nmr-processing 6.0.2 → 6.0.3
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/prediction/predictProton.js +1 -1
- package/lib/prediction/predictProton.js.map +1 -1
- package/lib/prediction/utils/getPredictions.js +1 -1
- package/lib/prediction/utils/getPredictions.js.map +1 -1
- package/lib/ranges/rangesToACS.js +8 -9
- package/lib/ranges/rangesToACS.js.map +1 -1
- package/lib/signals/simulation/simulate1D.js +2 -1
- package/lib/signals/simulation/simulate1D.js.map +1 -1
- package/lib-esm/prediction/predictProton.js +1 -1
- package/lib-esm/prediction/predictProton.js.map +1 -1
- package/lib-esm/prediction/utils/getPredictions.js +1 -1
- package/lib-esm/prediction/utils/getPredictions.js.map +1 -1
- package/lib-esm/ranges/rangesToACS.js +8 -9
- package/lib-esm/ranges/rangesToACS.js.map +1 -1
- package/lib-esm/signals/simulation/simulate1D.js +2 -1
- package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
- package/package.json +15 -27
- package/src/prediction/predictProton.ts +1 -1
- package/src/prediction/utils/getPredictions.ts +1 -1
- package/src/ranges/rangesToACS.ts +18 -11
- package/src/signals/simulation/simulate1D.ts +2 -1
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@@ -24,7 +24,7 @@ async function predictProton(molecule, options = {}) {
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formData.append('molfile', molfile);
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const response = await (0, cross_fetch_1.default)('https://www.nmrdb.org/service/predictor', {
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method: 'POST',
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-
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+
// @ts-expect-error RequestInit type does not include FormData.
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body: formData,
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});
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result = await response.text();
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAgC;AAChC,0DAAiC;AAEjC,yDAI2B;AAG3B,wDAAqD;AACrD,gEAA6D;AAkBtD,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC1B,QAAQ,GAAG,QAAQ,CAAC,cAAc,EAAE,CAAC;IACrC,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,mBAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,IAAA,qBAAK,EAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd
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+
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAgC;AAChC,0DAAiC;AAEjC,yDAI2B;AAG3B,wDAAqD;AACrD,gEAA6D;AAkBtD,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC1B,QAAQ,GAAG,QAAQ,CAAC,cAAc,EAAE,CAAC;IACrC,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,mBAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,IAAA,qBAAK,EAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd,+DAA+D;YAC/D,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;QACH,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,IAAI,KAAK,EAAE;YACT,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;SACxB;KACF;IAED,MAAM,MAAM,GAAG,IAAA,4CAAwB,EAAC,QAAQ,CAAC,CAAC;IAClD,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IACvD,MAAM,aAAa,GAAG,IAAA,yBAAW,EAAC,OAAO,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO;QACP,MAAM;QACN,OAAO,EAAE,IAAI;QACb,aAAa;QACb,OAAO;QACP,MAAM,EAAE,IAAA,iCAAe,EAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AAxCD,sCAwCC;AAED,SAAS,YAAY,CACnB,MAAc,EACd,QAAkB,EAClB,MAAgB;IAEhB,IAAI,QAAQ,CAAC,WAAW,EAAE,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE;QAC1B,MAAM,KAAK,CAAC,wBAAwB,MAAM,EAAE,CAAC,CAAC;KAC/C;IACD,IAAI,cAAc,GAAG,IAAA,yCAAqB,EAAC,QAAQ,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3E,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;IACtD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,IAAI,IAAI,IAAI,KAAK,EAAE;QACtB,IAAI,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACxC,IAAI,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAChC,IAAI,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACjC,IAAI,MAAM,GAAgB;YACxB,KAAK,EAAE,CAAC,IAAI,CAAC;YACb,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;YACtB,OAAO,EAAE,CAAC;YACV,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,EAAE;SACP,CAAC;QAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;SACvD;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,IAAI,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACtC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;gBACb,QAAQ,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClC,KAAK,EAAE,CAAC,MAAM,CAAC;gBACf,MAAM,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,YAAY,EAAE,GAAG;gBACjB,UAAU,EAAE,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC;aACzC,CAAC,CAAC;YACH,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC;SACnD;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
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@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
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exports.getPredictions = void 0;
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async function getPredictions(key, molecule, predictOptions, predictor, predictions) {
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let prediction;
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if (predictions
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if (predictions === null || predictions === void 0 ? void 0 : predictions[key]) {
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prediction = predictions[key];
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}
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else if (predictor) {
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@@ -1 +1 @@
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-
{"version":3,"file":"getPredictions.js","sourceRoot":"","sources":["../../../src/prediction/utils/getPredictions.ts"],"names":[],"mappings":";;;AAMO,KAAK,UAAU,cAAc,CAClC,GAAW,EACX,QAAkB,EAClB,cAA8B,EAC9B,SAAsB,EACtB,WAAyB;IAEzB,IAAI,UAAoC,CAAC;IACzC,IAAI,WAAW,
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{"version":3,"file":"getPredictions.js","sourceRoot":"","sources":["../../../src/prediction/utils/getPredictions.ts"],"names":[],"mappings":";;;AAMO,KAAK,UAAU,cAAc,CAClC,GAAW,EACX,QAAkB,EAClB,cAA8B,EAC9B,SAAsB,EACtB,WAAyB;IAEzB,IAAI,UAAoC,CAAC;IACzC,IAAI,WAAW,aAAX,WAAW,uBAAX,WAAW,CAAG,GAAG,CAAC,EAAE;QACtB,UAAU,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC;KAC/B;SAAM,IAAI,SAAS,EAAE;QACpB,MAAM,aAAa,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC;QACrC,UAAU,GAAG,aAAa;YACxB,CAAC,CAAC,MAAM,aAAa,CAAC,QAAQ,EAAE,cAAc,CAAC,GAAG,CAAC,CAAC;YACpD,CAAC,CAAC,SAAS,CAAC;KACf;IACD,OAAO,UAAU,CAAC;AACpB,CAAC;AAjBD,wCAiBC"}
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@@ -26,15 +26,14 @@ const globalOptions = {
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function rangesToACS(ranges, options = {}) {
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if (!options.nucleus)
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options.nucleus = '1H';
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-
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let defaultOptions = globalOptions[nucleus];
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const nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
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const defaultOptions = globalOptions[nucleus];
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options = Object.assign({}, defaultOptions, { ascending: false, format: 'IMJA' }, options);
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ranges = JSON.parse(JSON.stringify(ranges));
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if (options.ascending === true) {
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ranges.sort((a, b) => {
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const fromA = Math.min(a.from, a.to);
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const fromB = Math.min(b.from, b.to);
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return fromA - fromB;
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});
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}
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@@ -48,8 +47,8 @@ function formatAcs(ranges, options) {
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let acs = spectroInformation(options);
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if (acs.length === 0)
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acs = 'δ ';
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-
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for (
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const acsRanges = [];
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for (const range of ranges) {
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if (uselessKind(range.kind, options.filter))
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continue;
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pushDelta(range, acsRanges, options);
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@@ -62,7 +61,7 @@ function formatAcs(ranges, options) {
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}
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}
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function spectroInformation(options) {
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const parenthesis = [];
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let strings = `${formatNucleus(options.nucleus)} NMR`;
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if (options.solvent) {
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parenthesis.push(formatMF(options.solvent));
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@@ -81,7 +80,7 @@ function spectroInformation(options) {
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function pushDelta(range, acsRanges, options) {
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let strings = '';
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let parenthesis = [];
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const fromTo = [range.from, range.to];
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if (range.signals) {
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range.signals = range.signals.filter((signal) => !uselessKind(signal.kind, options.filter));
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}
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{"version":3,"file":"rangesToACS.js","sourceRoot":"","sources":["../../src/ranges/rangesToACS.ts"],"names":[],"mappings":";;;AAAA,uEAAoE;AACpE,mFAAgF;AAIhF,MAAM,aAAa,
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+
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@@ -68,7 +68,8 @@ spinSystem, options = {}) {
|
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|
68
68
|
else {
|
|
69
69
|
const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants, multiplicity, spinSystem.connectivity, clusterFake);
|
|
70
70
|
const hamSize = hamiltonian.rows;
|
|
71
|
-
|
|
71
|
+
// TODO: add support for sparse matrix in matrix types.
|
|
72
|
+
// @ts-expect-error sparse matrix not supported
|
|
72
73
|
const evd = new ml_matrix_1.EVD(hamiltonian);
|
|
73
74
|
const V = evd.eigenvectorMatrix;
|
|
74
75
|
const diagB = evd.realEigenvalues;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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@@ -18,7 +18,7 @@ export async function predictProton(molecule, options = {}) {
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18
18
|
formData.append('molfile', molfile);
|
|
19
19
|
const response = await fetch('https://www.nmrdb.org/service/predictor', {
|
|
20
20
|
method: 'POST',
|
|
21
|
-
|
|
21
|
+
// @ts-expect-error RequestInit type does not include FormData.
|
|
22
22
|
body: formData,
|
|
23
23
|
});
|
|
24
24
|
result = await response.text();
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,aAAa,CAAC;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAC;AAEjC,OAAO,EACL,iCAAiC,EACjC,qBAAqB,EACrB,wBAAwB,GACzB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAkB7D,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC1B,QAAQ,GAAG,QAAQ,CAAC,cAAc,EAAE,CAAC;IACrC,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,QAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd
|
|
1
|
+
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,aAAa,CAAC;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAC;AAEjC,OAAO,EACL,iCAAiC,EACjC,qBAAqB,EACrB,wBAAwB,GACzB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAkB7D,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC1B,QAAQ,GAAG,QAAQ,CAAC,cAAc,EAAE,CAAC;IACrC,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,QAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd,+DAA+D;YAC/D,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;QACH,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,IAAI,KAAK,EAAE;YACT,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;SACxB;KACF;IAED,MAAM,MAAM,GAAG,wBAAwB,CAAC,QAAQ,CAAC,CAAC;IAClD,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IACvD,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO;QACP,MAAM;QACN,OAAO,EAAE,IAAI;QACb,aAAa;QACb,OAAO;QACP,MAAM,EAAE,eAAe,CAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CACnB,MAAc,EACd,QAAkB,EAClB,MAAgB;IAEhB,IAAI,QAAQ,CAAC,WAAW,EAAE,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE;QAC1B,MAAM,KAAK,CAAC,wBAAwB,MAAM,EAAE,CAAC,CAAC;KAC/C;IACD,IAAI,cAAc,GAAG,qBAAqB,CAAC,QAAQ,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3E,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;IACtD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,IAAI,IAAI,IAAI,KAAK,EAAE;QACtB,IAAI,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACxC,IAAI,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAChC,IAAI,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACjC,IAAI,MAAM,GAAgB;YACxB,KAAK,EAAE,CAAC,IAAI,CAAC;YACb,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;YACtB,OAAO,EAAE,CAAC;YACV,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,EAAE;SACP,CAAC;QAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;SACvD;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,IAAI,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACtC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;gBACb,QAAQ,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClC,KAAK,EAAE,CAAC,MAAM,CAAC;gBACf,MAAM,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,YAAY,EAAE,GAAG;gBACjB,UAAU,EAAE,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC;aACzC,CAAC,CAAC;YACH,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC;SACnD;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
export async function getPredictions(key, molecule, predictOptions, predictor, predictions) {
|
|
2
2
|
let prediction;
|
|
3
|
-
if (predictions
|
|
3
|
+
if (predictions === null || predictions === void 0 ? void 0 : predictions[key]) {
|
|
4
4
|
prediction = predictions[key];
|
|
5
5
|
}
|
|
6
6
|
else if (predictor) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getPredictions.js","sourceRoot":"","sources":["../../../src/prediction/utils/getPredictions.ts"],"names":[],"mappings":"AAMA,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,GAAW,EACX,QAAkB,EAClB,cAA8B,EAC9B,SAAsB,EACtB,WAAyB;IAEzB,IAAI,UAAoC,CAAC;IACzC,IAAI,WAAW,
|
|
1
|
+
{"version":3,"file":"getPredictions.js","sourceRoot":"","sources":["../../../src/prediction/utils/getPredictions.ts"],"names":[],"mappings":"AAMA,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,GAAW,EACX,QAAkB,EAClB,cAA8B,EAC9B,SAAsB,EACtB,WAAyB;IAEzB,IAAI,UAAoC,CAAC;IACzC,IAAI,WAAW,aAAX,WAAW,uBAAX,WAAW,CAAG,GAAG,CAAC,EAAE;QACtB,UAAU,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC;KAC/B;SAAM,IAAI,SAAS,EAAE;QACpB,MAAM,aAAa,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC;QACrC,UAAU,GAAG,aAAa;YACxB,CAAC,CAAC,MAAM,aAAa,CAAC,QAAQ,EAAE,cAAc,CAAC,GAAG,CAAC,CAAC;YACpD,CAAC,CAAC,SAAS,CAAC;KACf;IACD,OAAO,UAAU,CAAC;AACpB,CAAC"}
|
|
@@ -23,15 +23,14 @@ const globalOptions = {
|
|
|
23
23
|
export function rangesToACS(ranges, options = {}) {
|
|
24
24
|
if (!options.nucleus)
|
|
25
25
|
options.nucleus = '1H';
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
let defaultOptions = globalOptions[nucleus];
|
|
26
|
+
const nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
|
|
27
|
+
const defaultOptions = globalOptions[nucleus];
|
|
29
28
|
options = Object.assign({}, defaultOptions, { ascending: false, format: 'IMJA' }, options);
|
|
30
29
|
ranges = JSON.parse(JSON.stringify(ranges));
|
|
31
30
|
if (options.ascending === true) {
|
|
32
31
|
ranges.sort((a, b) => {
|
|
33
|
-
|
|
34
|
-
|
|
32
|
+
const fromA = Math.min(a.from, a.to);
|
|
33
|
+
const fromB = Math.min(b.from, b.to);
|
|
35
34
|
return fromA - fromB;
|
|
36
35
|
});
|
|
37
36
|
}
|
|
@@ -44,8 +43,8 @@ function formatAcs(ranges, options) {
|
|
|
44
43
|
let acs = spectroInformation(options);
|
|
45
44
|
if (acs.length === 0)
|
|
46
45
|
acs = 'δ ';
|
|
47
|
-
|
|
48
|
-
for (
|
|
46
|
+
const acsRanges = [];
|
|
47
|
+
for (const range of ranges) {
|
|
49
48
|
if (uselessKind(range.kind, options.filter))
|
|
50
49
|
continue;
|
|
51
50
|
pushDelta(range, acsRanges, options);
|
|
@@ -58,7 +57,7 @@ function formatAcs(ranges, options) {
|
|
|
58
57
|
}
|
|
59
58
|
}
|
|
60
59
|
function spectroInformation(options) {
|
|
61
|
-
|
|
60
|
+
const parenthesis = [];
|
|
62
61
|
let strings = `${formatNucleus(options.nucleus)} NMR`;
|
|
63
62
|
if (options.solvent) {
|
|
64
63
|
parenthesis.push(formatMF(options.solvent));
|
|
@@ -77,7 +76,7 @@ function spectroInformation(options) {
|
|
|
77
76
|
function pushDelta(range, acsRanges, options) {
|
|
78
77
|
let strings = '';
|
|
79
78
|
let parenthesis = [];
|
|
80
|
-
|
|
79
|
+
const fromTo = [range.from, range.to];
|
|
81
80
|
if (range.signals) {
|
|
82
81
|
range.signals = range.signals.filter((signal) => !uselessKind(signal.kind, options.filter));
|
|
83
82
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"rangesToACS.js","sourceRoot":"","sources":["../../src/ranges/rangesToACS.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,yBAAyB,EAAE,MAAM,qCAAqC,CAAC;AAIhF,MAAM,aAAa,
|
|
1
|
+
{"version":3,"file":"rangesToACS.js","sourceRoot":"","sources":["../../src/ranges/rangesToACS.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,yBAAyB,EAAE,MAAM,qCAAqC,CAAC;AAIhF,MAAM,aAAa,GAQf;IACF,CAAC,EAAE;QACD,OAAO,EAAE,IAAI;QACb,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;IACD,CAAC,EAAE;QACD,OAAO,EAAE,KAAK;QACd,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;IACD,CAAC,EAAE;QACD,OAAO,EAAE,KAAK;QACd,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;CACF,CAAC;AAmCF,MAAM,UAAU,WAAW,CACzB,MAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,CAAC,OAAO,CAAC,OAAO;QAAE,OAAO,CAAC,OAAO,GAAG,IAAI,CAAC;IAC7C,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;IACpE,MAAM,cAAc,GAAG,aAAa,CAAC,OAAO,CAAC,CAAC;IAC9C,OAAO,GAAG,MAAM,CAAC,MAAM,CACrB,EAAE,EACF,cAAc,EACd,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,EACpC,OAAO,CACR,CAAC;IAEF,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;IAC5C,IAAI,OAAO,CAAC,SAAS,KAAK,IAAI,EAAE;QAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACnB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;YACrC,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;YACrC,OAAO,KAAK,GAAG,KAAK,CAAC;QACvB,CAAC,CAAC,CAAC;KACJ;IAED,IAAI,SAAS,GAAG,SAAS,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC3C,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC;QAAE,SAAS,IAAI,GAAG,CAAC;IAE3C,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,SAAS,CAAC,MAAkB,EAAE,OAAY;IACjD,IAAI,GAAG,GAAG,kBAAkB,CAAC,OAAO,CAAC,CAAC;IACtC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;QAAE,GAAG,GAAG,IAAI,CAAC;IACjC,MAAM,SAAS,GAAa,EAAE,CAAC;IAC/B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,IAAI,WAAW,CAAC,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC;YAAE,SAAS;QACtD,SAAS,CAAC,KAAK,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;KACtC;IACD,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE;QACxB,OAAO,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;KACnC;SAAM;QACL,OAAO,EAAE,CAAC;KACX;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAY;IACtC,MAAM,WAAW,GAAG,EAAE,CAAC;IACvB,IAAI,OAAO,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC;IACtD,IAAI,OAAO,CAAC,OAAO,EAAE;QACnB,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC;KAC7C;IACD,IAAI,OAAO,CAAC,iBAAiB,EAAE;QAC7B,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,iBAAiB,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;KACvE;IACD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE;QAC1B,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;KAC/C;SAAM;QACL,OAAO,IAAI,MAAM,CAAC;KACnB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,SAAS,CAAC,KAAe,EAAE,SAAmB,EAAE,OAAY;IACnE,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,IAAI,WAAW,GAAQ,EAAE,CAAC;IAC1B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,CAAC,CAAC;IAEtC,IAAI,KAAK,CAAC,OAAO,EAAE;QACjB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAClC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC,CACtD,CAAC;KACH;IAED,IAAI,KAAK,CAAC,OAAO,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;QAC7C,IAAI,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC;QAC5B,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;YACtB,IAAI,OAAO,CAAC,SAAS,KAAK,IAAI,EAAE;gBAC9B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;oBACpB,OAAO,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;gBAC3B,CAAC,CAAC,CAAC;aACJ;YACD,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;YAC3D,OAAO,IAAI,KAAK,WAAW,CAAC,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC;YAC9C,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;gBAC1B,WAAW,GAAG,EAAE,CAAC;gBACjB,IAAI,MAAM,CAAC,KAAK,KAAK,SAAS,EAAE;oBAC9B,OAAO,GAAG,eAAe,CAAC,OAAO,CAAC,CAAC;oBACnC,OAAO,IAAI,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;iBACzD;gBACD,MAAM,KAAK,GAAa;oBACtB,IAAI,EAAE,MAAM,CAAC,gBAAgB;oBAC7B,EAAE,EAAE,MAAM,CAAC,gBAAgB;iBAC5B,CAAC;gBACF,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBAClD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;aACvE;YACD,OAAO,IAAI,GAAG,CAAC;SAChB;aAAM;YACL,WAAW,GAAG,EAAE,CAAC;YACjB,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,EAAE;gBAClC,OAAO,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;gBAC5D,YAAY,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBACtD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;aACvE;iBAAM;gBACL,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;gBAC3D,YAAY,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBACtD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,GAAG,CAAC;aAC5D;SACF;KACF;SAAM;QACL,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;QAC3D,MAAM,MAAM,GAAQ,EAAE,CAAC;QACvB,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;QAClD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;YAAE,OAAO,IAAI,KAAK,WAAW,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@@ -63,7 +63,8 @@ spinSystem, options = {}) {
|
|
|
63
63
|
else {
|
|
64
64
|
const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants, multiplicity, spinSystem.connectivity, clusterFake);
|
|
65
65
|
const hamSize = hamiltonian.rows;
|
|
66
|
-
|
|
66
|
+
// TODO: add support for sparse matrix in matrix types.
|
|
67
|
+
// @ts-expect-error sparse matrix not supported
|
|
67
68
|
const evd = new EVD(hamiltonian);
|
|
68
69
|
const V = evd.eigenvectorMatrix;
|
|
69
70
|
const diagB = evd.realEigenvalues;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "6.0.
|
|
3
|
+
"version": "6.0.3",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -37,55 +37,43 @@
|
|
|
37
37
|
"url": "https://github.com/cheminfo/nmr-processing/issues"
|
|
38
38
|
},
|
|
39
39
|
"homepage": "https://github.com/cheminfo/nmr-processing#readme",
|
|
40
|
-
"jest": {
|
|
41
|
-
"preset": "ts-jest",
|
|
42
|
-
"testEnvironment": "node"
|
|
43
|
-
},
|
|
44
|
-
"prettier": {
|
|
45
|
-
"arrowParens": "always",
|
|
46
|
-
"semi": true,
|
|
47
|
-
"singleQuote": true,
|
|
48
|
-
"tabWidth": 2,
|
|
49
|
-
"trailingComma": "all"
|
|
50
|
-
},
|
|
51
40
|
"devDependencies": {
|
|
52
|
-
"@types/jest": "^27.0
|
|
41
|
+
"@types/jest": "^27.4.0",
|
|
53
42
|
"cheminfo-build": "^1.1.11",
|
|
54
43
|
"cheminfo-types": "^0.9.1",
|
|
55
|
-
"eslint": "^8.
|
|
56
|
-
"eslint-config-cheminfo-typescript": "^10.
|
|
57
|
-
"
|
|
58
|
-
"jest": "^27.4.5",
|
|
44
|
+
"eslint": "^8.7.0",
|
|
45
|
+
"eslint-config-cheminfo-typescript": "^10.3.0",
|
|
46
|
+
"jest": "^27.4.7",
|
|
59
47
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
60
48
|
"md5": "^2.3.0",
|
|
61
|
-
"ml-array-median": "^1.1.
|
|
49
|
+
"ml-array-median": "^1.1.6",
|
|
62
50
|
"nmr-xy-testdata": "^0.2.1",
|
|
63
51
|
"openchemlib": "^7.4.3",
|
|
64
52
|
"prettier": "^2.5.1",
|
|
65
53
|
"rimraf": "^3.0.2",
|
|
66
|
-
"ts-jest": "^27.1.
|
|
67
|
-
"typescript": "^4.5.
|
|
54
|
+
"ts-jest": "^27.1.3",
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"cross-fetch": "^3.1.
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"ml-array-mean": "^1.1.6",
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"ml-array-rescale": "^1.3.7",
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"ml-array-sequential-fill": "^1.1.8",
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"ml-array-sum": "^1.1.6",
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"ml-gsd": "^9.1.0",
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"ml-hclust": "^3.1.0",
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"ml-levenberg-marquardt": "^4.0.0",
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"ml-matrix": "^6.8.2",
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"ml-matrix-convolution": "^1.0.0",
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"ml-matrix-peaks-finder": "^1.0.0",
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"ml-peak-shape-generator": "^4.0.1",
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"ml-sparse-matrix": "^2.1.0",
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"ml-spectra-processing": "^8.0
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"ml-tree-set": "^0.1.1",
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"openchemlib-utils": "^1.8.0",
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"spectrum-generator": "^6.0.2"
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@@ -46,7 +46,7 @@ export async function predictProton(
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formData.append('molfile', molfile);
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const response = await fetch('https://www.nmrdb.org/service/predictor', {
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method: 'POST',
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predictions?: Predictions,
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) {
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let prediction: Prediction1D | undefined;
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if (predictions
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if (predictions?.[key]) {
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prediction = predictions[key];
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} else if (predictor) {
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const fromPredictor = predictor[key];
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@@ -3,7 +3,15 @@ import { signalMultiplicityPattern } from '../signal/signalMultiplicityPattern';
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import type { NMRSignal1D } from '../signals/NMRSignal1D';
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import type { NMRRange } from '../xy/NMRRange';
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const globalOptions
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const globalOptions: Record<
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string,
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{
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nucleus: string;
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nbDecimalDelta: number;
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nbDecimalJ: number;
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observedFrequency: number;
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}
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> = {
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h: {
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nucleus: '1H',
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nbDecimalDelta: 2,
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@@ -62,9 +70,8 @@ export function rangesToACS(
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options: RangesToACSOptions = {},
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let defaultOptions = globalOptions[nucleus];
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const nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
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const defaultOptions = globalOptions[nucleus];
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options = Object.assign(
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{},
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defaultOptions,
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@@ -75,13 +82,13 @@ export function rangesToACS(
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if (options.ascending === true) {
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const fromB = Math.min(b.from, b.to);
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return fromA - fromB;
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});
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}
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let acsString = formatAcs(ranges, options);
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+
let acsString = formatAcs(ranges, options);
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|
if (acsString.length > 0) acsString += '.';
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|
return acsString;
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|
@@ -90,8 +97,8 @@ export function rangesToACS(
|
|
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90
97
|
function formatAcs(ranges: NMRRange[], options: any) {
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91
98
|
let acs = spectroInformation(options);
|
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99
|
if (acs.length === 0) acs = 'δ ';
|
|
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|
-
|
|
94
|
-
for (
|
|
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
|
}
|
|
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111
|
|
|
105
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|
function spectroInformation(options: any) {
|
|
106
|
-
|
|
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|
+
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
|
-
|
|
132
|
+
const fromTo = [range.from, range.to];
|
|
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133
|
|
|
127
134
|
if (range.signals) {
|
|
128
135
|
range.signals = range.signals.filter(
|
|
@@ -133,7 +133,8 @@ export default function simulate1D(
|
|
|
133
133
|
clusterFake,
|
|
134
134
|
);
|
|
135
135
|
const hamSize = hamiltonian.rows;
|
|
136
|
-
|
|
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;
|