[WIP] Add overlay command for multi-structure visualizations #13
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Add comprehensive overlay functionality that combines multiple protein structures into single visualization with automatic clustering and alignment capabilities. Features: - Multiple file input via glob patterns (e.g., "folder/*.cif") - Automatic Foldseek-based clustering with opacity scaling - Two alignment modes: family-identity and inertia-based - Multiple output formats: SVG, PNG, PDF (PNG/PDF require Cairo) - Configurable canvas size, DPI, and styling - Built-in error handling and validation Implementation: - CLI command: src/flatprot/cli/overlay.py - Core utilities: src/flatprot/utils/overlay_utils.py - Comprehensive test suite: 41 tests (5 CLI + 19 integration + 17 unit) - Documentation: docs/commands/overlay.md - Integration with main CLI via src/flatprot/cli/main.py Replaces example script klk_overlay.py with production-ready command integrated into FlatProt's CLI ecosystem.
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Summary
Adds a new
flatprot overlaycommand that combines multiple protein structures into single visualization with automatic clustering and alignment capabilities.This replaces the example
klk_overlay.pyscript with a production-ready CLI command fully integrated into FlatProt's ecosystem.Features
"folder/*.cif")Implementation
src/flatprot/cli/overlay.pysrc/flatprot/utils/overlay_utils.pydocs/commands/overlay.mdsrc/flatprot/cli/main.pyExamples
Testing Status
✅ All 357 tests passing
✅ Complete test coverage for overlay functionality
✅ Integration tests for CLI interface
✅ Unit tests for utility functions
✅ Error handling and edge cases covered
Requirements
For PNG/PDF output, Cairo graphics library is required:
brew install cairosudo apt-get install libcairo2-devTODO