Exhaustive fragmenter saturation fix and optimization#1

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ToLeWeiss wants to merge 47 commits intomainfrom

exhaustive_fragmenter

Commits on Oct 28, 2024

work in progress: implemented the option for the fragmenter to return saturated or unsaturated fragments, added a test and renamed some tests to prepare for the tests for unsaturated fragments
ToLeWeiss
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added tests for unsaturated setting and fixed unsaturated run
ToLeWeiss
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Commits on Nov 28, 2024

work in progress: first copy approaches to fix saturation problem and algorithm changes to use a power set to reduce computations
ToLeWeiss
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fix subset generation for case where initial capacity might be negative or too small because of truncation of BigInt to int
ToLeWeiss
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switching to primitive integers because java Lists are indexed by these and therefore cant have more elements than 2^31 - 1
ToLeWeiss
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work in progress: fixed indexing and fix of check for size constraint
ToLeWeiss
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work in progress: switch to primitive int matrices for subset generation and added more comprehensive comments for subset generation
ToLeWeiss
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work in progress: fix size limitation of the subset generation
ToLeWeiss
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Commits on Dec 10, 2024

work in progress: figuring out why the end atoms are in a different container
ToLeWeiss
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Commits on Dec 13, 2024

work in progress: fixing for end atoms not in container
ToLeWeiss
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Commits on Feb 3, 2025

work in progress: working reimplementation of the exhaustive fragmenter
ToLeWeiss
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Commits on Apr 6, 2025

work in progress: first tries to add an saturation option with R-Atoms
ToLeWeiss
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Commits on Apr 25, 2025

work in progress: added tests for pseudo-R-atom saturation and first tries to implement the pseudo-R-atom saturation
ToLeWeiss
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Commits on May 9, 2025

Merge remote-tracking branch 'origin/main' into exhaustive_fragmenter
ToLeWeiss
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Commits on May 23, 2025

refactored splitting function to improve saturation and improved documentation
ToLeWeiss
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Commits on Jun 4, 2025

Commits on Jul 9, 2025

WIP fixing issues in documentation and conformities in the code
ToLeWeiss
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Commits on Jul 23, 2025

Commits on Aug 4, 2025

removed useless comments and imports and added documentation if it is not possible to generate any fragments
ToLeWeiss
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Commits on Aug 14, 2025

improved comments and removed dependencies in the test class
ToLeWeiss
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Commits on Aug 20, 2025

implemented test for double bonds, cleaned up code and tests
ToLeWeiss
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Commits on Aug 21, 2025

Commits on Sep 3, 2025

Commits on Sep 17, 2025

switching to big integers to lift the upper limit of 31 splittable Bonds per fragmentation
ToLeWeiss
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Commits on Oct 23, 2025