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- Implement BioProtein as a subclass of BioSequence. - Implement BioEnzyme and BioRestrictionEnzyme classes. - Implement BioReaction and BioCatalysis for many-to-many relationships. - Implement BioCircularSequence decorator for virtual circularity. - Add digestWith: extensions to BioSequence. - Add BioREBASEParser for emboss_e.dat format. - Add BioRestrictionTest with comprehensive test cases. - Use 1-based indexing for all site and fragment calculations. - Leverage IUPAC mapping for site searching. Co-authored-by: hernanmd <4825959+hernanmd@users.noreply.github.com>
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Implemented restriction enzyme module including: - BioProtein, BioEnzyme, BioRestrictionEnzyme (Flyweight). - Many-to-many ER relationship model (BioReaction, BioCatalysis). - BioCircularSequence decorator for wrap-around handling. - BioREBASEParser for emboss_e.dat. - BioRestrictionTest suite. - 1-based indexing consistency. Co-authored-by: hernanmd <4825959+hernanmd@users.noreply.github.com>
Implemented restriction enzyme module including: - BioProtein, BioEnzyme, BioRestrictionEnzyme (Flyweight). - Many-to-many ER relationship model (BioReaction, BioCatalysis) with inverse links. - BioCircularSequence decorator for wrap-around handling. - BioREBASEParser for emboss_e.dat. - BioRestrictionTest suite. - 1-based indexing consistency. Co-authored-by: hernanmd <4825959+hernanmd@users.noreply.github.com>
- Implement core hierarchy: BioProtein > BioEnzyme > BioRestrictionEnzyme. - Implement ER relationship model: BioReaction & BioCatalysis (association class). - Implement Flyweight pattern for efficient enzyme management via registry. - Implement Decorator pattern for circular sequences (BioCircularSequence). - Add support for multi-enzyme digestion and IUPAC-aware site searching. - Implement BioREBASEParser for emboss_e.dat format. - Implement BioRestrictionMapFormatter for human-readable reports. - Add comprehensive SUnit tests (BioRestrictionTest) covering linear/circular DNA, multi-enzyme digests, and relationship consistency. - Fix CI dependency conflict by updating .smalltalk.ston. - Use Smalltalk-native 1-based indexing for all biological coordinates. Co-authored-by: hernanmd <4825959+hernanmd@users.noreply.github.com>
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This PR ports the restriction enzyme logic from Biopython to BioSmalltalk, re-engineered for Smalltalk-native idioms. It addresses long-standing issues in the original Python implementation by using 1-based indexing, a decorator pattern for circularity, and a flyweight pattern for efficient enzyme management. It also implements a robust many-to-many relationship between enzymes and reactions using an association class for catalytic attributes like Km. Comprehensive tests and a REBASE data parser are included.
PR created automatically by Jules for task 195259426181153767 started by @hernanmd