AMDockVS 0.1.0__tar.gz

amdockvs-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

amdockvs-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

amdockvs-0.1.0/.gitignore

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+### JetBrains template
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### Python template
+# 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/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/
+
+
+### AMDock project-specific
+# Vendor compound libraries: 257 MB, one file is over GitHub's 100 MB hard limit.
+data/Enamine_*/
+# Scratch outputs from notebooks and the MolSuite chunk payload spool.
+notebooks/_tmp/
+chunk_payloads/
+# Local runtime state
+*.db
+*.db-journal
+*.db-wal
+.local/
+# Tooling / assistant scratch
+.aiassistant/
+.claude/
+.ruff_cache/
+# IDE: keep nothing but the shared inspection profiles
+.idea/
+
+# scripts/ is local scratch by its own README: 21 MB of design mockups, duplicated splash
+# assets and pre-ms_contactmap diagram prototypes (including their PLIP sample report).
+# Only the maintenance helpers are published.
+scripts/*
+!scripts/README.md
+!scripts/build_tools_check.py
+!scripts/bootstrap_ray_worker.py

amdockvs-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.

amdockvs-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: AMDockVS
+Version: 0.1.0
+Summary: AMDock — chemistry-focused virtual screening and docking desktop app built on the MolSuite orchestrator.
+Author: Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco, Ernesto Moreno, Pedro A. Valiente
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/AMDockVS/AMDockVS
+Project-URL: Documentation, https://amdockvs.github.io/
+Project-URL: Issues, https://github.com/AMDockVS/AMDockVS/issues
+Keywords: docking,virtual-screening,autodock-vina,cheminformatics,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
+Classifier: Environment :: X11 Applications :: Qt
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ms_flow
+Requires-Dist: ms_components
+Requires-Dist: ms_contactmap
+Requires-Dist: rdkit>=2025.3.5
+Requires-Dist: dimorphite-dl<3,>=2.0.2
+Requires-Dist: meeko>=0.7.1
+Requires-Dist: vina>=1.2.7
+Requires-Dist: gemmi>=0.6
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: scipy>=1.15
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: pyarrow>=15
+Requires-Dist: pydantic>=2.0
+Requires-Dist: scikit-learn>=1.5
+Requires-Dist: joblib>=1.3
+Requires-Dist: sqlalchemy>=2.0
+Requires-Dist: sqlmodel>=0.0.24
+Requires-Dist: PySide6>=6.5
+Requires-Dist: pyqtgraph>=0.13
+Provides-Extra: bblean
+Requires-Dist: bblean>=0.10; extra == "bblean"
+Provides-Extra: pockets
+Requires-Dist: jdk4py~=21.0; extra == "pockets"
+Provides-Extra: receptors
+Requires-Dist: openmm>=8.1; extra == "receptors"
+Requires-Dist: pdbfixer>=1.9; extra == "receptors"
+Requires-Dist: prody>=2.4; extra == "receptors"
+Provides-Extra: all
+Requires-Dist: amdock-vs[bblean,pockets,receptors]; extra == "all"
+Dynamic: license-file
+
+# AMDockVS
+
+`AMDockVS` exposes a composite runtime on top of MolSuite. The official entry point is:
+
+```python
+from amdockvs import AMDockVSRuntime
+```
+
+The active public API is organised by domain:
+
+- `runtime.loader`: ligand and receptor loading
+- `runtime.molecules`: scopes, filters, sets and access to the general molecular inventory
+- `runtime.complexes`: explicit receptor-ligand relations for redocking and rescoring
+- `runtime.chemistry`: optional chemical preparation tools for ligands and receptors
+- `runtime.qsar`: descriptors, activities, datasets and QSAR models
+- `runtime.pockets`: P2Rank installation and cavity prediction
+- `runtime.docking`: Meeko preparation, grids, docking and result queries
+
+## Installation
+
+Python >= 3.12. The three MolSuite dependencies are not on PyPI yet, so they are
+installed from git first. PyMOL is required and must be installed from
+conda-forge because it is not distributed on PyPI:
+
+```bash
+conda create -n amdockvs -c conda-forge python=3.12 pymol-open-source
+conda activate amdockvs
+pip install "ms_flow @ git+https://github.com/MolSuite/ms_flow"
+pip install "ms_components @ git+https://github.com/MolSuite/ms_components"
+pip install "ms_contactmap @ git+https://github.com/MolSuite/ms_contactmap"
+pip install "amdock-vs @ git+https://github.com/AMDockVS/AMDockVS"
+```
+
+Start the GUI:
+
+```bash
+amdockvs
+```
+
+### Optional extras
+
+```bash
+pip install "amdock-vs[all]"   # or pick one: bblean, pockets, receptors
+```
+
+| Extra | What it adds |
+|---|---|
+| `bblean` | BitBIRCH clustering (GPL, invoked through its CLI, never imported) |
+| `pockets` | the jlink-trimmed JDK that P2Rank runs on |
+| `receptors` | OpenMM/PDBFixer receptor rebuilding and minimisation, ProDy fallbacks |
+
+### Non-pip dependencies (optional)
+
+| Tool | What for | Installation |
+|---|---|---|
+| `autogrid4` | ad4 scoring | `conda install -c conda-forge autogrid` |
+| `reduce` | `runtime.chemistry.protonate_receptors(method="reduce")` | `conda install -c conda-forge reduce` |
+| `pdb2pqr` | `runtime.chemistry.protonate_receptors(method="pdb2pqr")` | `pip install pdb2pqr` |
+
+P2Rank 2.5.1 is installed on demand from **Molecule Tools → Pocket Detection**.
+AMDockVS first reuses `~/Downloads/p2rank_2.5.1.tar.gz` if it exists, and
+otherwise downloads the official distribution and verifies its checksum. Java 17
+is likewise installed on demand into the active Conda environment, after a
+`dry-run` check that the transaction will not replace Python, RDKit, PyMOL,
+PySide, NumPy, Vina or Meeko. P2Rank is not redistributed inside the application.
+
+The same operation is available from the backend:
+
+```python
+runtime.pockets.install_p2rank()
+job_id = runtime.pockets.predict(
+    receptor_ids=[receptor_id],
+    profile="default",
+    threads=1,
+)
+runtime.wait_for_job(job_id)
+sites = runtime.pockets.list_predictions(receptor_id=receptor_id)
+```
+
+## Minimal workflow
+
+```python
+from pathlib import Path
+
+from amdockvs import AMDockVSRuntime
+
+runtime = AMDockVSRuntime()
+try:
+    runtime.create_project(name="demo", folder=Path("./demo_project"))
+
+    load_jobs = [
+        *runtime.loader.load_ligands(["./ligands.sdf"], executor_name="thread"),
+        *runtime.loader.load_receptors(["./receptor.pdb"], executor_name="thread"),
+    ]
+    runtime.wait_for_jobs(load_jobs)
+
+    chemistry_job = runtime.chemistry.standardize_ligands(executor_name="thread")
+    runtime.wait_for_job(chemistry_job)
+
+    ligand_scope = runtime.molecules.select(role="ligand")
+    receptor_scope = runtime.molecules.select(role="receptor", limit=1)
+
+    descriptor_job = runtime.qsar.compute_descriptors(molecule_set=ligand_scope, executor_name="thread")
+    runtime.wait_for_job(descriptor_job)
+
+    receptor = next(runtime.molecules.stream(receptor_scope))
+    runtime.docking.set_grid(
+        receptor_id=int(receptor.id or 0),
+        center=(12.0, 13.0, 10.0),
+        size=(20.0, 20.0, 20.0),
+    )
+
+    prep_jobs = [
+        runtime.docking.prepare_ligands(executor_name="thread"),
+        runtime.docking.prepare_receptors(executor_name="thread"),
+    ]
+    runtime.wait_for_jobs(prep_jobs)
+
+    receptor_set = runtime.molecules.create_set(receptor_scope, name="default_receptor_set")
+    docking_job = runtime.docking.run(
+        ligand_set=ligand_scope,
+        receptor_set=receptor_set,
+        executor_name="thread",
+    )
+    runtime.wait_for_job(docking_job)
+
+    results = runtime.docking.list_results()
+finally:
+    runtime.shutdown()
+```
+
+## Async semantics
+
+- `loader.*`, `qsar.compute_descriptors()`, `docking.prepare_*()` and `docking.run()` submit jobs and return a `job_id` or a `list[job_id]`.
+- `chemistry.*` also submits jobs by default; use `wait=True` or `runtime.wait_for_job(...)` to block in notebooks.
+- Waiting is explicit, through `runtime.wait_for_job(...)` or `runtime.wait_for_jobs(...)`.
+- `runtime.docking.screen(...)` is async by default too. Use `wait=True` only when you want a blocking composite helper.
+
+## Design notes
+
+- `stored_path` keeps pointing at the base imported artifact.
+- `chemistry.*` records a current chemical path in metadata; later steps consume it when present.
+- Vina preparation is stored on `amdock_molecules`, without a separate per-state traceability layer.
+- Inventory reads go through `molsuite.query.project_rows(...)`; they do not depend on the private `DataAccess` helper.
+
+## Examples
+
+- [examples/pipeline_demo.py](examples/pipeline_demo.py)
+- [examples/runtime_quickstart.py](examples/runtime_quickstart.py)
+
+## License
+
+MIT — see [LICENSE](LICENSE).