@datagrok/bio 1.7.8 → 1.7.12

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Files changed (16) hide show
  1. package/detectors.js +17 -2
  2. package/dist/package-test.js +373 -81
  3. package/dist/package.js +289 -62
  4. package/files/tests/testSpgi100.csv +8437 -0
  5. package/files/tests/testUnichemSources.csv +36 -0
  6. package/package.json +3 -3
  7. package/src/const.ts +5 -0
  8. package/src/package.ts +83 -4
  9. package/src/tests/activity-cliffs-tests.ts +3 -0
  10. package/src/tests/convert-test.ts +55 -22
  11. package/src/tests/detectors-test.ts +37 -4
  12. package/src/utils/cell-renderer.ts +114 -1
  13. package/src/utils/constants.ts +2 -1
  14. package/src/utils/convert.ts +8 -6
  15. package/src/utils/utils.ts +29 -2
  16. package/{test-Bio-34f75e5127b8-cdc230d8.html → test-Bio-34f75e5127b8-6fa72ec4.html} +22 -14
package/src/utils/utils.ts CHANGED
@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
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  import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
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  import * as grok from 'datagrok-api/grok';
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  import {
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- CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL,
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+ CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, MONOMER_SYMBOL,
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  RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME
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  } from '../const';
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@@ -11,6 +11,33 @@ export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
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  export const HELM_CORE_LIB_MOLFILE = 'molfile';
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  export const HELM_CORE_FIELDS = ['symbol', 'molfile', 'rgroups', 'name'];
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+
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+ export function encodeMonomers(col: DG.Column): DG.Column | null {
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+ let encodeSymbol = MONOMER_ENCODE_MIN;
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+ const monomerSymbolDict: { [key: string]: number }= {};
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+ const units = col.tags[DG.TAGS.UNITS];
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+ const sep = col.getTag('separator');
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+ const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, sep);
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+ const encodedStringArray = [];
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+ for (let i = 0; i < col.length; ++i) {
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+ let encodedMonomerStr = '';
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+ const monomers = splitterFunc(col.get(i));
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+ monomers.forEach(m => {
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+ if(!monomerSymbolDict[m]) {
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+ if(encodeSymbol > MONOMER_ENCODE_MAX) {
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+ grok.shell.error(`Not enougth symbols to encode monomers`);
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+ return null;
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+ }
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+ monomerSymbolDict[m] = encodeSymbol;
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+ encodeSymbol++;
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+ }
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+ encodedMonomerStr += String.fromCodePoint(monomerSymbolDict[m]);
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+ })
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+ encodedStringArray.push(encodedMonomerStr);
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+ }
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+ return DG.Column.fromStrings('encodedMolecules', encodedStringArray);
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+ }
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+
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  export function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[]): any[][] | null {
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  const units = col.tags[DG.TAGS.UNITS];
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  const sep = col.getTag('separator');
@@ -79,4 +106,4 @@ export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
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  resultLib.push(monomer);
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  }
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  return resultLib;
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- }
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+ }
package/{test-Bio-34f75e5127b8-cdc230d8.html → test-Bio-34f75e5127b8-6fa72ec4.html} RENAMED
@@ -1,4 +1,4 @@
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- <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit cdc230d8.</title><style type="text/css">html,
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+ <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 6fa72ec4.</title><style type="text/css">html,
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  body {
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  font-family: Arial, Helvetica, sans-serif;
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  font-size: 1rem;
@@ -229,14 +229,8 @@ header {
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  font-size: 1rem;
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  padding: 0 0.5rem;
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  }
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- </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit cdc230d8.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-19 10:23:49</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 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 summary-empty">0 passed</div><div class="summary-failed">1 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/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">179.806s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">168.85s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
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- Test result : Bio.splitters.testHelm1 : Error: Expected R(U)P at position 0, got U
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- Test result : Bio.splitters.testHelm2 : Error: Expected R(U)P at position 1, got U
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- Test result : Bio.splitters.testHelm3 : Error: Expected R(U) at position 1, got U)
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- Test result : Bio.converters.testFastaGapsToSeparator : Error: Units are not specified in column
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- Test result : Bio.converters.testFastaGapsToHelm : Error: Units are not specified in column
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- Test result : Bio.converters.HelmDnaToFasta : Error: Units are not specified in column
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- Test result : Bio.converters.HelmDnaToSeparator : Error: Units are not specified in column
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+ </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 6fa72ec4.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-22 13:03:45</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 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 summary-empty">0 passed</div><div class="summary-failed">1 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/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">213.603s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">199.146s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
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+ Test result : Bio.activityCliffs.activityCliffsOpen : Error: Expected "105 cliffs", got "2362 cliffs"
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  at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:67:20
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  at Generator.next (&lt;anonymous&gt;)
@@ -310,20 +304,29 @@ Test result : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
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  Test result : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
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  Test result : Bio.detectors.samplesFastaPtPosSequence : OK
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  Test result : Bio.detectors.samplesTestCerealNegativeCerealName : OK
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+ Test result : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
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+ Test result : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
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+ Test result : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
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+ Test result : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
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+ Test result : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
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  Test result : Bio.MSA.test_table.is_not_empty : OK
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  Test result : Bio.sequenceSpace.sequenceSpaceOpens : OK
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- Test result : Bio.activityCliffs.activityCliffsOpen : OK
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  Test result : Bio.splitters.helm1 : OK
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  Test result : Bio.splitters.helm2 : OK
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  Test result : Bio.splitters.helm3-multichar : OK
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+ Test result : Bio.splitters.testHelm1 : OK
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+ Test result : Bio.splitters.testHelm2 : OK
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+ Test result : Bio.splitters.testHelm3 : OK
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  Test result : Bio.renderers.afterMsa : OK
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  Test result : Bio.renderers.afterConvert : OK
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  Test result : Bio.converters.testFastaPtToSeparator : OK
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  Test result : Bio.converters.testFastaDnaToSeparator : OK
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  Test result : Bio.converters.testFastaRnaToSeparator : OK
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+ Test result : Bio.converters.testFastaGapsToSeparator : OK
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  Test result : Bio.converters.testFastaPtToHelm : OK
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  Test result : Bio.converters.testFastaDnaToHelm : OK
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  Test result : Bio.converters.testFastaRnaToHelm : OK
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+ Test result : Bio.converters.testFastaGapsToHelm : OK
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  Test result : Bio.converters.testSeparatorPtToFasta : OK
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  Test result : Bio.converters.testSeparatorDnaToFasta : OK
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  Test result : Bio.converters.testSeparatorRnaToFasta : OK
@@ -332,8 +335,13 @@ Test result : Bio.converters.testSeparatorPtToHelm : OK
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  Test result : Bio.converters.testSeparatorDnaToHelm : OK
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  Test result : Bio.converters.testSeparatorRnaToHelm : OK
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  Test result : Bio.converters.testSeparatorGapsToHelm : OK
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- Test result : Bio.converters.HelmRnaToFasta : OK
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- Test result : Bio.converters.HelmPtToFasta : OK
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- Test result : Bio.converters.HelmRnaToSeparator : OK
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- Test result : Bio.converters.HelmPtToSeparator : OK
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+ Test result : Bio.converters.testHelmDnaToFasta : OK
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+ Test result : Bio.converters.testHelmRnaToFasta : OK
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+ Test result : Bio.converters.testHelmPtToFasta : OK
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+ Test result : Bio.converters.testHelmDnaToSeparator : OK
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+ Test result : Bio.converters.testHelmRnaToSeparator : OK
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+ Test result : Bio.converters.testHelmPtToSeparator : OK
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+ Test result : Bio.converters.testHelmLoneRibose : OK
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+ Test result : Bio.converters.testHelmLoneDeoxyribose : OK
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+ Test result : Bio.converters.testHelmLonePhosphorus : OK
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  </pre></div></div></div></div></body></html>