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AlkylStructureFragmenter Implementation #10
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0d207da
added new algorithm AlkylStructureFragmenter.java; exemplary added fi…
Mila1004 8011316
added further algorithm settings without functionality
Mila1004 e796701
WIP, Does not Compile! started implementing filter for alkyl structures
Mila1004 89988ad
added alkyl structure filter functionality in shouldBeFiltered;
Mila1004 5c283d3
added carbohydrate filter; added longest chain detection; added ring …
Mila1004 9555f0a
added different ring detection algorithm;
Mila1004 a3f5ab2
WIP! working on ring/chain detection
Mila1004 543f941
WIP! working on carbon chain detection
Mila1004 41b8474
added new algorithm AlkylStructureFragmenter.java; exemplary added fi…
Mila1004 9326006
added further algorithm settings without functionality
Mila1004 6b71b46
WIP, Does not Compile! started implementing filter for alkyl structures
Mila1004 c563270
added alkyl structure filter functionality in shouldBeFiltered;
Mila1004 7139641
added carbohydrate filter; added longest chain detection; added ring …
Mila1004 c0ae663
added different ring detection algorithm;
Mila1004 1800a8e
WIP! working on ring/chain detection
Mila1004 ca4a5c8
WIP! working on carbon chain detection
Mila1004 9c9d1ca
Merge branch 'dev-Max-alkylfragmentation' of github.com:FelixBaensch/…
FelixBaensch 23cc8e5
Depict structure image with fill to fit depending on atom count;
FelixBaensch 2e328bb
WIP! working on chain detection and extraction
Mila1004 7c75ece
WIP! working on carbon chain detection
Mila1004 cbc1c84
WIP! Does not compile!
Mila1004 e59e0f7
WIP! working on alkyl chain detection
Mila1004 b49017c
WIP! fixed alkyl detection bug;
Mila1004 e06b346
added detection of conjugated pi systems; fixed filter bug;
Mila1004 0c83d87
WIP! working on ring system detection
Mila1004 02d12d6
WIP! working on chain detection and extraction
Mila1004 7eaa4d2
added ConjugatedPiSystemDetector implementation as ConjugatedPiSystem…
Mila1004 276e9f7
WIP! working on ring detection and fragment return;
Mila1004 a5645d4
WIP! added hydrogen saturation; added ring system detection;
Mila1004 31a2788
WIP! overhauled ring and ring system detection; working on removal of…
Mila1004 2e7d7b6
WIP! overhauled ring and ring system detection; working on removal of…
Mila1004 dfd4063
Merge branch 'dev-Max-alkylfragmentation' of https://github.com/Felix…
Mila1004 a6df6bb
WIP! working on ring system mapping;
Mila1004 93c4d8b
added ring system mapping;
Mila1004 50737bb
added ring and conjugated pi system mapping; added non-ring alkyl ret…
Mila1004 7480fe8
cleaned code of unnecessary parts;
Mila1004 66b79db
WIP! working on ring system extraction bug;
Mila1004 14ff3c0
WIP! working on bond extraction bug for connected rings and ring systems
Mila1004 c4015db
WIP! working on extraction bug
Mila1004 204d4df
WIP! working on fragment extraction;
Mila1004 59aaf45
overhauled molecule mapping;
Mila1004 ebe88e8
WIP! on hashmap implementation for molecule mapping;
Mila1004 66e8c10
added hashmap implementation for molecule mapping;
Mila1004 98f5564
WIP! on extraction from HashMap;
Mila1004 3c6fd9e
Merge branch 'master' into dev-Max-alkylfragmentation
JonasSchaub 736d007
WIP! on Fragment Extraction;
Mila1004 ceb9227
fixed ring_bond_ring extraction bug; fragmentation now done inside ar…
Mila1004 dd3eb2d
cleaned code of deprecated and unnecessary parts;
Mila1004 27f8952
WIP! on merge changes;
Mila1004 994119c
WIP! on further merge changes;
Mila1004 fe10aa3
WIP! on merge changes; reworked fragmentation to include properties;
Mila1004 37ac325
WIP! on merge changes for AlkylStructureFragmenter;
Mila1004 fc98e64
added final merge changes;
Mila1004 e55f047
WIP! started test implementation;
Mila1004 8457307
WIP! separate fragmentation into private methods;
Mila1004 975b890
WIP! fragmentation separation into private methods;
Mila1004 92abad3
added further private methods;
Mila1004 faba162
added missing JavaDoc;
Mila1004 91b0ae1
added test classes for ASF and CPSF; added test structures as mol fil…
Mila1004 722a79c
added extraction functionality for tertiary and quaternary carbons fr…
Mila1004 9de9877
WIP! overhaul test classes for ASF and CPSF;
Mila1004 0167c04
WIP! dissect side chains into smaller fragments;
Mila1004 9c67569
WIP! dissect side chains into smaller fragments;
Mila1004 1b2ae70
added dissection of linear chains into separate molecules of defined …
Mila1004 b0ff2cc
added setting for maximum chain length;
Mila1004 6753a04
fixed ASF test class;
Mila1004 ad4945b
fixed linear dissection bug; fixed ASF test;
Mila1004 80ad1bd
pushed ASF test file;
Mila1004 9745ee6
Merge branch 'master' into dev-Max-alkylfragmentation
JonasSchaub c898b01
code cleanup;
Mila1004 be7c4d1
added further pull request changes;
Mila1004 295d5c3
pull request changes;
Mila1004 3761c2c
added restriction turn off setting; further pull request changes;
Mila1004 1610a50
WIP! started test rework;
Mila1004 6037327
changed side chain fragmentation setting;
Mila1004 f35de14
further test rework; code cleanup;
Mila1004 a6bc0aa
WIP! test coverage for private methods;
Mila1004 79a8c52
Does not Compile! Switch to protected methods and variables;
Mila1004 facaa7d
WIP! on test coverage; extracted array filling into methods;
Mila1004 68928fc
WIP! on test coverage and fragmentation architecture rework;
Mila1004 a0a417b
reworked data stream architecture for atom- and bondarray in all meth…
Mila1004 9dcab44
Merge branch 'production' into dev-Max-alkylfragmentation
JonasSchaub 5002211
applied IMoleculeFragmenter changes to AlkylStructureFragmenter and C…
Mila1004 60848fb
solved FileNotFoundException in AlkylStructureFragmenterTest; impleme…
Mila1004 df30210
WIP! changed test resource getter; changing comparison of resulting a…
Mila1004 69fa1c0
fixed issue with hydrogen saturation in ASF and its test class;
Mila1004 26c6481
added check for correct molecular formula/atom count after fragmentat…
Mila1004 b06caac
added rule in molecular formula check for ignoring CDK pseudo atoms;
Mila1004 74574d8
added switch/setting for alternative single carbon handling;
Mila1004 7bca034
fixed bug in ASF test class imported molecule saturation;
Mila1004 4d4f007
added tests for different ring detection methods;
Mila1004 f38737d
WIP! spiro carbon detection and extraction;
Mila1004 bba7d15
WIP! on isolated double-triple bond extraction; WIP! on spiro carbon …
Mila1004 cc96daa
WIP! on isolated double and triple bond extraction;
Mila1004 d04d734
added extraction of isolated double and triple bonds;
Mila1004 1ad9741
WIP extraction of neighbor atoms of tertiary and quaternary carbons;
Mila1004 cd9aa96
WIP extraction of neighbor atoms of tertiary and quaternary carbons;
Mila1004 b363891
WIP! in general; added neighbor extraction for tertiary and quaternar…
Mila1004 9064e97
WIP! rework of general fragment extraction;
Mila1004 9bf6a3e
reworked ring and conjugated pi system marking; WIP! on test class;
Mila1004 0e47cc6
fixed falsely placed isolated rings in fused ring systems bug; WIP! o…
Mila1004 1e5c822
added toggleable extraction of spiro configuration carbons; WIP! on t…
Mila1004 4bcfa15
reworked basic tests for AlkylStructureFragmenter;
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The two new fragmenter variables should go to the final class constants like the others.