@datagrok/bio 2.13.8 → 2.14.2

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Files changed (32) hide show
  1. package/.eslintrc.json +10 -2
  2. package/CHANGELOG.md +15 -0
  3. package/dist/248.js.map +1 -1
  4. package/dist/package-test.js +6 -6
  5. package/dist/package-test.js.map +1 -1
  6. package/dist/package.js +3 -3
  7. package/dist/package.js.map +1 -1
  8. package/files/monomer-sets/monomer-set-PEPTIDE.json +93 -0
  9. package/files/monomer-sets/monomer-set-RNA.json +29 -0
  10. package/files/schemas/monomer-set-schema.json +48 -0
  11. package/package.json +5 -5
  12. package/src/analysis/sequence-similarity-viewer.ts +5 -2
  13. package/src/demo/bio01-similarity-diversity.ts +3 -2
  14. package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts +1 -1
  15. package/src/package.ts +12 -7
  16. package/src/tests/activity-cliffs-tests.ts +2 -2
  17. package/src/tests/detectors-tests.ts +14 -7
  18. package/src/tests/monomer-libraries-tests.ts +6 -6
  19. package/src/tests/renderers-monomer-placer-tests.ts +2 -2
  20. package/src/tests/scoring.ts +2 -2
  21. package/src/tests/substructure-filters-tests.ts +2 -2
  22. package/src/tests/to-atomic-level-tests.ts +3 -3
  23. package/src/utils/helm-to-molfile/converter/converter.ts +1 -1
  24. package/src/utils/monomer-lib/lib-manager.ts +118 -21
  25. package/src/utils/monomer-lib/library-file-manager/event-manager.ts +25 -8
  26. package/src/utils/monomer-lib/library-file-manager/file-manager.ts +122 -35
  27. package/src/utils/monomer-lib/library-file-manager/ui.ts +1 -1
  28. package/src/utils/monomer-lib/monomer-lib.ts +23 -6
  29. package/src/utils/monomer-lib/monomer-set.ts +61 -0
  30. package/src/widgets/bio-substructure-filter-helm.ts +2 -2
  31. package/src/widgets/bio-substructure-filter.ts +19 -14
  32. package/webpack.config.js +3 -2
package/src/widgets/bio-substructure-filter-helm.ts CHANGED
@@ -63,7 +63,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
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  .add(webEditorHost!)
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  .onOK(() => {
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  try {
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- const webEditorValue = webEditorApp!.canvas.getHelm(true)
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+ const webEditorValue = webEditorApp!.canvas!.getHelm(true)
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  .replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
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  this.props = new BioFilterProps(webEditorValue);
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  } catch (err: any) {
@@ -90,7 +90,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
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  this.viewSubs.push(ui.onSizeChanged(this._filterPanel).subscribe((_: any) => {
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  try {
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  if (!!webEditorApp) {
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- const helmString = webEditorApp.canvas.getHelm(true)
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+ const helmString = webEditorApp!.canvas!.getHelm(true)
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  .replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
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  this.updateFilterPanel(helmString);
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  }
package/src/widgets/bio-substructure-filter.ts CHANGED
@@ -111,7 +111,6 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
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  private filterToLog(): string { return `BioSubstructureFilter<${this.filterId}>`; }
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-
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  private viewSubs: Unsubscribable[] = [];
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  attach(dataFrame: DG.DataFrame): void {
@@ -296,10 +295,12 @@ export class FastaBioFilter extends BioFilterBase<BioFilterProps> {
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  constructor() {
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  super();
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- this.substructureInput = ui.input.string('', {value: '', onValueChanged: () => {
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- this.props = new BioFilterProps(this.substructureInput.value);
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- if (!this._propsChanging) this.onChanged.next();
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- }, placeholder: 'Substructure'});
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+ this.substructureInput = ui.input.string('', {
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+ value: '', onValueChanged: () => {
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+ this.props = new BioFilterProps(this.substructureInput.value);
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+ if (!this._propsChanging) this.onChanged.next();
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+ }, placeholder: 'Substructure'
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+ });
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  }
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  public applyProps() {
@@ -336,15 +337,19 @@ export class SeparatorBioFilter extends BioFilterBase<SeparatorFilterProps> {
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  constructor(colSeparator: string) {
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  super();
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- this.substructureInput = ui.input.string('', {value: '', onValueChanged: () => {
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- this.props = new SeparatorFilterProps(this.substructureInput.value, this.props.separator);
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- if (!this._propsChanging) this.onChanged.next();
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- }, placeholder: 'Substructure'});
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- this.separatorInput = ui.input.string('', {value: this.colSeparator = colSeparator, onValueChanged: () => {
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- const separator: string | undefined = !!this.separatorInput.value ? this.separatorInput.value : undefined;
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- this.props = new SeparatorFilterProps(this.props.substructure, separator);
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- if (!this._propsChanging) this.onChanged.next();
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- }, placeholder: 'Separator'});
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+ this.substructureInput = ui.input.string('', {
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+ value: '', onValueChanged: () => {
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+ this.props = new SeparatorFilterProps(this.substructureInput.value, this.props.separator);
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+ if (!this._propsChanging) this.onChanged.next();
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+ }, placeholder: 'Substructure'
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+ });
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+ this.separatorInput = ui.input.string('', {
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+ value: this.colSeparator = colSeparator, onValueChanged: () => {
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+ const separator: string | undefined = !!this.separatorInput.value ? this.separatorInput.value : undefined;
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+ this.props = new SeparatorFilterProps(this.props.substructure, separator);
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+ if (!this._propsChanging) this.onChanged.next();
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+ }, placeholder: 'Separator'
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+ });
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  }
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  applyProps(): void {
package/webpack.config.js CHANGED
@@ -7,7 +7,8 @@ if (mode !== 'production')
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  console.warn(`Building Bio in '${mode}' mode.`);
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  module.exports = {
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- ...(mode === 'production' ? {cache: {type: 'filesystem'}} : {}),
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+ // ...(mode === 'production' ? {cache: {type: 'filesystem'}} : {}),
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+ cache: {type: 'filesystem'},
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  mode: mode,
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  entry: {
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  package: ['./src/package.ts'],
@@ -19,7 +20,7 @@ module.exports = {
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  },
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  resolve: {
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  fallback: {'url': false},
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- extensions: ['.wasm', '.mjs', '.ts', '.tsx', '.js', '.json'],
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+ extensions: ['.ts', '.tsx', '.wasm', '.mjs', '.js', '.json'],
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  },
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  module: {
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  rules: [