows/publish.yml

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+# Publish to PyPI on a GitHub release.
+#
+# No secrets: the job authenticates to PyPI over OIDC (Trusted Publishing).
+# It has to be enabled on the PyPI side *before* the first upload -- for a
+# project that does not exist yet, that is a "pending publisher" under
+# Your projects > Publishing, and it must name this repo, `publish.yml`
+# and the `pypi` environment below.
+name: publish
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      # A permissions block sets every scope it does not name to none, so
+      # checkout needs contents spelled out or it cannot read a private repo.
+      contents: read
+      id-token: write  # mint the OIDC token PyPI checks; no secret involved
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0  # setuptools-scm reads the version off the tag
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - run: pipx run build
+      - uses: pypa/gh-action-pypi-publish@release/v1

ms_contactmap-0.1.0/.gitignore

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+### JetBrains template
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+# Flask stuff:
+instance/
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+# Sphinx documentation
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+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
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+# 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:
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+# pipenv
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+#Pipfile.lock
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+#   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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+
+# Maestro reference screenshots used only while tuning colours/layout (42 MB).
+data/*.png
+.idea/
+
+# Internal planning notes, not part of the published package.
+PLAN.md

ms_contactmap-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco, Ernesto Moreno, Pedro A. Valiente
+
+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.

ms_contactmap-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ms_contactmap
+Version: 0.1.0
+Summary: MolSuite Interaction Profiler 
+Author: Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco, Ernesto Moreno, Pedro A. Valiente
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/MolSuite/ms_contactmap
+Project-URL: Issues, https://github.com/MolSuite/ms_contactmap/issues
+Keywords: protein-ligand,interactions,contact-map,molsuite,structural-biology
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: PySide6>=6.10
+Requires-Dist: rdkit>=2025.3
+Requires-Dist: numpy>=2.0
+Requires-Dist: scipy>=1.15
+Requires-Dist: biopython>=1.86
+Dynamic: license-file
+
+# ms_contactmap
+
+MolSuite Contact Map: computes protein–ligand contact maps and renders
+2D interaction diagrams.
+
+Part of the [MolSuite](https://molsuite.github.io/) stack.
+
+## Install
+
+```bash
+pip install git+https://github.com/MolSuite/ms_contactmap
+```
+
+## Usage
+
+```bash
+ms_contactmap --help
+ms_contactmap complex.pdb --ligand LIG --smiles "CCO" --json contacts.json
+```
+
+Reference structures and ligand catalogs in `data/` are development and test
+fixtures; the installed package does not depend on them.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

ms_contactmap-0.1.0/README.md

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+# ms_contactmap
+
+MolSuite Contact Map: computes protein–ligand contact maps and renders
+2D interaction diagrams.
+
+Part of the [MolSuite](https://molsuite.github.io/) stack.
+
+## Install
+
+```bash
+pip install git+https://github.com/MolSuite/ms_contactmap
+```
+
+## Usage
+
+```bash
+ms_contactmap --help
+ms_contactmap complex.pdb --ligand LIG --smiles "CCO" --json contacts.json
+```
+
+Reference structures and ligand catalogs in `data/` are development and test
+fixtures; the installed package does not depend on them.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

ms_contactmap-0.1.0/docs/api.md

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+# Python API
+
+The package root exposes the supported high-level API through lazy imports.
+
+## Analysis pipeline
+
+`build_diagram()` is the normal entry point. It selects the requested ligand,
+detects interactions, computes pocket context and exposure, and returns a
+`Diagram` independent of Qt rendering.
+
+```python
+from ms_contactmap import build_diagram
+
+diagram = build_diagram(
+    pdb_path="complex.pdb",
+    resname="LIG",
+    smiles="CCO",
+    name="screening hit 17",
+    chain="A",
+    resnum=401,
+    compute_exposure=True,
+)
+
+for interaction in diagram.interactions:
+    print(interaction.kind, interaction.residue_key, interaction.distance)
+```
+
+Set `compute_exposure=False` when solvent accessibility is unnecessary. This
+does not change interaction detection.
+
+## Layout and persistence
+
+Analysis can be serialized before or after solving its layout:
+
+```python
+from ms_contactmap import load_json, save_json, solve_layout
+
+layout = solve_layout(diagram)
+save_json("hit-17.json", diagram, layout)
+
+restored_diagram, restored_layout, view = load_json("hit-17.json")
+```
+
+The JSON document includes a schema version. Prefer `save_json()` and
+`load_json()` over depending on its internal dictionary layout.
+
+## Qt widget
+
+```python
+from PySide6.QtWidgets import QApplication
+from ms_contactmap import InteractionDiagramWidget
+
+app = QApplication([])
+widget = InteractionDiagramWidget(diagram)
+widget.resize(1100, 780)
+widget.show()
+app.exec()
+```
+
+`set_diagram_async()` solves larger layouts in the Qt thread pool and emits
+`layoutStarted`, `layoutFinished`, or `layoutFailed`. Use the synchronous
+constructor for batch export and the asynchronous method for a responsive UI.
+
+## Low-level detection
+
+`ms_contactmap.detect.detect_interactions()` is available for integrations that
+already own a `LigandGeometry`. Most callers should use `build_diagram()` so
+residue context, exposure, and metadata remain consistent.

ms_contactmap-0.1.0/docs/api_reference.md

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+# API reference
+
+## Public facade
+
+::: ms_contactmap
+
+## Diagram model
+
+::: ms_contactmap.model
+
+## Interaction analysis
+
+::: ms_contactmap.interactions
+
+## Detection
+
+::: ms_contactmap.detect
+
+## Ligand and PDB chemistry
+
+::: ms_contactmap.chem
+
+## Layout
+
+::: ms_contactmap.layout
+
+## Qt widget
+
+::: ms_contactmap.widget.InteractionDiagramWidget
+
+## JSON persistence
+
+::: ms_contactmap.json_io
+
+## Image export
+
+::: ms_contactmap.export

ms_contactmap-0.1.0/docs/examples.md

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+# Examples
+
+## Batch JSON, PNG, and SVG export
+
+```python
+from PySide6.QtWidgets import QApplication
+
+from ms_contactmap import InteractionDiagramWidget, build_diagram
+
+app = QApplication.instance() or QApplication([])
+diagram = build_diagram(
+    "complex.pdb",
+    "LIG",
+    "CCO",
+    chain="A",
+    resnum=401,
+)
+widget = InteractionDiagramWidget(diagram)
+widget.export_json("contacts.json")
+widget.export_png("contacts.png", scale=2.0)
+widget.export_svg("contacts.svg")
+```
+
+The widget owns the solved scene used by the exporters. A Qt event loop does
+not need to be started for this synchronous batch case, but a `QApplication`
+must exist.
+
+## Reopen and edit a saved diagram
+
+```python
+from PySide6.QtWidgets import QApplication
+from ms_contactmap import InteractionDiagramWidget
+
+app = QApplication([])
+widget = InteractionDiagramWidget.from_json("contacts.json")
+widget.resize(1100, 780)
+widget.show()
+app.exec()
+```
+
+The interactive widget supports moving residues, rotating or mirroring the
+ligand, recalculating the layout, changing the legend position, and exporting
+the edited result.

ms_contactmap-0.1.0/docs/index.md

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+# ms_contactmap
+
+`ms_contactmap` detects protein-ligand interactions from a PDB complex and
+renders an editable two-dimensional contact map. Analysis, layout, JSON
+serialization, Qt presentation, and image export are separate layers, so the
+same result can be used in a batch process or an interactive application.
+
+## Install
+
+```bash
+pip install "ms_contactmap @ git+https://github.com/MolSuite/ms_contactmap"
+```
+
+The package requires Python 3.12, RDKit, Biopython, SciPy, NumPy, and PySide6.
+
+## Command line
+
+Build a diagram directly from a complex:
+
+```bash
+ms_contactmap complex.pdb \
+  --ligand LIG \
+  --smiles "CCO" \
+  --json contacts.json \
+  --png contacts.png
+```
+
+Open a saved analysis without detecting the interactions again:
+
+```bash
+ms_contactmap --from-json contacts.json --show
+```
+
+Use `--chain` and `--resnum` when the PDB contains more than one copy of the
+ligand. Use `--no-exposure` for a faster first pass without solvent-exposure
+halos.
+
+## Python entry point
+
+```python
+from ms_contactmap import build_diagram
+
+diagram = build_diagram(
+    "complex.pdb",
+    "LIG",
+    "CCO",
+    chain="A",
+    resnum=401,
+)
+print(len(diagram.interactions))
+```
+
+See the [Python API guide](api.md), [complete examples](examples.md), and
+[generated reference](api_reference.md).
+
+## License
+
+`ms_contactmap` is released under the MIT License.