@datagrok/sequence-translator 1.0.15 → 1.0.17

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Files changed (38) hide show
  1. package/.eslintrc.json +16 -3
  2. package/detectors.js +0 -28
  3. package/dist/package-test.js +4372 -3957
  4. package/dist/package.js +3875 -3460
  5. package/package.json +4 -2
  6. package/setup-unlink-clean.sh +21 -0
  7. package/src/apps/oligo-sd-file-app.ts +58 -0
  8. package/src/autostart/calculations.ts +11 -8
  9. package/src/autostart/constants.ts +0 -12
  10. package/src/autostart/registration.ts +194 -157
  11. package/src/{axolabs/define-pattern.ts → axolabs-tab/axolabs-tab.ts} +2 -2
  12. package/src/axolabs-tab/define-pattern.ts +874 -0
  13. package/src/{axolabs → axolabs-tab}/draw-svg.ts +1 -1
  14. package/src/{axolabs → axolabs-tab}/helpers.ts +2 -2
  15. package/src/{autostart → hardcode-to-be-eliminated}/ICDs.ts +0 -0
  16. package/src/{autostart → hardcode-to-be-eliminated}/IDPs.ts +0 -0
  17. package/src/{structures-works → hardcode-to-be-eliminated}/const.ts +0 -0
  18. package/src/{axolabs → hardcode-to-be-eliminated}/constants.ts +0 -0
  19. package/src/{structures-works → hardcode-to-be-eliminated}/converters.ts +1 -1
  20. package/src/{structures-works → hardcode-to-be-eliminated}/map.ts +2 -2
  21. package/src/{autostart → hardcode-to-be-eliminated}/salts.ts +0 -0
  22. package/src/{autostart → hardcode-to-be-eliminated}/sources.ts +0 -0
  23. package/src/{autostart → hardcode-to-be-eliminated}/users.ts +0 -0
  24. package/src/{main/main-view.ts → main-tab/main-tab.ts} +28 -80
  25. package/src/package.ts +77 -13
  26. package/src/sdf-tab/sdf-tab.ts +163 -0
  27. package/src/{structures-works → sdf-tab}/sequence-codes-tools.ts +8 -5
  28. package/src/tests/smiles-tests.ts +2 -2
  29. package/src/utils/const.ts +0 -0
  30. package/src/{helpers.ts → utils/helpers.ts} +3 -3
  31. package/src/utils/parse.ts +27 -0
  32. package/src/utils/sdf-add-columns.ts +118 -0
  33. package/src/utils/sdf-save-table.ts +56 -0
  34. package/src/utils/structures-works/draw-molecule.ts +84 -0
  35. package/src/{structures-works → utils/structures-works}/from-monomers.ts +15 -16
  36. package/src/{structures-works → utils/structures-works}/mol-transformations.ts +34 -52
  37. package/{test-SequenceTranslator-91c83d8913ff-f94596bc.html → test-SequenceTranslator-6288c2fbe346-695b7b55.html} +10 -10
  38. package/src/structures-works/save-sense-antisense.ts +0 -91
package/src/structures-works/save-sense-antisense.ts DELETED
@@ -1,91 +0,0 @@
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- import * as grok from 'datagrok-api/grok';
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- import * as ui from 'datagrok-api/ui';
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- import * as DG from 'datagrok-api/dg';
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-
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- import {download} from '../helpers';
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- import {sequenceToMolV3000} from '../structures-works/from-monomers';
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- import {linkStrandsV3000} from '../structures-works/mol-transformations';
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- import {getFormat} from '../structures-works/sequence-codes-tools';
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-
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- export function saveSdf(as: string, ss: string,
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- oneEntity: boolean, useChirality: boolean,
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- invertSS: boolean, invertAS: boolean,
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- as2: string | null = null, invertAS2: boolean | null) {
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- const formatAs = getFormat(as);
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- const formatSs = getFormat(ss);
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- let formatAs2: string | null = null;
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- let molAS2: string | null = null;
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-
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- const molSS = sequenceToMolV3000(ss, invertSS, false, formatSs!);
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- const molAS = sequenceToMolV3000(as, invertAS, false, formatAs!);
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-
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- if (as2 != null && as2 != '') {
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- formatAs2 = getFormat(as2!);
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- molAS2 = sequenceToMolV3000(as2, invertAS2!, false, formatAs2!);
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- }
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-
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- let result: string;
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- if (oneEntity) {
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- const antiStrands = molAS2 == null ? [molAS] : [molAS, molAS2];
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- result = linkStrandsV3000({senseStrands: [molSS], antiStrands: antiStrands}, useChirality) + '\n$$$$\n';
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-
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- } else {
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- result =
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- molSS + '\n' +
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- `> <Sequence>\nSense Strand\n$$$$\n` +
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- molAS + '\n' +
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- `> <Sequence>\nAnti Sense\n$$$$\n`;
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-
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- if (molAS2)
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- result += molAS2+ '\n' +
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- `> <Sequence>\nAnti Sense 2\n$$$$\n`;
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- }
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- download(ss.replace(/\s/g, '') + '.sdf', encodeURIComponent(result));
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- }
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-
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- export function saveSenseAntiSense() {
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- const moleculeSvgDiv = ui.block([]);
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- const ssInput = ui.textInput('Sense Strand', '');
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- const asInput = ui.textInput('Anti Sense', '');
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- const asInput2 = ui.textInput('Anti Sense 2', '');
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- const straight = "5 prime -> 3 prime";
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- const inverse = "3 prime -> 5 prime";
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- let ssInverse = false;
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- let asInverse = false;
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- let as2Inverse = false;
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-
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- const changeSense = ui.choiceInput('SS direction', straight, [straight, inverse]);
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- changeSense.onChanged(() => {ssInverse = changeSense.value == inverse;});
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- const changeAntiSense = ui.choiceInput('AS direction', straight, [straight, inverse]);
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- changeAntiSense.onChanged(() => {asInverse = changeAntiSense.value == inverse;});
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- const changeAntiSense2 = ui.choiceInput('AS 2 direction', straight, [straight, inverse]);
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- changeAntiSense2.onChanged(() => {asInverse = changeAntiSense.value == inverse;});
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-
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- const saveOption = ui.switchInput('Save as one entity', true);
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- const chirality = ui.switchInput('Use chiral', true);
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- const saveBtn = ui.button('Save SDF', () =>
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- saveSdf(asInput.value, ssInput.value, saveOption.value, chirality.value, ssInverse, asInverse, asInput2.value, as2Inverse));
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-
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- const saveSection = ui.panel([
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- ui.div([
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- ui.div([
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- ui.divH([ui.h1('Inputs')]),
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- ui.divV([
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- ssInput,
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- asInput,
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- asInput2,
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- ui.div([changeSense], {style: {width: '40'}}),
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- changeSense,
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- changeAntiSense,
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- changeAntiSense2,
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- saveOption,
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- chirality,
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- ui.buttonsInput([saveBtn]),
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- ], 'ui-form'),
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- ], 'ui-form'),
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- ], 'ui-form'),
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- moleculeSvgDiv,
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- ]);
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-
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- return saveSection;
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- }