First small bug fixes#1

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michaelwenk wants to merge 415 commits intosteinbeck:masterfrom michaelwenk:master

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Commits on Mar 30, 2021

minor
michaelwenk
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Commits on Apr 1, 2021

assignments can now hold more than only one single assignment index (equivalences); small optimisations
michaelwenk
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disabled SHIH in PyLSDInputFileBuilder.java
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added RankedResultSDFParser
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Match: when checkEquivalencesCount is set to true then check for equal number instead of less or equal
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fix: an error when passing conditions
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Commits on Apr 4, 2021

feat: changed "mf" to "mfOriginal" and added alphabetic sorted mf as "mf"
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moved try and catch around Tanimoto coefficient calculation
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Commits on Apr 7, 2021

feat: multiplicity check when adding a signal to a spectrum
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fix: multiplicity check when searching for equivalence signals; use median for predicted shift calculation instead of mean
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fix: added missing multiplicity check when searching for equivalence signals
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feat: added PyLSD ELIM P1 and P2 parameters
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feat: added useElim parameter and changed filter paths to array
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Commits on Apr 8, 2021

feat: added atom type check when parsing ranked SDF by PyLSD
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feat: re-added SHIH in PyLSD input file
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Commits on Apr 9, 2021

feat: added PyLSD HMBC P3, HMBC P4, COSY P3 and COSY P4 parameters
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Commits on Apr 10, 2021

Commits on Apr 13, 2021

fix: init non-empty arrays for equivalences
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Commits on Apr 19, 2021

fix: use own deep clone method Assignment
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Commits on Apr 23, 2021

fix: extended hetero atom list in aromatic cycles in isValidBondAddition
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chore: added UTF-8 encoding and updated two dependencies
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fix: switched from SmiFlavor.Absolute to SmiFlavor.Unique
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Commits on Apr 24, 2021

fix: buildFilters expects direct paths to filters
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Commits on Apr 25, 2021

feat: added parseRankedResultSDFile methods
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Commits on Apr 29, 2021

feat: integration of HOSECodeBuilder project
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feat: updated README.md
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Commits on May 5, 2021

fix: replaced HashSet by Set
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Commits on May 10, 2021

fix: wrong order if allowLowerEquivalencesCount is checked
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Commits on Jun 4, 2021

feat: added method to remove a node from connection tree
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fix: parse multiplicities with toLowerCase
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feat: added H to HOSE code node weight
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feat: added methods to add and convert implicit to explicit hydrogens and to calculate the RMS value
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fix: take implicit hydrogens into account when building root sphere
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feat: added method to build HOSE code statistics
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Commits on Jun 5, 2021

feat: added ExtendedHOSEGenerator
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feat: added Utils class for DB services
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feat: added COCONUT data set import
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Commits on Jun 6, 2021

chore: update of toString method
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chore: update of toString method
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fix: improvement in multiplicity picking
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fix: return lower case multiplicity string
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fix: wrong explicit H removals; optional second sprectrum property string
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feat: added HOSECodeShiftStatistics
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chore: added GSON and BSON as dependencies
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chore: use [email protected]
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feat: added method for simple signal addition
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fix: restore to previous multiplicity picking
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fix: multiple multiplicity filter when adding a signal
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fix: set node weight for explicit H to 0
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Commits on Jun 7, 2021

fix: crash when adding assignments in higher dimension
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Commits on Jun 8, 2021

feat: addSignal now returns the index of added signal and enables pick precision for each dimension
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chore: removed unused method
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feat: integration of 1D and 2D spectrum prediction based on HOSE code (no diastereotopic distinctions for now)
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chore: removed outputs
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Commits on Jun 10, 2021

feat: specified HSQC und edited HSQC methods
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Commits on Jun 15, 2021

feat: new fragmentation functionality and movement of connection tree (node) model classes
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feat: added getUnsaturatedAtomIndices method
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feat: added a wrapper method to build a fragment
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Commits on Jun 16, 2021

feat: added isPseudoNode property to ConnectionTreeNode
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fix: bugfixes and improvements when building fragments
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fix: fixed an issue when closing rings
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Commits on Jun 18, 2021

Commits on Jun 19, 2021

feat: added method for checking equivalences
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feat: added methods for building fragment trees and fragment datasets
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Commits on Jun 20, 2021

fix: fixed invalid atom index usage
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fix: ensure pseudo atom when converting ExtendedConnectionMatrix to IAtomContainer
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feat: addition and usage of method for removing identical fragment trees
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Commits on Jun 21, 2021

feat: consider fused ring systems in fragmentation too
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feat: implemented separated method buildRingFragmentTrees and method descriptions were added
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Commits on Jun 23, 2021

feat: added closeRings for IAtomContainer as input too
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feat: added initKeySet method to ConnectionTree
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chore: moved additional methods to FragmentationUtils
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chore: moved attachPseudoAtoms and addPseudoNode to FragmentationUtils
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Commits on Jun 27, 2021

fix: getIndex method in Assignment did not return all indices
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fix: thrown exception if both multiplicities are null while checking them
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fix: parse empty multiplicity as null
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feat: added methods for MF comparisons and allow different aromaticity models
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feat: added ErtlFunctionalGroup class containing helper methods regarding ErtlFunctionalGroupsFinder
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Delete LICENSE
Michael Wenk
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Create LICENSE
Michael Wenk
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Update README.md
Michael Wenk
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Merge branch 'master' into add-fragmentation
michaelwenk
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Commits on Jun 28, 2021

fix: adaption to changes of getIndices() in Assignment
michaelwenk
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Delete LICENSE
Michael Wenk
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Create LICENSE
Michael Wenk
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Merge branch 'master' into add-fragmentation
michaelwenk
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feat: pasted ErtlFunctionalGroupsFinder class
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feat: store RMSD and average deviation in sub-datasets via findMatches method
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chore: removed unused MongoDB class
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chore: moved methods from old Utils class to new Statistics and Utils class
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chore: moved calculation methods for RMSD and average deviation to Statistics class
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chore: moved "fragmentation" into new "fragments" package; moved general utility methods for fragments to new FragmentUtilities class
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chore: put classes from "utils" package to separate packages
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feat: extended findMatches in FragmentUtilities by goodlist and badlist
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Commits on Jun 30, 2021

fix: allow unsaturated fragments only
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feat: added general getDeviation method and possibility to use previous assignments
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chore: added notice to BFS method (book by Elyashberg, Williams and Blinov)
michaelwenk
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Merge pull request #1 from michaelwenk/add-fragmentation
Michael Wenk
authored

Commits on Jul 6, 2021

feat: introduction of maximum average deviation for dereplication and elucidation
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Commits on Jul 13, 2021

feat: added usePrediction to ElucidationOptions
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chore: improvement of outlier detection and removal methods
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feat: added general SDF parser
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chore: switched solvent and nucleus parameter
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feat: added withExplicitH parameter to HOSE code statistic collection and usage of outlier removal
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Commits on Jul 20, 2021

feat: added default values for fluorine
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fix: wrong number of proton equivalences, i.e. in case of CH3 groups
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Commits on Jul 21, 2021

feat: added methods for files cleanup and SMILES file parsing
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chore: marked RankedResultSDFParser.java as deprecated
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Commits on Jul 29, 2021

feat: added a method to build HOSE codes statistics by list of datasets
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feat: set the multiplicity of carbon atoms when predicting spectra
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chore: improvements in MultiplicitySectionsBuilder
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chore: added dimension of spectrum
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feat: added method to calculate the Tanimoto coefficient between two spectra
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Commits on Aug 6, 2021

feat: improvement of matching between two spectra by using minimal distances
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Commits on Aug 10, 2021

fix: insert missing equivalences in matchSpectra & small optimisations
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feat: added public method to calculate the steps & small optimisations
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Commits on Aug 16, 2021

Commits on Aug 18, 2021

Commits on Aug 19, 2021

chore: optimisation of ExtendedAdjacencyList
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fix: check for null value of hybridisation state
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Commits on Aug 22, 2021

fix: renaming to atomCount and bondCount to avoid storage in JSON format
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chore: optimisations on Spectrum class
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Commits on Aug 23, 2021

feat: usage of Concurrent class when building HOSE code statistics
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fix: pre-set carbon hybridization states when having at least two protons
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Commits on Aug 25, 2021

chore: use common parser method for COCONUT and NMRShiftDB
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Commits on Aug 26, 2021

chore: usage of more compact classes in DataSet
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Commits on Aug 27, 2021

chore: extracted buildConnectivityStatistics method
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Commits on Aug 28, 2021

feat: methods for extraction of neighbor atom types and hybridizations
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Commits on Aug 30, 2021

feat: use connectivity information to forbid bonds between an atom and a group of atoms
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Commits on Sep 1, 2021

chore: renamed nmrdisplayer package to nmrium
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chore: changed string values to numeric ones; hybridizationConversionMap contains atom type as key instead of nucleus
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feat: use hybridization statistics too to forbid bonds
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Commits on Sep 3, 2021

feat: use SHIX command in PyLSD to let it recognise equivalent atoms by shift values
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chore: added PLANAR3 for O to hybridizationConversionMap
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feat: simplified connectivity statistics filtering
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Commits on Sep 11, 2021

chore: simplification in Constants
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feat: use utility classes for LIST and PROP creation and extension of connection forbids; allow multiple hybridizations
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feat: ability to use of INADEQUATE information
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Commits on Sep 13, 2021

fix: use unique hybridization states in MULT
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fix: wrong if conditions for setting possible hybridizations of hetero atoms
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Commits on Sep 16, 2021

fix: enable max ring size when detecting rings for ring fragment trees building
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feat: added correlationListToSpectrum1D method to Utils
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Commits on Oct 11, 2021

feat: added getFileContent method to FileSystem
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feat: added MultiThreading class
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chore: NMRium signal classes use a common parent class
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chore: adoptions regarding change in correlation data structure in nmr-correlation package
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chore: changed "phase" class member to Integer
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fix: wrong if condition when checking signal for null value
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Commits on Oct 19, 2021

chore: made buildForbiddenNeighborHybridizationsAndProtonCounts more general to re-use it
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Commits on Oct 22, 2021

fix: do not start proton atom count at heavy atom count
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chore: receive forbidden neighbors from external
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Commits on Nov 2, 2021

chore: simplification of neighborhood -> occurrences without hybridization layer & use of set neighbors
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chore: renamed requestID to pattern
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Commits on Nov 15, 2021

feat: re-use hybridizations
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Commits on Nov 17, 2021

chore: separated DEFF and FEXP
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chore: use common method for forbidden or set neighbors LIST and PROP creation
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chore: use common method for forbidden or set neighbors LIST and PROP creation
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Commits on Nov 18, 2021

chore: moved buildFixedNeighborsByINADEQUATE method to Utilities class && created buildBONDByFixedNeighbors method
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chore: use Java 11
michaelwenk
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Merge pull request #2 from michaelwenk/re-insert-hybridzations
Michael Wenk
authored

Commits on Nov 23, 2021

feat: use path length information from 2D signal if given
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Commits on Nov 26, 2021

fix: do not check state of correlation data in buildPyLSDInputFileContent method anymore
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Commits on Dec 8, 2021

fix: simplification regarding equivalences and HSQC and HMBC section creation
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Commits on Dec 9, 2021

feat: introduction of Detections class
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Commits on Dec 12, 2021

chore: expect Correlations as input instead of Data in buildPyLSDInputFileContent
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Commits on Dec 14, 2021

chore: extension of LSD Constants
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fix: mentioning of casekit in PyLSD header builder
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Commits on Dec 15, 2021

chore: removed unused variables in PyLSDInputFileBuilder
michaelwenk
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chore: removed unused variables in PyLSDInputFileBuilder
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Commits on Dec 23, 2021

fix: set hybridizations of correlations too after detecting them
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chore: do not use specific neighbor hybridization states for now && simplifications
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Commits on Jan 4, 2022

feat: introduction of Grouping class
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fix: forbidden list was incomplete
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Commits on Jan 6, 2022

feat: allow flexible HMBC and COSY
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Commits on Jan 8, 2022

Commits on Jan 18, 2022

feat: added buildOccurrenceStatistics method in ConnectivityStatistics.java
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feat: use grouping information when building HMBC or COSY PyLSD input file section
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Commits on Jan 20, 2022

fix: do not insert incomplete HMBC or COSY lines in PyLSD file by missing proton attachments
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Commits on Jan 25, 2022

chore: introduction of MolecularConnectivity class && extended list of default atoms and use of all valencies in MULT section
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Commits on Jan 26, 2022

chore: added Si properties to Constants
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Commits on Jan 27, 2022

feat: filter group members when building HMBC and COSY section
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Commits on Jan 28, 2022

chore: moved Distance.java to model class
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Commits on Feb 4, 2022

chore: separation and movements to new elucidation package and lsd subpackage
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chore: use one proton index only instead of multiple ones
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Commits on Feb 10, 2022

chore: added PathLength to Signal class
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chore: added PathLength to Signal class (2)
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chore: use Lists in MolecularConnectivity.java instead of Sets
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chore: use MolecularConnectivity class
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Commits on Feb 11, 2022

fix: avoid NullPointerException and duplicated entries in PYLSD input file
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Commits on Feb 14, 2022

feat: enabling of flexibility in HSQC
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Commits on Feb 17, 2022

feat: check whether hetero atoms are present before disallowing hetero hetero bonds
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feat: added HMBC combinations
michaelwenk
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Merge pull request #3 from michaelwenk/allow-flexible-HSQC
Michael Wenk
authored

Commits on Feb 18, 2022

feat: added attachment of objects to DataSet
michaelwenk
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Commits on Feb 22, 2022

feat: enable 3D HOSE code in HOSECodeShiftStatistics
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Commits on Feb 26, 2022

feat: moved prediction, filter and rank methods from Sherlock to here
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Commits on Mar 2, 2022

chore: do not store molfiles during filtering and ranking & store similarity values in DataSet attachment and not meta
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fix: avoid exceptions when parsing doubles
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chore: allow to set the number of threads to use for prediction
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chore: rank results by number of hits at first and then by average deviation
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Commits on Mar 9, 2022

chore: return value directly
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Commits on Mar 11, 2022

chore: adoptions to new J and PathLength class (NMRium)
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Commits on Mar 12, 2022

feat: added methods to build heavy atom statistics
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Commits on Mar 15, 2022

chore: allow to pass the checkMultiplicity and checkEquivalencesCount
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Commits on Mar 22, 2022

chore: renaming in Assignment class
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feat: switch position of query and dataset spectrum in spectral assignment && added prediction method for SMILES strings
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Commits on Mar 29, 2022

feat: added prediction meta data to Prediction
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Commits on Apr 6, 2022

feat: extended spectral matching methods to consider structural constraints if given
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Commits on Apr 11, 2022

feat: added ID property to Signal
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Commits on Apr 25, 2022

chore: renamed Data class to NMRiumData
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Commits on May 3, 2022

chore: adoptions to current spectra format in NMRium
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Commits on May 10, 2022

fix: use manually set and detected hybridization in pyLSD input file
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Commits on May 12, 2022

chore: use capitalized AND for FEXP command
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Commits on May 13, 2022

chore: no use of concurrency classes in HOSECodeShiftStatistics
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Commits on May 17, 2022

feat: allow usage of Ertl functional groups (or fragments in general) in PyLSD
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Commits on May 18, 2022

chore: renamed FunctionalGroup to Fragment
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Commits on May 21, 2022

fix: use different DEFF files for fragment definition in LSD
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fix: use different DEFF files for fragment definition in LSD (2)
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Commits on May 22, 2022

fix: do not store stringified spectral match assignment
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Commits on May 23, 2022

fix: swapped query spectrum in first place with (sub)spectrum when doing spectral matching
michaelwenk
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Commits on Aug 28, 2022

chore: updated README.md
Michael Wenk
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Commits on Sep 27, 2022

fix: avoid bidirectional BOND commands in PyLSD input file; close #4
michaelwenk
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Merge pull request #5 from michaelwenk/fix-bidirectional-BOND-command
Michael Wenk
authored

Commits on Apr 11, 2023

fix: consider bond stereo configuration in StructureCompact class and during stereo HOSE code prediction
michaelwenk
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fix: close #6
michaelwenk
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Merge pull request #7 from michaelwenk/add-bond-stereo
Michael Wenk
authored

Commits on Apr 12, 2023

chore: use common method placeExplicitHydrogens
michaelwenk
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Commits on Apr 13, 2023

fix: configure structure atomContainerToDataSet method
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fix: remove unnecessary command
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Commits on Apr 14, 2023

fix: do not place explicit hydrogens when no bonds exist
michaelwenk
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Commits on Apr 18, 2023

chore: inserted separate buildAlphabeticMF method
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Commits on Jun 15, 2023

fix: enable no stereo bond information in StructureCompact class
michaelwenk
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Commits on Jun 20, 2023

chore: optimised getOutliers method
michaelwenk
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