nmr-processing 6.0.8 → 7.1.0
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.
- package/lib/index.d.ts +1 -0
- package/lib/index.js +6 -1
- package/lib/index.js.map +1 -1
- package/lib/peaks/NMRPeak1D.d.ts +5 -2
- package/lib/peaks/peaksToRanges.d.ts +3 -1
- package/lib/peaks/peaksToRanges.js.map +1 -1
- package/lib/peaks/util/jAnalyzer.d.ts +1 -1
- package/lib/peaks/util/jAnalyzer.js.map +1 -1
- package/lib/prediction/predictAllSpectra.d.ts +18 -0
- package/lib/prediction/predictAllSpectra.js +40 -0
- package/lib/prediction/predictAllSpectra.js.map +1 -0
- package/lib/prediction/utils/getFilteredIDiaIDs.d.ts +1 -1
- package/lib/utilities/resurrectRange.js +12 -16
- package/lib/utilities/resurrectRange.js.map +1 -1
- package/lib/xy/xyAutoPeaksPicking.d.ts +5 -4
- package/lib/xy/xyAutoPeaksPicking.js +14 -23
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib/xyz/xyzAutoZonesPicking.js +5 -1
- package/lib/xyz/xyzAutoZonesPicking.js.map +1 -1
- package/lib-esm/index.js +1 -0
- package/lib-esm/index.js.map +1 -1
- package/lib-esm/peaks/peaksToRanges.js.map +1 -1
- package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
- package/lib-esm/prediction/predictAllSpectra.js +36 -0
- package/lib-esm/prediction/predictAllSpectra.js.map +1 -0
- package/lib-esm/utilities/resurrectRange.js +12 -16
- package/lib-esm/utilities/resurrectRange.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +15 -24
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +14 -15
- package/src/index.ts +1 -0
- package/src/{openchemlib.d.ts → openchemlib-utils.d.ts} +0 -1
- package/src/peaks/NMRPeak1D.ts +5 -2
- package/src/peaks/peaksToRanges.ts +5 -3
- package/src/peaks/util/jAnalyzer.ts +3 -1
- package/src/prediction/predictAllSpectra.ts +48 -0
- package/src/utilities/resurrectRange.ts +17 -17
- package/src/xy/xyAutoPeaksPicking.ts +25 -36
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1
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|
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@@ -0,0 +1,36 @@
|
|
|
1
|
+
import { signalsToXY } from '../signals/signalsToXY';
|
|
2
|
+
import { predictAll } from './predictAll';
|
|
3
|
+
/**
|
|
4
|
+
* This function will generate an object compatible with NMR-ium
|
|
5
|
+
*
|
|
6
|
+
* @param molecule
|
|
7
|
+
* @param options
|
|
8
|
+
*/
|
|
9
|
+
export async function predictAllSpectra(molecule, options = {}) {
|
|
10
|
+
const predictions = await predictAll(molecule, options.prediction);
|
|
11
|
+
const spectra = [];
|
|
12
|
+
const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
|
|
13
|
+
spectra.push(getProton(predictions.proton, options.simulation));
|
|
14
|
+
return result;
|
|
15
|
+
}
|
|
16
|
+
function getProton(prediction, options) {
|
|
17
|
+
const { x, y } = signalsToXY(prediction.signals, options);
|
|
18
|
+
const spectrum = {
|
|
19
|
+
id: '',
|
|
20
|
+
// todo Array.from is temporary for the developement
|
|
21
|
+
data: { x: Array.from(x), re: Array.from(y), im: null },
|
|
22
|
+
info: {
|
|
23
|
+
nucleus: prediction.nucleus,
|
|
24
|
+
dimension: 1,
|
|
25
|
+
originFrequency: 400,
|
|
26
|
+
baseFrequency: 400,
|
|
27
|
+
pulseSequence: 'prediction',
|
|
28
|
+
experiment: 'proton',
|
|
29
|
+
isFt: true,
|
|
30
|
+
},
|
|
31
|
+
// todo: currently we disable the ranges because there is no ID
|
|
32
|
+
//ranges: { values: prediction.ranges },
|
|
33
|
+
};
|
|
34
|
+
return spectrum;
|
|
35
|
+
}
|
|
36
|
+
//# sourceMappingURL=predictAllSpectra.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"predictAllSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictAllSpectra.ts"],"names":[],"mappings":"AAEA,OAAO,EAAsB,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAEzE,OAAO,EAAqB,UAAU,EAAE,MAAM,cAAc,CAAC;AAC7D;;;;;GAKG;AAEH,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,QAAkB,EAClB,UAGI,EAAE;IAEN,MAAM,WAAW,GAAG,MAAM,UAAU,CAAC,QAAQ,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC;IACnE,MAAM,OAAO,GAAU,EAAE,CAAC;IAC1B,MAAM,MAAM,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,EAAE,CAAC,EAAE,CAAC;IAC1E,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC;IAEhE,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,SAAS,CAAC,UAAe,EAAE,OAA4B;IAC9D,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,WAAW,CAAC,UAAU,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IAC1D,MAAM,QAAQ,GAAG;QACf,EAAE,EAAE,EAAE;QACN,oDAAoD;QACpD,IAAI,EAAE,EAAE,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE;QACvD,IAAI,EAAE;YACJ,OAAO,EAAE,UAAU,CAAC,OAAO;YAC3B,SAAS,EAAE,CAAC;YACZ,eAAe,EAAE,GAAG;YACpB,aAAa,EAAE,GAAG;YAClB,aAAa,EAAE,YAAY;YAC3B,UAAU,EAAE,QAAQ;YACpB,IAAI,EAAE,IAAI;SACX;QACD,+DAA+D;QAC/D,wCAAwC;KACzC,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
|
@@ -6,16 +6,12 @@ export function resurrectRange(part, options = {}) {
|
|
|
6
6
|
const split = splitParenthesis(part);
|
|
7
7
|
if (!split.before)
|
|
8
8
|
return;
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
.split(/(?: |(?<=[0-9])-)/)
|
|
12
|
-
.map((part) => Number(part))
|
|
13
|
-
.filter((part) => !Number.isNaN(part));
|
|
14
|
-
if (beforeParts.length < 1 || beforeParts.length > 2) {
|
|
9
|
+
const beforeMatch = /.*?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.]*).*/.exec(split.before);
|
|
10
|
+
if (!beforeMatch || !beforeMatch.groups)
|
|
15
11
|
return;
|
|
16
|
-
|
|
17
|
-
const from =
|
|
18
|
-
const to =
|
|
12
|
+
const isARange = beforeMatch.groups.to !== '';
|
|
13
|
+
const from = Number(beforeMatch.groups.from);
|
|
14
|
+
const to = isARange ? Number(beforeMatch.groups.to) : from;
|
|
19
15
|
const insideParts = split.inside.split(/ *, */);
|
|
20
16
|
let signal = { delta: NaN, js: [] };
|
|
21
17
|
let range = { from, to, signals: [signal] };
|
|
@@ -27,22 +23,22 @@ export function resurrectRange(part, options = {}) {
|
|
|
27
23
|
if (multiplicityParts.length === 1) {
|
|
28
24
|
const multiplicity = multiplicityParts[0];
|
|
29
25
|
if (multiplicity === 'm') {
|
|
30
|
-
if (
|
|
31
|
-
// a
|
|
32
|
-
signal.delta =
|
|
26
|
+
if (isARange) {
|
|
27
|
+
// a real range
|
|
28
|
+
signal.delta = (from + to) / 2;
|
|
33
29
|
signal.multiplicity = multiplicity;
|
|
34
30
|
}
|
|
35
31
|
else {
|
|
36
|
-
// a
|
|
37
|
-
signal.delta =
|
|
32
|
+
// a complex signal
|
|
33
|
+
signal.delta = from;
|
|
38
34
|
signal.multiplicity = multiplicity;
|
|
39
35
|
}
|
|
40
36
|
}
|
|
41
37
|
else {
|
|
42
38
|
// looks like a real multiplicity, s, d, dd, etc..
|
|
43
|
-
if (
|
|
39
|
+
if (!isARange) {
|
|
44
40
|
// a complex signal
|
|
45
|
-
signal.delta =
|
|
41
|
+
signal.delta = from;
|
|
46
42
|
signal.multiplicity = multiplicity;
|
|
47
43
|
}
|
|
48
44
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"resurrectRange.js","sourceRoot":"","sources":["../../src/utilities/resurrectRange.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAEhD,MAAM,UAAU,cAAc,CAAC,IAAY,EAAE,UAAe,EAAE;IAC5D,MAAM,EAAE,OAAO,GAAG,IAAI,EAAE,SAAS,GAAG,GAAG,EAAE,GAAG,OAAO,CAAC;IACpD,MAAM,KAAK,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAC;IACrC,IAAI,CAAC,KAAK,CAAC,MAAM;QAAE,OAAO;
|
|
1
|
+
{"version":3,"file":"resurrectRange.js","sourceRoot":"","sources":["../../src/utilities/resurrectRange.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAEhD,MAAM,UAAU,cAAc,CAAC,IAAY,EAAE,UAAe,EAAE;IAC5D,MAAM,EAAE,OAAO,GAAG,IAAI,EAAE,SAAS,GAAG,GAAG,EAAE,GAAG,OAAO,CAAC;IACpD,MAAM,KAAK,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAC;IACrC,IAAI,CAAC,KAAK,CAAC,MAAM;QAAE,OAAO;IAE1B,MAAM,WAAW,GAAG,2CAA2C,CAAC,IAAI,CAClE,KAAK,CAAC,MAAM,CACb,CAAC;IAEF,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,CAAC,MAAM;QAAE,OAAO;IAEhD,MAAM,QAAQ,GAAG,WAAW,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,CAAC;IAE9C,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IAC7C,MAAM,EAAE,GAAG,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3D,MAAM,WAAW,GAAG,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IAChD,IAAI,MAAM,GAAgB,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC;IACjD,IAAI,KAAK,GAAa,EAAE,IAAI,EAAE,EAAE,EAAE,OAAO,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC;IAEtD,MAAM,gBAAgB,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC,IAAS,EAAE,EAAE,CACxD,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,CACxB,CAAC;IACF,IAAI,gBAAgB,CAAC,MAAM,KAAK,CAAC,EAAE;QACjC,KAAK,CAAC,WAAW,GAAG,MAAM,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC;KAClE;IAED,MAAM,iBAAiB,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC,IAAS,EAAE,EAAE,CACzD,IAAI,CAAC,KAAK,CAAC,aAAa,CAAC,CAC1B,CAAC;IACF,IAAI,iBAAiB,CAAC,MAAM,KAAK,CAAC,EAAE;QAClC,MAAM,YAAY,GAAG,iBAAiB,CAAC,CAAC,CAAC,CAAC;QAC1C,IAAI,YAAY,KAAK,GAAG,EAAE;YACxB,IAAI,QAAQ,EAAE;gBACZ,eAAe;gBACf,MAAM,CAAC,KAAK,GAAG,CAAC,IAAI,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC;gBAC/B,MAAM,CAAC,YAAY,GAAG,YAAY,CAAC;aACpC;iBAAM;gBACL,mBAAmB;gBACnB,MAAM,CAAC,KAAK,GAAG,IAAI,CAAC;gBACpB,MAAM,CAAC,YAAY,GAAG,YAAY,CAAC;aACpC;SACF;aAAM;YACL,kDAAkD;YAClD,IAAI,CAAC,QAAQ,EAAE;gBACb,mBAAmB;gBACnB,MAAM,CAAC,KAAK,GAAG,IAAI,CAAC;gBACpB,MAAM,CAAC,YAAY,GAAG,YAAY,CAAC;aACpC;SACF;KACF;IAED,MAAM,UAAU,GAAG,WAAW;SAC3B,MAAM,CAAC,CAAC,IAAS,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC;SACrD,GAAG,CAAC,CAAC,SAAiB,EAAE,EAAE,CAAC,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;IAEzE,MAAM,cAAc,GAAG,aAAa,CAAC,MAAM,CAAC,YAAY,IAAI,EAAE,CAAC,CAAC;IAChE,IAAI,cAAc,CAAC,MAAM,KAAK,UAAU,CAAC,MAAM,EAAE;QAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC9C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;gBACd,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAC;aACtC;YACD,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;gBACb,QAAQ,EAAE,UAAU,CAAC,CAAC,CAAC;gBACvB,YAAY,EAAE,cAAc,CAAC,CAAC,CAAC;aAChC,CAAC,CAAC;SACJ;KACF;IAED,IAAI,KAAK,CAAC,IAAI,KAAK,KAAK,CAAC,EAAE,EAAE;QAC3B,KAAK,GAAG,EAAE,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,MAAM,EAAE,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC,EAAE,CAAC;KAC1E;IAED,OAAO,KAAK,CAAC;AACf,CAAC"}
|
|
@@ -1,19 +1,21 @@
|
|
|
1
|
-
import { gsd, joinBroadPeaks,
|
|
1
|
+
import { gsd, optimizePeaks, joinBroadPeaks, appendShapeAndFWHM } from 'ml-gsd';
|
|
2
2
|
import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
|
|
3
3
|
export function xyAutoPeaksPicking(data, options = {}) {
|
|
4
|
-
const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false,
|
|
4
|
+
const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, lookNegative = false, } = options;
|
|
5
|
+
const { windowSize = 9, polynomial = 3 } = sgOptions;
|
|
5
6
|
if (from !== undefined && to !== undefined) {
|
|
6
7
|
data = xyExtract(data, { zones: [{ from, to }] });
|
|
7
8
|
}
|
|
8
|
-
if (data.x.length <
|
|
9
|
+
if (data.x.length < windowSize)
|
|
9
10
|
return [];
|
|
10
11
|
const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
|
|
11
12
|
let getPeakOptions = {
|
|
12
13
|
shape,
|
|
13
14
|
broadWidth,
|
|
14
15
|
optimize,
|
|
15
|
-
|
|
16
|
-
|
|
16
|
+
factorLimits,
|
|
17
|
+
maxCriteria: true,
|
|
18
|
+
sgOptions: { windowSize, polynomial },
|
|
17
19
|
minMaxRatio,
|
|
18
20
|
broadRatio,
|
|
19
21
|
noiseLevel: cutOff.positive,
|
|
@@ -24,22 +26,23 @@ export function xyAutoPeaksPicking(data, options = {}) {
|
|
|
24
26
|
let peaks = getPeakList(data, getPeakOptions);
|
|
25
27
|
if (lookNegative) {
|
|
26
28
|
getPeakOptions.noiseLevel = cutOff.negative;
|
|
27
|
-
|
|
29
|
+
getPeakOptions.maxCriteria = false;
|
|
30
|
+
peaks.push(...getPeakList(data, getPeakOptions));
|
|
28
31
|
}
|
|
29
32
|
return peaks;
|
|
30
33
|
}
|
|
31
34
|
function getPeakList(data, options) {
|
|
32
|
-
const { shape, broadWidth, optimize,
|
|
35
|
+
const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
|
|
33
36
|
let peakList = gsd(data, {
|
|
34
|
-
shape,
|
|
35
37
|
sgOptions,
|
|
38
|
+
maxCriteria,
|
|
36
39
|
minMaxRatio,
|
|
37
40
|
noiseLevel,
|
|
38
41
|
smoothY,
|
|
39
42
|
realTopDetection,
|
|
40
43
|
});
|
|
41
44
|
if (broadWidth) {
|
|
42
|
-
peakList = joinBroadPeaks(
|
|
45
|
+
peakList = joinBroadPeaks(peakList, {
|
|
43
46
|
broadRatio,
|
|
44
47
|
broadWidth,
|
|
45
48
|
shape,
|
|
@@ -47,25 +50,13 @@ function getPeakList(data, options) {
|
|
|
47
50
|
});
|
|
48
51
|
}
|
|
49
52
|
if (optimize) {
|
|
50
|
-
|
|
53
|
+
return optimizePeaks(data, peakList, {
|
|
51
54
|
shape,
|
|
52
|
-
|
|
55
|
+
factorLimits,
|
|
53
56
|
optimization,
|
|
54
57
|
});
|
|
55
58
|
}
|
|
56
|
-
return peakList;
|
|
57
|
-
}
|
|
58
|
-
function getNegativePeaks(data, options) {
|
|
59
|
-
let { x, y } = data;
|
|
60
|
-
let negativeDataY = new Float64Array(data.y.length);
|
|
61
|
-
for (let i = 0; i < negativeDataY.length; i++) {
|
|
62
|
-
negativeDataY[i] = -1 * y[i];
|
|
63
|
-
}
|
|
64
|
-
let peakList = getPeakList({ x, y: negativeDataY }, options);
|
|
65
|
-
for (const peak of peakList) {
|
|
66
|
-
peak.y *= -1;
|
|
67
|
-
}
|
|
68
|
-
return peakList;
|
|
59
|
+
return appendShapeAndFWHM(peakList, { shape });
|
|
69
60
|
}
|
|
70
61
|
function getCutOff(data, options) {
|
|
71
62
|
const { noiseLevel, useSanPlot, thresholdFactor } = options;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,cAAc,EAAE,
|
|
1
|
+
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,aAAa,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,QAAQ,CAAC;AAMhF,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAqD/B,MAAM,UAAU,kBAAkB,CAChC,IAAY,EACZ,UAAqC,EAAE;IAEvC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,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,YAAY,GAAG,KAAK,GACrB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;IAErD,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;IACD,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU;QAAE,OAAO,EAAE,CAAC;IAE1C,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,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,IAAI,KAAK,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;IAE9C,IAAI,YAAY,EAAE;QAChB,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;QAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;QACnC,KAAK,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC,CAAC;KAClD;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAA2B;IAC5D,MAAM,EACJ,KAAK,EACL,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,IAAI,QAAQ,GAAG,GAAG,CAAC,IAAI,EAAE;QACvB,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,IAAI,UAAU,EAAE;QACd,QAAQ,GAAG,cAAc,CAAC,QAAQ,EAAE;YAClC,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC;KACJ;IAED,IAAI,QAAQ,EAAE;QACZ,OAAO,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE;YACnC,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC;KACJ;IAED,OAAO,kBAAkB,CAAC,QAAQ,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC;AACjD,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"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "7.1.0",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -38,24 +38,23 @@
|
|
|
38
38
|
},
|
|
39
39
|
"homepage": "https://github.com/cheminfo/nmr-processing#readme",
|
|
40
40
|
"devDependencies": {
|
|
41
|
-
"@types/jest": "^27.4.
|
|
41
|
+
"@types/jest": "^27.4.1",
|
|
42
42
|
"cheminfo-build": "^1.1.11",
|
|
43
|
-
"cheminfo-types": "^
|
|
44
|
-
"eslint": "^8.
|
|
43
|
+
"cheminfo-types": "^1.1.0",
|
|
44
|
+
"eslint": "^8.10.0",
|
|
45
45
|
"eslint-config-cheminfo-typescript": "^10.3.0",
|
|
46
|
-
"jest": "^27.
|
|
46
|
+
"jest": "^27.5.1",
|
|
47
47
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
48
48
|
"md5": "^2.3.0",
|
|
49
49
|
"ml-array-median": "^1.1.6",
|
|
50
|
-
"nmr-xy-testdata": "^0.5.
|
|
50
|
+
"nmr-xy-testdata": "^0.5.1",
|
|
51
51
|
"openchemlib": "^7.4.3",
|
|
52
52
|
"prettier": "^2.5.1",
|
|
53
53
|
"rimraf": "^3.0.2",
|
|
54
54
|
"ts-jest": "^27.1.3",
|
|
55
|
-
"typescript": "^4.
|
|
55
|
+
"typescript": "^4.6.2"
|
|
56
56
|
},
|
|
57
57
|
"dependencies": {
|
|
58
|
-
"assign-deep": "^1.0.1",
|
|
59
58
|
"binary-search": "^1.3.6",
|
|
60
59
|
"cross-fetch": "^3.1.5",
|
|
61
60
|
"form-data": "^4.0.0",
|
|
@@ -64,18 +63,18 @@
|
|
|
64
63
|
"ml-array-rescale": "^1.3.7",
|
|
65
64
|
"ml-array-sequential-fill": "^1.1.8",
|
|
66
65
|
"ml-array-sum": "^1.1.6",
|
|
67
|
-
"ml-gsd": "^
|
|
66
|
+
"ml-gsd": "^10.1.2",
|
|
68
67
|
"ml-hclust": "^3.1.0",
|
|
69
|
-
"ml-levenberg-marquardt": "^4.
|
|
70
|
-
"ml-matrix": "^6.
|
|
68
|
+
"ml-levenberg-marquardt": "^4.1.0",
|
|
69
|
+
"ml-matrix": "^6.9.0",
|
|
71
70
|
"ml-matrix-convolution": "^1.0.0",
|
|
72
71
|
"ml-matrix-peaks-finder": "^1.0.0",
|
|
73
|
-
"ml-peak-shape-generator": "^4.
|
|
72
|
+
"ml-peak-shape-generator": "^4.1.1",
|
|
74
73
|
"ml-simple-clustering": "^0.1.0",
|
|
75
74
|
"ml-sparse-matrix": "^2.1.0",
|
|
76
|
-
"ml-spectra-processing": "^
|
|
75
|
+
"ml-spectra-processing": "^11.0.0",
|
|
77
76
|
"ml-tree-set": "^0.1.1",
|
|
78
|
-
"openchemlib-utils": "^1.
|
|
79
|
-
"spectrum-generator": "^
|
|
77
|
+
"openchemlib-utils": "^1.9.0",
|
|
78
|
+
"spectrum-generator": "^8.0.0"
|
|
80
79
|
}
|
|
81
80
|
}
|
package/src/index.ts
CHANGED
|
@@ -10,6 +10,7 @@ export * from './prediction/predictCOSY';
|
|
|
10
10
|
export * from './prediction/predictHSQC';
|
|
11
11
|
export * from './prediction/predictHMBC';
|
|
12
12
|
export * from './prediction/predictAll';
|
|
13
|
+
export * from './prediction/predictAllSpectra';
|
|
13
14
|
|
|
14
15
|
export * from './assignment/get1HAssignments';
|
|
15
16
|
export * from './assignment/get13CAssignments';
|
package/src/peaks/NMRPeak1D.ts
CHANGED
|
@@ -1,5 +1,8 @@
|
|
|
1
|
-
import type {
|
|
1
|
+
import type { PeakXYWidth } from 'cheminfo-types';
|
|
2
|
+
import type { Shape1D } from 'ml-peak-shape-generator';
|
|
2
3
|
|
|
3
|
-
export interface NMRPeak1D extends
|
|
4
|
+
export interface NMRPeak1D extends PeakXYWidth {
|
|
4
5
|
kind?: string;
|
|
6
|
+
fwhm?: number;
|
|
7
|
+
shape?: Shape1D;
|
|
5
8
|
}
|
|
@@ -70,6 +70,8 @@ type SignalInternMandatory = MakeMandatory<
|
|
|
70
70
|
'symRank' | 'mask' | 'peaksComp' | 'mask2' | 'maskPattern'
|
|
71
71
|
>;
|
|
72
72
|
|
|
73
|
+
type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
|
|
74
|
+
|
|
73
75
|
function checkSignalAfterCompilePattern(
|
|
74
76
|
signal: SignalIntern,
|
|
75
77
|
): asserts signal is SignalInternMandatory {
|
|
@@ -83,7 +85,7 @@ function checkSignalAfterCompilePattern(
|
|
|
83
85
|
}
|
|
84
86
|
|
|
85
87
|
const assignSignal = (
|
|
86
|
-
peak:
|
|
88
|
+
peak: NMRPeak1DIntern,
|
|
87
89
|
frequency: number,
|
|
88
90
|
nucleus: string,
|
|
89
91
|
): SignalIntern => {
|
|
@@ -115,7 +117,7 @@ const assignSignal = (
|
|
|
115
117
|
|
|
116
118
|
export function peaksToRanges(
|
|
117
119
|
data: DataXY,
|
|
118
|
-
peakList:
|
|
120
|
+
peakList: NMRPeak1DIntern[],
|
|
119
121
|
options: OptionsPeaksToRanges = {},
|
|
120
122
|
): NMRRange[] {
|
|
121
123
|
let {
|
|
@@ -280,7 +282,7 @@ export function peaksToRanges(
|
|
|
280
282
|
|
|
281
283
|
function detectSignals(
|
|
282
284
|
data: DataXY,
|
|
283
|
-
peakList:
|
|
285
|
+
peakList: NMRPeak1DIntern[],
|
|
284
286
|
options: OptionsDetectSignals = {},
|
|
285
287
|
): SignalIntern[] {
|
|
286
288
|
let {
|
|
@@ -29,7 +29,9 @@ interface IntergralData {
|
|
|
29
29
|
to: number;
|
|
30
30
|
}
|
|
31
31
|
|
|
32
|
-
export type Peak1DIntern = Omit<NMRPeak1D, 'y'> & {
|
|
32
|
+
export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape' | 'fwhm'> & {
|
|
33
|
+
intensity: number;
|
|
34
|
+
};
|
|
33
35
|
|
|
34
36
|
export interface SignalIntern {
|
|
35
37
|
delta: number;
|
|
@@ -0,0 +1,48 @@
|
|
|
1
|
+
import type { Molecule } from 'openchemlib';
|
|
2
|
+
|
|
3
|
+
import { OptionsSignalsToXY, signalsToXY } from '../signals/signalsToXY';
|
|
4
|
+
|
|
5
|
+
import { PredictAllOptions, predictAll } from './predictAll';
|
|
6
|
+
/**
|
|
7
|
+
* This function will generate an object compatible with NMR-ium
|
|
8
|
+
*
|
|
9
|
+
* @param molecule
|
|
10
|
+
* @param options
|
|
11
|
+
*/
|
|
12
|
+
|
|
13
|
+
export async function predictAllSpectra(
|
|
14
|
+
molecule: Molecule,
|
|
15
|
+
options: {
|
|
16
|
+
prediction?: PredictAllOptions;
|
|
17
|
+
simulation?: OptionsSignalsToXY;
|
|
18
|
+
} = {},
|
|
19
|
+
) {
|
|
20
|
+
const predictions = await predictAll(molecule, options.prediction);
|
|
21
|
+
const spectra: any[] = [];
|
|
22
|
+
const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
|
|
23
|
+
spectra.push(getProton(predictions.proton, options.simulation));
|
|
24
|
+
|
|
25
|
+
return result;
|
|
26
|
+
}
|
|
27
|
+
|
|
28
|
+
function getProton(prediction: any, options?: OptionsSignalsToXY) {
|
|
29
|
+
const { x, y } = signalsToXY(prediction.signals, options);
|
|
30
|
+
const spectrum = {
|
|
31
|
+
id: '',
|
|
32
|
+
// todo Array.from is temporary for the developement
|
|
33
|
+
data: { x: Array.from(x), re: Array.from(y), im: null },
|
|
34
|
+
info: {
|
|
35
|
+
nucleus: prediction.nucleus,
|
|
36
|
+
dimension: 1,
|
|
37
|
+
originFrequency: 400,
|
|
38
|
+
baseFrequency: 400,
|
|
39
|
+
pulseSequence: 'prediction',
|
|
40
|
+
experiment: 'proton',
|
|
41
|
+
isFt: true,
|
|
42
|
+
},
|
|
43
|
+
// todo: currently we disable the ranges because there is no ID
|
|
44
|
+
//ranges: { values: prediction.ranges },
|
|
45
|
+
};
|
|
46
|
+
|
|
47
|
+
return spectrum;
|
|
48
|
+
}
|
|
@@ -9,17 +9,17 @@ export function resurrectRange(part: string, options: any = {}) {
|
|
|
9
9
|
const { nucleus = '1h', frequency = 400 } = options;
|
|
10
10
|
const split = splitParenthesis(part);
|
|
11
11
|
if (!split.before) return;
|
|
12
|
-
// before parenthesis there should be only numbers but we will still split with space
|
|
13
|
-
const beforeParts = split.before
|
|
14
|
-
.split(/(?: |(?<=[0-9])-)/)
|
|
15
|
-
.map((part: string) => Number(part))
|
|
16
|
-
.filter((part: number) => !Number.isNaN(part));
|
|
17
|
-
if (beforeParts.length < 1 || beforeParts.length > 2) {
|
|
18
|
-
return;
|
|
19
|
-
}
|
|
20
|
-
const from = beforeParts[0];
|
|
21
|
-
const to = beforeParts.length > 1 ? beforeParts[1] : beforeParts[0];
|
|
22
12
|
|
|
13
|
+
const beforeMatch = /.*?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.]*).*/.exec(
|
|
14
|
+
split.before,
|
|
15
|
+
);
|
|
16
|
+
|
|
17
|
+
if (!beforeMatch || !beforeMatch.groups) return;
|
|
18
|
+
|
|
19
|
+
const isARange = beforeMatch.groups.to !== '';
|
|
20
|
+
|
|
21
|
+
const from = Number(beforeMatch.groups.from);
|
|
22
|
+
const to = isARange ? Number(beforeMatch.groups.to) : from;
|
|
23
23
|
const insideParts = split.inside.split(/ *, */);
|
|
24
24
|
let signal: NMRSignal1D = { delta: NaN, js: [] };
|
|
25
25
|
let range: NMRRange = { from, to, signals: [signal] };
|
|
@@ -37,20 +37,20 @@ export function resurrectRange(part: string, options: any = {}) {
|
|
|
37
37
|
if (multiplicityParts.length === 1) {
|
|
38
38
|
const multiplicity = multiplicityParts[0];
|
|
39
39
|
if (multiplicity === 'm') {
|
|
40
|
-
if (
|
|
41
|
-
// a
|
|
42
|
-
signal.delta =
|
|
40
|
+
if (isARange) {
|
|
41
|
+
// a real range
|
|
42
|
+
signal.delta = (from + to) / 2;
|
|
43
43
|
signal.multiplicity = multiplicity;
|
|
44
44
|
} else {
|
|
45
|
-
// a
|
|
46
|
-
signal.delta =
|
|
45
|
+
// a complex signal
|
|
46
|
+
signal.delta = from;
|
|
47
47
|
signal.multiplicity = multiplicity;
|
|
48
48
|
}
|
|
49
49
|
} else {
|
|
50
50
|
// looks like a real multiplicity, s, d, dd, etc..
|
|
51
|
-
if (
|
|
51
|
+
if (!isARange) {
|
|
52
52
|
// a complex signal
|
|
53
|
-
signal.delta =
|
|
53
|
+
signal.delta = from;
|
|
54
54
|
signal.multiplicity = multiplicity;
|
|
55
55
|
}
|
|
56
56
|
}
|