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First small bug fixes #1

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b3badc3
minor
Mar 30, 2021
a7ed157
assignments can now hold more than only one single assignment index (…
Apr 1, 2021
6f531ff
disabled SHIH in PyLSDInputFileBuilder.java
Apr 1, 2021
da49058
added RankedResultSDFParser
Apr 1, 2021
93861d0
Match: when checkEquivalencesCount is set to true then check for equa…
Apr 1, 2021
e731835
fix: an error when passing conditions
Apr 1, 2021
716dcff
feat: changed "mf" to "mfOriginal" and added alphabetic sorted mf as …
Apr 4, 2021
bde083d
moved try and catch around Tanimoto coefficient calculation
Apr 4, 2021
6b1b4ec
feat: multiplicity check when adding a signal to a spectrum
Apr 7, 2021
3545940
fix: multiplicity check when searching for equivalence signals; use m…
Apr 7, 2021
519bb94
fix: added missing multiplicity check when searching for equivalence …
Apr 7, 2021
2cbcec5
feat: added PyLSD ELIM P1 and P2 parameters
Apr 7, 2021
b5d758a
feat: added useElim parameter and changed filter paths to array
Apr 7, 2021
090cc43
feat: added atom type check when parsing ranked SDF by PyLSD
Apr 8, 2021
bf82a1a
feat: re-added SHIH in PyLSD input file
Apr 8, 2021
82c8f19
feat: added PyLSD HMBC P3, HMBC P4, COSY P3 and COSY P4 parameters
Apr 9, 2021
bd3818f
chore: replace default constructors, setters and getters by lombok an…
Apr 10, 2021
d041935
chore: replace default constructors, setters and getters by lombok an…
Apr 10, 2021
17d1ca9
feat: added allowLowerEquivalencesCount to spectra matching
Apr 10, 2021
6bb4077
feat: added setSignal method to Spectrum
Apr 10, 2021
f2711a3
fix: add equivalences count of newly added signal instead of one only
Apr 10, 2021
df12f85
feat: added addAssignment method to Assignment
Apr 10, 2021
561c0df
fix: too high index when checking the dimension
Apr 10, 2021
61b9d3b
fix: init non-empty arrays for equivalences
Apr 13, 2021
14c9469
fix: use own deep clone method Assignment
Apr 19, 2021
3be9b47
fix: extended hetero atom list in aromatic cycles in isValidBondAddition
Apr 23, 2021
287baf4
chore: added UTF-8 encoding and updated two dependencies
Apr 23, 2021
ec921de
fix: switched from SmiFlavor.Absolute to SmiFlavor.Unique
Apr 23, 2021
63ef95d
fix: buildFilters expects direct paths to filters
Apr 24, 2021
5434788
feat: added parseRankedResultSDFile methods
Apr 25, 2021
acc54ba
feat: integration of HOSECodeBuilder project
Apr 29, 2021
54afba9
feat: updated README.md
Apr 29, 2021
bcc849e
fix: replaced HashSet by Set
May 5, 2021
9b57ef0
fix: wrong order if allowLowerEquivalencesCount is checked
May 10, 2021
0327450
feat: added method to remove a node from connection tree
Jun 4, 2021
3f174f7
fix: parse multiplicities with toLowerCase
Jun 4, 2021
881fad3
feat: added H to HOSE code node weight
Jun 4, 2021
b3a0a6a
feat: added methods to add and convert implicit to explicit hydrogens…
Jun 4, 2021
af7a27e
fix: take implicit hydrogens into account when building root sphere
Jun 4, 2021
aa194fa
feat: added method to build HOSE code statistics
Jun 4, 2021
ad3c42f
feat: added ExtendedHOSEGenerator
Jun 5, 2021
ec2d00c
feat: added Utils class for DB services
Jun 5, 2021
76e24db
feat: added COCONUT data set import
Jun 5, 2021
82c0f99
chore: update of toString method
Jun 6, 2021
aa7ff8a
chore: update of toString method
Jun 6, 2021
337fc52
fix: improvement in multiplicity picking
Jun 6, 2021
e5794d1
fix: return lower case multiplicity string
Jun 6, 2021
46aa804
fix: wrong explicit H removals; optional second sprectrum property st…
Jun 6, 2021
e2185a6
feat: added HOSECodeShiftStatistics
Jun 6, 2021
14c5f0b
chore: added GSON and BSON as dependencies
Jun 6, 2021
ef42758
chore: use [email protected]
Jun 6, 2021
7022ed9
feat: added method for simple signal addition
Jun 6, 2021
b0ad16a
fix: restore to previous multiplicity picking
Jun 6, 2021
7188b4e
fix: multiple multiplicity filter when adding a signal
Jun 6, 2021
8da8922
fix: set node weight for explicit H to 0
Jun 6, 2021
ecd4c08
fix: crash when adding assignments in higher dimension
Jun 7, 2021
7f3abee
feat: addSignal now returns the index of added signal and enables pic…
Jun 8, 2021
c40b943
chore: removed unused method
Jun 8, 2021
51e35d1
feat: integration of 1D and 2D spectrum prediction based on HOSE code…
Jun 8, 2021
a89327c
chore: removed outputs
Jun 8, 2021
bba7784
feat: specified HSQC und edited HSQC methods
Jun 10, 2021
fefb9ef
feat: new fragmentation functionality and movement of connection tree…
Jun 15, 2021
f153caf
feat: added getUnsaturatedAtomIndices method
Jun 15, 2021
9fbcbf1
feat: added a wrapper method to build a fragment
Jun 15, 2021
f67787c
feat: added isPseudoNode property to ConnectionTreeNode
Jun 16, 2021
62a1e3a
fix: bugfixes and improvements when building fragments
Jun 16, 2021
3c171d0
fix: fixed an issue when closing rings
Jun 16, 2021
0e74ce2
feat: added toString method to ConnectionTreeNode and enabled to set …
Jun 18, 2021
ad054e2
feat: added addSubtree method to ConnectionTree class
Jun 18, 2021
8fc8044
feat: improvement of fragmentation by ring extension via a given maxS…
Jun 18, 2021
34ee705
feat: added method for checking equivalences
Jun 19, 2021
e3f6f76
feat: added methods for building fragment trees and fragment datasets
Jun 19, 2021
b19035c
fix: fixed invalid atom index usage
Jun 20, 2021
6f682a3
fix: ensure pseudo atom when converting ExtendedConnectionMatrix to I…
Jun 20, 2021
d45b897
feat: addition and usage of method for removing identical fragment trees
Jun 20, 2021
31c5c8b
feat: consider fused ring systems in fragmentation too
Jun 21, 2021
97311d1
feat: implemented separated method buildRingFragmentTrees and method …
Jun 21, 2021
b01d927
feat: added closeRings for IAtomContainer as input too
Jun 23, 2021
0d0652b
feat: added initKeySet method to ConnectionTree
Jun 23, 2021
03f4d2f
chore: moved additional methods to FragmentationUtils
Jun 23, 2021
1d7269f
chore: moved attachPseudoAtoms and addPseudoNode to FragmentationUtils
Jun 23, 2021
36781bc
fix: getIndex method in Assignment did not return all indices
Jun 27, 2021
47b9fad
fix: thrown exception if both multiplicities are null while checking …
Jun 27, 2021
7f521ed
fix: parse empty multiplicity as null
Jun 27, 2021
43a23aa
feat: added methods for MF comparisons and allow different aromaticit…
Jun 27, 2021
c3df5ba
feat: added ErtlFunctionalGroup class containing helper methods regar…
Jun 27, 2021
9565873
Delete LICENSE
Jun 27, 2021
5e225d5
Create LICENSE
Jun 27, 2021
184c760
Update README.md
Jun 27, 2021
ec7d2c6
Merge branch 'master' into add-fragmentation
Jun 27, 2021
f64bf37
fix: adaption to changes of getIndices() in Assignment
Jun 28, 2021
287e84c
Delete LICENSE
Jun 28, 2021
4a37bdd
Create LICENSE
Jun 28, 2021
24a6eba
Merge branch 'master' into add-fragmentation
Jun 28, 2021
95a8c77
feat: pasted ErtlFunctionalGroupsFinder class
Jun 28, 2021
ffa81d8
feat: store RMSD and average deviation in sub-datasets via findMatche…
Jun 28, 2021
3dd950c
chore: removed unused MongoDB class
Jun 28, 2021
0c5a1bd
chore: moved methods from old Utils class to new Statistics and Utils…
Jun 28, 2021
a555a9d
chore: moved calculation methods for RMSD and average deviation to St…
Jun 28, 2021
6bb045a
chore: moved "fragmentation" into new "fragments" package; moved gene…
Jun 28, 2021
2cf185d
chore: put classes from "utils" package to separate packages
Jun 28, 2021
65de333
feat: extended findMatches in FragmentUtilities by goodlist and badlist
Jun 28, 2021
2506cf4
fix: allow unsaturated fragments only
Jun 30, 2021
adc838a
feat: added general getDeviation method and possibility to use previo…
Jun 30, 2021
17b9b08
chore: added notice to BFS method (book by Elyashberg, Williams and B…
Jun 30, 2021
69b1635
Merge pull request #1 from michaelwenk/add-fragmentation
Jun 30, 2021
42722b0
feat: introduction of maximum average deviation for dereplication and…
Jul 6, 2021
866ccf4
feat: added usePrediction to ElucidationOptions
Jul 13, 2021
d9c1a6d
chore: improvement of outlier detection and removal methods
Jul 13, 2021
3d4a7f1
feat: added general SDF parser
Jul 13, 2021
abddd24
chore: switched solvent and nucleus parameter
Jul 13, 2021
cd4df4d
feat: added withExplicitH parameter to HOSE code statistic collection…
Jul 13, 2021
0f2b27f
feat: added default values for fluorine
Jul 20, 2021
01a681c
fix: wrong number of proton equivalences, i.e. in case of CH3 groups
Jul 20, 2021
7638f88
feat: added methods for files cleanup and SMILES file parsing
Jul 21, 2021
eb12c6a
chore: marked RankedResultSDFParser.java as deprecated
Jul 21, 2021
abfa9ca
feat: added a method to build HOSE codes statistics by list of datasets
Jul 29, 2021
0bfc272
feat: set the multiplicity of carbon atoms when predicting spectra
Jul 29, 2021
7190371
chore: improvements in MultiplicitySectionsBuilder
Jul 29, 2021
9d00efd
chore: added dimension of spectrum
Jul 29, 2021
5da296d
feat: added method to calculate the Tanimoto coefficient between two …
Jul 29, 2021
743d5b0
feat: improvement of matching between two spectra by using minimal di…
Aug 6, 2021
cc41b55
fix: insert missing equivalences in matchSpectra & small optimisations
Aug 10, 2021
c3a77d8
feat: added public method to calculate the steps & small optimisations
Aug 10, 2021
fe85d82
chore: optimisation of toString method in Assignment
Aug 16, 2021
bdd0053
fix: initialise meta map when adding an info in DataSet
Aug 16, 2021
ebd336e
fix: use case insensitive comparison of multiplicities
Aug 16, 2021
d996b77
feat: added atomContainerToDataSet method to Utils
Aug 16, 2021
f89a92c
feat: added methods to parse SMILES from file in Parser
Aug 16, 2021
04a3969
feat: added optional hybridizations to check when searching for goodl…
Aug 16, 2021
cc5505d
feat: added ConnectivityStatistics class
Aug 16, 2021
ef293a3
chore: use Utils.atomContainerToDataSet() in COCONUT.java
Aug 18, 2021
8a1fe38
chore: receive general dataSet list when collecting functional groups…
Aug 18, 2021
b9cfc9f
chore: simplification and renaming of ExtendedConnectionMatrix into E…
Aug 18, 2021
e03a404
chore: optimisation of ExtendedAdjacencyList
Aug 19, 2021
9eecafe
fix: check for null value of hybridisation state
Aug 19, 2021
856fe5a
fix: renaming to atomCount and bondCount to avoid storage in JSON format
Aug 22, 2021
ec92521
chore: optimisations on Spectrum class
Aug 22, 2021
d74ee7e
feat: usage of Concurrent class when building HOSE code statistics
Aug 23, 2021
ac7e74a
fix: pre-set carbon hybridization states when having at least two pro…
Aug 23, 2021
fbd8f51
chore: use common parser method for COCONUT and NMRShiftDB
Aug 25, 2021
5e5aa8b
chore: usage of more compact classes in DataSet
Aug 26, 2021
145c1c7
chore: extracted buildConnectivityStatistics method
Aug 27, 2021
7dea28c
feat: methods for extraction of neighbor atom types and hybridizations
Aug 28, 2021
22d2bd1
feat: use connectivity information to forbid bonds between an atom an…
Aug 30, 2021
6850f57
chore: renamed nmrdisplayer package to nmrium
Sep 1, 2021
f56ab3a
chore: changed string values to numeric ones; hybridizationConversion…
Sep 1, 2021
53d50eb
feat: use hybridization statistics too to forbid bonds
Sep 1, 2021
b3dc392
feat: use SHIX command in PyLSD to let it recognise equivalent atoms …
Sep 3, 2021
373d1b5
chore: added PLANAR3 for O to hybridizationConversionMap
Sep 3, 2021
e272d43
feat: simplified connectivity statistics filtering
Sep 3, 2021
168277e
chore: simplification in Constants
Sep 11, 2021
04e407f
feat: use utility classes for LIST and PROP creation and extension of…
Sep 11, 2021
deda39c
feat: ability to use of INADEQUATE information
Sep 11, 2021
d08bc3a
fix: use unique hybridization states in MULT
Sep 13, 2021
dd39bcd
fix: wrong if conditions for setting possible hybridizations of heter…
Sep 13, 2021
68aa8d2
fix: enable max ring size when detecting rings for ring fragment tree…
Sep 16, 2021
664fa34
feat: added correlationListToSpectrum1D method to Utils
Sep 16, 2021
e1bc684
feat: added getFileContent method to FileSystem
Oct 11, 2021
af01c1e
feat: added MultiThreading class
Oct 11, 2021
fdc155b
chore: NMRium signal classes use a common parent class
Oct 11, 2021
ad465b0
chore: adoptions regarding change in correlation data structure in nm…
Oct 11, 2021
1e71690
chore: changed "phase" class member to Integer
Oct 11, 2021
341f847
fix: wrong if condition when checking signal for null value
Oct 11, 2021
b97c87b
chore: made buildForbiddenNeighborHybridizationsAndProtonCounts more …
Oct 19, 2021
0f8b38a
fix: do not start proton atom count at heavy atom count
Oct 22, 2021
78f16f9
chore: receive forbidden neighbors from external
Oct 22, 2021
2e21330
chore: simplification of neighborhood -> occurrences without hybridiz…
Nov 2, 2021
8848e4e
chore: renamed requestID to pattern
Nov 2, 2021
7a760ec
feat: re-use hybridizations
Nov 15, 2021
02c9b83
chore: separated DEFF and FEXP
Nov 17, 2021
6dbb349
chore: use common method for forbidden or set neighbors LIST and PROP…
Nov 17, 2021
0cd0f95
chore: use common method for forbidden or set neighbors LIST and PROP…
Nov 17, 2021
337fb78
chore: moved buildFixedNeighborsByINADEQUATE method to Utilities clas…
Nov 18, 2021
08376c7
chore: use Java 11
Nov 18, 2021
b946cee
Merge pull request #2 from michaelwenk/re-insert-hybridzations
Nov 18, 2021
706b44a
feat: use path length information from 2D signal if given
Nov 23, 2021
caeb7eb
fix: do not check state of correlation data in buildPyLSDInputFileCon…
Nov 26, 2021
aeeb3fe
fix: simplification regarding equivalences and HSQC and HMBC section …
Dec 8, 2021
acc15f3
feat: introduction of Detections class
Dec 9, 2021
a72534b
chore: expect Correlations as input instead of Data in buildPyLSDInpu…
Dec 12, 2021
93549cc
chore: extension of LSD Constants
Dec 14, 2021
a38c399
fix: mentioning of casekit in PyLSD header builder
Dec 14, 2021
fb89655
chore: removed unused variables in PyLSDInputFileBuilder
Dec 15, 2021
4b3d4b3
chore: removed unused variables in PyLSDInputFileBuilder
Dec 15, 2021
e854c2c
fix: set hybridizations of correlations too after detecting them
Dec 23, 2021
1917470
chore: do not use specific neighbor hybridization states for now && s…
Dec 23, 2021
f9f6982
feat: introduction of Grouping class
Jan 4, 2022
953c7e3
fix: forbidden list was incomplete
Jan 4, 2022
be04b5a
feat: allow flexible HMBC and COSY
Jan 6, 2022
59de93b
chore: use common method for COSY and HMBC section build
Jan 8, 2022
f7bc142
feat: added onAtomTypeLevel parameter to filterExtractedConnectivitie…
Jan 8, 2022
cb121c5
feat: added buildOccurrenceStatistics method in ConnectivityStatistic…
Jan 18, 2022
e0f67b5
feat: use grouping information when building HMBC or COSY PyLSD input…
Jan 18, 2022
e7abbe1
fix: do not insert incomplete HMBC or COSY lines in PyLSD file by mis…
Jan 20, 2022
b93c91b
chore: introduction of MolecularConnectivity class && extended list o…
Jan 25, 2022
e1b3aec
chore: added Si properties to Constants
Jan 26, 2022
24e32e2
feat: filter group members when building HMBC and COSY section
Jan 27, 2022
52100c5
chore: moved Distance.java to model class
Jan 28, 2022
a5ea98c
chore: separation and movements to new elucidation package and lsd su…
Feb 4, 2022
725fa4c
chore: use one proton index only instead of multiple ones
Feb 4, 2022
020ba05
chore: added PathLength to Signal class
Feb 10, 2022
43451cd
chore: added PathLength to Signal class (2)
Feb 10, 2022
c54db34
chore: use Lists in MolecularConnectivity.java instead of Sets
Feb 10, 2022
1098b17
chore: use MolecularConnectivity class
Feb 10, 2022
caec677
fix: avoid NullPointerException and duplicated entries in PYLSD input…
Feb 11, 2022
e462d68
feat: enabling of flexibility in HSQC
Feb 14, 2022
db93021
feat: check whether hetero atoms are present before disallowing heter…
Feb 17, 2022
608c3a7
feat: added HMBC combinations
Feb 17, 2022
35e1978
Merge pull request #3 from michaelwenk/allow-flexible-HSQC
Feb 17, 2022
4979d8f
feat: added attachment of objects to DataSet
Feb 18, 2022
5afdcb1
feat: enable 3D HOSE code in HOSECodeShiftStatistics
Feb 22, 2022
35d66d1
feat: moved prediction, filter and rank methods from Sherlock to here
Feb 26, 2022
e47c3f4
chore: do not store molfiles during filtering and ranking & store sim…
Mar 2, 2022
a9eb4bb
fix: avoid exceptions when parsing doubles
Mar 2, 2022
0c9a594
chore: allow to set the number of threads to use for prediction
Mar 2, 2022
3ea00d1
chore: rank results by number of hits at first and then by average de…
Mar 2, 2022
bd9e7ca
chore: return value directly
Mar 9, 2022
4aa4c67
chore: adoptions to new J and PathLength class (NMRium)
Mar 11, 2022
f03d60c
feat: added methods to build heavy atom statistics
Mar 12, 2022
9e877b8
chore: allow to pass the checkMultiplicity and checkEquivalencesCount
Mar 15, 2022
64539cc
chore: renaming in Assignment class
Mar 22, 2022
d572c68
feat: switch position of query and dataset spectrum in spectral assig…
Mar 22, 2022
7ef8981
feat: added prediction meta data to Prediction
Mar 29, 2022
6d9f457
feat: extended spectral matching methods to consider structural const…
Apr 6, 2022
1e65f57
feat: added ID property to Signal
Apr 11, 2022
ffe2172
chore: renamed Data class to NMRiumData
Apr 25, 2022
a2f3553
chore: adoptions to current spectra format in NMRium
May 3, 2022
8f0daa3
fix: use manually set and detected hybridization in pyLSD input file
May 10, 2022
7b6a3be
chore: use capitalized AND for FEXP command
May 12, 2022
35afc07
chore: no use of concurrency classes in HOSECodeShiftStatistics
May 13, 2022
4be9003
feat: allow usage of Ertl functional groups (or fragments in general)…
May 17, 2022
e626ede
chore: renamed FunctionalGroup to Fragment
May 18, 2022
b3d7b23
fix: use different DEFF files for fragment definition in LSD
May 21, 2022
ec06241
fix: use different DEFF files for fragment definition in LSD (2)
May 21, 2022
608866a
fix: do not store stringified spectral match assignment
May 22, 2022
eafefc2
fix: swapped query spectrum in first place with (sub)spectrum when do…
May 23, 2022
99e2911
chore: updated README.md
Aug 28, 2022
f78392e
fix: avoid bidirectional BOND commands in PyLSD input file; close #4
Sep 27, 2022
6a5c78c
Merge pull request #5 from michaelwenk/fix-bidirectional-BOND-command
Sep 27, 2022
b680e23
fix: consider bond stereo configuration in StructureCompact class and…
Apr 11, 2023
aabccde
fix: close #6
Apr 11, 2023
ae5b813
Merge pull request #7 from michaelwenk/add-bond-stereo
Apr 11, 2023
35721e3
chore: use common method placeExplicitHydrogens
Apr 12, 2023
6da415b
fix: configure structure atomContainerToDataSet method
Apr 13, 2023
c81b222
fix: remove unnecessary command
Apr 13, 2023
8425573
fix: do not place explicit hydrogens when no bonds exist
Apr 14, 2023
83c4fce
chore: inserted separate buildAlphabeticMF method
Apr 18, 2023
7f44e3d
fix: enable no stereo bond information in StructureCompact class
Jun 15, 2023
b2a5de5
chore: optimised getOutliers method
Jun 20, 2023
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