@datagrok/sequence-translator 1.0.12 → 1.0.14

package/src/structures-works/save-sense-antisense.ts

@@ -1,48 +1,70 @@
+import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {download} from '../helpers';
 import {sequenceToMolV3000} from '../structures-works/from-monomers';
-import {linkV3000} from '../structures-works/mol-transformations';
+import {linkStrandsV3000} from '../structures-works/mol-transformations';
 import {getFormat} from '../structures-works/sequence-codes-tools';
 
-export function saveSdf(as: string, ss: string, oneEntity: boolean, useChirality: boolean, invertSS: boolean, invertAS: boolean) {
+export function saveSdf(as: string, ss: string,
+                        oneEntity: boolean, useChirality: boolean,
+                        invertSS: boolean, invertAS: boolean,
+                        as2: string | null = null, invertAS2: boolean | null) {
   const formatAs = getFormat(as);
   const formatSs = getFormat(ss);
+  let formatAs2: string | null = null;
+  let molAS2: string | null = null;
+
   const molSS = sequenceToMolV3000(ss, invertSS, false, formatSs!);
   const molAS = sequenceToMolV3000(as, invertAS, false, formatAs!);
+
+  if (as2 != null && as2 != '') {
+    formatAs2 = getFormat(as2!);
+    molAS2 = sequenceToMolV3000(as2, invertAS2!, false, formatAs2!);
+  }
+
   let result: string;
-  if (oneEntity)
-    result = linkV3000([molSS, molAS], true, useChirality) + '\n$$$$\n';
-  else {
+  if (oneEntity) {
+    const antiStrands = molAS2 == null ? [molAS] : [molAS, molAS2];
+    result = linkStrandsV3000({senseStrands: [molSS], antiStrands: antiStrands}, useChirality) + '\n$$$$\n';
+
+  } else {
     result =
     molSS + '\n' +
     `> <Sequence>\nSense Strand\n$$$$\n` +
     molAS + '\n' +
     `> <Sequence>\nAnti Sense\n$$$$\n`;
-  }
 
-  const element = document.createElement('a');
-  element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
-  element.setAttribute('download', ss.replace(/\s/g, '') + '.sdf');
-  element.click();
+    if (molAS2)
+      result += molAS2+ '\n' +
+      `> <Sequence>\nAnti Sense 2\n$$$$\n`;
+  }
+  download(ss.replace(/\s/g, '') + '.sdf', encodeURIComponent(result));
 }
 
 export function saveSenseAntiSense() {
   const moleculeSvgDiv = ui.block([]);
   const ssInput = ui.textInput('Sense Strand', '');
   const asInput = ui.textInput('Anti Sense', '');
+  const asInput2 = ui.textInput('Anti Sense 2', '');
   const straight = "5 prime -> 3 prime";
   const inverse = "3 prime -> 5 prime";
   let ssInverse = false;
   let asInverse = false;
+  let as2Inverse = false;
 
   const changeSense = ui.choiceInput('SS direction', straight, [straight, inverse]);
   changeSense.onChanged(() => {ssInverse = changeSense.value == inverse;});
   const changeAntiSense = ui.choiceInput('AS direction', straight, [straight, inverse]);
   changeAntiSense.onChanged(() => {asInverse = changeAntiSense.value == inverse;});
+  const changeAntiSense2 = ui.choiceInput('AS 2 direction', straight, [straight, inverse]);
+  changeAntiSense2.onChanged(() => {asInverse = changeAntiSense.value == inverse;});
 
   const saveOption = ui.switchInput('Save as one entity', true);
   const chirality = ui.switchInput('Use chiral', true);
   const saveBtn = ui.button('Save SDF', () =>
-    saveSdf(asInput.value, ssInput.value, saveOption.value, chirality.value, ssInverse, asInverse));
+    saveSdf(asInput.value, ssInput.value, saveOption.value, chirality.value, ssInverse, asInverse, asInput2.value, as2Inverse));
 
   const saveSection = ui.panel([
     ui.div([
@@ -51,9 +73,11 @@ export function saveSenseAntiSense() {
         ui.divV([
           ssInput,
           asInput,
+          asInput2,
           ui.div([changeSense], {style: {width: '40'}}),
           changeSense,
           changeAntiSense,
+          changeAntiSense2,
           saveOption,
           chirality,
           ui.buttonsInput([saveBtn]),

package/src/structures-works/sequence-codes-tools.ts

@@ -1,5 +1,6 @@
 
-import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, delimiter, gcrsCodesWithoutSmiles} from './map';
+import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, DELIMITER, gcrsCodesWithoutSmiles, NUCLEOTIDES} from './map';
+import {sortByStringLengthInDescendingOrder} from '../helpers';
 import {asoGapmersNucleotidesToBioSpring, asoGapmersNucleotidesToGcrs,
   asoGapmersBioSpringToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12, siRnaNucleotideToBioSpringSenseStrand,
   siRnaNucleotideToAxolabsSenseStrand, siRnaNucleotidesToGcrs, siRnaBioSpringToNucleotides,
@@ -19,7 +20,6 @@ export function getFormat(sequence: string): string | null {
   let outputIndex = 0;
 
   const firstUniqueCharacters = ['r', 'd'];
-  const nucleotides = ['A', 'U', 'T', 'C', 'G'];
 
   possibleSynthesizers.forEach((synthesizer) => {
     const codes = getAllCodesOfSynthesizer(synthesizer);
@@ -31,13 +31,13 @@ export function getFormat(sequence: string): string | null {
 
       if ( // for mistake pattern 'rAA'
         outputIndex > 1 &&
-        nucleotides.includes(sequence[outputIndex]) &&
+        NUCLEOTIDES.includes(sequence[outputIndex]) &&
         firstUniqueCharacters.includes(sequence[outputIndex - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
         firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-        nucleotides.includes(sequence[outputIndex])
+        NUCLEOTIDES.includes(sequence[outputIndex])
       ) {
         outputIndex++;
         break;
@@ -68,13 +68,13 @@ export function getFormat(sequence: string): string | null {
 
       if ( // for mistake pattern 'rAA'
         outputIndex > 1 &&
-        nucleotides.includes(sequence[outputIndex]) &&
+        NUCLEOTIDES.includes(sequence[outputIndex]) &&
         firstUniqueCharacters.includes(sequence[outputIndex - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
         firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-        nucleotides.includes(sequence[outputIndex])
+        NUCLEOTIDES.includes(sequence[outputIndex])
       ) {
         outputIndex++;
         break;
@@ -87,9 +87,6 @@ export function getFormat(sequence: string): string | null {
   return possibleSynthesizers[0];
 }
 
-function sortByStringLengthInDescendingOrder(array: string[]): string[] {
-  return array.sort(function(a: string, b: string) {return b.length - a.length;});
-}
 
 export function isValidSequence(sequence: string, format: string | null): {
   indexOfFirstNotValidChar: number,
@@ -118,7 +115,6 @@ export function isValidSequence(sequence: string, format: string | null): {
   const outputIndices = Array(possibleSynthesizers.length).fill(0);
 
   const firstUniqueCharacters = ['r', 'd'];
-  const nucleotides = ['A', 'U', 'T', 'C', 'G'];
   possibleSynthesizers.forEach(function(synthesizer, i) {
     const codes = sortByStringLengthInDescendingOrder(getAllCodesOfSynthesizer(synthesizer));
     while (outputIndices[i] < sequence.length) {
@@ -129,13 +125,13 @@ export function isValidSequence(sequence: string, format: string | null): {
 
       if ( // for mistake pattern 'rAA'
         outputIndices[i] > 1 &&
-        nucleotides.includes(sequence[outputIndices[i]]) &&
+        NUCLEOTIDES.includes(sequence[outputIndices[i]]) &&
         firstUniqueCharacters.includes(sequence[outputIndices[i] - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
         firstUniqueCharacters.includes(sequence[outputIndices[i] + 1]) &&
-        nucleotides.includes(sequence[outputIndices[i]])
+        NUCLEOTIDES.includes(sequence[outputIndices[i]])
       ) {
         outputIndices[i]++;
         break;
@@ -213,7 +209,7 @@ export function getAllCodesOfSynthesizer(synthesizer: string): string[] {
   let codes: string[] = [];
   for (const technology of Object.keys(map[synthesizer]))
     codes = codes.concat(Object.keys(map[synthesizer][technology]));
-  return codes.concat(Object.keys(MODIFICATIONS)).concat(delimiter);
+  return codes.concat(Object.keys(MODIFICATIONS)).concat(DELIMITER);
 }
 
 function getListOfPossibleSynthesizersByFirstMatchedCode(sequence: string): string[] {

package/{test-SequenceTranslator-49ff04f38f57-128d0678.html → test-SequenceTranslator-e8c06047b7e7-eb4db608.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=49ff04f38f57. Commit 128d0678.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=e8c06047b7e7. Commit eb4db608.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=49ff04f38f57. Commit 128d0678.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-24 16:17:41</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">15.882s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">1.582s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=e8c06047b7e7. Commit eb4db608.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-22 12:28:58</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">15.587s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">3.952s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:40:11
@@ -239,7 +239,7 @@ header {
     at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:27:12)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:38:23)
     at Promise.then.completed (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:66:11
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:72:11
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
@@ -249,8 +249,11 @@ Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu
 Test result : Success : 0 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.acacacsacsac : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.cccgggusug : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
-</pre></div></div></div></div></body></html>
+</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:74:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>