@datagrok/bio 2.7.1 → 2.7.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.7.1",
+  "version": "2.7.2",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -53,9 +53,9 @@
     "source-map-loader": "^4.0.1",
     "ts-loader": "^9.2.5",
     "typescript": "^4.8.4",
-    "webpack": "^5.76.0",
+    "webpack": "^5.76.3",
     "webpack-bundle-analyzer": "latest",
-    "webpack-cli": "^4.6.0",
+    "webpack-cli": "^4.9.1",
     "@datagrok/chem": "1.4.21",
     "@datagrok/helm": "2.1.7"
   },

package/src/package.ts

@@ -262,7 +262,7 @@ export function SeqActivityCliffsEditor(call: DG.FuncCall) {
     .show();
 }
 
-//top-menu: Bio | SAR | Activity Cliffs...
+//top-menu: Bio | Analyze | Activity Cliffs...
 //name: Sequence Activity Cliffs
 //description: detect activity cliffs
 //input: dataframe table [Input data table]
@@ -356,7 +356,7 @@ export function SequenceSpaceEditor(call: DG.FuncCall) {
     .show();
 }
 
-//top-menu: Bio | Structure | Sequence Space...
+//top-menu: Bio | Analyze | Sequence Space...
 //name: Sequence Space
 //input: dataframe table
 //input: column molecules { semType: Macromolecule }
@@ -454,7 +454,7 @@ export async function sequenceSpaceTopMenu(
   } */
 };
 
-//top-menu: Bio | Atomic Level | To Atomic Level...
+//top-menu: Bio | Convert | To Atomic Level...
 //name: To Atomic Level
 //description: returns molfiles for each monomer from HELM library
 //input: dataframe df [Input data table]
@@ -477,8 +477,8 @@ export async function toAtomicLevel(df: DG.DataFrame, macroMolecule: DG.Column):
     grok.shell.warning(ui.list(atomicLevelRes.warnings));
 }
 
-//top-menu: Bio | Alignment | MSA...
-//name: MSA...
+//top-menu: Bio | Analyze | MSA...
+//name: MSA
 //tags: bio, panel
 export function multipleSequenceAlignmentDialog(): void {
   multipleSequenceAlignmentUI();
@@ -495,7 +495,7 @@ export async function alignSequences(sequenceCol: DG.Column<string> | null = nul
   return multipleSequenceAlignmentUI({col: sequenceCol, clustersCol});
 }
 
-//top-menu: Bio | Structure | Composition Analysis
+//top-menu: Bio | Analyze | Composition
 //name: Composition Analysis
 //meta.icon: files/icons/composition-analysis.svg
 //output: viewer result
@@ -554,7 +554,7 @@ export async function compositionAnalysis(): Promise<void> {
   await handler(col);
 }
 
-//top-menu: Bio | Atomic Level | SDF to JSON Library...
+//top-menu: Bio | Convert | SDF to JSON Library...
 //name: SDF to JSON Library
 //input: dataframe table
 export async function sdfToJsonLib(table: DG.DataFrame) {
@@ -595,7 +595,7 @@ export function importBam(fileContent: string): DG.DataFrame [] {
   return [];
 }
 
-//top-menu: Bio | Convert...
+//top-menu: Bio | Convert | Notation...
 //name: convertDialog
 export function convertDialog() {
   const col = getMacromoleculeColumn();
@@ -675,7 +675,7 @@ export function SplitToMonomersEditor(call: DG.FuncCall): void {
     .show();
 }
 
-//top-menu: Bio | Split to Monomers
+//top-menu: Bio | Convert | Split to Monomers...
 //name: Split to Monomers
 //input: dataframe table
 //input: column sequence { semType: Macromolecule }
@@ -702,7 +702,7 @@ export function similaritySearchViewer(): SequenceSimilarityViewer {
   return new SequenceSimilarityViewer();
 }
 
-//top-menu: Bio | Search | Similarity Search
+//top-menu: Bio | Search | Similarity
 //name: similaritySearch
 //description: finds the most similar sequence
 //output: viewer result
@@ -720,7 +720,7 @@ export function diversitySearchViewer(): SequenceDiversityViewer {
   return new SequenceDiversityViewer();
 }
 
-//top-menu: Bio | Search | Diversity Search
+//top-menu: Bio | Search | Diversity
 //name: diversitySearch
 //description: finds the most diverse molecules
 //output: viewer result
@@ -730,7 +730,7 @@ export function diversitySearchTopMenu() {
   view.dockManager.dock(viewer, 'down');
 }
 
-//top-menu: Bio | Structure | Substructure Search ...
+//top-menu: Bio | Search | Substructure...
 //name: bioSubstructureSearch
 export function bioSubstructureSearch(): void {
   const col = getMacromoleculeColumn();

package/src/substructure-search/substructure-search.ts

@@ -105,6 +105,7 @@ export async function helmSubstructureSearch(substructure: string, col: DG.Colum
   if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
     await invalidateMols(col, true);
   const substructureCol: DG.Column<string> = DG.Column.string('helm', 1).init((_i) => substructure);
+  substructureCol.semType = DG.SEMTYPE.MACROMOLECULE;
   substructureCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
   const substructureMolsCol =
     await getMonomericMols(substructureCol, true, col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT]);

package/tsconfig.json

@@ -4,7 +4,7 @@
 
     /* Basic Options */
     // "incremental": true,                         /* Enable incremental compilation */
-    "target": "es2020",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
+    "target": "es2020",                             /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
     "module": "es2020",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
     "lib": ["ES2022", "dom"],      /* Specify library files to be included in the compilation. */
     // "allowJs": true,                             /* Allow javascript files to be compiled. */
@@ -66,8 +66,7 @@
 
     /* Advanced Options */
     "skipLibCheck": false,                          /* Skip type checking of declaration files. */
-    "forceConsistentCasingInFileNames": true,
-    /* Disallow inconsistently-cased references to the same file. */
+    "forceConsistentCasingInFileNames": true,       /* Disallow inconsistently-cased references to the same file. */
     //"jsx": "react"
   }
 }

package/webpack.config.js

@@ -36,7 +36,7 @@ module.exports = {
   },
   output: {
     filename: '[name].js',
-    library: 'bio',
+    library: packageName,
     libraryTarget: 'var',
     path: path.resolve(__dirname, 'dist'),
   },