First small bug fixes #1

michaelwenk · 2018-03-09T13:58:55Z

bug fixes in following two functions:

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

…l number instead of less or equal

…"mf"

…edian for predicted shift calculation instead of mean

…signals

…notations

…notations (2)

…nment && added prediction method for SMILES strings

…raints if given

… in PyLSD

…ing spectral matching

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

… during stereo HOSE code prediction

Add and consider bond stereo

…lly install casekit & updated README

michaelwenk added 30 commits April 1, 2021 17:44

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

feat: integration of HOSECodeBuilder project

acc54ba

feat: updated README.md

54afba9

michaelwenk and others added 30 commits March 22, 2022 16:04

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

chore: included predictorc.jar from NMRShiftDB & added script to loca…

3884fbd

…lly install casekit & updated README

chore: fixed different issues coming with newer CDK and nmrshiftdb data

af192ed

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michaelwenk commented Mar 9, 2018

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michaelwenk commented Mar 9, 2018

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