nmr-processing 9.1.0 → 9.2.0

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 (127) hide show
  1. package/lib/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
  2. package/lib/index.d.ts +3 -2
  3. package/lib/index.js +1 -0
  4. package/lib/index.js.map +1 -1
  5. package/lib/prediction/{prediction1D.d.ts → Prediction1D.d.ts} +0 -0
  6. package/lib/prediction/{prediction1D.js → Prediction1D.js} +1 -1
  7. package/lib/prediction/Prediction1D.js.map +1 -0
  8. package/lib/prediction/predictAll.d.ts +1 -1
  9. package/lib/prediction/predictAll.js.map +1 -1
  10. package/lib/prediction/predictAllSpectra.js +2 -2
  11. package/lib/prediction/predictAllSpectra.js.map +1 -1
  12. package/lib/prediction/predictCOSY.d.ts +1 -1
  13. package/lib/prediction/predictCOSY.js.map +1 -1
  14. package/lib/prediction/predictCarbon.d.ts +1 -1
  15. package/lib/prediction/predictHMBC.d.ts +1 -1
  16. package/lib/prediction/predictHMBC.js.map +1 -1
  17. package/lib/prediction/predictHSQC.d.ts +1 -1
  18. package/lib/prediction/predictHSQC.js.map +1 -1
  19. package/lib/prediction/predictProton.d.ts +1 -1
  20. package/lib/prediction/utils/fetchPrediction.d.ts +1 -1
  21. package/lib/prediction/utils/getPredictions.d.ts +1 -1
  22. package/lib/prediction/utils/predict2D.d.ts +1 -1
  23. package/lib/prediction/utils/predict2D.js +1 -1
  24. package/lib/prediction/utils/predict2D.js.map +1 -1
  25. package/lib/signals/{jcoupling.d.ts → Jcoupling.d.ts} +0 -0
  26. package/lib/signals/{jcoupling.js → Jcoupling.js} +1 -1
  27. package/lib/signals/Jcoupling.js.map +1 -0
  28. package/lib/signals/NMRSignal1D.d.ts +1 -1
  29. package/lib/signals/addDummySignals.js +12 -7
  30. package/lib/signals/addDummySignals.js.map +1 -1
  31. package/lib/signals/optimization/defaultParameters.d.ts +1 -0
  32. package/lib/signals/optimization/defaultParameters.js +36 -0
  33. package/lib/signals/optimization/defaultParameters.js.map +1 -0
  34. package/lib/signals/optimization/directOptimization.d.ts +20 -0
  35. package/lib/signals/optimization/directOptimization.js +32 -0
  36. package/lib/signals/optimization/directOptimization.js.map +1 -0
  37. package/lib/signals/optimization/getInternalSignals.d.ts +54 -0
  38. package/lib/signals/optimization/getInternalSignals.js +150 -0
  39. package/lib/signals/optimization/getInternalSignals.js.map +1 -0
  40. package/lib/signals/optimization/getSumOfShapes.d.ts +4 -0
  41. package/lib/signals/optimization/getSumOfShapes.js +46 -0
  42. package/lib/signals/optimization/getSumOfShapes.js.map +1 -0
  43. package/lib/signals/optimization/signalsToPointXY.d.ts +9 -0
  44. package/lib/signals/optimization/signalsToPointXY.js +24 -0
  45. package/lib/signals/optimization/signalsToPointXY.js.map +1 -0
  46. package/lib/signals/optimizeSignals.d.ts +40 -0
  47. package/lib/signals/optimizeSignals.js +108 -0
  48. package/lib/signals/optimizeSignals.js.map +1 -0
  49. package/lib/signals/signalsJoin.d.ts +1 -1
  50. package/lib/signals/simulation/simulateXYPeaks.js +1 -1
  51. package/lib/signals/simulation/simulateXYPeaks.js.map +1 -1
  52. package/lib/xy/xyAutoPeaksPicking.d.ts +2 -2
  53. package/lib/xy/xyAutoPeaksPicking.js +2 -2
  54. package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
  55. package/lib/xy/xyPeaksOptimization.js +2 -1
  56. package/lib/xy/xyPeaksOptimization.js.map +1 -1
  57. package/lib-esm/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
  58. package/lib-esm/index.js +1 -0
  59. package/lib-esm/index.js.map +1 -1
  60. package/lib-esm/prediction/Prediction1D.js +2 -0
  61. package/lib-esm/prediction/Prediction1D.js.map +1 -0
  62. package/lib-esm/prediction/predictAll.js.map +1 -1
  63. package/lib-esm/prediction/predictAllSpectra.js +2 -2
  64. package/lib-esm/prediction/predictAllSpectra.js.map +1 -1
  65. package/lib-esm/prediction/predictCOSY.js.map +1 -1
  66. package/lib-esm/prediction/predictHMBC.js.map +1 -1
  67. package/lib-esm/prediction/predictHSQC.js.map +1 -1
  68. package/lib-esm/prediction/utils/predict2D.js +1 -1
  69. package/lib-esm/prediction/utils/predict2D.js.map +1 -1
  70. package/lib-esm/signals/Jcoupling.js +2 -0
  71. package/lib-esm/signals/Jcoupling.js.map +1 -0
  72. package/lib-esm/signals/addDummySignals.js +12 -7
  73. package/lib-esm/signals/addDummySignals.js.map +1 -1
  74. package/lib-esm/signals/optimization/defaultParameters.js +33 -0
  75. package/lib-esm/signals/optimization/defaultParameters.js.map +1 -0
  76. package/lib-esm/signals/optimization/directOptimization.js +25 -0
  77. package/lib-esm/signals/optimization/directOptimization.js.map +1 -0
  78. package/lib-esm/signals/optimization/getInternalSignals.js +146 -0
  79. package/lib-esm/signals/optimization/getInternalSignals.js.map +1 -0
  80. package/lib-esm/signals/optimization/getSumOfShapes.js +42 -0
  81. package/lib-esm/signals/optimization/getSumOfShapes.js.map +1 -0
  82. package/lib-esm/signals/optimization/signalsToPointXY.js +20 -0
  83. package/lib-esm/signals/optimization/signalsToPointXY.js.map +1 -0
  84. package/lib-esm/signals/optimizeSignals.js +104 -0
  85. package/lib-esm/signals/optimizeSignals.js.map +1 -0
  86. package/lib-esm/signals/simulation/simulateXYPeaks.js +1 -1
  87. package/lib-esm/signals/simulation/simulateXYPeaks.js.map +1 -1
  88. package/lib-esm/xy/xyAutoPeaksPicking.js +3 -3
  89. package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
  90. package/lib-esm/xy/xyPeaksOptimization.js +2 -1
  91. package/lib-esm/xy/xyPeaksOptimization.js.map +1 -1
  92. package/package.json +3 -2
  93. package/src/assignment/utils/getAssignment/buildAssignments.ts +1 -1
  94. package/src/index.ts +3 -2
  95. package/src/prediction/{prediction1D.ts → Prediction1D.ts} +0 -0
  96. package/src/prediction/predictAll.ts +1 -1
  97. package/src/prediction/predictAllSpectra.ts +2 -2
  98. package/src/prediction/predictCOSY.ts +1 -1
  99. package/src/prediction/predictCarbon.ts +1 -1
  100. package/src/prediction/predictHMBC.ts +1 -1
  101. package/src/prediction/predictHSQC.ts +1 -1
  102. package/src/prediction/predictProton.ts +1 -1
  103. package/src/prediction/utils/fetchPrediction.ts +1 -1
  104. package/src/prediction/utils/getPredictions.ts +1 -1
  105. package/src/prediction/utils/predict2D.ts +2 -2
  106. package/src/signal/signalJoinCouplings.ts +1 -1
  107. package/src/signals/{jcoupling.ts → Jcoupling.ts} +0 -0
  108. package/src/signals/NMRSignal1D.ts +1 -1
  109. package/src/signals/addDummySignals.ts +17 -7
  110. package/src/signals/optimization/defaultParameters.ts +45 -0
  111. package/src/signals/optimization/directOptimization.ts +49 -0
  112. package/src/signals/optimization/getInternalSignals.ts +287 -0
  113. package/src/signals/optimization/getSumOfShapes.ts +54 -0
  114. package/src/signals/optimization/signalsToPointXY.ts +37 -0
  115. package/src/signals/optimizeSignals.ts +173 -0
  116. package/src/signals/signalsJoin.ts +1 -1
  117. package/src/signals/signalsToXY.ts +1 -1
  118. package/src/signals/simulation/signalsToSpinSystem.ts +1 -1
  119. package/src/signals/simulation/simulateXYPeaks.ts +1 -2
  120. package/src/xy/xyAutoPeaksPicking.ts +10 -6
  121. package/src/xy/xyPeaksOptimization.ts +3 -1
  122. package/lib/prediction/prediction1D.js.map +0 -1
  123. package/lib/signals/jcoupling.js.map +0 -1
  124. package/lib-esm/prediction/prediction1D.js +0 -2
  125. package/lib-esm/prediction/prediction1D.js.map +0 -1
  126. package/lib-esm/signals/jcoupling.js +0 -2
  127. package/lib-esm/signals/jcoupling.js.map +0 -1
package/lib-esm/signals/simulation/simulateXYPeaks.js.map CHANGED
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package/lib-esm/xy/xyAutoPeaksPicking.js CHANGED
@@ -1,4 +1,4 @@
1
- import { gsd, optimizePeaks, joinBroadPeaks, } from 'ml-gsd';
1
+ import { gsd, optimizePeaks, joinBroadPeaks, setShape, } from 'ml-gsd';
2
2
  import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
3
3
  import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
4
4
  export function xyAutoPeaksPicking(data, options) {
@@ -52,8 +52,7 @@ function getNegativePeaks(data, cutOff, getPeakOptions) {
52
52
  }
53
53
  function getPeakList(data, options) {
54
54
  const { shape, frequency, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
55
- let peakList = gsd(data, {
56
- shape,
55
+ const peaks = gsd(data, {
57
56
  sgOptions,
58
57
  maxCriteria,
59
58
  minMaxRatio,
@@ -61,6 +60,7 @@ function getPeakList(data, options) {
61
60
  smoothY,
62
61
  realTopDetection,
63
62
  });
63
+ const peakList = setShape(peaks, { output: peaks, shape });
64
64
  const newPeaks = broadWidth
65
65
  ? joinBroadPeaks(peakList, {
66
66
  broadRatio,
package/lib-esm/xy/xyAutoPeaksPicking.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EACL,GAAG,EACH,aAAa,EACb,cAAc,EAMd,QAAQ,GACT,MAAM,QAAQ,CAAC;AAEhB,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAG/B,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAgElE,MAAM,UAAU,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;IAErD,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU;QAAE,OAAO,EAAE,CAAC;IAE1C,IAAI,IAAI,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE;QAC1C,IAAI,GAAG,SAAS,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC;KACnD;IAED,MAAM,MAAM,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,CAAC,CAAC;IAE9E,IAAI,cAAc,GAAuB;QACvC,KAAK;QACL,SAAS;QACT,UAAU;QACV,QAAQ;QACR,YAAY;QACZ,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE;QACrC,WAAW;QACX,UAAU;QACV,UAAU,EAAE,MAAM,CAAC,QAAQ;QAC3B,OAAO;QACP,YAAY;QACZ,gBAAgB;KACjB,CAAC;IAEF,QAAQ,SAAS,EAAE;QACjB,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;SAC1C;QACD,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC,CAAC;SACvD;QACD,KAAK,MAAM,CAAC,CAAC;YACX,OAAO;gBACL,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC;gBACpC,GAAG,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC;aAClD,CAAC;SACH;QACD,OAAO,CAAC,CAAC;YACP,MAAM,SAAS,GAAU,SAAS,CAAC;YACnC,4EAA4E;YAC5E,MAAM,KAAK,CAAC,wBAAwB,SAAS,EAAE,CAAC,CAAC;SAClD;KACF;AACH,CAAC;AAED,SAAS,gBAAgB,CACvB,IAAY,EACZ,MAA4B,EAC5B,cAAkC;IAElC,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;IAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;IACnC,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;AAC3C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAA2B;IAC5D,MAAM,EACJ,KAAK,EACL,SAAS,EACT,UAAU,EACV,QAAQ,EACR,WAAW,EACX,YAAY,EACZ,SAAS,EACT,WAAW,EACX,UAAU,EACV,UAAU,EACV,OAAO,EACP,YAAY,EACZ,gBAAgB,GACjB,GAAG,OAAO,CAAC;IAEZ,MAAM,KAAK,GAAG,GAAG,CAAC,IAAI,EAAE;QACtB,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;IAE3D,MAAM,QAAQ,GAAG,UAAU;QACzB,CAAC,CAAC,cAAc,CAAC,QAAQ,EAAE;YACvB,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,oBAAoB,CAAC,CAAC;IAEvC,OAAO,gBAAgB,CACrB,QAAQ;QACN,CAAC,CAAC,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE;YAC5B,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,EACZ,EAAE,SAAS,EAAE,CACd,CAAC;AACJ,CAAC;AAED,SAAS,SAAS,CAAC,IAA6B,EAAE,OAAyB;IACzE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAC;IAE5D,MAAM,YAAY,GAAG,CAAC,UAAkB,EAAE,EAAE,CAC1C,OAAO,UAAU,KAAK,QAAQ;QAC5B,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,CAAC,UAAU,EAAE;QACjD,CAAC,CAAC,UAAU,CAAC;IAEjB,IAAI,UAAU,EAAE;QACd,OAAO,YAAY,CAAC,UAAU,CAAC,CAAC;KACjC;SAAM;QACL,OAAO,UAAU;YACf,CAAC,CAAC,aAAa,CAAC,IAAI,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC;YACrD,CAAC,CAAC,YAAY,CAAC,eAAe,CAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAC;KAC3D;AACH,CAAC;AAED,SAAS,oBAAoB,CAC3B,IAAyC;IAEzC,MAAM,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,GAAG,IAAI,CAAC;IACxC,OAAO;QACL,EAAE;QACF,CAAC;QACD,CAAC;QACD,KAAK;QACL,KAAK;KACN,CAAC;AACJ,CAAC"}
package/lib-esm/xy/xyPeaksOptimization.js CHANGED
@@ -5,9 +5,10 @@ export function xyPeaksOptimization(data, peaks, options) {
5
5
  const { frequency } = options;
6
6
  const newPeaks = convertWidthToPPM(peaks, { frequency });
7
7
  const optimizedPeaks = optimizePeaks(data, newPeaks, options);
8
- return convertWidthToHz(optimizedPeaks, {
8
+ const result = convertWidthToHz(optimizedPeaks, {
9
9
  frequency,
10
10
  output: optimizedPeaks,
11
11
  });
12
+ return result;
12
13
  }
13
14
  //# sourceMappingURL=xyPeaksOptimization.js.map
package/lib-esm/xy/xyPeaksOptimization.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"xyPeaksOptimization.js","sourceRoot":"","sources":["../../src/xy/xyPeaksOptimization.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAwB,MAAM,QAAQ,CAAC;AAE7D,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,iBAAiB,EAAE,MAAM,iCAAiC,CAAC;AAQpE,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,KAAU,EACV,OAAmC;IAEnC,MAAM,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC;IAC9B,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;IACzD,MAAM,cAAc,GAAG,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC9D,OAAO,gBAAgB,CAAC,cAAc,EAAE;QACtC,SAAS;QACT,MAAM,EAAE,cAAc;KACvB,CAAC,CAAC;AACL,CAAC"}
1
+ {"version":3,"file":"xyPeaksOptimization.js","sourceRoot":"","sources":["../../src/xy/xyPeaksOptimization.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAwB,MAAM,QAAQ,CAAC;AAE7D,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,iBAAiB,EAAE,MAAM,iCAAiC,CAAC;AASpE,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,KAAU,EACV,OAAmC;IAEnC,MAAM,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC;IAC9B,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;IACzD,MAAM,cAAc,GAAG,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC9D,MAAM,MAAM,GAAG,gBAAgB,CAAC,cAAc,EAAE;QAC9C,SAAS;QACT,MAAM,EAAE,cAAc;KACvB,CAAC,CAAC;IACH,OAAO,MAAM,CAAC;AAChB,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "nmr-processing",
3
- "version": "9.1.0",
3
+ "version": "9.2.0",
4
4
  "description": "Pure functions allowing to process NMR spectra.",
5
5
  "main": "./lib/index.js",
6
6
  "module": "./lib-esm/index.js",
@@ -64,7 +64,8 @@
64
64
  "ml-array-mean": "^1.1.6",
65
65
  "ml-array-rescale": "^1.3.7",
66
66
  "ml-array-sum": "^1.1.6",
67
- "ml-gsd": "^12.1.0",
67
+ "ml-direct": "^0.1.1",
68
+ "ml-gsd": "^12.1.2",
68
69
  "ml-hclust": "^3.1.0",
69
70
  "ml-levenberg-marquardt": "^4.1.0",
70
71
  "ml-matrix": "^6.10.2",
package/src/assignment/utils/getAssignment/buildAssignments.ts CHANGED
@@ -337,7 +337,7 @@ function initializePartials(
337
337
  }
338
338
 
339
339
  function fillPartial(nSources: number, value: string | null = null) {
340
- const partial: Array<string | null> = new Array(nSources);
340
+ const partial = new Array<string | null>(nSources);
341
341
  for (let i = 0; i < nSources; i++) {
342
342
  partial[i] = value;
343
343
  }
package/src/index.ts CHANGED
@@ -24,6 +24,7 @@ export * from './ranges/rangesToXY';
24
24
  export * from './signals/signalsToRanges';
25
25
  export * from './signals/signalsToXY';
26
26
  export * from './signals/signals2DToZ';
27
+ export * from './signals/optimizeSignals';
27
28
 
28
29
  export * from './utilities/resurrect';
29
30
  export * from './utilities/rangeFromSignal';
@@ -50,8 +51,8 @@ export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
50
51
  export type { NMRRange } from './xy/NMRRange';
51
52
  export type { NMRZone } from './xyz/NMRZone';
52
53
  export type { NMRPeak1D } from './peaks/NMRPeak1D';
53
- export type { Prediction1D } from './prediction/prediction1D';
54
- export type { Jcoupling } from './signals/jcoupling';
54
+ export type { Prediction1D } from './prediction/Prediction1D';
55
+ export type { Jcoupling } from './signals/Jcoupling';
55
56
  export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
56
57
  export type {
57
58
  DataBaseLevelStructure,
package/src/prediction/predictAll.ts CHANGED
@@ -1,11 +1,11 @@
1
1
  import type { Molecule } from 'openchemlib';
2
2
 
3
+ import type { Prediction1D } from './Prediction1D';
3
4
  import { predictCOSY } from './predictCOSY';
4
5
  import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
5
6
  import { predictHMBC } from './predictHMBC';
6
7
  import { predictHSQC } from './predictHSQC';
7
8
  import { predictProton, PredictProtonOptions } from './predictProton';
8
- import type { Prediction1D } from './prediction1D';
9
9
  import { getPredictions } from './utils/getPredictions';
10
10
  import type { Predictor } from './utils/predict2D';
11
11
 
package/src/prediction/predictAllSpectra.ts CHANGED
@@ -52,8 +52,8 @@ export async function predictAllSpectra(
52
52
  ...{
53
53
  proton: { from: 0, to: 14 },
54
54
  carbon: { from: 0, to: 200 },
55
- nbPoints: 4098,
56
- lineWidth: 0.03,
55
+ nbPoints: 65536,
56
+ lineWidth: 1,
57
57
  },
58
58
  ...(simulationOptions.oneD || {}),
59
59
  };
package/src/prediction/predictCOSY.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import { Molecule } from 'openchemlib';
2
2
 
3
+ import type { Prediction1D } from './Prediction1D';
3
4
  import { predictProton, PredictProtonOptions } from './predictProton';
4
- import type { Prediction1D } from './prediction1D';
5
5
  import { predict2D, Predictor } from './utils/predict2D';
6
6
 
7
7
  export interface PredictCOSYOptions {
package/src/prediction/predictCarbon.ts CHANGED
@@ -7,8 +7,8 @@ import type { NMRSignal1D } from '../signals/NMRSignal1D';
7
7
  import { signalsToRanges } from '../signals/signalsToRanges';
8
8
  import type { MakeMandatory } from '../utilities/MakeMandatory';
9
9
 
10
+ import type { Prediction1D } from './Prediction1D';
10
11
  import type { DataBaseStructure } from './dataStructure';
11
- import type { Prediction1D } from './prediction1D';
12
12
  import { fetchPrediction } from './utils/fetchPrediction';
13
13
  import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
14
14
  import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
package/src/prediction/predictHMBC.ts CHANGED
@@ -1,10 +1,10 @@
1
1
  import { Molecule } from 'openchemlib';
2
2
 
3
+ import type { Prediction1D } from './Prediction1D';
3
4
  import { predictCarbon } from './predictCarbon';
4
5
  import type { PredictCarbonOptions } from './predictCarbon';
5
6
  import { predictProton } from './predictProton';
6
7
  import type { PredictProtonOptions } from './predictProton';
7
- import type { Prediction1D } from './prediction1D';
8
8
  import { predict2D } from './utils/predict2D';
9
9
  import type { Predictor } from './utils/predict2D';
10
10
 
package/src/prediction/predictHSQC.ts CHANGED
@@ -1,8 +1,8 @@
1
1
  import { Molecule } from 'openchemlib';
2
2
 
3
+ import type { Prediction1D } from './Prediction1D';
3
4
  import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
4
5
  import { predictProton, PredictProtonOptions } from './predictProton';
5
- import type { Prediction1D } from './prediction1D';
6
6
  import { predict2D, Predictor } from './utils/predict2D';
7
7
 
8
8
  export interface PredictHSQCOptions {
package/src/prediction/predictProton.ts CHANGED
@@ -12,7 +12,7 @@ import type { NMRSignal1D } from '../signals/NMRSignal1D';
12
12
  import { signalsJoin } from '../signals/signalsJoin';
13
13
  import { signalsToRanges } from '../signals/signalsToRanges';
14
14
 
15
- import type { Prediction1D } from './prediction1D';
15
+ import type { Prediction1D } from './Prediction1D';
16
16
 
17
17
  /**
18
18
  * Makes a prediction using proton.
package/src/prediction/utils/fetchPrediction.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import { fetch } from 'cross-fetch';
2
2
  import { Molecule } from 'openchemlib';
3
3
 
4
- import type { Prediction1D } from '../prediction1D';
4
+ import type { Prediction1D } from '../Prediction1D';
5
5
 
6
6
  interface FetchPredictionOptions {
7
7
  webserviceURL: string;
package/src/prediction/utils/getPredictions.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import type { Molecule } from 'openchemlib';
2
2
 
3
- import type { Prediction1D } from '../prediction1D';
3
+ import type { Prediction1D } from '../Prediction1D';
4
4
 
5
5
  import type { Predictions, PredictOptions, Predictors } from './predict2D';
6
6
 
package/src/prediction/utils/predict2D.ts CHANGED
@@ -12,16 +12,16 @@ import type {
12
12
  PathInfo,
13
13
  } from 'openchemlib-utils';
14
14
 
15
+ import { setIDs } from '../../peaks/util/setIDs';
15
16
  import type { NMRSignal1D } from '../../signals/NMRSignal1D';
16
17
  import type { MakeMandatory } from '../../utilities/MakeMandatory';
17
18
  import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
19
+ import type { Prediction1D } from '../Prediction1D';
18
20
  import type { PredictCarbon, PredictCarbonOptions } from '../predictCarbon';
19
21
  import type { PredictProton, PredictProtonOptions } from '../predictProton';
20
- import type { Prediction1D } from '../prediction1D';
21
22
 
22
23
  import { getNuclei } from './getNuclei';
23
24
  import { getPredictions } from './getPredictions';
24
- import { setIDs } from '../../peaks/util/setIDs';
25
25
 
26
26
  /**
27
27
  * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
package/src/signal/signalJoinCouplings.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import sum from 'ml-array-sum';
2
2
 
3
+ import type { Jcoupling } from '../signals/Jcoupling';
3
4
  import type { NMRSignal1D } from '../signals/NMRSignal1D';
4
- import type { Jcoupling } from '../signals/jcoupling';
5
5
  import type { MakeMandatory } from '../utilities/MakeMandatory';
6
6
  import { joinPatterns } from '../utilities/joinPatterns';
7
7
 
package/src/signals/{jcoupling.ts → Jcoupling.ts} RENAMED
File without changes
package/src/signals/NMRSignal1D.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import type { NMRPeak1D } from '../peaks/NMRPeak1D';
2
2
 
3
- import type { Jcoupling } from './jcoupling';
3
+ import type { Jcoupling } from './Jcoupling';
4
4
 
5
5
  export interface NMRSignal1D {
6
6
  delta: number;
package/src/signals/addDummySignals.ts CHANGED
@@ -1,18 +1,28 @@
1
1
  import { couplingPatterns } from '../constants/couplingPatterns';
2
2
 
3
+ import type { Jcoupling } from './Jcoupling';
3
4
  import { NMRSignal1D } from './NMRSignal1D';
4
- import type { Jcoupling } from './jcoupling';
5
5
 
6
6
  export function addDummySignals(signals: NMRSignal1D[]) {
7
7
  let newSignals: NMRSignal1D[] = JSON.parse(JSON.stringify(signals));
8
8
 
9
+ let nextAtomToAssign =
10
+ signals.reduce((nextAtomToAssign, signal) => {
11
+ const { atoms = [] } = signal;
12
+ return Math.max(...atoms) > nextAtomToAssign
13
+ ? Math.max(...atoms)
14
+ : nextAtomToAssign;
15
+ }, 0) + 1;
9
16
  signals.forEach((signal, s) => {
10
- const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
11
-
17
+ const {
18
+ js: jCouplings = [],
19
+ atoms: signalAssignment = [nextAtomToAssign++],
20
+ } = signal;
12
21
  let { newCouplings, tempSignals } = checkCouplings(
13
22
  jCouplings,
14
23
  newSignals,
15
24
  signalAssignment,
25
+ nextAtomToAssign + signals.length,
16
26
  );
17
27
 
18
28
  if (tempSignals.length > 0) newSignals.push(...tempSignals);
@@ -28,8 +38,8 @@ function checkCouplings(
28
38
  jCouplings: Jcoupling[],
29
39
  signals: NMRSignal1D[],
30
40
  signalAssignment: number[],
41
+ nextAtomToAssign: number,
31
42
  ) {
32
- let newSignalAssignment = signals.length - 1;
33
43
  let tempSignals: NMRSignal1D[] = [];
34
44
  const newCouplings = jCouplings.reduce<Jcoupling[]>(
35
45
  (newCouplings, jCoupling) => {
@@ -39,13 +49,13 @@ function checkCouplings(
39
49
  let tempCouplings: Jcoupling[] = [];
40
50
  const nbLinks = couplingPatterns.indexOf(multiplicity);
41
51
  for (let i = 0; i < nbLinks; i++) {
42
- newSignalAssignment++;
52
+ nextAtomToAssign++;
43
53
  tempCouplings.push({
44
54
  coupling,
45
- atoms: [newSignalAssignment],
55
+ atoms: [nextAtomToAssign],
46
56
  });
47
57
  tempSignals.push(
48
- formatSignal(coupling, [newSignalAssignment], signalAssignment),
58
+ formatSignal(coupling, [nextAtomToAssign], signalAssignment),
49
59
  );
50
60
  }
51
61
  } else {
package/src/signals/optimization/defaultParameters.ts ADDED
@@ -0,0 +1,45 @@
1
+ import { PseudoVoigtShape1D, Shape1D } from 'ml-peak-shape-generator';
2
+
3
+ import { Jcoupling } from '../Jcoupling';
4
+ import { Signal } from '../optimizeSignals';
5
+
6
+ type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & { fwhm: number };
7
+
8
+ export const defaultParameters: Record<
9
+ string,
10
+ Record<string, (...args: any) => number>
11
+ > = {
12
+ delta: {
13
+ init: (data: { signal: Signal }) => data.signal.delta,
14
+ min: (data: { signal: Signal; shape: Shape1DWithFWHM }) =>
15
+ data.signal.delta - data.shape.fwhm * 2,
16
+ max: (data: { signal: Signal; shape: Shape1DWithFWHM }) =>
17
+ data.signal.delta + data.shape.fwhm * 2,
18
+ gradientDifference: () => 2e-3,
19
+ },
20
+ intensity: {
21
+ init: (data: { signal: Signal }) => data.signal.intensity || 1,
22
+ min: () => 0,
23
+ max: () => 1.5,
24
+ gradientDifference: () => 1e-3,
25
+ },
26
+ fwhm: {
27
+ init: (data: { shape: Shape1DWithFWHM }) => data.shape.fwhm,
28
+ min: (data: { shape: Shape1DWithFWHM }) => data.shape.fwhm * 0.25,
29
+ max: (data: { shape: Shape1DWithFWHM }) => data.shape.fwhm * 4,
30
+ gradientDifference: (data: { shape: Shape1DWithFWHM }) =>
31
+ data.shape.fwhm * 2e-3,
32
+ },
33
+ mu: {
34
+ init: (data: { shape: PseudoVoigtShape1D }) => data.shape.mu || 0.5,
35
+ min: () => 0,
36
+ max: () => 1,
37
+ gradientDifference: () => 0.01,
38
+ },
39
+ coupling: {
40
+ init: (data: { jCoupling: Jcoupling }) => data.jCoupling.coupling,
41
+ min: (data: { jCoupling: Jcoupling }) => data.jCoupling.coupling * 0.8,
42
+ max: (data: { jCoupling: Jcoupling }) => data.jCoupling.coupling * 1.2,
43
+ gradientDifference: () => 0.01,
44
+ },
45
+ };
package/src/signals/optimization/directOptimization.ts ADDED
@@ -0,0 +1,49 @@
1
+ import { DataXY } from 'cheminfo-types';
2
+ import direct from 'ml-direct';
3
+
4
+ import { SumOfShapes } from './getSumOfShapes';
5
+
6
+ interface DirectOptions {
7
+ iterations?: number;
8
+ epsilon?: number;
9
+ tolerance?: number;
10
+ tolerance2?: number;
11
+ initialState?: any;
12
+ }
13
+
14
+ interface DirectOptimizationOptions extends DirectOptions {
15
+ directOptions?: DirectOptions;
16
+ minValues: number[];
17
+ maxValues: number[];
18
+ }
19
+
20
+ export function directOptimization(
21
+ data: DataXY,
22
+ sumOfShapes: SumOfShapes,
23
+ options: DirectOptimizationOptions,
24
+ ) {
25
+ const { minValues, maxValues, directOptions = {} } = options;
26
+ const objectiveFunction = getObjectiveFunction(data, sumOfShapes);
27
+ const result = direct(objectiveFunction, minValues, maxValues, directOptions);
28
+
29
+ const { optima } = result;
30
+
31
+ return {
32
+ error: result.minFunctionValue,
33
+ iterations: result.iterations,
34
+ parameterValues: optima[0],
35
+ };
36
+ }
37
+
38
+ function getObjectiveFunction(data: DataXY, sumOfShapes: SumOfShapes) {
39
+ const { x, y } = data;
40
+ const nbPoints = x.length;
41
+ return (parameters: number[]) => {
42
+ const fct = sumOfShapes(parameters);
43
+ let error = 0;
44
+ for (let i = 0; i < nbPoints; i++) {
45
+ error += Math.pow(y[i] - fct(x[i]), 2);
46
+ }
47
+ return error;
48
+ };
49
+ }