nmr-processing 6.0.0 → 6.0.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (232) hide show
  1. package/lib/assignment/get1HAssignments.d.ts +2 -2
  2. package/lib/{types → assignment}/nmrAssigment.d.ts +2 -2
  3. package/lib/{types → assignment}/nmrAssigment.js +0 -0
  4. package/lib/assignment/nmrAssigment.js.map +1 -0
  5. package/lib/assignment/utils/createMapPossibleAssignments.d.ts +1 -1
  6. package/lib/databases/DatabaseNMREntry.d.ts +1 -1
  7. package/lib/index.d.ts +8 -9
  8. package/lib/ml-matrix-convolution.d.ts +8 -0
  9. package/lib/ml-matrix-convolution.js +2 -0
  10. package/lib/ml-matrix-convolution.js.map +1 -0
  11. package/lib/ml-simple-clustering.d.ts +8 -0
  12. package/lib/ml-simple-clustering.js +2 -0
  13. package/lib/ml-simple-clustering.js.map +1 -0
  14. package/lib/{types → peaks}/NMRPeak1D.d.ts +0 -0
  15. package/lib/{types → peaks}/NMRPeak1D.js +0 -0
  16. package/{lib-esm/types → lib/peaks}/NMRPeak1D.js.map +1 -1
  17. package/lib/peaks/peaksFilterImpurities.d.ts +1 -1
  18. package/lib/peaks/peaksFilterImpurities.js.map +1 -1
  19. package/lib/peaks/peaksToRanges.d.ts +2 -2
  20. package/lib/peaks/util/determineRealTop.js +2 -5
  21. package/lib/peaks/util/determineRealTop.js.map +1 -1
  22. package/lib/peaks/util/jAnalyzer.d.ts +2 -2
  23. package/lib/peaks/util/joinRanges.d.ts +1 -1
  24. package/lib/peaks/util/peakOptimizer.d.ts +1 -1
  25. package/lib/{types → prediction}/dataStructure.d.ts +0 -0
  26. package/lib/{types → prediction}/dataStructure.js +0 -0
  27. package/lib/prediction/dataStructure.js.map +1 -0
  28. package/lib/prediction/predictAll.d.ts +1 -1
  29. package/lib/prediction/predictAll.js.map +1 -1
  30. package/lib/prediction/predictCOSY.d.ts +1 -1
  31. package/lib/prediction/predictCOSY.js.map +1 -1
  32. package/lib/prediction/predictCarbon.d.ts +2 -2
  33. package/lib/prediction/predictCarbon.js.map +1 -1
  34. package/lib/prediction/predictHMBC.d.ts +1 -1
  35. package/lib/prediction/predictHMBC.js.map +1 -1
  36. package/lib/prediction/predictHSQC.d.ts +1 -1
  37. package/lib/prediction/predictHSQC.js.map +1 -1
  38. package/lib/prediction/predictProton.d.ts +1 -1
  39. package/lib/prediction/predictProton.js +1 -1
  40. package/lib/prediction/predictProton.js.map +1 -1
  41. package/lib/{types → prediction}/prediction1D.d.ts +2 -2
  42. package/lib/{types → prediction}/prediction1D.js +0 -0
  43. package/lib/prediction/prediction1D.js.map +1 -0
  44. package/lib/prediction/utils/fetchPrediction.d.ts +1 -1
  45. package/lib/prediction/utils/getFilteredIDiaIDs.d.ts +1 -1
  46. package/lib/prediction/utils/getPredictions.d.ts +1 -1
  47. package/lib/prediction/utils/getPredictions.js +1 -1
  48. package/lib/prediction/utils/getPredictions.js.map +1 -1
  49. package/lib/prediction/utils/predict2D.d.ts +2 -2
  50. package/lib/prediction/utils/queryByHOSE.d.ts +1 -1
  51. package/lib/ranges/rangesToACS.d.ts +1 -1
  52. package/lib/ranges/rangesToACS.js +8 -9
  53. package/lib/ranges/rangesToACS.js.map +1 -1
  54. package/lib/ranges/rangesToXY.d.ts +1 -1
  55. package/lib/ranges/rangesToXY.js.map +1 -1
  56. package/lib/signal/signalJoinCouplings.d.ts +1 -1
  57. package/lib/signal/signalMultiplicityPattern.d.ts +1 -1
  58. package/lib/{types → signals}/NMRSignal1D.d.ts +1 -1
  59. package/lib/{types → signals}/NMRSignal1D.js +0 -0
  60. package/lib/{types → signals}/NMRSignal1D.js.map +1 -1
  61. package/lib/signals/hackSignalsToXY.d.ts +1 -1
  62. package/lib/{types → signals}/jcoupling.d.ts +0 -0
  63. package/lib/{types → signals}/jcoupling.js +0 -0
  64. package/lib/{types → signals}/jcoupling.js.map +1 -1
  65. package/lib/signals/signals2DToZ.d.ts +1 -1
  66. package/lib/signals/signalsJoin.d.ts +3 -3
  67. package/lib/signals/signalsJoin.js.map +1 -1
  68. package/lib/signals/signalsToRanges.d.ts +2 -2
  69. package/lib/signals/signalsToRanges.js.map +1 -1
  70. package/lib/signals/signalsToXY.d.ts +1 -1
  71. package/lib/signals/simulation/signalsToSpinSystem.d.ts +2 -2
  72. package/lib/signals/simulation/simulate1D.d.ts +1 -1
  73. package/lib/signals/simulation/simulate1D.js +2 -1
  74. package/lib/signals/simulation/simulate1D.js.map +1 -1
  75. package/lib/signals/simulation/splitSpinSystem.d.ts +1 -1
  76. package/lib/{types → signals}/spinSystem.d.ts +0 -0
  77. package/lib/{types → signals}/spinSystem.js +0 -0
  78. package/lib/{types → signals}/spinSystem.js.map +1 -1
  79. package/lib/{types → utilities}/MakeMandatory.d.ts +0 -0
  80. package/lib/{types → utilities}/MakeMandatory.js +0 -0
  81. package/lib/utilities/MakeMandatory.js.map +1 -0
  82. package/lib/utilities/rangeFromSignal.d.ts +1 -1
  83. package/lib/utilities/resurrect.d.ts +1 -1
  84. package/lib/utilities/resurrectRange.d.ts +1 -1
  85. package/lib/{types → xy}/NMRRange.d.ts +1 -1
  86. package/lib/{types → xy}/NMRRange.js +0 -0
  87. package/lib/{types → xy}/NMRRange.js.map +1 -1
  88. package/lib/xy/xyAutoRangesPicking.d.ts +2 -2
  89. package/lib/xy/xyAutoRangesPicking.js.map +1 -1
  90. package/lib/{types → xyz}/NMRSignal2D.d.ts +0 -1
  91. package/lib/{types → xyz}/NMRSignal2D.js +0 -0
  92. package/lib/{types → xyz}/NMRSignal2D.js.map +1 -1
  93. package/lib/{types → xyz}/NMRZone.d.ts +0 -0
  94. package/lib/{types → xyz}/NMRZone.js +0 -0
  95. package/lib/{types → xyz}/NMRZone.js.map +1 -1
  96. package/lib/xyz/xyzAutoZonesPicking.d.ts +2 -2
  97. package/lib/xyz/xyzAutoZonesPicking.js.map +1 -1
  98. package/lib/xyz/xyzJResAnalyzer.d.ts +1 -1
  99. package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
  100. package/lib-esm/{types → assignment}/nmrAssigment.js +0 -0
  101. package/lib-esm/assignment/nmrAssigment.js.map +1 -0
  102. package/lib-esm/ml-matrix-convolution.js +2 -0
  103. package/lib-esm/ml-matrix-convolution.js.map +1 -0
  104. package/lib-esm/ml-simple-clustering.js +2 -0
  105. package/lib-esm/ml-simple-clustering.js.map +1 -0
  106. package/lib-esm/{types → peaks}/NMRPeak1D.js +0 -0
  107. package/{lib/types → lib-esm/peaks}/NMRPeak1D.js.map +1 -1
  108. package/lib-esm/peaks/peaksFilterImpurities.js.map +1 -1
  109. package/lib-esm/peaks/util/determineRealTop.js +2 -2
  110. package/lib-esm/peaks/util/determineRealTop.js.map +1 -1
  111. package/lib-esm/{types → prediction}/dataStructure.js +0 -0
  112. package/lib-esm/prediction/dataStructure.js.map +1 -0
  113. package/lib-esm/prediction/predictAll.js.map +1 -1
  114. package/lib-esm/prediction/predictCOSY.js.map +1 -1
  115. package/lib-esm/prediction/predictCarbon.js.map +1 -1
  116. package/lib-esm/prediction/predictHMBC.js.map +1 -1
  117. package/lib-esm/prediction/predictHSQC.js.map +1 -1
  118. package/lib-esm/prediction/predictProton.js +1 -1
  119. package/lib-esm/prediction/predictProton.js.map +1 -1
  120. package/lib-esm/{types → prediction}/prediction1D.js +0 -0
  121. package/lib-esm/prediction/prediction1D.js.map +1 -0
  122. package/lib-esm/prediction/utils/getPredictions.js +1 -1
  123. package/lib-esm/prediction/utils/getPredictions.js.map +1 -1
  124. package/lib-esm/ranges/rangesToACS.js +8 -9
  125. package/lib-esm/ranges/rangesToACS.js.map +1 -1
  126. package/lib-esm/ranges/rangesToXY.js.map +1 -1
  127. package/lib-esm/{types → signals}/NMRSignal1D.js +0 -0
  128. package/lib-esm/{types → signals}/NMRSignal1D.js.map +1 -1
  129. package/lib-esm/{types → signals}/jcoupling.js +0 -0
  130. package/lib-esm/{types → signals}/jcoupling.js.map +1 -1
  131. package/lib-esm/signals/signalsJoin.js.map +1 -1
  132. package/lib-esm/signals/signalsToRanges.js.map +1 -1
  133. package/lib-esm/signals/simulation/simulate1D.js +2 -1
  134. package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
  135. package/lib-esm/{types → signals}/spinSystem.js +0 -0
  136. package/lib-esm/{types → signals}/spinSystem.js.map +1 -1
  137. package/lib-esm/{types → utilities}/MakeMandatory.js +0 -0
  138. package/lib-esm/utilities/MakeMandatory.js.map +1 -0
  139. package/lib-esm/{types → xy}/NMRRange.js +0 -0
  140. package/lib-esm/{types → xy}/NMRRange.js.map +1 -1
  141. package/lib-esm/xy/xyAutoRangesPicking.js.map +1 -1
  142. package/lib-esm/{types → xyz}/NMRSignal2D.js +0 -0
  143. package/lib-esm/{types → xyz}/NMRSignal2D.js.map +1 -1
  144. package/lib-esm/{types → xyz}/NMRZone.js +0 -0
  145. package/lib-esm/{types → xyz}/NMRZone.js.map +1 -1
  146. package/lib-esm/xyz/xyzAutoZonesPicking.js.map +1 -1
  147. package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
  148. package/package.json +20 -32
  149. package/src/assignment/get13CAssignments.ts +1 -1
  150. package/src/assignment/get1HAssignments.ts +2 -2
  151. package/src/{types → assignment}/nmrAssigment.ts +2 -2
  152. package/src/assignment/utils/createMapPossibleAssignments.ts +1 -1
  153. package/src/databases/DatabaseNMREntry.ts +1 -1
  154. package/src/index.ts +8 -9
  155. package/src/{types/ml-matrix-convolution/index.d.ts → ml-matrix-convolution.ts} +0 -0
  156. package/src/{types/ml-matrix-peaks-finder/index.d.ts → ml-matrix-peaks-finder.d.ts} +0 -0
  157. package/src/{types/ml-simple-clustering/index.d.ts → ml-simple-clustering.ts} +0 -0
  158. package/src/{types/ml-sparse-matrix/index.d.ts → ml-sparse-matrix.d.ts} +0 -0
  159. package/src/{types/ml-tree-set/index.d.ts → ml-tree-set.d.ts} +0 -0
  160. package/src/{types/modules/nmr-parser.ts → nmr-parser.d.ts} +0 -0
  161. package/src/{types/openchemlib-utils/index..d.ts → openchemlib.d.ts} +0 -0
  162. package/src/{types → peaks}/NMRPeak1D.ts +0 -0
  163. package/src/peaks/peaksFilterImpurities.ts +2 -1
  164. package/src/peaks/peaksToRanges.ts +4 -4
  165. package/src/peaks/util/determineRealTop.ts +2 -2
  166. package/src/peaks/util/jAnalyzer.ts +2 -2
  167. package/src/peaks/util/joinRanges.ts +1 -1
  168. package/src/peaks/util/peakOptimizer.ts +1 -1
  169. package/src/{types → prediction}/dataStructure.ts +0 -0
  170. package/src/prediction/predictAll.ts +1 -2
  171. package/src/prediction/predictCOSY.ts +1 -2
  172. package/src/prediction/predictCarbon.ts +4 -4
  173. package/src/prediction/predictHMBC.ts +1 -2
  174. package/src/prediction/predictHSQC.ts +1 -2
  175. package/src/prediction/predictProton.ts +4 -3
  176. package/src/{types → prediction}/prediction1D.ts +2 -2
  177. package/src/prediction/utils/fetchPrediction.ts +1 -1
  178. package/src/prediction/utils/getPredictions.ts +2 -2
  179. package/src/prediction/utils/predict2D.ts +4 -4
  180. package/src/prediction/utils/queryByHOSE.ts +1 -1
  181. package/src/ranges/rangesToACS.ts +20 -13
  182. package/src/ranges/rangesToXY.ts +3 -3
  183. package/src/signal/signalJoinCouplings.ts +3 -3
  184. package/src/signal/signalMultiplicityPattern.ts +1 -1
  185. package/src/{types → signals}/NMRSignal1D.ts +2 -1
  186. package/src/signals/hackSignalsToXY.ts +2 -2
  187. package/src/{types → signals}/jcoupling.ts +0 -0
  188. package/src/signals/signals2DToZ.ts +1 -1
  189. package/src/signals/signalsJoin.ts +4 -3
  190. package/src/signals/signalsToRanges.ts +4 -3
  191. package/src/signals/signalsToXY.ts +3 -3
  192. package/src/signals/simulation/signalsToSpinSystem.ts +4 -4
  193. package/src/signals/simulation/simulate1D.ts +3 -2
  194. package/src/signals/simulation/splitSpinSystem.ts +1 -1
  195. package/src/{types → signals}/spinSystem.ts +0 -0
  196. package/src/{types → utilities}/MakeMandatory.ts +0 -0
  197. package/src/utilities/rangeFromSignal.ts +1 -1
  198. package/src/utilities/resurrect.ts +1 -1
  199. package/src/utilities/resurrectRange.ts +2 -2
  200. package/src/{types → xy}/NMRRange.ts +1 -1
  201. package/src/xy/xyAutoRangesPicking.ts +3 -2
  202. package/src/{types → xyz}/NMRSignal2D.ts +0 -2
  203. package/src/{types → xyz}/NMRZone.ts +0 -0
  204. package/src/xyz/xyzAutoZonesPicking.ts +4 -3
  205. package/src/xyz/xyzJResAnalyzer.ts +3 -2
  206. package/lib/types/MakeMandatory.js.map +0 -1
  207. package/lib/types/XYNumberArray.d.ts +0 -4
  208. package/lib/types/XYNumberArray.js +0 -3
  209. package/lib/types/XYNumberArray.js.map +0 -1
  210. package/lib/types/dataStructure.js.map +0 -1
  211. package/lib/types/modules/nmr-parser.d.ts +0 -11
  212. package/lib/types/modules/nmr-parser.js +0 -2
  213. package/lib/types/modules/nmr-parser.js.map +0 -1
  214. package/lib/types/nmrAssigment.js.map +0 -1
  215. package/lib/types/prediction1D.js.map +0 -1
  216. package/lib/types/prediction2D.d.ts +0 -0
  217. package/lib/types/prediction2D.js +0 -2
  218. package/lib/types/prediction2D.js.map +0 -1
  219. package/lib-esm/types/MakeMandatory.js.map +0 -1
  220. package/lib-esm/types/XYNumberArray.js +0 -2
  221. package/lib-esm/types/XYNumberArray.js.map +0 -1
  222. package/lib-esm/types/dataStructure.js.map +0 -1
  223. package/lib-esm/types/modules/nmr-parser.js +0 -2
  224. package/lib-esm/types/modules/nmr-parser.js.map +0 -1
  225. package/lib-esm/types/nmrAssigment.js.map +0 -1
  226. package/lib-esm/types/prediction1D.js.map +0 -1
  227. package/lib-esm/types/prediction2D.js +0 -2
  228. package/lib-esm/types/prediction2D.js.map +0 -1
  229. package/src/types/XYNumberArray.ts +0 -4
  230. package/src/types/ml-levenberg-marquardt/index.d.ts +0 -13
  231. package/src/types/ml-spectra-processing/index.d.ts +0 -57
  232. package/src/types/prediction2D.ts +0 -0
@@ -1,12 +1,11 @@
1
1
  import type { Molecule } from 'openchemlib';
2
2
 
3
- import type { Prediction1D } from '../types/prediction1D';
4
-
5
3
  import { predictCOSY } from './predictCOSY';
6
4
  import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
7
5
  import { predictHMBC } from './predictHMBC';
8
6
  import { predictHSQC } from './predictHSQC';
9
7
  import { predictProton, PredictProtonOptions } from './predictProton';
8
+ import type { Prediction1D } from './prediction1D';
10
9
  import { getPredictions } from './utils/getPredictions';
11
10
  import type { Predictor } from './utils/predict2D';
12
11
 
@@ -1,8 +1,7 @@
1
1
  import { Molecule } from 'openchemlib';
2
2
 
3
- import type { Prediction1D } from '../types/prediction1D';
4
-
5
3
  import { predictProton, PredictProtonOptions } from './predictProton';
4
+ import type { Prediction1D } from './prediction1D';
6
5
  import { predict2D, Predictor } from './utils/predict2D';
7
6
 
8
7
  export interface PredictCOSYOptions {
@@ -1,12 +1,12 @@
1
1
  import fetch from 'cross-fetch';
2
2
  import type { Molecule } from 'openchemlib';
3
3
 
4
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
4
5
  import { signalsToRanges } from '../signals/signalsToRanges';
5
- import type { MakeMandatory } from '../types/MakeMandatory';
6
- import type { NMRSignal1D } from '../types/NMRSignal1D';
7
- import type { DataBaseStructure } from '../types/dataStructure';
8
- import type { Prediction1D } from '../types/prediction1D';
6
+ import type { MakeMandatory } from '../utilities/MakeMandatory';
9
7
 
8
+ import type { DataBaseStructure } from './dataStructure';
9
+ import type { Prediction1D } from './prediction1D';
10
10
  import { fetchPrediction } from './utils/fetchPrediction';
11
11
  import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
12
12
  import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
@@ -1,11 +1,10 @@
1
1
  import { Molecule } from 'openchemlib';
2
2
 
3
- import type { Prediction1D } from '../types/prediction1D';
4
-
5
3
  import { predictCarbon } from './predictCarbon';
6
4
  import type { PredictCarbonOptions } from './predictCarbon';
7
5
  import { predictProton } from './predictProton';
8
6
  import type { PredictProtonOptions } from './predictProton';
7
+ import type { Prediction1D } from './prediction1D';
9
8
  import { predict2D } from './utils/predict2D';
10
9
  import type { Predictor } from './utils/predict2D';
11
10
 
@@ -1,9 +1,8 @@
1
1
  import { Molecule } from 'openchemlib';
2
2
 
3
- import type { Prediction1D } from '../types/prediction1D';
4
-
5
3
  import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
6
4
  import { predictProton, PredictProtonOptions } from './predictProton';
5
+ import type { Prediction1D } from './prediction1D';
7
6
  import { predict2D, Predictor } from './utils/predict2D';
8
7
 
9
8
  export interface PredictHSQCOptions {
@@ -7,10 +7,11 @@ import {
7
7
  getDiastereotopicAtomIDs,
8
8
  } from 'openchemlib-utils';
9
9
 
10
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
10
11
  import { signalsJoin } from '../signals/signalsJoin';
11
12
  import { signalsToRanges } from '../signals/signalsToRanges';
12
- import type { NMRSignal1D } from '../types/NMRSignal1D';
13
- import type { Prediction1D } from '../types/prediction1D';
13
+
14
+ import type { Prediction1D } from './prediction1D';
14
15
 
15
16
  /**
16
17
  * Makes a prediction using proton.
@@ -45,7 +46,7 @@ export async function predictProton(
45
46
  formData.append('molfile', molfile);
46
47
  const response = await fetch('https://www.nmrdb.org/service/predictor', {
47
48
  method: 'POST',
48
- //@ts-expect-error
49
+ // @ts-expect-error RequestInit type does not include FormData.
49
50
  body: formData,
50
51
  });
51
52
  result = await response.text();
@@ -1,7 +1,7 @@
1
1
  import type { Molecule } from 'openchemlib';
2
2
 
3
- import type { NMRRange } from './NMRRange';
4
- import type { NMRSignal1D } from './NMRSignal1D';
3
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
4
+ import type { NMRRange } from '../xy/NMRRange';
5
5
 
6
6
  export interface Prediction1D {
7
7
  molfile: string;
@@ -1,7 +1,7 @@
1
1
  import { fetch } from 'cross-fetch';
2
2
  import { Molecule } from 'openchemlib';
3
3
 
4
- import type { Prediction1D } from '../../types/prediction1D';
4
+ import type { Prediction1D } from '../prediction1D';
5
5
 
6
6
  interface FetchPredictionOptions {
7
7
  webserviceURL: string;
@@ -1,6 +1,6 @@
1
1
  import type { Molecule } from 'openchemlib';
2
2
 
3
- import type { Prediction1D } from '../../types/prediction1D';
3
+ import type { Prediction1D } from '../prediction1D';
4
4
 
5
5
  import type { Predictions, PredictOptions, Predictors } from './predict2D';
6
6
 
@@ -12,7 +12,7 @@ export async function getPredictions(
12
12
  predictions?: Predictions,
13
13
  ) {
14
14
  let prediction: Prediction1D | undefined;
15
- if (predictions && predictions[key]) {
15
+ if (predictions?.[key]) {
16
16
  prediction = predictions[key];
17
17
  } else if (predictor) {
18
18
  const fromPredictor = predictor[key];
@@ -11,12 +11,12 @@ import type {
11
11
  PathInfo,
12
12
  } from 'openchemlib-utils';
13
13
 
14
- import type { MakeMandatory } from '../../types/MakeMandatory';
15
- import type { NMRSignal1D } from '../../types/NMRSignal1D';
16
- import type { NMRSignal2D } from '../../types/NMRSignal2D';
17
- import type { Prediction1D } from '../../types/prediction1D';
14
+ import type { NMRSignal1D } from '../../signals/NMRSignal1D';
15
+ import type { MakeMandatory } from '../../utilities/MakeMandatory';
16
+ import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
18
17
  import type { PredictCarbon, PredictCarbonOptions } from '../predictCarbon';
19
18
  import type { PredictProton, PredictProtonOptions } from '../predictProton';
19
+ import type { Prediction1D } from '../prediction1D';
20
20
 
21
21
  import { getNuclei } from './getNuclei';
22
22
  import { getPredictions } from './getPredictions';
@@ -1,4 +1,4 @@
1
- import type { DataBaseStructure } from '../../types/dataStructure';
1
+ import type { DataBaseStructure } from '../dataStructure';
2
2
 
3
3
  import type { GroupedDiaIDsWithHose } from './getFilteredIDiaIDs';
4
4
 
@@ -1,9 +1,17 @@
1
1
  import { signalJoinCouplings } from '../signal/signalJoinCouplings';
2
2
  import { signalMultiplicityPattern } from '../signal/signalMultiplicityPattern';
3
- import type { NMRRange } from '../types/NMRRange';
4
- import type { NMRSignal1D } from '../types/NMRSignal1D';
3
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
4
+ import type { NMRRange } from '../xy/NMRRange';
5
5
 
6
- const globalOptions = {
6
+ const globalOptions: Record<
7
+ string,
8
+ {
9
+ nucleus: string;
10
+ nbDecimalDelta: number;
11
+ nbDecimalJ: number;
12
+ observedFrequency: number;
13
+ }
14
+ > = {
7
15
  h: {
8
16
  nucleus: '1H',
9
17
  nbDecimalDelta: 2,
@@ -62,9 +70,8 @@ export function rangesToACS(
62
70
  options: RangesToACSOptions = {},
63
71
  ) {
64
72
  if (!options.nucleus) options.nucleus = '1H';
65
- let nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
66
- //@ts-expect-error
67
- let defaultOptions = globalOptions[nucleus];
73
+ const nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
74
+ const defaultOptions = globalOptions[nucleus];
68
75
  options = Object.assign(
69
76
  {},
70
77
  defaultOptions,
@@ -75,13 +82,13 @@ export function rangesToACS(
75
82
  ranges = JSON.parse(JSON.stringify(ranges));
76
83
  if (options.ascending === true) {
77
84
  ranges.sort((a, b) => {
78
- let fromA = Math.min(a.from, a.to);
79
- let fromB = Math.min(b.from, b.to);
85
+ const fromA = Math.min(a.from, a.to);
86
+ const fromB = Math.min(b.from, b.to);
80
87
  return fromA - fromB;
81
88
  });
82
89
  }
83
- let acsString = formatAcs(ranges, options);
84
90
 
91
+ let acsString = formatAcs(ranges, options);
85
92
  if (acsString.length > 0) acsString += '.';
86
93
 
87
94
  return acsString;
@@ -90,8 +97,8 @@ export function rangesToACS(
90
97
  function formatAcs(ranges: NMRRange[], options: any) {
91
98
  let acs = spectroInformation(options);
92
99
  if (acs.length === 0) acs = 'δ ';
93
- let acsRanges: string[] = [];
94
- for (let range of ranges) {
100
+ const acsRanges: string[] = [];
101
+ for (const range of ranges) {
95
102
  if (uselessKind(range.kind, options.filter)) continue;
96
103
  pushDelta(range, acsRanges, options);
97
104
  }
@@ -103,7 +110,7 @@ function formatAcs(ranges: NMRRange[], options: any) {
103
110
  }
104
111
 
105
112
  function spectroInformation(options: any) {
106
- let parenthesis = [];
113
+ const parenthesis = [];
107
114
  let strings = `${formatNucleus(options.nucleus)} NMR`;
108
115
  if (options.solvent) {
109
116
  parenthesis.push(formatMF(options.solvent));
@@ -122,7 +129,7 @@ function spectroInformation(options: any) {
122
129
  function pushDelta(range: NMRRange, acsRanges: string[], options: any) {
123
130
  let strings = '';
124
131
  let parenthesis: any = [];
125
- let fromTo = [range.from, range.to];
132
+ const fromTo = [range.from, range.to];
126
133
 
127
134
  if (range.signals) {
128
135
  range.signals = range.signals.filter(
@@ -3,10 +3,10 @@ import arraySequentialFill from 'ml-array-sequential-fill';
3
3
  import type { Shape1D } from 'ml-peak-shape-generator';
4
4
  import { SpectrumGenerator } from 'spectrum-generator';
5
5
 
6
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
6
7
  import { hackSignalsToXY } from '../signals/hackSignalsToXY';
7
- import type { MakeMandatory } from '../types/MakeMandatory';
8
- import type { NMRRange } from '../types/NMRRange';
9
- import type { NMRSignal1D } from '../types/NMRSignal1D';
8
+ import type { MakeMandatory } from '../utilities/MakeMandatory';
9
+ import type { NMRRange } from '../xy/NMRRange';
10
10
 
11
11
  type RangeWithSignal = MakeMandatory<NMRRange, 'signals'>;
12
12
 
@@ -1,8 +1,8 @@
1
1
  import sum from 'ml-array-sum';
2
2
 
3
- import type { MakeMandatory } from '../types/MakeMandatory';
4
- import type { NMRSignal1D } from '../types/NMRSignal1D';
5
- import type { Jcoupling } from '../types/jcoupling';
3
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
4
+ import type { Jcoupling } from '../signals/jcoupling';
5
+ import type { MakeMandatory } from '../utilities/MakeMandatory';
6
6
  import { joinPatterns } from '../utilities/joinPatterns';
7
7
 
8
8
  export interface SignalJoinCouplingsOptions {
@@ -1,4 +1,4 @@
1
- import type { NMRSignal1D } from '../types/NMRSignal1D';
1
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
2
2
  /**
3
3
  * Return
4
4
  * @param {*} signal
@@ -1,4 +1,5 @@
1
- import type { NMRPeak1D } from './NMRPeak1D';
1
+ import type { NMRPeak1D } from '../peaks/NMRPeak1D';
2
+
2
3
  import type { Jcoupling } from './jcoupling';
3
4
 
4
5
  export interface NMRSignal1D {
@@ -1,7 +1,7 @@
1
1
  import { couplingPatterns } from '../constants/couplingPatterns';
2
- import type { NMRSignal1D } from '../types/NMRSignal1D';
3
- import type { Jcoupling } from '../types/jcoupling';
4
2
 
3
+ import type { NMRSignal1D } from './NMRSignal1D';
4
+ import type { Jcoupling } from './jcoupling';
5
5
  import { OptionsSignalsToXY, signalsToXY } from './signalsToXY';
6
6
 
7
7
  /**
File without changes
@@ -1,7 +1,7 @@
1
1
  import { generateSpectrum2D } from 'spectrum-generator';
2
2
  import type { XYNumber } from 'spectrum-generator';
3
3
 
4
- import type { NMRSignal2D } from '../types/NMRSignal2D';
4
+ import type { NMRSignal2D } from '../xyz/NMRSignal2D';
5
5
 
6
6
  interface Signals2DToZOptions {
7
7
  /**
@@ -3,9 +3,10 @@ import sum from 'ml-array-sum';
3
3
 
4
4
  import { signalJoinCouplings } from '../signal/signalJoinCouplings';
5
5
  import type { SignalJoinCouplingsOptions } from '../signal/signalJoinCouplings';
6
- import type { MakeMandatory } from '../types/MakeMandatory';
7
- import type { NMRSignal1D } from '../types/NMRSignal1D';
8
- import type { Jcoupling } from '../types/jcoupling';
6
+ import type { MakeMandatory } from '../utilities/MakeMandatory';
7
+
8
+ import type { NMRSignal1D } from './NMRSignal1D';
9
+ import type { Jcoupling } from './jcoupling';
9
10
 
10
11
  export interface SignalsJoinOptions {
11
12
  /**
@@ -1,7 +1,8 @@
1
- import type { MakeMandatory } from '../types/MakeMandatory';
2
- import type { NMRRange } from '../types/NMRRange';
3
- import type { NMRSignal1D } from '../types/NMRSignal1D';
1
+ import type { MakeMandatory } from '../utilities/MakeMandatory';
4
2
  import { rangeFromSignal } from '../utilities/rangeFromSignal';
3
+ import type { NMRRange } from '../xy/NMRRange';
4
+
5
+ import type { NMRSignal1D } from './NMRSignal1D';
5
6
 
6
7
  interface SignalsToRangesOptions {
7
8
  /**
@@ -2,10 +2,10 @@ import rescale from 'ml-array-rescale';
2
2
  import arraySequentialFill from 'ml-array-sequential-fill';
3
3
  import type { Shape1D } from 'ml-peak-shape-generator';
4
4
 
5
- import type { MakeMandatory } from '../types/MakeMandatory';
6
- import type { NMRSignal1D } from '../types/NMRSignal1D';
7
- import type { Jcoupling } from '../types/jcoupling';
5
+ import type { MakeMandatory } from '../utilities/MakeMandatory';
8
6
 
7
+ import type { NMRSignal1D } from './NMRSignal1D';
8
+ import type { Jcoupling } from './jcoupling';
9
9
  import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
10
10
  import simulate1D from './simulation/simulate1D';
11
11
  import { splitSpinSystem } from './simulation/splitSpinSystem';
@@ -1,10 +1,10 @@
1
1
  import { Matrix } from 'ml-matrix';
2
2
  import simpleClustering from 'ml-simple-clustering';
3
3
 
4
- import type { MakeMandatory } from '../../types/MakeMandatory';
5
- import type { NMRSignal1D } from '../../types/NMRSignal1D';
6
- import type { Jcoupling } from '../../types/jcoupling';
7
- import type { SpinSystem } from '../../types/spinSystem';
4
+ import type { MakeMandatory } from '../../utilities/MakeMandatory';
5
+ import type { NMRSignal1D } from '../NMRSignal1D';
6
+ import type { Jcoupling } from '../jcoupling';
7
+ import type { SpinSystem } from '../spinSystem';
8
8
 
9
9
  interface Ids {
10
10
  [index: number]: number;
@@ -6,7 +6,7 @@ import type { Shape1D } from 'ml-peak-shape-generator';
6
6
  import { SparseMatrix } from 'ml-sparse-matrix';
7
7
  import { SpectrumGenerator } from 'spectrum-generator';
8
8
 
9
- import type { SpinSystem } from '../../types/spinSystem';
9
+ import type { SpinSystem } from '../spinSystem';
10
10
 
11
11
  import getPauliMatrix from './getPauliMatrix';
12
12
 
@@ -133,7 +133,8 @@ export default function simulate1D(
133
133
  clusterFake,
134
134
  );
135
135
  const hamSize = hamiltonian.rows;
136
- //@ts-expect-error
136
+ // TODO: add support for sparse matrix in matrix types.
137
+ // @ts-expect-error sparse matrix not supported
137
138
  const evd = new EVD(hamiltonian);
138
139
  const V = evd.eigenvectorMatrix;
139
140
  const diagB = evd.realEigenvalues;
@@ -2,7 +2,7 @@ import { agnes } from 'ml-hclust';
2
2
  import type { Cluster } from 'ml-hclust';
3
3
  import { Matrix } from 'ml-matrix';
4
4
 
5
- import type { SpinSystem } from '../../types/spinSystem';
5
+ import type { SpinSystem } from '../spinSystem';
6
6
 
7
7
  export interface SplitSpinSystemOptions {
8
8
  /**
File without changes
File without changes
@@ -1,5 +1,5 @@
1
1
  import { couplingValues } from '../constants/couplingValues';
2
- import type { NMRSignal1D } from '../types/NMRSignal1D';
2
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
3
3
 
4
4
  export interface RangeFromSignalOptions {
5
5
  /**
@@ -1,4 +1,4 @@
1
- import type { NMRRange } from '../types/NMRRange';
1
+ import type { NMRRange } from '../xy/NMRRange';
2
2
 
3
3
  import { resurrectRange } from './resurrectRange';
4
4
  import { splitParenthesis } from './splitParenthesis';
@@ -1,5 +1,5 @@
1
- import type { NMRRange } from '../types/NMRRange';
2
- import type { NMRSignal1D } from '../types/NMRSignal1D';
1
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
2
+ import type { NMRRange } from '../xy/NMRRange';
3
3
 
4
4
  import { rangeFromSignal } from './rangeFromSignal';
5
5
  import { splitParenthesis } from './splitParenthesis';
@@ -1,4 +1,4 @@
1
- import type { NMRSignal1D } from './NMRSignal1D';
1
+ import type { NMRSignal1D } from '../signals/NMRSignal1D';
2
2
 
3
3
  export interface NMRRange {
4
4
  from: number;
@@ -1,7 +1,8 @@
1
+ import type { DataXY } from 'cheminfo-types';
2
+
1
3
  import { peaksFilterImpurities } from '../peaks/peaksFilterImpurities';
2
4
  import type { OptionsPeaksFilterImpurities } from '../peaks/peaksFilterImpurities';
3
5
  import { OptionsPeaksToRanges, peaksToRanges } from '../peaks/peaksToRanges';
4
- import type { XYNumberArray } from '../types/XYNumberArray';
5
6
 
6
7
  import { xyAutoPeaksPicking } from './xyAutoPeaksPicking';
7
8
  import type { OptionsXYAutoPeaksPicking } from './xyAutoPeaksPicking';
@@ -16,7 +17,7 @@ interface OptionsXYAutoRangesPicking {
16
17
  * Detect peaks, optimize parameters and compile multiplicity if required.
17
18
  */
18
19
  export function xyAutoRangesPicking(
19
- data: XYNumberArray,
20
+ data: DataXY,
20
21
  options: OptionsXYAutoRangesPicking = {},
21
22
  ) {
22
23
  let peaks = xyAutoPeaksPicking(data, options.peakPicking);
@@ -17,6 +17,4 @@ export interface NMRSignal2D {
17
17
  id?: string;
18
18
  peaks?: Peak2D[];
19
19
  kind?: string;
20
-
21
- _highlight?: (number | string)[];
22
20
  }
File without changes
@@ -9,7 +9,8 @@ import { determineRealTop } from '../peaks/util/determineRealTop';
9
9
  import { getKernel } from '../peaks/util/getKernel';
10
10
  import type { GetKernelOptions } from '../peaks/util/getKernel';
11
11
  import * as PeakOptimizer from '../peaks/util/peakOptimizer';
12
- import type { NMRSignal2D } from '../types/NMRSignal2D';
12
+
13
+ import type { NMRSignal2D } from './NMRSignal2D';
13
14
 
14
15
  const smallFilter = [
15
16
  [0, 0, 1, 2, 2, 2, 1, 0, 0],
@@ -31,7 +32,7 @@ export interface Data2D {
31
32
  maxY: number;
32
33
  }
33
34
 
34
- export interface XYZAutoPeaksPickingOptions {
35
+ export interface XYZAutoZonesPickingOptions {
35
36
  /**
36
37
  * max number of points in any dimension to pad the input data, this is needed to avoid lost peaks when the input matrix is too small.
37
38
  * @default 14
@@ -89,7 +90,7 @@ export interface XYZAutoPeaksPickingOptions {
89
90
 
90
91
  export function xyzAutoZonesPicking(
91
92
  spectraData: Data2D,
92
- options: XYZAutoPeaksPickingOptions,
93
+ options: XYZAutoZonesPickingOptions,
93
94
  ) {
94
95
  let {
95
96
  sizeToPad = 14,
@@ -3,8 +3,9 @@ import simpleClustering from 'ml-simple-clustering';
3
3
 
4
4
  import type { JAxisKeys } from '../peaks/util/jAnalyzer';
5
5
  import jAnalyzer from '../peaks/util/jAnalyzer';
6
- import type { MakeMandatory } from '../types/MakeMandatory';
7
- import type { NMRSignal2D } from '../types/NMRSignal2D';
6
+ import type { MakeMandatory } from '../utilities/MakeMandatory';
7
+
8
+ import type { NMRSignal2D } from './NMRSignal2D';
8
9
 
9
10
  interface CompilePatternOptions {
10
11
  observedFrequencies?: number[] | Float64Array;
@@ -1 +0,0 @@
1
- {"version":3,"file":"MakeMandatory.js","sourceRoot":"","sources":["../../src/types/MakeMandatory.ts"],"names":[],"mappings":""}
@@ -1,4 +0,0 @@
1
- export interface XYNumberArray {
2
- x: Array<number> | Float64Array;
3
- y: Array<number> | Float64Array;
4
- }
@@ -1,3 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- //# sourceMappingURL=XYNumberArray.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"XYNumberArray.js","sourceRoot":"","sources":["../../src/types/XYNumberArray.ts"],"names":[],"mappings":""}
@@ -1 +0,0 @@
1
- {"version":3,"file":"dataStructure.js","sourceRoot":"","sources":["../../src/types/dataStructure.ts"],"names":[],"mappings":""}
@@ -1,11 +0,0 @@
1
- declare module 'nmr-parser' {
2
- interface FromBrukerOptions {
3
- base64?: boolean;
4
- shiftX?: number;
5
- info?: any;
6
- name?: string;
7
- }
8
- function fromBruker(zipFile: ArrayBuffer | string, options?: Partial<FromBrukerOptions>): Promise<Array<any>>;
9
- function fromJCAMP(buffer: string | ArrayBuffer, options?: any): Array<any>;
10
- function fromJEOL(buffer: ArrayBuffer): any;
11
- }
@@ -1,2 +0,0 @@
1
- "use strict";
2
- //# sourceMappingURL=nmr-parser.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"nmr-parser.js","sourceRoot":"","sources":["../../../src/types/modules/nmr-parser.ts"],"names":[],"mappings":""}
@@ -1 +0,0 @@
1
- {"version":3,"file":"nmrAssigment.js","sourceRoot":"","sources":["../../src/types/nmrAssigment.ts"],"names":[],"mappings":""}
@@ -1 +0,0 @@
1
- {"version":3,"file":"prediction1D.js","sourceRoot":"","sources":["../../src/types/prediction1D.ts"],"names":[],"mappings":""}
File without changes
@@ -1,2 +0,0 @@
1
- "use strict";
2
- //# sourceMappingURL=prediction2D.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"prediction2D.js","sourceRoot":"","sources":["../../src/types/prediction2D.ts"],"names":[],"mappings":""}
@@ -1 +0,0 @@
1
- {"version":3,"file":"MakeMandatory.js","sourceRoot":"","sources":["../../src/types/MakeMandatory.ts"],"names":[],"mappings":""}
@@ -1,2 +0,0 @@
1
- export {};
2
- //# sourceMappingURL=XYNumberArray.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"XYNumberArray.js","sourceRoot":"","sources":["../../src/types/XYNumberArray.ts"],"names":[],"mappings":""}
@@ -1 +0,0 @@
1
- {"version":3,"file":"dataStructure.js","sourceRoot":"","sources":["../../src/types/dataStructure.ts"],"names":[],"mappings":""}
@@ -1,2 +0,0 @@
1
- "use strict";
2
- //# sourceMappingURL=nmr-parser.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"nmr-parser.js","sourceRoot":"","sources":["../../../src/types/modules/nmr-parser.ts"],"names":[],"mappings":""}
@@ -1 +0,0 @@
1
- {"version":3,"file":"nmrAssigment.js","sourceRoot":"","sources":["../../src/types/nmrAssigment.ts"],"names":[],"mappings":""}
@@ -1 +0,0 @@
1
- {"version":3,"file":"prediction1D.js","sourceRoot":"","sources":["../../src/types/prediction1D.ts"],"names":[],"mappings":""}
@@ -1,2 +0,0 @@
1
- "use strict";
2
- //# sourceMappingURL=prediction2D.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"prediction2D.js","sourceRoot":"","sources":["../../src/types/prediction2D.ts"],"names":[],"mappings":""}
@@ -1,4 +0,0 @@
1
- export interface XYNumberArray {
2
- x: Array<number> | Float64Array;
3
- y: Array<number> | Float64Array;
4
- }
@@ -1,13 +0,0 @@
1
- declare module 'ml-levenberg-marquardt' {
2
- import type { DataXY } from 'cheminfo-types';
3
-
4
- export default function levenbergMarquardt(
5
- data: DataXY,
6
- parametrizedFunction: (p: number[]) => (t: number) => number,
7
- options?: any,
8
- ): {
9
- parameterValues: Array<number>;
10
- parameterError: number;
11
- iterations: number;
12
- };
13
- }