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Add fragmentation and functional groups #1

Merged
merged 39 commits into from
Jun 30, 2021
Merged

Add fragmentation and functional groups #1

merged 39 commits into from
Jun 30, 2021

Commits on Jun 15, 2021

  1. feat: new fragmentation functionality and movement of connection tree… 

    … (node) model classes
    michaelwenk committed Jun 15, 2021
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  2. feat: added getUnsaturatedAtomIndices method

    michaelwenk committed Jun 15, 2021
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  3. feat: added a wrapper method to build a fragment

    michaelwenk committed Jun 15, 2021
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Commits on Jun 16, 2021

  1. feat: added isPseudoNode property to ConnectionTreeNode

    michaelwenk committed Jun 16, 2021
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  2. fix: bugfixes and improvements when building fragments

    michaelwenk committed Jun 16, 2021
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  3. fix: fixed an issue when closing rings

    michaelwenk committed Jun 16, 2021
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Commits on Jun 18, 2021

  1. feat: added toString method to ConnectionTreeNode and enabled to set … 

    …parent node and bond to parent node
    michaelwenk committed Jun 18, 2021
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  2. feat: added addSubtree method to ConnectionTree class

    michaelwenk committed Jun 18, 2021
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  3. feat: improvement of fragmentation by ring extension via a given maxS… 

    …phereRing and bugfixes
    michaelwenk committed Jun 18, 2021
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Commits on Jun 19, 2021

  1. feat: added method for checking equivalences

    michaelwenk committed Jun 19, 2021
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  2. feat: added methods for building fragment trees and fragment datasets

    michaelwenk committed Jun 19, 2021
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Commits on Jun 20, 2021

  1. fix: fixed invalid atom index usage

    michaelwenk committed Jun 20, 2021
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  2. fix: ensure pseudo atom when converting ExtendedConnectionMatrix to I… 

    …AtomContainer
    michaelwenk committed Jun 20, 2021
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  3. feat: addition and usage of method for removing identical fragment trees

    michaelwenk committed Jun 20, 2021
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Commits on Jun 21, 2021

  1. feat: consider fused ring systems in fragmentation too

    michaelwenk committed Jun 21, 2021
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  2. feat: implemented separated method buildRingFragmentTrees and method … 

    …descriptions were added
    michaelwenk committed Jun 21, 2021
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Commits on Jun 23, 2021

  1. feat: added closeRings for IAtomContainer as input too

    michaelwenk committed Jun 23, 2021
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  2. feat: added initKeySet method to ConnectionTree

    michaelwenk committed Jun 23, 2021
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  3. chore: moved additional methods to FragmentationUtils

    michaelwenk committed Jun 23, 2021
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  4. chore: moved attachPseudoAtoms and addPseudoNode to FragmentationUtils

    michaelwenk committed Jun 23, 2021
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Commits on Jun 27, 2021

  1. fix: getIndex method in Assignment did not return all indices

    michaelwenk committed Jun 27, 2021
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  2. fix: thrown exception if both multiplicities are null while checking … 

    …them
    michaelwenk committed Jun 27, 2021
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  3. fix: parse empty multiplicity as null

    michaelwenk committed Jun 27, 2021
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  4. feat: added methods for MF comparisons and allow different aromaticit… 

    …y models
    michaelwenk committed Jun 27, 2021
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  5. feat: added ErtlFunctionalGroup class containing helper methods regar… 

    …ding ErtlFunctionalGroupsFinder
    michaelwenk committed Jun 27, 2021
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  6. Merge branch 'master' into add-fragmentation

    michaelwenk committed Jun 27, 2021
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Commits on Jun 28, 2021

  1. fix: adaption to changes of getIndices() in Assignment

    michaelwenk committed Jun 28, 2021
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  2. Merge branch 'master' into add-fragmentation

    michaelwenk committed Jun 28, 2021
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  3. feat: pasted ErtlFunctionalGroupsFinder class

    michaelwenk committed Jun 28, 2021
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  4. feat: store RMSD and average deviation in sub-datasets via findMatche… 

    …s method
    michaelwenk committed Jun 28, 2021
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  5. chore: removed unused MongoDB class

    michaelwenk committed Jun 28, 2021
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  6. chore: moved methods from old Utils class to new Statistics and Utils… 

    … class
    michaelwenk committed Jun 28, 2021
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  7. chore: moved calculation methods for RMSD and average deviation to St… 

    …atistics class
    michaelwenk committed Jun 28, 2021
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  8. chore: moved "fragmentation" into new "fragments" package; moved gene… 

    …ral utility methods for fragments to new FragmentUtilities class
    michaelwenk committed Jun 28, 2021
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  9. chore: put classes from "utils" package to separate packages

    michaelwenk committed Jun 28, 2021
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  10. feat: extended findMatches in FragmentUtilities by goodlist and badlist

    michaelwenk committed Jun 28, 2021
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Commits on Jun 30, 2021

  1. fix: allow unsaturated fragments only

    michaelwenk committed Jun 30, 2021
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  2. feat: added general getDeviation method and possibility to use previo… 

    …us assignments
    michaelwenk committed Jun 30, 2021
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  3. chore: added notice to BFS method (book by Elyashberg, Williams and B… 

    …linov)
    michaelwenk committed Jun 30, 2021
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