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First small bug fixes #1

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First small bug fixes #1

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michaelwenk
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bug fixes in following two functions:

  • predict: addition of a missing strokes
  • fixExplicitHydrogens: did not work properly, now corrected with additional remove list

michaelwenk added 30 commits March 30, 2021 02:43
minor
b3badc3
assignments can now hold more than only one single assignment index (…
a7ed157 
…equivalences); small optimisations
disabled SHIH in PyLSDInputFileBuilder.java
6f531ff
added RankedResultSDFParser
da49058
Match: when checkEquivalencesCount is set to true then check for equa…
93861d0 
…l number instead of less or equal
fix: an error when passing conditions
e731835
feat: changed "mf" to "mfOriginal" and added alphabetic sorted mf as …
716dcff 
…"mf"
moved try and catch around Tanimoto coefficient calculation
bde083d
feat: multiplicity check when adding a signal to a spectrum
6b1b4ec
fix: multiplicity check when searching for equivalence signals; use m…
3545940 
…edian for predicted shift calculation instead of mean
fix: added missing multiplicity check when searching for equivalence …
519bb94 
…signals
feat: added PyLSD ELIM P1 and P2 parameters
2cbcec5
feat: added useElim parameter and changed filter paths to array
b5d758a
feat: added atom type check when parsing ranked SDF by PyLSD
090cc43
feat: re-added SHIH in PyLSD input file
bf82a1a
feat: added PyLSD HMBC P3, HMBC P4, COSY P3 and COSY P4 parameters
82c8f19
chore: replace default constructors, setters and getters by lombok an…
bd3818f 
…notations
chore: replace default constructors, setters and getters by lombok an…
d041935 
…notations (2)
feat: added allowLowerEquivalencesCount to spectra matching
17d1ca9
feat: added setSignal method to Spectrum
6bb4077
fix: add equivalences count of newly added signal instead of one only
f2711a3
feat: added addAssignment method to Assignment
df12f85
fix: too high index when checking the dimension
561c0df
fix: init non-empty arrays for equivalences
61b9d3b
fix: use own deep clone method Assignment
14c9469
fix: extended hetero atom list in aromatic cycles in isValidBondAddition
3be9b47
chore: added UTF-8 encoding and updated two dependencies
287baf4
fix: switched from SmiFlavor.Absolute to SmiFlavor.Unique
ec921de
fix: buildFilters expects direct paths to filters
63ef95d
feat: added parseRankedResultSDFile methods
5434788
michaelwenk added 30 commits March 15, 2022 12:34
chore: allow to pass the checkMultiplicity and checkEquivalencesCount
9e877b8
chore: renaming in Assignment class
64539cc
feat: switch position of query and dataset spectrum in spectral assig…
d572c68 
…nment && added prediction method for SMILES strings
feat: added prediction meta data to Prediction
7ef8981
feat: extended spectral matching methods to consider structural const…
6d9f457 
…raints if given
feat: added ID property to Signal
1e65f57
chore: renamed Data class to NMRiumData
ffe2172
chore: adoptions to current spectra format in NMRium
a2f3553
fix: use manually set and detected hybridization in pyLSD input file
8f0daa3
chore: use capitalized AND for FEXP command
7b6a3be
chore: no use of concurrency classes in HOSECodeShiftStatistics
35afc07
feat: allow usage of Ertl functional groups (or fragments in general)…
4be9003 
… in PyLSD
chore: renamed FunctionalGroup to Fragment
e626ede
fix: use different DEFF files for fragment definition in LSD
b3d7b23
fix: use different DEFF files for fragment definition in LSD (2)
ec06241
fix: do not store stringified spectral match assignment
608866a
fix: swapped query spectrum in first place with (sub)spectrum when do…
eafefc2 
…ing spectral matching
chore: updated README.md
99e2911
fix: avoid bidirectional BOND commands in PyLSD input file; close #4
f78392e
Merge pull request #5 from michaelwenk/fix-bidirectional-BOND-command
6a5c78c 
fix: avoid bidirectional BOND commands in PyLSD input file; close #4
fix: consider bond stereo configuration in StructureCompact class and…
b680e23 
… during stereo HOSE code prediction
fix: close #6
aabccde
Merge pull request #7 from michaelwenk/add-bond-stereo
ae5b813 
Add and consider bond stereo
chore: use common method placeExplicitHydrogens
35721e3
fix: configure structure atomContainerToDataSet method
6da415b
fix: remove unnecessary command
c81b222
fix: do not place explicit hydrogens when no bonds exist
8425573
chore: inserted separate buildAlphabeticMF method
83c4fce
fix: enable no stereo bond information in StructureCompact class
7f44e3d
chore: optimised getOutliers method
b2a5de5
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@michaelwenk