@datagrok/sequence-translator 1.0.15 → 1.0.16

package/src/utils/sdf-add-columns.ts

@@ -0,0 +1,118 @@
+import * as DG from 'datagrok-api/dg';
+import {COL_NAMES, GENERATED_COL_NAMES, SEQUENCE_TYPES} from '../autostart/constants';
+import * as grok from 'datagrok-api/grok';
+import {removeEmptyRows} from '../helpers';
+import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
+import {isValidSequence} from '../structures-works/sequence-codes-tools';
+import {batchMolWeight, molecularWeight, saltMass, saltMolWeigth} from '../autostart/calculations';
+import {weightsObj} from '../structures-works/map';
+
+export class SdfColumnsExistsError extends Error {
+  constructor(message: string) {
+    super();
+  }
+}
+
+export function sdfAddColumns(
+  df: DG.DataFrame, saltNamesList: string[], saltsMolWeightList: number[], onError: (rowI: number, err: any) => void
+): DG.DataFrame {
+  const sequenceCol = df.getCol(COL_NAMES.SEQUENCE);
+  const saltCol = df.getCol(COL_NAMES.SALT);
+  const equivalentsCol = df.getCol(COL_NAMES.EQUIVALENTS);
+  const typeCol = df.getCol(COL_NAMES.TYPE);
+  const chemistryNameCol = df.getCol(COL_NAMES.CHEMISTRY_NAME);
+
+  if (GENERATED_COL_NAMES.some((colName) => df.columns.contains(colName)))
+    throw new SdfColumnsExistsError('Columns already exist');
+
+  df = removeEmptyRows(df, sequenceCol);
+
+  df.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => {
+    let res: string = '';
+    try {
+      res = ([SEQUENCE_TYPES.DUPLEX, SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) ?
+        chemistryNameCol.get(i) :
+        sequenceCol.get(i);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => {
+    let res: string = '';
+    try {
+      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i))) {
+        res = sequenceCol.get(i);
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        res = `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS: ${obj.AS}`;
+      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        res = `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS1: ${obj.AS1} and AS2: ${obj.AS2}`;
+      }
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewFloat(COL_NAMES.COMPOUND_MOL_WEIGHT).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i))) {
+        res = (isValidSequence(sequenceCol.get(i), null).indexOfFirstNotValidChar == -1) ?
+          molecularWeight(sequenceCol.get(i), weightsObj) :
+          DG.FLOAT_NULL;
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        res = (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
+          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS, weightsObj) :
+          DG.FLOAT_NULL;
+      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        res = (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
+          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS1, weightsObj) +
+          molecularWeight(obj.AS2, weightsObj) :
+          DG.FLOAT_NULL;
+      }
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      res = saltMass(saltNamesList, saltsMolWeightList, equivalentsCol, i, saltCol);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewFloat(COL_NAMES.SALT_MOL_WEIGHT).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      res = saltMolWeigth(saltNamesList, saltCol, saltsMolWeightList, i);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  const compoundMolWeightCol = df.getCol(COL_NAMES.COMPOUND_MOL_WEIGHT);
+  const saltMassCol = df.getCol(COL_NAMES.SALT_MASS);
+  df.columns.addNewFloat(COL_NAMES.BATCH_MOL_WEIGHT).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      res = batchMolWeight(compoundMolWeightCol, saltMassCol, i);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  return df;
+}

package/src/utils/sdf-save-table.ts

@@ -0,0 +1,56 @@
+import * as DG from 'datagrok-api/dg';
+import {COL_NAMES, GENERATED_COL_NAMES, SEQUENCE_TYPES} from '../autostart/constants';
+import {differenceOfTwoArrays, download} from '../helpers';
+import * as grok from 'datagrok-api/grok';
+import {SYNTHESIZERS} from '../structures-works/map';
+import {sequenceToMolV3000} from '../structures-works/from-monomers';
+import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
+import {linkStrandsV3000} from '../structures-works/mol-transformations';
+
+export async function sdfSaveTable(table: DG.DataFrame, onError: (rowI: number, err: any) => void) {
+  if (GENERATED_COL_NAMES.some((colName) => !table.columns.contains(colName))) {
+    const absentColNames = differenceOfTwoArrays(GENERATED_COL_NAMES, table.columns.names()).join(`', '`);
+    grok.shell.warning(`File saved without columns '${absentColNames}'`);
+  }
+
+  const sequenceCol = table.getCol(COL_NAMES.SEQUENCE);
+  const typeCol = table.getCol(COL_NAMES.TYPE);
+
+  let resultStr = '';
+  const rowCount = table.rowCount;
+  for (let i = 0; i < rowCount; i++) {
+    try {
+      let rowStr = '';
+      const format = SYNTHESIZERS.GCRS; //getFormat(sequenceCol.get(i))!;
+      if (typeCol.get(i) == SEQUENCE_TYPES.SENSE_STRAND) {
+        rowStr += `${sequenceToMolV3000(sequenceCol.get(i), false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.ANTISENSE_STRAND) {
+        rowStr += `${sequenceToMolV3000(sequenceCol.get(i), true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        const as = `${sequenceToMolV3000(obj.AS, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+        const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+        rowStr += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as]}, true)}\n\n`;
+      } else if ([SEQUENCE_TYPES.TRIPLEX, SEQUENCE_TYPES.DIMER].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        const as1 = `${sequenceToMolV3000(obj.AS1, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+        const as2 = `${sequenceToMolV3000(obj.AS2, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+        const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+        rowStr += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as1, as2]}, true)}\n\n`;
+      }
+
+      for (const col of table.columns) {
+        if (col.name != COL_NAMES.SEQUENCE)
+          rowStr += `> <${col.name}>\n${col.get(i)}\n\n`;
+      }
+
+      rowStr += '$$$$\n';
+
+      resultStr += rowStr;
+    } catch (err: any) {
+      onError(i, err);
+    }
+  }
+
+  download(`${table.name}.sdf`, encodeURIComponent(resultStr));
+}

package/{test-SequenceTranslator-91c83d8913ff-f94596bc.html → test-SequenceTranslator-6288c2fbe346-cce4ac1d.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=91c83d8913ff. Commit f94596bc.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=6288c2fbe346. Commit cce4ac1d.</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=91c83d8913ff. Commit f94596bc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-29 11:55:21</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">18.993s</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">5.501s</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=6288c2fbe346. Commit cce4ac1d.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-12-12 14:55:37</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">21.067s</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">6.276s</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
@@ -242,16 +242,16 @@ header {
     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
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 2 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.acacacsacsac : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.cccgggusug : OK
+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 : 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 : 1 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
 </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;)