nmr-processing 7.4.3 → 8.0.0

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Files changed (22) hide show
  1. package/lib/assignment/getAssignments.js +1 -1
  2. package/lib/assignment/getAssignments.js.map +1 -1
  3. package/lib/databases/getDatabase.d.ts +6 -1
  4. package/lib/databases/getDatabase.js +13 -3
  5. package/lib/databases/getDatabase.js.map +1 -1
  6. package/lib/index.d.ts +1 -1
  7. package/lib/prediction/predictAllSpectra.d.ts +22 -4
  8. package/lib/prediction/predictAllSpectra.js +102 -16
  9. package/lib/prediction/predictAllSpectra.js.map +1 -1
  10. package/lib/xyz/NMRSignal2D.d.ts +3 -3
  11. package/lib-esm/assignment/getAssignments.js +1 -1
  12. package/lib-esm/assignment/getAssignments.js.map +1 -1
  13. package/lib-esm/databases/getDatabase.js +13 -3
  14. package/lib-esm/databases/getDatabase.js.map +1 -1
  15. package/lib-esm/prediction/predictAllSpectra.js +102 -16
  16. package/lib-esm/prediction/predictAllSpectra.js.map +1 -1
  17. package/package.json +12 -12
  18. package/src/assignment/getAssignments.ts +1 -1
  19. package/src/databases/getDatabase.ts +19 -2
  20. package/src/index.ts +1 -1
  21. package/src/prediction/predictAllSpectra.ts +151 -14
  22. package/src/xyz/NMRSignal2D.ts +3 -3
package/lib/assignment/getAssignments.js CHANGED
@@ -10,7 +10,7 @@ const checkIDs_1 = require("./utils/getAssignment/checkIDs");
10
10
  const getTargetsAndCorrelations_1 = require("./utils/getAssignment/getTargetsAndCorrelations");
11
11
  const getWorkFlow_1 = __importDefault(require("./utils/getAssignment/getWorkFlow"));
12
12
  async function getAssignments(input, options = {}) {
13
- let { restrictionByCS = {}, justAssign, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
13
+ let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
14
14
  const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
15
15
  const molecule = input.molecule;
16
16
  if (!molecule)
package/lib/assignment/getAssignments.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;AACA,yDAAsE;AAQtE,6EAIgD;AAChD,6DAA0D;AAC1D,+FAA4F;AAC5F,oFAA4D;AA0ErD,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,CAAC,EACZ,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAA,mBAAQ,EAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAA,qDAAyB,EACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,qBAAW,EAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,IAAA,mCAAgB,EAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC;AAzDD,wCAyDC"}
1
+ {"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;AACA,yDAAsE;AAQtE,6EAIgD;AAChD,6DAA0D;AAC1D,+FAA4F;AAC5F,oFAA4D;AA0ErD,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,IAAI,EACf,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAA,mBAAQ,EAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAA,qDAAyB,EACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,qBAAW,EAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,IAAA,mCAAgB,EAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC;AAzDD,wCAyDC"}
package/lib/databases/getDatabase.d.ts CHANGED
@@ -1,2 +1,7 @@
1
1
  import { DatabaseNMREntry } from './DatabaseNMREntry';
2
- export declare function getDatabase(url?: string): Promise<DatabaseNMREntry[]>;
2
+ export declare function getDatabase(url?: string, options?: {
3
+ /**
4
+ * @default 'tsv'
5
+ */
6
+ format?: 'tsv' | 'json';
7
+ }): Promise<DatabaseNMREntry[]>;
package/lib/databases/getDatabase.js CHANGED
@@ -3,13 +3,23 @@ Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.getDatabase = void 0;
4
4
  const cross_fetch_1 = require("cross-fetch");
5
5
  const resurrectRange_1 = require("../utilities/resurrectRange");
6
- async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
6
+ async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
7
+ const { format = 'tsv' } = options;
7
8
  if (url.includes('google.com')) {
8
9
  url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(url)}/export?format=tsv`;
9
10
  }
11
+ let parsed;
10
12
  const response = await (0, cross_fetch_1.fetch)(url);
11
- const result = await response.text();
12
- const parsed = parseData(result);
13
+ switch (format) {
14
+ case 'tsv':
15
+ parsed = parseData(await response.text());
16
+ break;
17
+ case 'json':
18
+ parsed = await response.json();
19
+ break;
20
+ default:
21
+ throw new Error('unknown database format');
22
+ }
13
23
  const results = [];
14
24
  for (let line of parsed.data) {
15
25
  const result = {
package/lib/databases/getDatabase.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"getDatabase.js","sourceRoot":"","sources":["../../src/databases/getDatabase.ts"],"names":[],"mappings":";;;AAAA,6CAAoC;AAEpC,gEAA6D;AAItD,KAAK,UAAU,WAAW,CAC/B,GAAG,GAAG,sGAAsG;IAE5G,IAAI,GAAG,CAAC,QAAQ,CAAC,YAAY,CAAC,EAAE;QAC9B,GAAG,GAAG,kDAAkD,iBAAiB,CACvE,GAAG,CACJ,oBAAoB,CAAC;KACvB;IAED,MAAM,QAAQ,GAAG,MAAM,IAAA,mBAAK,EAAC,GAAG,CAAC,CAAC;IAClC,MAAM,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;IACrC,MAAM,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC;IAEjC,MAAM,OAAO,GAAG,EAAE,CAAC;IAEnB,KAAK,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;QAC5B,MAAM,MAAM,GAAqB;YAC/B,MAAM,EAAE,EAAE;YACV,OAAO,EAAE,EAAE;YACX,OAAO,EAAE,EAAE;YACX,QAAQ,EAAE,EAAE;YACZ,KAAK,EAAE,EAAE;YACT,IAAI,EAAE,EAAE;YACR,MAAM,EAAE,EAAE;SACX,CAAC;QACF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACpC,QAAQ,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACvB,KAAK,QAAQ;oBACX,MAAM,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,UAAU;oBACb,MAAM,CAAC,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC1B,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,KAAK;wBAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBAC7C,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,IAAI;wBAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzD,MAAM;gBACR,KAAK,QAAQ,CAAC,CAAC;oBACb,MAAM,KAAK,GAAG,IAAA,+BAAc,EAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBACtC,IAAI,KAAK;wBAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;oBACrC,MAAM;iBACP;gBACD;oBACE,MAAM,IAAI,KAAK,CAAC,wBAAwB,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;aAC9D;SACF;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAzDD,kCAyDC;AAED,SAAS,iBAAiB,CAAC,GAAW;IACpC,OAAO,GAAG,CAAC,OAAO,CAAC,4BAA4B,EAAE,SAAS,CAAC,CAAC;AAC9D,CAAC;AAED,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,MAAM,GAAG,IAAI;SAChB,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;SACrC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IAE9E,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACxB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAC7B,OAAO;QACL,MAAM;QACN,KAAK;QACL,IAAI;KACL,CAAC;AACJ,CAAC"}
1
+ {"version":3,"file":"getDatabase.js","sourceRoot":"","sources":["../../src/databases/getDatabase.ts"],"names":[],"mappings":";;;AAAA,6CAAoC;AAEpC,gEAA6D;AAItD,KAAK,UAAU,WAAW,CAC/B,GAAG,GAAG,sGAAsG,EAC5G,UAKI,EAAE;IAEN,MAAM,EAAE,MAAM,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEnC,IAAI,GAAG,CAAC,QAAQ,CAAC,YAAY,CAAC,EAAE;QAC9B,GAAG,GAAG,kDAAkD,iBAAiB,CACvE,GAAG,CACJ,oBAAoB,CAAC;KACvB;IAED,IAAI,MAAM,CAAC;IACX,MAAM,QAAQ,GAAG,MAAM,IAAA,mBAAK,EAAC,GAAG,CAAC,CAAC;IAClC,QAAQ,MAAM,EAAE;QACd,KAAK,KAAK;YACR,MAAM,GAAG,SAAS,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC;YAC1C,MAAM;QACR,KAAK,MAAM;YACT,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YAC/B,MAAM;QACR;YACE,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;KAC9C;IAED,MAAM,OAAO,GAAG,EAAE,CAAC;IAEnB,KAAK,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;QAC5B,MAAM,MAAM,GAAqB;YAC/B,MAAM,EAAE,EAAE;YACV,OAAO,EAAE,EAAE;YACX,OAAO,EAAE,EAAE;YACX,QAAQ,EAAE,EAAE;YACZ,KAAK,EAAE,EAAE;YACT,IAAI,EAAE,EAAE;YACR,MAAM,EAAE,EAAE;SACX,CAAC;QACF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACpC,QAAQ,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACvB,KAAK,QAAQ;oBACX,MAAM,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,UAAU;oBACb,MAAM,CAAC,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC1B,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,KAAK;wBAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBAC7C,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,IAAI;wBAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzD,MAAM;gBACR,KAAK,QAAQ,CAAC,CAAC;oBACb,MAAM,KAAK,GAAG,IAAA,+BAAc,EAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBACtC,IAAI,KAAK;wBAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;oBACrC,MAAM;iBACP;gBACD;oBACE,MAAM,IAAI,KAAK,CAAC,wBAAwB,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;aAC9D;SACF;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AA1ED,kCA0EC;AAED,SAAS,iBAAiB,CAAC,GAAW;IACpC,OAAO,GAAG,CAAC,OAAO,CAAC,4BAA4B,EAAE,SAAS,CAAC,CAAC;AAC9D,CAAC;AAED,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,MAAM,GAAG,IAAI;SAChB,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;SACrC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IAE9E,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACxB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAC7B,OAAO;QACL,MAAM;QACN,KAAK;QACL,IAAI;KACL,CAAC;AACJ,CAAC"}
package/lib/index.d.ts CHANGED
@@ -28,7 +28,7 @@ export * from './databases/getDatabase';
28
28
  export * from './databases/carbonImpurities';
29
29
  export * from './databases/protonImpurities';
30
30
  export type { NMRSignal1D } from './signals/NMRSignal1D';
31
- export type { NMRSignal2D, Signal2DAxisData } from './xyz/NMRSignal2D';
31
+ export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
32
32
  export type { NMRRange } from './xy/NMRRange';
33
33
  export type { NMRZone } from './xyz/NMRZone';
34
34
  export type { NMRPeak1D } from './peaks/NMRPeak1D';
package/lib/prediction/predictAllSpectra.d.ts CHANGED
@@ -1,5 +1,5 @@
1
+ import { FromTo, PointXY } from 'cheminfo-types';
1
2
  import type { Molecule } from 'openchemlib';
2
- import { OptionsSignalsToXY } from '../signals/signalsToXY';
3
3
  import { PredictAllOptions } from './predictAll';
4
4
  /**
5
5
  * This function will generate an object compatible with NMR-ium
@@ -7,12 +7,30 @@ import { PredictAllOptions } from './predictAll';
7
7
  * @param molecule
8
8
  * @param options
9
9
  */
10
- export declare function predictAllSpectra(molecule: Molecule, options?: {
10
+ interface OneDOptions {
11
+ proton: FromTo;
12
+ carbon: FromTo;
13
+ nbPoints: number;
14
+ lineWidth: number;
15
+ }
16
+ interface TwoDOptions {
17
+ from: PointXY;
18
+ to: PointXY;
19
+ nbPoints: PointXY;
20
+ }
21
+ interface SimulationOptions {
22
+ frequency: number;
23
+ oneD?: Partial<OneDOptions>;
24
+ twoD?: Partial<TwoDOptions>;
25
+ }
26
+ interface PredictAllSpectraOptions {
11
27
  prediction?: PredictAllOptions;
12
- simulation?: OptionsSignalsToXY;
13
- }): Promise<{
28
+ simulation?: SimulationOptions;
29
+ }
30
+ export declare function predictAllSpectra(molecule: Molecule, options?: PredictAllSpectraOptions): Promise<{
14
31
  spectra: any[];
15
32
  molecules: {
16
33
  molfile: any;
17
34
  }[];
18
35
  }>;
36
+ export {};
package/lib/prediction/predictAllSpectra.js CHANGED
@@ -1,40 +1,126 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.predictAllSpectra = void 0;
4
+ const signals2DToZ_1 = require("../signals/signals2DToZ");
4
5
  const signalsToXY_1 = require("../signals/signalsToXY");
6
+ const getFrequency_1 = require("../utilities/getFrequency");
5
7
  const predictAll_1 = require("./predictAll");
6
- /**
7
- * This function will generate an object compatible with NMR-ium
8
- *
9
- * @param molecule
10
- * @param options
11
- */
12
8
  async function predictAllSpectra(molecule, options = {}) {
13
- const predictions = await (0, predictAll_1.predictAll)(molecule, options.prediction);
9
+ const { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictionOptions = {}, } = options;
10
+ const predictions = await (0, predictAll_1.predictAll)(molecule, predictionOptions);
14
11
  const spectra = [];
15
12
  const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
16
- spectra.push(getProton(predictions.proton, options.simulation));
13
+ const oneDOptions = {
14
+ ...{
15
+ proton: { from: 0, to: 14 },
16
+ carbon: { from: 0, to: 200 },
17
+ nbPoints: 4098,
18
+ lineWidth: 0.03,
19
+ },
20
+ ...(simulationOptions.oneD || {}),
21
+ };
22
+ const twoDOptions = {
23
+ ...{
24
+ from: { x: oneDOptions.proton.from, y: oneDOptions.carbon.from },
25
+ to: { x: oneDOptions.proton.to, y: oneDOptions.carbon.to },
26
+ nbPoints: { x: 1024, y: 1024 },
27
+ },
28
+ ...(simulationOptions.twoD || {}),
29
+ };
30
+ for (const experiment in predictions) {
31
+ switch (experiment) {
32
+ case 'carbon':
33
+ case 'proton': {
34
+ spectra.push(get1DSpectrum(predictions[experiment], {
35
+ nbPoints: oneDOptions.nbPoints,
36
+ lineWidth: oneDOptions.lineWidth,
37
+ ...oneDOptions[experiment],
38
+ experiment,
39
+ frequency: simulationOptions.frequency,
40
+ }));
41
+ break;
42
+ }
43
+ case 'cosy':
44
+ case 'hsqc':
45
+ case 'hmbc': {
46
+ spectra.push(get2DSpectrum(predictions[experiment], {
47
+ ...twoDOptions,
48
+ experiment,
49
+ frequency: simulationOptions.frequency,
50
+ }));
51
+ break;
52
+ }
53
+ default:
54
+ break;
55
+ }
56
+ }
17
57
  return result;
18
58
  }
19
59
  exports.predictAllSpectra = predictAllSpectra;
20
- function getProton(prediction, options) {
21
- const { x, y } = (0, signalsToXY_1.signalsToXY)(prediction.signals, options);
60
+ function get2DSpectrum(prediction, options) {
61
+ const { signals, zones, nuclei } = prediction;
62
+ const { frequency: baseFrequency, experiment } = options;
63
+ const width = get2DWidth(nuclei);
64
+ const frequency = calculateFrequency(nuclei, baseFrequency);
65
+ const spectrumData = (0, signals2DToZ_1.signals2DToZ)(signals, {
66
+ ...options,
67
+ width,
68
+ factor: 3,
69
+ });
70
+ const spectrum = {
71
+ data: { ...spectrumData, noise: 0.01 },
72
+ info: {
73
+ nucleus: nuclei,
74
+ originFrequency: frequency,
75
+ baseFrequency: frequency,
76
+ pulseSequence: experiment,
77
+ experiment: '2d',
78
+ },
79
+ zones: { values: zones },
80
+ };
81
+ return spectrum;
82
+ }
83
+ function get2DWidth(nucleus) {
84
+ return nucleus[0] === nucleus[1] ? 0.02 : { x: 0.02, y: 0.2133 };
85
+ }
86
+ function get1DSpectrum(prediction, options) {
87
+ const { frequency = 400, experiment } = options;
88
+ const { signals, nucleus } = prediction;
89
+ const realFrequency = calculateFrequency(nucleus, frequency);
90
+ const { x, y } = (0, signalsToXY_1.signalsToXY)(signals, {
91
+ ...options,
92
+ frequency: realFrequency,
93
+ });
22
94
  const spectrum = {
23
- id: '',
24
95
  // todo Array.from is temporary for the developement
25
96
  data: { x: Array.from(x), re: Array.from(y), im: null },
26
97
  info: {
27
98
  nucleus: prediction.nucleus,
28
99
  dimension: 1,
29
- originFrequency: 400,
30
- baseFrequency: 400,
100
+ originFrequency: realFrequency,
101
+ baseFrequency: realFrequency,
31
102
  pulseSequence: 'prediction',
32
- experiment: 'proton',
103
+ experiment,
33
104
  isFt: true,
34
105
  },
35
- // todo: currently we disable the ranges because there is no ID
36
- //ranges: { values: prediction.ranges },
106
+ ranges: { values: prediction.ranges },
37
107
  };
38
108
  return spectrum;
39
109
  }
110
+ function calculateFrequency(nucleus, frequency) {
111
+ if (typeof nucleus === 'string') {
112
+ return (0, getFrequency_1.getFrequency)(nucleus, { nucleus: '1H', frequency });
113
+ }
114
+ else {
115
+ if (nucleus[0] === nucleus[1]) {
116
+ return `${frequency},${frequency}`;
117
+ }
118
+ else {
119
+ return `${frequency},${(0, getFrequency_1.getFrequency)(nucleus[1], {
120
+ nucleus: nucleus[0],
121
+ frequency,
122
+ })}`;
123
+ }
124
+ }
125
+ }
40
126
  //# sourceMappingURL=predictAllSpectra.js.map
package/lib/prediction/predictAllSpectra.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"predictAllSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictAllSpectra.ts"],"names":[],"mappings":";;;AAGA,0DAAuD;AACvD,wDAAyE;AACzE,4DAAyD;AAEzD,6CAA6D;AA8BtD,KAAK,UAAU,iBAAiB,CACrC,QAAkB,EAClB,UAAoC,EAAE;IAEtC,MAAM,EACJ,UAAU,EAAE,iBAAiB,GAAG,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAuB,EAC3E,UAAU,EAAE,iBAAiB,GAAG,EAAE,GACnC,GAAG,OAAO,CAAC;IAEZ,MAAM,WAAW,GAAG,MAAM,IAAA,uBAAU,EAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;IAClE,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;IAE1E,MAAM,WAAW,GAAgB;QAC/B,GAAG;YACD,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;YAC3B,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE;YAC5B,QAAQ,EAAE,IAAI;YACd,SAAS,EAAE,IAAI;SAChB;QACD,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,EAAE,CAAC;KAClC,CAAC;IAEF,MAAM,WAAW,GAAgB;QAC/B,GAAG;YACD,IAAI,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE;YAChE,EAAE,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,EAAE,EAAE;YAC1D,QAAQ,EAAE,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE;SAC/B;QACD,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,EAAE,CAAC;KAClC,CAAC;IAEF,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;QACpC,QAAQ,UAAU,EAAE;YAClB,KAAK,QAAQ,CAAC;YACd,KAAK,QAAQ,CAAC,CAAC;gBACb,OAAO,CAAC,IAAI,CACV,aAAa,CAAC,WAAW,CAAC,UAAU,CAAC,EAAE;oBACrC,QAAQ,EAAE,WAAW,CAAC,QAAQ;oBAC9B,SAAS,EAAE,WAAW,CAAC,SAAS;oBAChC,GAAG,WAAW,CAAC,UAAU,CAAC;oBAC1B,UAAU;oBACV,SAAS,EAAE,iBAAiB,CAAC,SAAS;iBACvC,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC,CAAC;gBACX,OAAO,CAAC,IAAI,CACV,aAAa,CAAC,WAAW,CAAC,UAAU,CAAC,EAAE;oBACrC,GAAG,WAAW;oBACd,UAAU;oBACV,SAAS,EAAE,iBAAiB,CAAC,SAAS;iBACvC,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD;gBACE,MAAM;SACT;KACF;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAjED,8CAiEC;AAOD,SAAS,aAAa,CAAC,UAAe,EAAE,OAA6B;IACnE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC;IAC9C,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;IAEzD,MAAM,KAAK,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC;IACjC,MAAM,SAAS,GAAG,kBAAkB,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC;IAE5D,MAAM,YAAY,GAAG,IAAA,2BAAY,EAAC,OAAO,EAAE;QACzC,GAAG,OAAO;QACV,KAAK;QACL,MAAM,EAAE,CAAC;KACV,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG;QACf,IAAI,EAAE,EAAE,GAAG,YAAY,EAAE,KAAK,EAAE,IAAI,EAAE;QACtC,IAAI,EAAE;YACJ,OAAO,EAAE,MAAM;YACf,eAAe,EAAE,SAAS;YAC1B,aAAa,EAAE,SAAS;YACxB,aAAa,EAAE,UAAU;YACzB,UAAU,EAAE,IAAI;SACjB;QACD,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;KACzB,CAAC;IACF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,UAAU,CAAC,OAAiB;IACnC,OAAO,OAAO,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC;AACnE,CAAC;AAID,SAAS,aAAa,CAAC,UAAe,EAAE,OAA6B;IACnE,MAAM,EAAE,SAAS,GAAG,GAAG,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;IAChD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC;IACxC,MAAM,aAAa,GAAG,kBAAkB,CAAC,OAAO,EAAE,SAAS,CAAW,CAAC;IACvE,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,IAAA,yBAAW,EAAC,OAAO,EAAE;QACpC,GAAG,OAAO;QACV,SAAS,EAAE,aAAa;KACzB,CAAC,CAAC;IACH,MAAM,QAAQ,GAAG;QACf,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,aAAa;YAC9B,aAAa,EAAE,aAAa;YAC5B,aAAa,EAAE,YAAY;YAC3B,UAAU;YACV,IAAI,EAAE,IAAI;SACX;QACD,MAAM,EAAE,EAAE,MAAM,EAAE,UAAU,CAAC,MAAM,EAAE;KACtC,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,kBAAkB,CACzB,OAA0B,EAC1B,SAAiB;IAEjB,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE;QAC/B,OAAO,IAAA,2BAAY,EAAC,OAAO,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,CAAC,CAAC;KAC5D;SAAM;QACL,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,EAAE;YAC7B,OAAO,GAAG,SAAS,IAAI,SAAS,EAAE,CAAC;SACpC;aAAM;YACL,OAAO,GAAG,SAAS,IAAI,IAAA,2BAAY,EAAC,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC9C,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC;gBACnB,SAAS;aACV,CAAC,EAAE,CAAC;SACN;KACF;AACH,CAAC"}
package/lib/xyz/NMRSignal2D.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import type { FromTo } from 'cheminfo-types';
2
2
  import type { Peak2D } from 'ml-matrix-peaks-finder';
3
- export interface Signal2DAxisData {
3
+ export interface Signal2DProjection {
4
4
  nucleus?: string;
5
5
  delta: number;
6
6
  resolution?: number;
@@ -8,8 +8,8 @@ export interface Signal2DAxisData {
8
8
  diaIDs?: string[];
9
9
  }
10
10
  export interface NMRSignal2D {
11
- x: Signal2DAxisData;
12
- y: Signal2DAxisData;
11
+ x: Signal2DProjection;
12
+ y: Signal2DProjection;
13
13
  j?: {
14
14
  pathLength?: number | FromTo;
15
15
  };
package/lib-esm/assignment/getAssignments.js CHANGED
@@ -4,7 +4,7 @@ import { checkIDs } from './utils/getAssignment/checkIDs';
4
4
  import { getTargetsAndCorrelations } from './utils/getAssignment/getTargetsAndCorrelations';
5
5
  import getWorkFlow from './utils/getAssignment/getWorkFlow';
6
6
  export async function getAssignments(input, options = {}) {
7
- let { restrictionByCS = {}, justAssign, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
7
+ let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
8
8
  const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
9
9
  const molecule = input.molecule;
10
10
  if (!molecule)
package/lib-esm/assignment/getAssignments.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iCAAiC,EAAE,MAAM,mBAAmB,CAAC;AAQtE,OAAO,EAEL,gBAAgB,GAEjB,MAAM,wCAAwC,CAAC;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAC;AAC1D,OAAO,EAAE,yBAAyB,EAAE,MAAM,iDAAiD,CAAC;AAC5F,OAAO,WAAW,MAAM,mCAAmC,CAAC;AA0E5D,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,IAAI,EACf,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,yBAAyB,CACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,WAAW,CAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,gBAAgB,CAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC"}
package/lib-esm/databases/getDatabase.js CHANGED
@@ -1,12 +1,22 @@
1
1
  import { fetch } from 'cross-fetch';
2
2
  import { resurrectRange } from '../utilities/resurrectRange';
3
- export async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
3
+ export async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
4
+ const { format = 'tsv' } = options;
4
5
  if (url.includes('google.com')) {
5
6
  url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(url)}/export?format=tsv`;
6
7
  }
8
+ let parsed;
7
9
  const response = await fetch(url);
8
- const result = await response.text();
9
- const parsed = parseData(result);
10
+ switch (format) {
11
+ case 'tsv':
12
+ parsed = parseData(await response.text());
13
+ break;
14
+ case 'json':
15
+ parsed = await response.json();
16
+ break;
17
+ default:
18
+ throw new Error('unknown database format');
19
+ }
10
20
  const results = [];
11
21
  for (let line of parsed.data) {
12
22
  const result = {
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package/lib-esm/prediction/predictAllSpectra.js CHANGED
@@ -1,36 +1,122 @@
1
+ import { signals2DToZ } from '../signals/signals2DToZ';
1
2
  import { signalsToXY } from '../signals/signalsToXY';
3
+ import { getFrequency } from '../utilities/getFrequency';
2
4
  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
5
  export async function predictAllSpectra(molecule, options = {}) {
10
- const predictions = await predictAll(molecule, options.prediction);
6
+ const { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictionOptions = {}, } = options;
7
+ const predictions = await predictAll(molecule, predictionOptions);
11
8
  const spectra = [];
12
9
  const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
13
- spectra.push(getProton(predictions.proton, options.simulation));
10
+ const oneDOptions = {
11
+ ...{
12
+ proton: { from: 0, to: 14 },
13
+ carbon: { from: 0, to: 200 },
14
+ nbPoints: 4098,
15
+ lineWidth: 0.03,
16
+ },
17
+ ...(simulationOptions.oneD || {}),
18
+ };
19
+ const twoDOptions = {
20
+ ...{
21
+ from: { x: oneDOptions.proton.from, y: oneDOptions.carbon.from },
22
+ to: { x: oneDOptions.proton.to, y: oneDOptions.carbon.to },
23
+ nbPoints: { x: 1024, y: 1024 },
24
+ },
25
+ ...(simulationOptions.twoD || {}),
26
+ };
27
+ for (const experiment in predictions) {
28
+ switch (experiment) {
29
+ case 'carbon':
30
+ case 'proton': {
31
+ spectra.push(get1DSpectrum(predictions[experiment], {
32
+ nbPoints: oneDOptions.nbPoints,
33
+ lineWidth: oneDOptions.lineWidth,
34
+ ...oneDOptions[experiment],
35
+ experiment,
36
+ frequency: simulationOptions.frequency,
37
+ }));
38
+ break;
39
+ }
40
+ case 'cosy':
41
+ case 'hsqc':
42
+ case 'hmbc': {
43
+ spectra.push(get2DSpectrum(predictions[experiment], {
44
+ ...twoDOptions,
45
+ experiment,
46
+ frequency: simulationOptions.frequency,
47
+ }));
48
+ break;
49
+ }
50
+ default:
51
+ break;
52
+ }
53
+ }
14
54
  return result;
15
55
  }
16
- function getProton(prediction, options) {
17
- const { x, y } = signalsToXY(prediction.signals, options);
56
+ function get2DSpectrum(prediction, options) {
57
+ const { signals, zones, nuclei } = prediction;
58
+ const { frequency: baseFrequency, experiment } = options;
59
+ const width = get2DWidth(nuclei);
60
+ const frequency = calculateFrequency(nuclei, baseFrequency);
61
+ const spectrumData = signals2DToZ(signals, {
62
+ ...options,
63
+ width,
64
+ factor: 3,
65
+ });
66
+ const spectrum = {
67
+ data: { ...spectrumData, noise: 0.01 },
68
+ info: {
69
+ nucleus: nuclei,
70
+ originFrequency: frequency,
71
+ baseFrequency: frequency,
72
+ pulseSequence: experiment,
73
+ experiment: '2d',
74
+ },
75
+ zones: { values: zones },
76
+ };
77
+ return spectrum;
78
+ }
79
+ function get2DWidth(nucleus) {
80
+ return nucleus[0] === nucleus[1] ? 0.02 : { x: 0.02, y: 0.2133 };
81
+ }
82
+ function get1DSpectrum(prediction, options) {
83
+ const { frequency = 400, experiment } = options;
84
+ const { signals, nucleus } = prediction;
85
+ const realFrequency = calculateFrequency(nucleus, frequency);
86
+ const { x, y } = signalsToXY(signals, {
87
+ ...options,
88
+ frequency: realFrequency,
89
+ });
18
90
  const spectrum = {
19
- id: '',
20
91
  // todo Array.from is temporary for the developement
21
92
  data: { x: Array.from(x), re: Array.from(y), im: null },
22
93
  info: {
23
94
  nucleus: prediction.nucleus,
24
95
  dimension: 1,
25
- originFrequency: 400,
26
- baseFrequency: 400,
96
+ originFrequency: realFrequency,
97
+ baseFrequency: realFrequency,
27
98
  pulseSequence: 'prediction',
28
- experiment: 'proton',
99
+ experiment,
29
100
  isFt: true,
30
101
  },
31
- // todo: currently we disable the ranges because there is no ID
32
- //ranges: { values: prediction.ranges },
102
+ ranges: { values: prediction.ranges },
33
103
  };
34
104
  return spectrum;
35
105
  }
106
+ function calculateFrequency(nucleus, frequency) {
107
+ if (typeof nucleus === 'string') {
108
+ return getFrequency(nucleus, { nucleus: '1H', frequency });
109
+ }
110
+ else {
111
+ if (nucleus[0] === nucleus[1]) {
112
+ return `${frequency},${frequency}`;
113
+ }
114
+ else {
115
+ return `${frequency},${getFrequency(nucleus[1], {
116
+ nucleus: nucleus[0],
117
+ frequency,
118
+ })}`;
119
+ }
120
+ }
121
+ }
36
122
  //# sourceMappingURL=predictAllSpectra.js.map
package/lib-esm/prediction/predictAllSpectra.js.map CHANGED
@@ -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": "7.4.3",
3
+ "version": "8.0.0",
4
4
  "description": "Pure functions allowing to process NMR spectra.",
5
5
  "main": "./lib/index.js",
6
6
  "module": "./lib-esm/index.js",
@@ -38,21 +38,21 @@
38
38
  },
39
39
  "homepage": "https://github.com/cheminfo/nmr-processing#readme",
40
40
  "devDependencies": {
41
- "@types/jest": "^27.4.1",
41
+ "@types/jest": "^27.5.0",
42
42
  "cheminfo-build": "^1.1.11",
43
43
  "cheminfo-types": "^1.1.0",
44
- "eslint": "^8.11.0",
44
+ "eslint": "^8.14.0",
45
45
  "eslint-config-cheminfo-typescript": "^10.4.0",
46
- "jest": "^27.5.1",
46
+ "jest": "^28.0.3",
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
50
  "nmr-xy-testdata": "^0.5.1",
51
51
  "openchemlib": "^7.4.3",
52
- "prettier": "^2.6.1",
52
+ "prettier": "^2.6.2",
53
53
  "rimraf": "^3.0.2",
54
- "ts-jest": "^27.1.4",
55
- "typescript": "^4.6.3"
54
+ "ts-jest": "^28.0.1",
55
+ "typescript": "^4.6.4"
56
56
  },
57
57
  "dependencies": {
58
58
  "binary-search": "^1.3.6",
@@ -63,19 +63,19 @@
63
63
  "ml-array-rescale": "^1.3.7",
64
64
  "ml-array-sequential-fill": "^1.1.8",
65
65
  "ml-array-sum": "^1.1.6",
66
- "ml-gsd": "^10.2.0",
66
+ "ml-gsd": "^11.2.0",
67
67
  "ml-hclust": "^3.1.0",
68
68
  "ml-levenberg-marquardt": "^4.1.0",
69
- "ml-matrix": "^6.9.0",
69
+ "ml-matrix": "^6.10.0",
70
70
  "ml-matrix-convolution": "^1.0.0",
71
71
  "ml-matrix-peaks-finder": "^1.0.0",
72
72
  "ml-peak-shape-generator": "^4.1.1",
73
73
  "ml-simple-clustering": "^0.1.0",
74
74
  "ml-sparse-matrix": "^2.1.0",
75
- "ml-spectra-processing": "^11.1.0",
75
+ "ml-spectra-processing": "^11.5.0",
76
76
  "ml-tree-set": "^0.1.1",
77
77
  "nmr-correlation": "^2.2.5",
78
- "openchemlib-utils": "^1.10.0",
79
- "spectrum-generator": "^8.0.0"
78
+ "openchemlib-utils": "^1.11.0",
79
+ "spectrum-generator": "^8.0.1"
80
80
  }
81
81
  }
package/src/assignment/getAssignments.ts CHANGED
@@ -95,7 +95,7 @@ export async function getAssignments(
95
95
  let {
96
96
  restrictionByCS = {},
97
97
  justAssign,
98
- minScore = 1,
98
+ minScore = 0.01,
99
99
  maxSolutions = 10,
100
100
  nbAllowedUnAssigned,
101
101
  timeout = 6000,
package/src/databases/getDatabase.ts CHANGED
@@ -6,16 +6,33 @@ import { DatabaseNMREntry } from './DatabaseNMREntry';
6
6
 
7
7
  export async function getDatabase(
8
8
  url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing',
9
+ options: {
10
+ /**
11
+ * @default 'tsv'
12
+ */
13
+ format?: 'tsv' | 'json';
14
+ } = {},
9
15
  ) {
16
+ const { format = 'tsv' } = options;
17
+
10
18
  if (url.includes('google.com')) {
11
19
  url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(
12
20
  url,
13
21
  )}/export?format=tsv`;
14
22
  }
15
23
 
24
+ let parsed;
16
25
  const response = await fetch(url);
17
- const result = await response.text();
18
- const parsed = parseData(result);
26
+ switch (format) {
27
+ case 'tsv':
28
+ parsed = parseData(await response.text());
29
+ break;
30
+ case 'json':
31
+ parsed = await response.json();
32
+ break;
33
+ default:
34
+ throw new Error('unknown database format');
35
+ }
19
36
 
20
37
  const results = [];
21
38
 
package/src/index.ts CHANGED
@@ -38,7 +38,7 @@ export * from './databases/carbonImpurities';
38
38
  export * from './databases/protonImpurities';
39
39
 
40
40
  export type { NMRSignal1D } from './signals/NMRSignal1D';
41
- export type { NMRSignal2D, Signal2DAxisData } from './xyz/NMRSignal2D';
41
+ export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
42
42
  export type { NMRRange } from './xy/NMRRange';
43
43
  export type { NMRZone } from './xyz/NMRZone';
44
44
  export type { NMRPeak1D } from './peaks/NMRPeak1D';
package/src/prediction/predictAllSpectra.ts CHANGED
@@ -1,6 +1,9 @@
1
+ import { FromTo, PointXY } from 'cheminfo-types';
1
2
  import type { Molecule } from 'openchemlib';
2
3
 
4
+ import { signals2DToZ } from '../signals/signals2DToZ';
3
5
  import { OptionsSignalsToXY, signalsToXY } from '../signals/signalsToXY';
6
+ import { getFrequency } from '../utilities/getFrequency';
4
7
 
5
8
  import { PredictAllOptions, predictAll } from './predictAll';
6
9
  /**
@@ -10,39 +13,173 @@ import { PredictAllOptions, predictAll } from './predictAll';
10
13
  * @param options
11
14
  */
12
15
 
16
+ interface OneDOptions {
17
+ proton: FromTo;
18
+ carbon: FromTo;
19
+ nbPoints: number;
20
+ lineWidth: number;
21
+ }
22
+
23
+ interface TwoDOptions {
24
+ from: PointXY;
25
+ to: PointXY;
26
+ nbPoints: PointXY;
27
+ }
28
+ interface SimulationOptions {
29
+ frequency: number;
30
+ oneD?: Partial<OneDOptions>;
31
+ twoD?: Partial<TwoDOptions>;
32
+ }
33
+ interface PredictAllSpectraOptions {
34
+ prediction?: PredictAllOptions;
35
+ simulation?: SimulationOptions;
36
+ }
37
+
13
38
  export async function predictAllSpectra(
14
39
  molecule: Molecule,
15
- options: {
16
- prediction?: PredictAllOptions;
17
- simulation?: OptionsSignalsToXY;
18
- } = {},
40
+ options: PredictAllSpectraOptions = {},
19
41
  ) {
20
- const predictions = await predictAll(molecule, options.prediction);
42
+ const {
43
+ simulation: simulationOptions = { oneD: {}, twoD: {} } as SimulationOptions,
44
+ prediction: predictionOptions = {},
45
+ } = options;
46
+
47
+ const predictions = await predictAll(molecule, predictionOptions);
21
48
  const spectra: any[] = [];
22
49
  const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
23
- spectra.push(getProton(predictions.proton, options.simulation));
50
+
51
+ const oneDOptions: OneDOptions = {
52
+ ...{
53
+ proton: { from: 0, to: 14 },
54
+ carbon: { from: 0, to: 200 },
55
+ nbPoints: 4098,
56
+ lineWidth: 0.03,
57
+ },
58
+ ...(simulationOptions.oneD || {}),
59
+ };
60
+
61
+ const twoDOptions: TwoDOptions = {
62
+ ...{
63
+ from: { x: oneDOptions.proton.from, y: oneDOptions.carbon.from },
64
+ to: { x: oneDOptions.proton.to, y: oneDOptions.carbon.to },
65
+ nbPoints: { x: 1024, y: 1024 },
66
+ },
67
+ ...(simulationOptions.twoD || {}),
68
+ };
69
+
70
+ for (const experiment in predictions) {
71
+ switch (experiment) {
72
+ case 'carbon':
73
+ case 'proton': {
74
+ spectra.push(
75
+ get1DSpectrum(predictions[experiment], {
76
+ nbPoints: oneDOptions.nbPoints,
77
+ lineWidth: oneDOptions.lineWidth,
78
+ ...oneDOptions[experiment],
79
+ experiment,
80
+ frequency: simulationOptions.frequency,
81
+ }),
82
+ );
83
+ break;
84
+ }
85
+ case 'cosy':
86
+ case 'hsqc':
87
+ case 'hmbc': {
88
+ spectra.push(
89
+ get2DSpectrum(predictions[experiment], {
90
+ ...twoDOptions,
91
+ experiment,
92
+ frequency: simulationOptions.frequency,
93
+ }),
94
+ );
95
+ break;
96
+ }
97
+ default:
98
+ break;
99
+ }
100
+ }
24
101
 
25
102
  return result;
26
103
  }
27
104
 
28
- function getProton(prediction: any, options?: OptionsSignalsToXY) {
29
- const { x, y } = signalsToXY(prediction.signals, options);
105
+ type Get2DSpectrumOptions = TwoDOptions & {
106
+ experiment: string;
107
+ frequency: number;
108
+ };
109
+
110
+ function get2DSpectrum(prediction: any, options: Get2DSpectrumOptions) {
111
+ const { signals, zones, nuclei } = prediction;
112
+ const { frequency: baseFrequency, experiment } = options;
113
+
114
+ const width = get2DWidth(nuclei);
115
+ const frequency = calculateFrequency(nuclei, baseFrequency);
116
+
117
+ const spectrumData = signals2DToZ(signals, {
118
+ ...options,
119
+ width,
120
+ factor: 3,
121
+ });
122
+
123
+ const spectrum = {
124
+ data: { ...spectrumData, noise: 0.01 },
125
+ info: {
126
+ nucleus: nuclei,
127
+ originFrequency: frequency,
128
+ baseFrequency: frequency,
129
+ pulseSequence: experiment,
130
+ experiment: '2d',
131
+ },
132
+ zones: { values: zones },
133
+ };
134
+ return spectrum;
135
+ }
136
+
137
+ function get2DWidth(nucleus: string[]) {
138
+ return nucleus[0] === nucleus[1] ? 0.02 : { x: 0.02, y: 0.2133 };
139
+ }
140
+
141
+ type Get1DSpectrumOptions = OptionsSignalsToXY & { experiment: string };
142
+
143
+ function get1DSpectrum(prediction: any, options: Get1DSpectrumOptions) {
144
+ const { frequency = 400, experiment } = options;
145
+ const { signals, nucleus } = prediction;
146
+ const realFrequency = calculateFrequency(nucleus, frequency) as number;
147
+ const { x, y } = signalsToXY(signals, {
148
+ ...options,
149
+ frequency: realFrequency,
150
+ });
30
151
  const spectrum = {
31
- id: '',
32
152
  // todo Array.from is temporary for the developement
33
153
  data: { x: Array.from(x), re: Array.from(y), im: null },
34
154
  info: {
35
155
  nucleus: prediction.nucleus,
36
156
  dimension: 1,
37
- originFrequency: 400,
38
- baseFrequency: 400,
157
+ originFrequency: realFrequency,
158
+ baseFrequency: realFrequency,
39
159
  pulseSequence: 'prediction',
40
- experiment: 'proton',
160
+ experiment,
41
161
  isFt: true,
42
162
  },
43
- // todo: currently we disable the ranges because there is no ID
44
- //ranges: { values: prediction.ranges },
163
+ ranges: { values: prediction.ranges },
45
164
  };
46
165
 
47
166
  return spectrum;
48
167
  }
168
+
169
+ function calculateFrequency(
170
+ nucleus: string | string[],
171
+ frequency: number,
172
+ ): number | string {
173
+ if (typeof nucleus === 'string') {
174
+ return getFrequency(nucleus, { nucleus: '1H', frequency });
175
+ } else {
176
+ if (nucleus[0] === nucleus[1]) {
177
+ return `${frequency},${frequency}`;
178
+ } else {
179
+ return `${frequency},${getFrequency(nucleus[1], {
180
+ nucleus: nucleus[0],
181
+ frequency,
182
+ })}`;
183
+ }
184
+ }
185
+ }
package/src/xyz/NMRSignal2D.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import type { FromTo } from 'cheminfo-types';
2
2
  import type { Peak2D } from 'ml-matrix-peaks-finder';
3
3
 
4
- export interface Signal2DAxisData {
4
+ export interface Signal2DProjection {
5
5
  nucleus?: string;
6
6
  delta: number;
7
7
  resolution?: number;
@@ -9,8 +9,8 @@ export interface Signal2DAxisData {
9
9
  diaIDs?: string[];
10
10
  }
11
11
  export interface NMRSignal2D {
12
- x: Signal2DAxisData;
13
- y: Signal2DAxisData;
12
+ x: Signal2DProjection;
13
+ y: Signal2DProjection;
14
14
  j?: {
15
15
  pathLength?: number | FromTo;
16
16
  };