@datagrok/sequence-translator 1.0.12 → 1.0.14

package/src/structures-works/map.ts

@@ -1,7 +1,9 @@
 import * as DG from 'datagrok-api/dg';
 import {getAllCodesOfSynthesizer} from './sequence-codes-tools';
+import {differenceOfTwoArrays} from '../helpers';
 
-export const delimiter = ';';
+export const DELIMITER = ';';
+export const NUCLEOTIDES = ['A', 'G', 'C', 'U', 'T'];
 export const SYNTHESIZERS = {
   RAW_NUCLEOTIDES: 'Raw Nucleotides',
   BIOSPRING: 'BioSpring Codes',
@@ -16,29 +18,6 @@ export const TECHNOLOGIES = {
   ASO_GAPMERS: 'For ASO Gapmers',
   SI_RNA: 'For 2\'-OMe and 2\'-F modified siRNA',
 };
-export const COL_NAMES = {
-  CHEMISTRY: 'Chemistry',
-  NUMBER: 'Number',
-  TYPE: 'Type',
-  CHEMISTRY_NAME: 'Chemistry Name',
-  INTERNAL_COMPOUND_ID: 'Internal compound ID',
-  IDP: 'IDP',
-  SEQUENCE: 'Sequence',
-  COMPOUND_NAME: 'Compound Name',
-  COMPOUND_COMMENTS: 'Compound Comments',
-  SALT: 'Salt',
-  EQUIVALENTS: 'Equivalents',
-  PURITY: 'Purity',
-  CPD_MW: 'Cpd MW',
-  SALT_MOL_WEIGHT: 'Salt MW',
-  SALT_MASS: 'Salt mass',
-  BATCH_MW: 'Batch MW',
-  SOURCE: 'Source',
-  ICD: 'ICD',
-  OWNER: 'Owner',
-};
-// interface CODES {
-// }
 export const MODIFICATIONS: {[index: string]: {molecularWeight: number, left: string, right: string}} = {
   '(invabasic)': {
     molecularWeight: 118.13,
@@ -58,7 +37,7 @@ export const MODIFICATIONS: {[index: string]: {molecularWeight: number, left: st
 export const stadardPhosphateLinkSmiles = 'OP(=O)(O)O';
 export const map: {[synthesizer: string]:
   {[technology: string]: {[code: string]:
-    {'name'?: string, 'weight'?: number, 'normalized'?: string, 'SMILES': string}}}} = {
+    {'name': string, 'weight': number, 'normalized': string, 'SMILES': string}}}} = {
       'Raw Nucleotides': {
         'DNA': {
           'A': {
@@ -68,7 +47,7 @@ export const map: {[synthesizer: string]:
             'SMILES': 'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[C@@H]1O',
           },
           'T': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
@@ -170,7 +149,7 @@ export const map: {[synthesizer: string]:
             'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'T': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
@@ -384,13 +363,13 @@ export const map: {[synthesizer: string]:
             'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'T': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
           },
           'dT': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
@@ -572,8 +551,6 @@ export const map: {[synthesizer: string]:
           },
         },
       },
-      // 'LCMS': {
-      //   'For 2\'-OMe and 2\'-F modified siRNA': {
     };
 
 export const lcmsToGcrs = `LCMS, GCRS
@@ -724,12 +701,20 @@ fU, fU
 /J-CbCS/, J-CbCS
 /J-MtCD/, J-MtCD`;
 
-function differenceOfTwoArrays(a: string[], b: string[]): string[] {
-  return a.filter((x) => !b.includes(x));
-}
 
 const codesWithSmiles = getAllCodesOfSynthesizer(SYNTHESIZERS.GCRS);
 const allGcrsCodes = DG.DataFrame.fromCsv(lcmsToGcrs).getCol('GCRS').toList();
 export const gcrsCodesWithoutSmiles = differenceOfTwoArrays(allGcrsCodes, codesWithSmiles);
 for (const e of gcrsCodesWithoutSmiles)
-  map[SYNTHESIZERS.GCRS]['Others'][e] = {'SMILES': ''};
+  map[SYNTHESIZERS.GCRS]['Others'][e] = {name: '', weight: 0, normalized: '', SMILES: ''};
+
+
+export const weightsObj: {[code: string]: number} = {};
+for (const synthesizer of Object.keys(map)) {
+  for (const technology of Object.keys(map[synthesizer])) {
+    for (const code of Object.keys(map[synthesizer][technology]))
+      weightsObj[code] = map[synthesizer][technology][code].weight;
+  }
+}
+for (const [key, value] of Object.entries(MODIFICATIONS))
+  weightsObj[key] = value.molecularWeight;