Integration/implementation of RECAP algorithm#143
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JonasSchaub wants to merge 43 commits intoproductionfrom
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Integration/implementation of RECAP algorithm#143JonasSchaub wants to merge 43 commits intoproductionfrom
JonasSchaub wants to merge 43 commits intoproductionfrom
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Closes #127 |
…cks for rings to determine still allowed, small fragments
…do not match cleavage results of previous rounds and lead to a forever loop; adds test structure described in RDKit doc and test structure from the RECAP paper, which helped elucidating the infinity loop bug
…hy node class, adds more tests and a lot of to-dos
…easier access and makes more methods of the inner classes public
…now return more sensible educts
…ore details to them, and tests them individually
…ng a double bond to any atom
…rbon atoms for the environment atoms) and re-works urea rule and tests it
…vised overarching concept
* production: MORTAR v1.3 adds dependencies that were implicitly included in cdk-fragment explicitly updates aromaticity settings and handling to new CDK 2.10 aromaticity API updates JUnit to 5.11.4 updates spotless to 7.0.2 and removes redundant specifiers in interfaces because spotless complains about them now updates librepdf/openpdf to 2.0.3 corrects small things in ScaffoldGeneratorFragmenter corrects small details in SRUFragmenter finished adjustment of EFGFFragmenter to CDK 2.10 WIP, closer to fixing the problem now but env Cs will still be copied in the resulting fragments WIP, replaces external EFGF with CDK FunctionalGroupsFinder but the generation of alkyl remnants does not work currently updates CDK from 2.9 to 2.10 and discards SRU artifact in favour of using the new CDK implementation # Conflicts: # build.gradle # src/test/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/ErtlFunctionalGroupsFinderFragmenterTest.java
…re open questions
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https://doi.org/10.1021/ci970429i