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Merge pull request #117 from RosettaCommons/codex/msa-cli-docs-public
docs: finish MSA CLI and preprocessing documentation for 3.0
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‎docs/conf.py‎

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"sphinx.ext.viewcode", # Add source code links
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"sphinx.ext.napoleon", # Google/NumPy style docstrings
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"sphinx_gallery.gen_gallery", # Generates auto_examples/ from examples/
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"sphinxcontrib.typer",
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"myst_parser", # Support Markdown tutorial pages
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"sphinx_design", # Render collapsible tutorial code examples
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]
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html_favicon = "_static/favicon-32x32.png"
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templates_path = ["_templates"]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/GALLERY_HEADER.rst", "ml/preprocessing.rst"]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/GALLERY_HEADER.rst"]
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napoleon_use_ivar = True
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# -- Options for HTML output -------------------------------------------------

‎docs/docs_requirements.txt‎

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pandoc>=2.0.0,<3
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myst-parser>=5.0.0
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sphinx-design>=0.6.0,<1
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sphinxcontrib-typer>=0.7.2,<1

‎docs/index.rst‎

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auto_examples/index
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contributor_guide
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mirrors
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msa

‎docs/ml.rst‎

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ml/msa_server
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ml/transforms/msa
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ml/utils
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ml/preprocessing

‎docs/ml/preprocessing.rst‎

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Core Preprocessing Functions
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----------------------------
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.. automodule:: atomworks.ml.preprocessing.get_pn_unit_data_from_structure
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.. automodule:: atomworks.ml.preprocessing.preprocess
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:members:
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:undoc-members:
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:show-inheritance:
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.. automodule:: atomworks.ml.preprocessing.utils
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:members:
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:undoc-members:
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:show-inheritance:
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:show-inheritance:
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MSA
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---
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Note that the following functions can be called via the command line. See :doc:`../msa`
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for more details.
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Finding
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^^^^^^^
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.. automodule:: atomworks.ml.preprocessing.msa.finding
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:members:
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:undoc-members:
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:show-inheritance:
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Filtering
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^^^^^^^^^
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.. automodule:: atomworks.ml.preprocessing.msa.filtering
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:members:
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:undoc-members:
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:show-inheritance:
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Generating
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^^^^^^^^^^
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.. automodule:: atomworks.ml.preprocessing.msa.generating
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:members:
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:undoc-members:
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:show-inheritance:
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Organizing
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^^^^^^^^^^
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.. automodule:: atomworks.ml.preprocessing.msa.organizing
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/msa.rst‎

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Multiple Sequence Alignment in AtomWorks
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========================================
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AtomWorks provides several command-line tools for Multiple Sequence Alignment (MSA) operations.
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Install AtomWorks with the ML extra. Filtering requires hhfilter from HH-suite
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on PATH. Local generation requires the selected MMseqs2 or HHblits backend and
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configured sequence databases, plus hhfilter for filtering the results. The
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ColabFold Python API supports remote generation; see :doc:`ml/msa_server`.
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Finding and organizing existing files do not run a sequence search.
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Find
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----
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Provide ``--existing-msa-dirs`` or set ``PROTEIN_MSA_DIRS`` to the directories
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containing your MSA files.
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.. typer:: atomworks_cli.find:app
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:prog: atomworks msa find
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:show-nested:
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Filter
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------
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.. typer:: atomworks_cli.filter:app
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:prog: atomworks msa filter
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:show-nested:
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Generate
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--------
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.. typer:: atomworks_cli.generate:app
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:prog: atomworks msa generate
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:show-nested:
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Organize
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--------
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.. typer:: atomworks_cli.organize:app
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:prog: atomworks msa organize
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:show-nested:

‎pyproject.toml‎

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docs = [
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"sphinxcontrib-typer>=0.7.2,<1",
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"sphinx>=8.0.0",
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"sphinx-gallery>=0.19.0",
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"pydata-sphinx-theme>=0.16.1",

‎src/atomworks/ml/preprocessing/msa/finding.py‎

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Args:
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sequences: Protein sequences to find template alignments for.
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template_dirs: Directories to search. Accepts:
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- None: No directories (all sequences reported missing).
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- list[PathLike]: Auto-assumes ``.m8`` / directory_depth=2 (matching
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`organize_template_alignments`'s defaults).

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