AlkylStructureFragmenter Implementation#10

Draft

Mila1004 wants to merge 231 commits intoproductionfrom

dev-Max-alkylfragmentation

Commits on Apr 20, 2023

added new algorithm AlkylStructureFragmenter.java; exemplary added first algorithm setting
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Commits on Apr 21, 2023

added further algorithm settings without functionality
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Commits on Apr 24, 2023

WIP, Does not Compile! started implementing filter for alkyl structures
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Commits on Apr 25, 2023

added alkyl structure filter functionality in shouldBeFiltered;
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Commits on Apr 26, 2023

added carbohydrate filter; added longest chain detection; added ring detection;
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Commits on May 2, 2023

added different ring detection algorithm;
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Commits on May 3, 2023

WIP! working on ring/chain detection
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Commits on May 5, 2023

WIP! working on carbon chain detection
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added new algorithm AlkylStructureFragmenter.java; exemplary added first algorithm setting

Mila1004
authored and
FelixBaensch
committed
added further algorithm settings without functionality

Mila1004
authored and
FelixBaensch
committed
WIP, Does not Compile! started implementing filter for alkyl structures

Mila1004
authored and
FelixBaensch
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added alkyl structure filter functionality in shouldBeFiltered;

Mila1004
authored and
FelixBaensch
committed
added carbohydrate filter; added longest chain detection; added ring detection;

Mila1004
authored and
FelixBaensch
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added different ring detection algorithm;

Mila1004
authored and
FelixBaensch
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WIP! working on ring/chain detection

Mila1004
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FelixBaensch
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WIP! working on carbon chain detection

Mila1004
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FelixBaensch
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Merge branch 'dev-Max-alkylfragmentation' of github.com:FelixBaensch/MORTAR into dev-Max-alkylfragmentation
FelixBaensch
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Depict structure image with fill to fit depending on atom count;
FelixBaensch
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Commits on May 9, 2023

WIP! working on chain detection and extraction
Mila1004
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Commits on May 10, 2023

WIP! working on carbon chain detection
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Commits on May 11, 2023

WIP! Does not compile!
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Commits on May 12, 2023

WIP! working on alkyl chain detection
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Commits on May 15, 2023

WIP! fixed alkyl detection bug;
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Commits on May 17, 2023

added detection of conjugated pi systems; fixed filter bug;
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Commits on May 22, 2023

WIP! working on ring system detection
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Commits on May 23, 2023

Commits on May 24, 2023

WIP! working on ring detection and fragment return;
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Commits on May 25, 2023

WIP! added hydrogen saturation; added ring system detection;
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Commits on May 26, 2023

WIP! overhauled ring and ring system detection; working on removal of duplicate rings;
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Commits on May 30, 2023

Commits on May 31, 2023

WIP! working on ring system mapping;
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Commits on Jun 1, 2023

added ring system mapping;
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Commits on Jun 2, 2023

added ring and conjugated pi system mapping; added non-ring alkyl return;
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Commits on Jun 5, 2023

cleaned code of unnecessary parts;
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Commits on Jun 7, 2023

WIP! working on ring system extraction bug;
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Commits on Jun 14, 2023

WIP! working on bond extraction bug for connected rings and ring systems
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Commits on Jun 21, 2023

WIP! working on extraction bug
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Commits on Jun 22, 2023

WIP! working on fragment extraction;
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Commits on Jun 23, 2023

overhauled molecule mapping;
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Commits on Jun 28, 2023

WIP! on hashmap implementation for molecule mapping;
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Commits on Jun 29, 2023

added hashmap implementation for molecule mapping;
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Commits on Jul 4, 2023

WIP! on extraction from HashMap;
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Commits on Jul 5, 2023

Commits on Jul 6, 2023

Commits on Jul 16, 2023

WIP! on merge changes;
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Commits on Jul 17, 2023

WIP! on further merge changes;
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Commits on Jul 18, 2023

WIP! on merge changes; reworked fragmentation to include properties;
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Commits on Jul 19, 2023

WIP! on merge changes for AlkylStructureFragmenter;
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Commits on Jul 20, 2023

added final merge changes;
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Commits on Jul 21, 2023

WIP! started test implementation;
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Commits on Jul 24, 2023

WIP! separate fragmentation into private methods;
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Commits on Jul 25, 2023

WIP! fragmentation separation into private methods;
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Commits on Jul 26, 2023

added further private methods;
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Commits on Jul 28, 2023

added missing JavaDoc;
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Commits on Jul 31, 2023

added test classes for ASF and CPSF; added test structures as mol files; fixed CPSF H-saturation bug; cleaned code;
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Commits on Aug 1, 2023

added extraction functionality for tertiary and quaternary carbons from chains;
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Commits on Aug 8, 2023

WIP! overhaul test classes for ASF and CPSF;
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Commits on Aug 10, 2023

WIP! dissect side chains into smaller fragments;
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Commits on Aug 11, 2023

WIP! dissect side chains into smaller fragments;
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Commits on Aug 12, 2023

added dissection of linear chains into separate molecules of defined length;
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Commits on Aug 13, 2023

added setting for maximum chain length;
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Commits on Aug 14, 2023

fixed ASF test class;
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Commits on Aug 23, 2023

fixed linear dissection bug; fixed ASF test;
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Commits on Sep 18, 2023

pushed ASF test file;
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Commits on Oct 10, 2023

Merge branch 'master' into dev-Max-alkylfragmentation
JonasSchaub
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Commits on Oct 25, 2023

code cleanup;
Mila1004
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Commits on Oct 26, 2023

added further pull request changes;
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Commits on Oct 27, 2023

pull request changes;
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Commits on Nov 3, 2023

added restriction turn off setting; further pull request changes;
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Commits on Nov 6, 2023

WIP! started test rework;
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Commits on Nov 10, 2023

changed side chain fragmentation setting;
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Commits on Nov 14, 2023

further test rework; code cleanup;
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Commits on Nov 16, 2023

WIP! test coverage for private methods;
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Commits on Nov 17, 2023

Does not Compile! Switch to protected methods and variables;
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Commits on Dec 18, 2023

WIP! on test coverage; extracted array filling into methods;
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Commits on Dec 20, 2023

WIP! on test coverage and fragmentation architecture rework;
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Commits on Jan 19, 2024

reworked data stream architecture for atom- and bondarray in all methods (former implicit, now explicit usage);
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Commits on Apr 19, 2024

Merge branch 'production' into dev-Max-alkylfragmentation
JonasSchaub
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Commits on Apr 22, 2024

applied IMoleculeFragmenter changes to AlkylStructureFragmenter and ConjugatedPiSystemFragmenter classes; WIP: test coverage, not clear why Build fails;
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Commits on Apr 24, 2024

solved FileNotFoundException in AlkylStructureFragmenterTest; implemented default fragmentation test for AlkylStructureFragmenter;
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Commits on Apr 26, 2024

WIP! changed test resource getter; changing comparison of resulting and expected fragments;
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Commits on Jun 11, 2024

Commits on Jun 12, 2024

added rule in molecular formula check for ignoring CDK pseudo atoms;
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Commits on Jun 13, 2024

added switch/setting for alternative single carbon handling;
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Commits on Jun 14, 2024

fixed bug in ASF test class imported molecule saturation;
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Commits on Jul 6, 2024

added tests for different ring detection methods;
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Commits on Jul 8, 2024

Commits on Jul 15, 2024

WIP! on isolated double and triple bond extraction;
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Commits on Jul 17, 2024

added extraction of isolated double and triple bonds;
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Commits on Jul 18, 2024

WIP extraction of neighbor atoms of tertiary and quaternary carbons;
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Commits on Jul 19, 2024

WIP extraction of neighbor atoms of tertiary and quaternary carbons;
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Commits on Jul 22, 2024

WIP! in general; added neighbor extraction for tertiary and quaternary carbons;
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Commits on Jul 26, 2024

WIP! rework of general fragment extraction;
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Commits on Jul 30, 2024

reworked ring and conjugated pi system marking; WIP! on test class;
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Commits on Aug 1, 2024

fixed falsely placed isolated rings in fused ring systems bug; WIP! on test class;
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Commits on Sep 3, 2024

added toggleable extraction of spiro configuration carbons; WIP! on test class;
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Commits on Sep 5, 2024

reworked basic tests for AlkylStructureFragmenter;
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Commits on Oct 14, 2024

merge branch 'production' into dev-Max-alkylfragmentation;
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Commits on Oct 29, 2024

minor adjustments and changes to fragmentation and settings;
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Commits on Oct 31, 2024

further adjustments regarding code quality;
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Commits on Nov 7, 2024

WIP! fixed bug in extraction of double bonded carbon connected to ring structures;
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Commits on Nov 14, 2024

WIP! further code improvements and settings tweaking;
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Commits on Nov 15, 2024

Commits on Nov 19, 2024

fixed a bug in retention of non-fragmentable molecules; applied code improvements;
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Commits on Nov 21, 2024

WIP! bug with false fragment saturation after separation of double bonded carbon with ring structure;
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Commits on Nov 22, 2024

WIP! on methods to create deep copies of atoms and bonds;
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Commits on Nov 26, 2024

WIP! deep copy of bonds to add;
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Commits on Nov 28, 2024

WIP! further testing deepCopyBond() method;
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Commits on Nov 29, 2024

WIP! added further tests for double bond extraction; located faulty extraction in fragmenter;
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Commits on Dec 2, 2024

WIP! fixing faulty extraction and saturation of double bonds connected to rings;
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Commits on Dec 4, 2024

implemented deep copy methods for atoms and bonds; fixed bug with false saturation after removing residues from double bonds connected to ring structures;
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Commits on Dec 12, 2024

replaced atomcontainer.getID with internal molecule name property;
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Commits on Apr 7, 2025

Commits on Apr 9, 2025

WIP! test coverage;
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Commits on Apr 14, 2025

WIP! test coverage;
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Commits on Apr 23, 2025

WIP! test coverage;
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Commits on Apr 25, 2025

Commits on Apr 28, 2025

failing tests! added tests;
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Commits on Apr 29, 2025

working on default test for atom and bond marking;
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Commits on Apr 30, 2025

added basic tests for ASF base functionalities;
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Commits on May 1, 2025

localized scope by switching to temporary ASF instances in each test;
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Commits on May 2, 2025

minor changes (mainly formatting);
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Commits on May 5, 2025

fixed bug in dissection of linear chains;
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Commits on May 6, 2025

added proper documentation for algorithm;
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Commits on May 12, 2025

further code improvements;
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Commits on May 13, 2025

Commits on May 14, 2025

Commits on May 18, 2025

added setting to separate tertiary and quaternary carbons from rings;
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Commits on May 19, 2025

removed unnecessary keepRings setting;
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Commits on May 20, 2025

WIP! new tertiary/quaternary carbon handling;
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Commits on May 21, 2025

Commits on May 22, 2025

WIP! Isolation of tertiary and quaternary carbons;
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Commits on May 23, 2025

added isolation of tertiary and quaternary atoms; added support for all cross-activation of fragmentation settings;
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Commits on May 25, 2025

work on code quality;
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Commits on May 27, 2025

WIP! on fragmentation setting hierarchy;
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Commits on May 28, 2025

WIP! on isolation setting;
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Commits on May 30, 2025

WIP! on isolation setting;
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Commits on May 31, 2025

WIP! on isolation setting;
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Commits on Jun 2, 2025

WIP! on correct extraction depending on settings;
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Commits on Jun 4, 2025

WIP! on isolation setting;
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Commits on Jun 5, 2025

WIP! on isolation setting;
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Commits on Jun 6, 2025

fixed tertiary and quaternary isolation and ring separation hierarchy issue;
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Commits on Jul 2, 2025

WIP! Investigation of strange pseudo atom exception; located problematic code line - no fix yet;
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Commits on Jul 3, 2025

WIP! exception in neighbor bond extraction;
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Commits on Jul 4, 2025

added pseudo atom representation of former bond between tertiary/quaternary carbons and ring structures;
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Commits on Jul 7, 2025

WIP! on inner class MolecularArrays;
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Commits on Jul 8, 2025

simplified data transfer with inner class MolecularArrays;
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Commits on Jul 9, 2025

work on code quality;
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Commits on Jul 11, 2025

added deep copy of atom and bond properties;
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Commits on Jul 14, 2025

Commits on Jul 15, 2025

code improvements; Failed Tests! due to issue in separation of disconnected structures;
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Commits on Jul 18, 2025

WIP! Failed Tests! due to ongoing work on ConjPiSys detection;
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Commits on Jul 21, 2025

Commits on Jul 22, 2025

WIP! CPSD SMILES detection incongruity;
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Commits on Jul 23, 2025

WIP! started implementation of conjugated pi bond systems detection;
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Commits on Jul 24, 2025

WIP! added first steps of conjugated pi bond systems detection;
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Commits on Jul 25, 2025

implementation of conjugated pi system detection;
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Commits on Jul 29, 2025

WIP! on issue with connectivity checker;
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Commits on Jul 30, 2025

WIP! on fragmentation issues in tests;
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Commits on Aug 1, 2025

WIP! investigation of tertiary and quaternary extraction issue;
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Commits on Aug 5, 2025

WIP! added logging environment for finest level;
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Commits on Aug 6, 2025

WIP! still ongoing investigation of occurring NoSuchAtomException;
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Commits on Aug 7, 2025

WIP! still ongoing investigation of occurring exception;
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Commits on Aug 10, 2025

Failing Tests! Fixed NoSuchAtomException occurrences;
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Commits on Aug 11, 2025

Commits on Aug 12, 2025

Commits on Aug 13, 2025

fixed bug in extraction of ring-chain-conj._pi configurated atoms when tert/quat isolation is turned off; added according test case;
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Commits on Aug 14, 2025

Commits on Aug 15, 2025

Commits on Aug 19, 2025

Small fixes as part of the review;
JonasSchaub
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Commits on Aug 20, 2025

Commits on Aug 21, 2025

refactoring and putting test resources where they belong
JonasSchaub
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Commits on Aug 26, 2025

Merge pull request #185 from FelixBaensch/alkylfragmentation-jonas
Mila1004
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Commits on Aug 27, 2025

first changes from code review;
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Commits on Aug 28, 2025

Commits on Sep 1, 2025

code review changes;
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Commits on Sep 2, 2025

Commits on Sep 3, 2025

more code review changes;
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Commits on Sep 4, 2025

Commits on Sep 10, 2025

code improvements;
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Commits on Sep 11, 2025

Commits on Sep 12, 2025

Commits on Sep 15, 2025

Commits on Sep 16, 2025

Commits on Sep 17, 2025

WIP! implementation of stereo chemistry;
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Commits on Sep 18, 2025

preservation of stereo chemistry added; stereo chemistry preservation setting added;
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Commits on Sep 19, 2025

Commits on Sep 23, 2025

Commits on Sep 25, 2025

WIP! stereo chemistry implementation;
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Commits on Sep 30, 2025

WIP! stereo chemistry implementation;
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Commits on Oct 1, 2025

added stereo chemistry support;
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Commits on Oct 5, 2025

fixed bug in stereo chemistry remap;
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Commits on Oct 6, 2025

small addition to MolecularArrays for preserving original Importer-given molecule name;
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Commits on Oct 8, 2025

WIP! issue with tert/quat and neighbor atoms
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Commits on Oct 9, 2025

fixed bug within neighbor and linear chain interaction of combined substructure of ring-connected tertiary or quaternary atoms;
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Commits on Oct 16, 2025

bonds with 'unset' order will now be filtered and not fragmented;
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