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First small bug fixes #1

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First small bug fixes #1

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Commits on Mar 30, 2021

  1. minor

    michaelwenk committed Mar 30, 2021
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Commits on Apr 1, 2021

  1. assignments can now hold more than only one single assignment index (… 

    …equivalences); small optimisations
    michaelwenk committed Apr 1, 2021
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  2. disabled SHIH in PyLSDInputFileBuilder.java

    michaelwenk committed Apr 1, 2021
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  3. added RankedResultSDFParser

    michaelwenk committed Apr 1, 2021
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  4. Match: when checkEquivalencesCount is set to true then check for equa… 

    …l number instead of less or equal
    michaelwenk committed Apr 1, 2021
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  5. fix: an error when passing conditions

    michaelwenk committed Apr 1, 2021
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Commits on Apr 4, 2021

  1. feat: changed "mf" to "mfOriginal" and added alphabetic sorted mf as … 

    …"mf"
    michaelwenk committed Apr 4, 2021
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  2. moved try and catch around Tanimoto coefficient calculation

    michaelwenk committed Apr 4, 2021
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Commits on Apr 7, 2021

  1. feat: multiplicity check when adding a signal to a spectrum

    michaelwenk committed Apr 7, 2021
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  2. fix: multiplicity check when searching for equivalence signals; use m… 

    …edian for predicted shift calculation instead of mean
    michaelwenk committed Apr 7, 2021
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  3. fix: added missing multiplicity check when searching for equivalence … 

    …signals
    michaelwenk committed Apr 7, 2021
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  4. feat: added PyLSD ELIM P1 and P2 parameters

    michaelwenk committed Apr 7, 2021
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  5. feat: added useElim parameter and changed filter paths to array

    michaelwenk committed Apr 7, 2021
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Commits on Apr 8, 2021

  1. feat: added atom type check when parsing ranked SDF by PyLSD

    michaelwenk committed Apr 8, 2021
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  2. feat: re-added SHIH in PyLSD input file

    michaelwenk committed Apr 8, 2021
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Commits on Apr 9, 2021

  1. feat: added PyLSD HMBC P3, HMBC P4, COSY P3 and COSY P4 parameters

    michaelwenk committed Apr 9, 2021
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Commits on Apr 10, 2021

  1. chore: replace default constructors, setters and getters by lombok an… 

    …notations
    michaelwenk committed Apr 10, 2021
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  2. chore: replace default constructors, setters and getters by lombok an… 

    …notations (2)
    michaelwenk committed Apr 10, 2021
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  3. feat: added allowLowerEquivalencesCount to spectra matching

    michaelwenk committed Apr 10, 2021
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  4. feat: added setSignal method to Spectrum

    michaelwenk committed Apr 10, 2021
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  5. fix: add equivalences count of newly added signal instead of one only

    michaelwenk committed Apr 10, 2021
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  6. feat: added addAssignment method to Assignment

    michaelwenk committed Apr 10, 2021
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  7. fix: too high index when checking the dimension

    michaelwenk committed Apr 10, 2021
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Commits on Apr 13, 2021

  1. fix: init non-empty arrays for equivalences

    michaelwenk committed Apr 13, 2021
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Commits on Apr 19, 2021

  1. fix: use own deep clone method Assignment

    michaelwenk committed Apr 19, 2021
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Commits on Apr 23, 2021

  1. fix: extended hetero atom list in aromatic cycles in isValidBondAddition

    michaelwenk committed Apr 23, 2021
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  2. chore: added UTF-8 encoding and updated two dependencies

    michaelwenk committed Apr 23, 2021
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  3. fix: switched from SmiFlavor.Absolute to SmiFlavor.Unique

    michaelwenk committed Apr 23, 2021
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Commits on Apr 24, 2021

  1. fix: buildFilters expects direct paths to filters

    michaelwenk committed Apr 24, 2021
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Commits on Apr 25, 2021

  1. feat: added parseRankedResultSDFile methods

    michaelwenk committed Apr 25, 2021
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Commits on Apr 29, 2021

  1. feat: integration of HOSECodeBuilder project

    michaelwenk committed Apr 29, 2021
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  2. feat: updated README.md

    michaelwenk committed Apr 29, 2021
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Commits on May 5, 2021

  1. fix: replaced HashSet by Set

    michaelwenk committed May 5, 2021
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Commits on May 10, 2021

  1. fix: wrong order if allowLowerEquivalencesCount is checked

    michaelwenk committed May 10, 2021
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Commits on Jun 4, 2021

  1. feat: added method to remove a node from connection tree

    michaelwenk committed Jun 4, 2021
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  2. fix: parse multiplicities with toLowerCase

    michaelwenk committed Jun 4, 2021
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  3. feat: added H to HOSE code node weight

    michaelwenk committed Jun 4, 2021
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  4. feat: added methods to add and convert implicit to explicit hydrogens… 

    … and to calculate the RMS value
    michaelwenk committed Jun 4, 2021
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  5. fix: take implicit hydrogens into account when building root sphere

    michaelwenk committed Jun 4, 2021
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  6. feat: added method to build HOSE code statistics

    michaelwenk committed Jun 4, 2021
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Commits on Jun 5, 2021

  1. feat: added ExtendedHOSEGenerator

    michaelwenk committed Jun 5, 2021
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  2. feat: added Utils class for DB services

    michaelwenk committed Jun 5, 2021
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  3. feat: added COCONUT data set import

    michaelwenk committed Jun 5, 2021
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Commits on Jun 6, 2021

  1. chore: update of toString method

    michaelwenk committed Jun 6, 2021
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  2. chore: update of toString method

    michaelwenk committed Jun 6, 2021
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  3. fix: improvement in multiplicity picking

    michaelwenk committed Jun 6, 2021
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  4. fix: return lower case multiplicity string

    michaelwenk committed Jun 6, 2021
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  5. fix: wrong explicit H removals; optional second sprectrum property st… 

    …ring
    michaelwenk committed Jun 6, 2021
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  6. feat: added HOSECodeShiftStatistics

    michaelwenk committed Jun 6, 2021
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  7. chore: added GSON and BSON as dependencies

    michaelwenk committed Jun 6, 2021
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  8. chore: use CDK@2.5

    michaelwenk committed Jun 6, 2021
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  9. feat: added method for simple signal addition

    michaelwenk committed Jun 6, 2021
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  10. fix: restore to previous multiplicity picking

    michaelwenk committed Jun 6, 2021
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  11. fix: multiple multiplicity filter when adding a signal

    michaelwenk committed Jun 6, 2021
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  12. fix: set node weight for explicit H to 0

    michaelwenk committed Jun 6, 2021
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Commits on Jun 7, 2021

  1. fix: crash when adding assignments in higher dimension

    michaelwenk committed Jun 7, 2021
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Commits on Jun 8, 2021

  1. feat: addSignal now returns the index of added signal and enables pic… 

    …k precision for each dimension
    michaelwenk committed Jun 8, 2021
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  2. chore: removed unused method

    michaelwenk committed Jun 8, 2021
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  3. feat: integration of 1D and 2D spectrum prediction based on HOSE code… 

    … (no diastereotopic distinctions for now)
    michaelwenk committed Jun 8, 2021
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  4. chore: removed outputs

    michaelwenk committed Jun 8, 2021
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Commits on Jun 10, 2021

  1. feat: specified HSQC und edited HSQC methods

    michaelwenk committed Jun 10, 2021
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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. Delete LICENSE

    Michael Wenk authored Jun 27, 2021
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  7. Create LICENSE

    Michael Wenk authored Jun 27, 2021
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  8. Update README.md

    Michael Wenk authored Jun 27, 2021
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  9. 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. Delete LICENSE

    Michael Wenk authored Jun 28, 2021
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  3. Create LICENSE

    Michael Wenk authored Jun 28, 2021
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  4. Merge branch 'master' into add-fragmentation

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

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

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

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

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

    …atistics class
    michaelwenk committed Jun 28, 2021
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  10. 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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  11. chore: put classes from "utils" package to separate packages

    michaelwenk committed Jun 28, 2021
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  12. 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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  4. Merge pull request #1 from michaelwenk/add-fragmentation 

    feat: add fragmentation and functional groups
    Michael Wenk authored Jun 30, 2021
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Commits on Jul 6, 2021

  1. feat: introduction of maximum average deviation for dereplication and… 

    … elucidation
    michaelwenk committed Jul 6, 2021
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Commits on Jul 13, 2021

  1. feat: added usePrediction to ElucidationOptions

    michaelwenk committed Jul 13, 2021
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  2. chore: improvement of outlier detection and removal methods

    michaelwenk committed Jul 13, 2021
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  3. feat: added general SDF parser

    michaelwenk committed Jul 13, 2021
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  4. chore: switched solvent and nucleus parameter

    michaelwenk committed Jul 13, 2021
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  5. feat: added withExplicitH parameter to HOSE code statistic collection… 

    … and usage of outlier removal
    michaelwenk committed Jul 13, 2021
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Commits on Jul 20, 2021

  1. feat: added default values for fluorine

    michaelwenk committed Jul 20, 2021
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  2. fix: wrong number of proton equivalences, i.e. in case of CH3 groups

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

  1. feat: added methods for files cleanup and SMILES file parsing

    michaelwenk committed Jul 21, 2021
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  2. chore: marked RankedResultSDFParser.java as deprecated

    michaelwenk committed Jul 21, 2021
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Commits on Jul 29, 2021

  1. feat: added a method to build HOSE codes statistics by list of datasets

    michaelwenk committed Jul 29, 2021
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  2. feat: set the multiplicity of carbon atoms when predicting spectra

    michaelwenk committed Jul 29, 2021
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  3. chore: improvements in MultiplicitySectionsBuilder

    michaelwenk committed Jul 29, 2021
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  4. chore: added dimension of spectrum

    michaelwenk committed Jul 29, 2021
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  5. feat: added method to calculate the Tanimoto coefficient between two … 

    …spectra
    michaelwenk committed Jul 29, 2021
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Commits on Aug 6, 2021

  1. feat: improvement of matching between two spectra by using minimal di… 

    …stances
    michaelwenk committed Aug 6, 2021
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Commits on Aug 10, 2021

  1. fix: insert missing equivalences in matchSpectra & small optimisations

    michaelwenk committed Aug 10, 2021
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  2. feat: added public method to calculate the steps & small optimisations

    michaelwenk committed Aug 10, 2021
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Commits on Aug 16, 2021

  1. chore: optimisation of toString method in Assignment

    michaelwenk committed Aug 16, 2021
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  2. fix: initialise meta map when adding an info in DataSet

    michaelwenk committed Aug 16, 2021
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  3. fix: use case insensitive comparison of multiplicities

    michaelwenk committed Aug 16, 2021
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  4. feat: added atomContainerToDataSet method to Utils

    michaelwenk committed Aug 16, 2021
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  5. feat: added methods to parse SMILES from file in Parser

    michaelwenk committed Aug 16, 2021
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  6. feat: added optional hybridizations to check when searching for goodl… 

    …ist and badlist elements; added matchAssignment to meta info
    michaelwenk committed Aug 16, 2021
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  7. feat: added ConnectivityStatistics class

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

  1. chore: use Utils.atomContainerToDataSet() in COCONUT.java

    michaelwenk committed Aug 18, 2021
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  2. chore: receive general dataSet list when collecting functional groups… 

    … (instead of path to NMRShiftDB)
    michaelwenk committed Aug 18, 2021
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  3. chore: simplification and renaming of ExtendedConnectionMatrix into E… 

    …xtendedAdjacencyList
    michaelwenk committed Aug 18, 2021
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Commits on Aug 19, 2021

  1. chore: optimisation of ExtendedAdjacencyList

    michaelwenk committed Aug 19, 2021
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  2. fix: check for null value of hybridisation state

    michaelwenk committed Aug 19, 2021
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Commits on Aug 22, 2021

  1. fix: renaming to atomCount and bondCount to avoid storage in JSON format

    michaelwenk committed Aug 22, 2021
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  2. chore: optimisations on Spectrum class

    michaelwenk committed Aug 22, 2021
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Commits on Aug 23, 2021

  1. feat: usage of Concurrent class when building HOSE code statistics

    michaelwenk committed Aug 23, 2021
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  2. fix: pre-set carbon hybridization states when having at least two pro… 

    …tons
    michaelwenk committed Aug 23, 2021
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Commits on Aug 25, 2021

  1. chore: use common parser method for COCONUT and NMRShiftDB

    michaelwenk committed Aug 25, 2021
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Commits on Aug 26, 2021

  1. chore: usage of more compact classes in DataSet

    michaelwenk committed Aug 26, 2021
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Commits on Aug 27, 2021

  1. chore: extracted buildConnectivityStatistics method

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

  1. feat: methods for extraction of neighbor atom types and hybridizations

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

  1. feat: use connectivity information to forbid bonds between an atom an… 

    …d a group of atoms
    michaelwenk committed Aug 30, 2021
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Commits on Sep 1, 2021

  1. chore: renamed nmrdisplayer package to nmrium

    michaelwenk committed Sep 1, 2021
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  2. chore: changed string values to numeric ones; hybridizationConversion… 

    …Map contains atom type as key instead of nucleus
    michaelwenk committed Sep 1, 2021
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  3. feat: use hybridization statistics too to forbid bonds

    michaelwenk committed Sep 1, 2021
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Commits on Sep 3, 2021

  1. feat: use SHIX command in PyLSD to let it recognise equivalent atoms … 

    …by shift values
    michaelwenk committed Sep 3, 2021
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  2. chore: added PLANAR3 for O to hybridizationConversionMap

    michaelwenk committed Sep 3, 2021
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  3. feat: simplified connectivity statistics filtering

    michaelwenk committed Sep 3, 2021
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Commits on Sep 11, 2021

  1. chore: simplification in Constants

    michaelwenk committed Sep 11, 2021
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  2. feat: use utility classes for LIST and PROP creation and extension of… 

    … connection forbids; allow multiple hybridizations
    michaelwenk committed Sep 11, 2021
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  3. feat: ability to use of INADEQUATE information

    michaelwenk committed Sep 11, 2021
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Commits on Sep 13, 2021

  1. fix: use unique hybridization states in MULT

    michaelwenk committed Sep 13, 2021
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  2. fix: wrong if conditions for setting possible hybridizations of heter… 

    …o atoms
    michaelwenk committed Sep 13, 2021
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Commits on Sep 16, 2021

  1. fix: enable max ring size when detecting rings for ring fragment tree… 

    …s building
    michaelwenk committed Sep 16, 2021
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  2. feat: added correlationListToSpectrum1D method to Utils

    michaelwenk committed Sep 16, 2021
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Commits on Oct 11, 2021

  1. feat: added getFileContent method to FileSystem

    michaelwenk committed Oct 11, 2021
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  2. feat: added MultiThreading class

    michaelwenk committed Oct 11, 2021
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  3. chore: NMRium signal classes use a common parent class

    michaelwenk committed Oct 11, 2021
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  4. chore: adoptions regarding change in correlation data structure in nm… 

    …r-correlation package
    michaelwenk committed Oct 11, 2021
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  5. chore: changed "phase" class member to Integer

    michaelwenk committed Oct 11, 2021
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  6. fix: wrong if condition when checking signal for null value

    michaelwenk committed Oct 11, 2021
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Commits on Oct 19, 2021

  1. chore: made buildForbiddenNeighborHybridizationsAndProtonCounts more … 

    …general to re-use it
    michaelwenk committed Oct 19, 2021
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Commits on Oct 22, 2021

  1. fix: do not start proton atom count at heavy atom count

    michaelwenk committed Oct 22, 2021
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  2. chore: receive forbidden neighbors from external

    michaelwenk committed Oct 22, 2021
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Commits on Nov 2, 2021

  1. chore: simplification of neighborhood -> occurrences without hybridiz… 

    …ation layer & use of set neighbors
    michaelwenk committed Nov 2, 2021
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  2. chore: renamed requestID to pattern

    michaelwenk committed Nov 2, 2021
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Commits on Nov 15, 2021

  1. feat: re-use hybridizations

    michaelwenk committed Nov 15, 2021
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Commits on Nov 17, 2021

  1. chore: separated DEFF and FEXP

    michaelwenk committed Nov 17, 2021
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  2. chore: use common method for forbidden or set neighbors LIST and PROP… 

    … creation
    michaelwenk committed Nov 17, 2021
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  3. chore: use common method for forbidden or set neighbors LIST and PROP… 

    … creation
    michaelwenk committed Nov 17, 2021
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Commits on Nov 18, 2021

  1. chore: moved buildFixedNeighborsByINADEQUATE method to Utilities clas… 

    …s && created buildBONDByFixedNeighbors method
    michaelwenk committed Nov 18, 2021
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  2. chore: use Java 11

    michaelwenk committed Nov 18, 2021
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  3. Merge pull request #2 from michaelwenk/re-insert-hybridzations 

    feat: re-use hybridzations
    Michael Wenk authored Nov 18, 2021
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Commits on Nov 23, 2021

  1. feat: use path length information from 2D signal if given

    michaelwenk committed Nov 23, 2021
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Commits on Nov 26, 2021

  1. fix: do not check state of correlation data in buildPyLSDInputFileCon… 

    …tent method anymore
    michaelwenk committed Nov 26, 2021
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Commits on Dec 8, 2021

  1. fix: simplification regarding equivalences and HSQC and HMBC section … 

    …creation
    michaelwenk committed Dec 8, 2021
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Commits on Dec 9, 2021

  1. feat: introduction of Detections class

    michaelwenk committed Dec 9, 2021
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Commits on Dec 12, 2021

  1. chore: expect Correlations as input instead of Data in buildPyLSDInpu… 

    …tFileContent
    michaelwenk committed Dec 12, 2021
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Commits on Dec 14, 2021

  1. chore: extension of LSD Constants

    michaelwenk committed Dec 14, 2021
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  2. fix: mentioning of casekit in PyLSD header builder

    michaelwenk committed Dec 14, 2021
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Commits on Dec 15, 2021

  1. chore: removed unused variables in PyLSDInputFileBuilder

    michaelwenk committed Dec 15, 2021
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  2. chore: removed unused variables in PyLSDInputFileBuilder

    michaelwenk committed Dec 15, 2021
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Commits on Dec 23, 2021

  1. fix: set hybridizations of correlations too after detecting them

    michaelwenk committed Dec 23, 2021
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  2. chore: do not use specific neighbor hybridization states for now && s… 

    …implifications
    michaelwenk committed Dec 23, 2021
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Commits on Jan 4, 2022

  1. feat: introduction of Grouping class

    michaelwenk committed Jan 4, 2022
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  2. fix: forbidden list was incomplete

    michaelwenk committed Jan 4, 2022
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Commits on Jan 6, 2022

  1. feat: allow flexible HMBC and COSY

    michaelwenk committed Jan 6, 2022
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Commits on Jan 8, 2022

  1. chore: use common method for COSY and HMBC section build

    michaelwenk committed Jan 8, 2022
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  2. feat: added onAtomTypeLevel parameter to filterExtractedConnectivitie… 

    …s method & added convertToNumericHybridizationMapKeys method
    michaelwenk committed Jan 8, 2022
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Commits on Jan 18, 2022

  1. feat: added buildOccurrenceStatistics method in ConnectivityStatistic… 

    …s.java
    michaelwenk committed Jan 18, 2022
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  2. feat: use grouping information when building HMBC or COSY PyLSD input… 

    … file section
    michaelwenk committed Jan 18, 2022
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Commits on Jan 20, 2022

  1. fix: do not insert incomplete HMBC or COSY lines in PyLSD file by mis… 

    …sing proton attachments
    michaelwenk committed Jan 20, 2022
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Commits on Jan 25, 2022

  1. chore: introduction of MolecularConnectivity class && extended list o… 

    …f default atoms and use of all valencies in MULT section
    michaelwenk committed Jan 25, 2022
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Commits on Jan 26, 2022

  1. chore: added Si properties to Constants

    michaelwenk committed Jan 26, 2022
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Commits on Jan 27, 2022

  1. feat: filter group members when building HMBC and COSY section

    michaelwenk committed Jan 27, 2022
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Commits on Jan 28, 2022

  1. chore: moved Distance.java to model class

    michaelwenk committed Jan 28, 2022
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Commits on Feb 4, 2022

  1. chore: separation and movements to new elucidation package and lsd su… 

    …bpackage
    michaelwenk committed Feb 4, 2022
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  2. chore: use one proton index only instead of multiple ones

    michaelwenk committed Feb 4, 2022
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Commits on Feb 10, 2022

  1. chore: added PathLength to Signal class

    michaelwenk committed Feb 10, 2022
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  2. chore: added PathLength to Signal class (2)

    michaelwenk committed Feb 10, 2022
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  3. chore: use Lists in MolecularConnectivity.java instead of Sets

    michaelwenk committed Feb 10, 2022
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  4. chore: use MolecularConnectivity class

    michaelwenk committed Feb 10, 2022
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Commits on Feb 11, 2022

  1. fix: avoid NullPointerException and duplicated entries in PYLSD input… 

    … file
    michaelwenk committed Feb 11, 2022
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Commits on Feb 14, 2022

  1. feat: enabling of flexibility in HSQC

    michaelwenk committed Feb 14, 2022
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Commits on Feb 17, 2022

  1. feat: check whether hetero atoms are present before disallowing heter… 

    …o hetero bonds
    michaelwenk committed Feb 17, 2022
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  2. feat: added HMBC combinations

    michaelwenk committed Feb 17, 2022
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  3. Merge pull request #3 from michaelwenk/allow-flexible-HSQC 

    feat: implementation of combinatorics for HSQC and HMBC
    Michael Wenk authored Feb 17, 2022
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Commits on Feb 18, 2022

  1. feat: added attachment of objects to DataSet

    michaelwenk committed Feb 18, 2022
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Commits on Feb 22, 2022

  1. feat: enable 3D HOSE code in HOSECodeShiftStatistics

    michaelwenk committed Feb 22, 2022
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Commits on Feb 26, 2022

  1. feat: moved prediction, filter and rank methods from Sherlock to here

    michaelwenk committed Feb 26, 2022
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Commits on Mar 2, 2022

  1. chore: do not store molfiles during filtering and ranking & store sim… 

    …ilarity values in DataSet attachment and not meta
    michaelwenk committed Mar 2, 2022
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  2. fix: avoid exceptions when parsing doubles

    michaelwenk committed Mar 2, 2022
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  3. chore: allow to set the number of threads to use for prediction

    michaelwenk committed Mar 2, 2022
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  4. chore: rank results by number of hits at first and then by average de… 

    …viation
    michaelwenk committed Mar 2, 2022
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Commits on Mar 9, 2022

  1. chore: return value directly

    michaelwenk committed Mar 9, 2022
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Commits on Mar 11, 2022

  1. chore: adoptions to new J and PathLength class (NMRium)

    michaelwenk committed Mar 11, 2022
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Commits on Mar 12, 2022

  1. feat: added methods to build heavy atom statistics

    michaelwenk committed Mar 12, 2022
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Commits on Mar 15, 2022

  1. chore: allow to pass the checkMultiplicity and checkEquivalencesCount

    michaelwenk committed Mar 15, 2022
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Commits on Mar 22, 2022

  1. chore: renaming in Assignment class

    michaelwenk committed Mar 22, 2022
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  2. feat: switch position of query and dataset spectrum in spectral assig… 

    …nment && added prediction method for SMILES strings
    michaelwenk committed Mar 22, 2022
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Commits on Mar 29, 2022

  1. feat: added prediction meta data to Prediction

    michaelwenk committed Mar 29, 2022
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Commits on Apr 6, 2022

  1. feat: extended spectral matching methods to consider structural const… 

    …raints if given
    michaelwenk committed Apr 6, 2022
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Commits on Apr 11, 2022

  1. feat: added ID property to Signal

    michaelwenk committed Apr 11, 2022
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Commits on Apr 25, 2022

  1. chore: renamed Data class to NMRiumData

    michaelwenk committed Apr 25, 2022
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Commits on May 3, 2022

  1. chore: adoptions to current spectra format in NMRium

    michaelwenk committed May 3, 2022
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Commits on May 10, 2022

  1. fix: use manually set and detected hybridization in pyLSD input file

    michaelwenk committed May 10, 2022
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Commits on May 12, 2022

  1. chore: use capitalized AND for FEXP command

    michaelwenk committed May 12, 2022
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Commits on May 13, 2022

  1. chore: no use of concurrency classes in HOSECodeShiftStatistics

    michaelwenk committed May 13, 2022
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Commits on May 17, 2022

  1. feat: allow usage of Ertl functional groups (or fragments in general)… 

    … in PyLSD
    michaelwenk committed May 17, 2022
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Commits on May 18, 2022

  1. chore: renamed FunctionalGroup to Fragment

    michaelwenk committed May 18, 2022
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Commits on May 21, 2022

  1. fix: use different DEFF files for fragment definition in LSD

    michaelwenk committed May 21, 2022
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  2. fix: use different DEFF files for fragment definition in LSD (2)

    michaelwenk committed May 21, 2022
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Commits on May 22, 2022

  1. fix: do not store stringified spectral match assignment

    michaelwenk committed May 22, 2022
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Commits on May 23, 2022

  1. fix: swapped query spectrum in first place with (sub)spectrum when do… 

    …ing spectral matching
    michaelwenk committed May 23, 2022
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Commits on Aug 28, 2022

  1. chore: updated README.md

    Michael Wenk authored Aug 28, 2022
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Commits on Sep 27, 2022

  1. fix: avoid bidirectional BOND commands in PyLSD input file; close #4

    michaelwenk committed Sep 27, 2022
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  2. Merge pull request #5 from michaelwenk/fix-bidirectional-BOND-command 

    fix: avoid bidirectional BOND commands in PyLSD input file; close #4
    Michael Wenk authored Sep 27, 2022
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Commits on Apr 11, 2023

  1. fix: consider bond stereo configuration in StructureCompact class and… 

    … during stereo HOSE code prediction
    michaelwenk committed Apr 11, 2023
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  2. fix: close #6

    michaelwenk committed Apr 11, 2023
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  3. Merge pull request #7 from michaelwenk/add-bond-stereo 

    Add and consider bond stereo
    Michael Wenk authored Apr 11, 2023
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Commits on Apr 12, 2023

  1. chore: use common method placeExplicitHydrogens

    michaelwenk committed Apr 12, 2023
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Commits on Apr 13, 2023

  1. fix: configure structure atomContainerToDataSet method

    michaelwenk committed Apr 13, 2023
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  2. fix: remove unnecessary command

    michaelwenk committed Apr 13, 2023
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Commits on Apr 14, 2023

  1. fix: do not place explicit hydrogens when no bonds exist

    michaelwenk committed Apr 14, 2023
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Commits on Apr 18, 2023

  1. chore: inserted separate buildAlphabeticMF method

    michaelwenk committed Apr 18, 2023
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Commits on Jun 15, 2023

  1. fix: enable no stereo bond information in StructureCompact class

    michaelwenk committed Jun 15, 2023
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Commits on Jun 20, 2023

  1. chore: optimised getOutliers method

    michaelwenk committed Jun 20, 2023
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