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Version 1.3 #21

Merged
merged 30 commits into from
Feb 2, 2024
Merged

Version 1.3 #21

merged 30 commits into from
Feb 2, 2024

Commits on Jan 5, 2024

  1. Commented-out input restrictions;

    @JonasSchaub
    JonasSchaub committed Jan 5, 2024
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  2. Moved test classes into the same folder as the tested classes; moved … 

    …test resources into the respective package structure; added tests to EFGFTest for cases that formerly represented illegal inputs;
    @JonasSchaub
    JonasSchaub committed Jan 5, 2024
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Commits on Jan 8, 2024

  1. Updated copyright year

    @JonasSchaub
    JonasSchaub committed Jan 8, 2024
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  2. Started refactoring code according to internal conventions;

    @JonasSchaub
    JonasSchaub committed Jan 8, 2024
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Commits on Jan 9, 2024

  1. Continued refactoring;

    @JonasSchaub
    JonasSchaub committed Jan 9, 2024
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Commits on Jan 10, 2024

  1. Refactoring of markAtoms method

    @JonasSchaub
    JonasSchaub committed Jan 10, 2024
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  2. Overhaul of extractGroups

    @JonasSchaub
    JonasSchaub committed Jan 10, 2024
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Commits on Jan 11, 2024

  1. Overhaul of expandGeneralizedEnvironments, WIP

    @JonasSchaub
    JonasSchaub committed Jan 11, 2024
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Commits on Jan 12, 2024

  1. Continued refactoring

    @JonasSchaub
    JonasSchaub committed Jan 12, 2024
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  2. Overhaul of more methods, WIP

    @JonasSchaub
    JonasSchaub committed Jan 12, 2024
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Commits on Jan 15, 2024

  1. Overhaul of partitionIntoGroups()

    @JonasSchaub
    JonasSchaub committed Jan 15, 2024
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  2. Finished refactoring of EFGF for now;

    @JonasSchaub
    JonasSchaub committed Jan 15, 2024
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  3. Added new environment mode to only extract marked atoms; added factor… 

    …y methods; added convenience method for accessing valid atomic numbers
    @JonasSchaub
    JonasSchaub committed Jan 15, 2024
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  4. Transferred some utility methods for input testing and preprocessing … 

    …from utility class to EFGF;
    @JonasSchaub
    JonasSchaub committed Jan 15, 2024
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Commits on Jan 16, 2024

  1. Additional documentation;

    @JonasSchaub
    JonasSchaub committed Jan 16, 2024
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  2. Overhaul of EFGFTest;

    @JonasSchaub
    JonasSchaub committed Jan 16, 2024
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Commits on Jan 17, 2024

  1. Fixed failing javadoc build

    @JonasSchaub
    JonasSchaub committed Jan 17, 2024
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  2. Pseudo atoms are not identified as hetero atoms anymore;

    @JonasSchaub
    JonasSchaub committed Jan 17, 2024
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  3. Moved ChEBI analysis to evaluation test;

    @JonasSchaub
    JonasSchaub committed Jan 17, 2024
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Commits on Jan 22, 2024

  1. Added molecule from test find 1 to test for extracting only marked at… 

    …oms;
    @JonasSchaub
    JonasSchaub committed Jan 22, 2024
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Commits on Jan 24, 2024

  1. Test for charge neutralization;

    @JonasSchaub
    JonasSchaub committed Jan 24, 2024
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Commits on Jan 31, 2024

  1. Merge branch 'main' into production 

    * main:
  Update Performance usage instructions.txt
  Update README.md
    @JonasSchaub
    JonasSchaub committed Jan 31, 2024
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  2. Started cleaning up tests;

    @JonasSchaub
    JonasSchaub committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. Started looking at evaluation test;

    @JonasSchaub
    JonasSchaub committed Feb 1, 2024
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  2. Finished cleaning up the evaluation test; some more refactoring and d… 

    …ocumentation;
    @JonasSchaub
    JonasSchaub committed Feb 1, 2024
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  3. Fixed hydrogen bug and disabled evaluation test;

    @JonasSchaub
    JonasSchaub committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. Removed duplicated test methods from evaluation test;

    @JonasSchaub
    JonasSchaub committed Feb 2, 2024
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  2. Removed unused imports;

    @JonasSchaub
    JonasSchaub committed Feb 2, 2024
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  3. Merge pull request #20 from JonasSchaub/input_restrictions 

    Input restrictions for EFGF lifted and some general refactoring and fixing
    @JonasSchaub
    JonasSchaub authored Feb 2, 2024
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  4. ErtlFunctionalGroupsFinder version 1.3

    @JonasSchaub
    JonasSchaub committed Feb 2, 2024
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