@datagrok/bio 2.22.6 → 2.22.8

package/src/package.g.ts

@@ -1 +1,629 @@
+import {PackageFunctions} from './package';
 import * as DG from 'datagrok-api/dg';
+
+//name: getMonomerLibHelper
+//description: Returns an instance of the monomer library helper
+//output: object result
+export async function getMonomerLibHelper() {
+  return PackageFunctions.getMonomerLibHelper();
+}
+
+//name: initBio
+//tags: init
+export async function initBio() {
+  return PackageFunctions.initBio();
+}
+
+//name: sequenceTooltip
+//tags: tooltip
+//input: column col { semType: Macromolecule }
+//output: widget result
+export function sequenceTooltip(col: DG.Column) {
+  return PackageFunctions.sequenceTooltip(col);
+}
+
+//name: getBioLib
+//output: object monomerLib
+export function getBioLib() {
+  return PackageFunctions.getBioLib();
+}
+
+//name: getSeqHandler
+//input: column sequence { semType: Macromolecule }
+//output: object result
+export function getSeqHandler(sequence: any) {
+  return PackageFunctions.getSeqHandler(sequence);
+}
+
+//name: Bioinformatics | Get Region
+//description: Creates a new column with sequences of the region between start and end
+//tags: panel
+//input: column seqCol { semType: Macromolecule }
+//output: widget result
+export function getRegionPanel(seqCol: any) {
+  return PackageFunctions.getRegionPanel(seqCol);
+}
+
+//name: Bioinformatics | Manage Monomer Libraries
+//tags: panel, exclude-actions-panel
+//input: column seqColumn { semType: Macromolecule }
+//output: widget result
+export async function libraryPanel(_seqColumn: DG.Column) {
+  return PackageFunctions.libraryPanel(_seqColumn);
+}
+
+//name: GetRegionEditor
+//tags: editor
+//input: funccall call 
+export function GetRegionEditor(call: DG.FuncCall) {
+  return PackageFunctions.GetRegionEditor(call);
+}
+
+//name: SplitToMonomersEditor
+//tags: editor
+//input: funccall call 
+export function SplitToMonomersEditor(call: DG.FuncCall) {
+  return PackageFunctions.SplitToMonomersEditor(call);
+}
+
+//name: SequenceSpaceEditor
+//tags: editor
+//input: funccall call 
+export function SequenceSpaceEditor(call: DG.FuncCall) {
+  return PackageFunctions.SequenceSpaceEditor(call);
+}
+
+//name: SeqActivityCliffsEditor
+//tags: editor
+//input: funccall call 
+export function SeqActivityCliffsEditor(call: DG.FuncCall) {
+  return PackageFunctions.SeqActivityCliffsEditor(call);
+}
+
+//name: customSequenceCellRenderer
+//tags: cellRenderer
+//output: grid_cell_renderer result
+//meta.cellType: sequence
+//meta.columnTags: quality=Macromolecule, units=custom
+export function customSequenceCellRenderer() {
+  return PackageFunctions.customSequenceCellRenderer();
+}
+
+//name: fastaSequenceCellRenderer
+//tags: cellRenderer
+//output: grid_cell_renderer result
+//meta.cellType: sequence
+//meta.columnTags: quality=Macromolecule, units=fasta
+export function fastaSequenceCellRenderer() {
+  return PackageFunctions.fastaSequenceCellRenderer();
+}
+
+//name: separatorSequenceCellRenderer
+//tags: cellRenderer
+//output: grid_cell_renderer result
+//meta.cellType: sequence
+//meta.columnTags: quality=Macromolecule, units=separator
+export function separatorSequenceCellRenderer() {
+  return PackageFunctions.separatorSequenceCellRenderer();
+}
+
+//name: Bioinformatics | Sequence Renderer
+//tags: panel
+//input: column molColumn { semType: Macromolecule }
+//output: widget result
+export function macroMolColumnPropertyPanel(molColumn: DG.Column) {
+  return PackageFunctions.macroMolColumnPropertyPanel(molColumn);
+}
+
+//name: Composition analysis
+//tags: panel, bio, widgets
+//input: semantic_value sequence { semType: Macromolecule }
+//output: widget result
+export function compositionAnalysisWidget(sequence: DG.SemanticValue) {
+  return PackageFunctions.compositionAnalysisWidget(sequence);
+}
+
+//name: MacromoleculeDifferenceCellRenderer
+//tags: cellRenderer
+//output: grid_cell_renderer result
+//meta.cellType: MacromoleculeDifference
+//meta.columnTags: quality=MacromoleculeDifference
+export function macromoleculeDifferenceCellRenderer() {
+  return PackageFunctions.macromoleculeDifferenceCellRenderer();
+}
+
+//name: sequenceAlignment
+//input: string alignType { choices: ['Local alignment','Global alignment'] }
+//input: string alignTable { choices: ['AUTO','NUCLEOTIDES','BLOSUM45','BLOSUM50','BLOSUM62','BLOSUM80','BLOSUM90','PAM30','PAM70','PAM250','SCHNEIDER','TRANS'] }
+//input: double gap 
+//input: string seq1 
+//input: string seq2 
+//output: object result
+export function sequenceAlignment(alignType: string, alignTable: string, gap: number, seq1: string, seq2: string) {
+  return PackageFunctions.sequenceAlignment(alignType, alignTable, gap, seq1, seq2);
+}
+
+//name: WebLogo
+//description: WebLogo
+//tags: panel, viewer
+//output: viewer result
+//meta.icon: files/icons/weblogo-viewer.svg
+export function webLogoViewer() {
+  return PackageFunctions.webLogoViewer();
+}
+
+//name: VdRegions
+//description: V-Domain regions viewer
+//tags: panel, viewer
+//output: viewer result
+//meta.icon: files/icons/vdregions-viewer.svg
+export function vdRegionsViewer() {
+  return PackageFunctions.vdRegionsViewer();
+}
+
+//name: getRegion
+//description: Gets a new column with sequences of the region between start and end
+//input: column sequence 
+//input: string start { optional: true }
+//input: string end { optional: true }
+//input: string name { optional: true; description: Name of the column to be created }
+//output: column result
+export function getRegion(sequence: any, start: any, end: any, name: any) {
+  return PackageFunctions.getRegion(sequence, start, end, name);
+}
+
+//name: Get Region Top Menu
+//description: Get sequences for a region specified from a Macromolecule
+//input: dataframe table { description: Input data table }
+//input: column sequence { semType: Macromolecule; description: Sequence column }
+//input: string start { optional: true; description: Region start position name }
+//input: string end { optional: true; description: Region end position name }
+//input: string name { optional: true; description: Region column name }
+//top-menu: Bio | Calculate | Get Region...
+//editor: Bio:GetRegionEditor
+export async function getRegionTopMenu(table: DG.DataFrame, sequence: DG.Column, start: any, end: any, name: any) {
+  return PackageFunctions.getRegionTopMenu(table, sequence, start, end, name);
+}
+
+//name: Sequence Activity Cliffs
+//description: Detects pairs of molecules with similar structure and significant difference in any given property
+//input: dataframe table { description: Input data table }
+//input: string molecules { semType: Macromolecule; description: Input data table }
+//input: column activities 
+//input: double similarity { default: 80; description: Similarity cutoff }
+//input: string methodName { choices: ['UMAP','t-SNE'] }
+//input: string similarityMetric { choices: ['Hamming','Levenshtein','Monomer chemical distance'] }
+//input: func preprocessingFunction 
+//input: object options { optional: true }
+//input: bool demo { optional: true }
+//top-menu: Bio | Analyze | Activity Cliffs...
+//editor: Bio:SeqActivityCliffsEditor
+export async function activityCliffs(table: DG.DataFrame, molecules: any, activities: DG.Column, similarity: number, methodName: any, similarityMetric: any, preprocessingFunction: any, options?: any, demo?: boolean) {
+  return PackageFunctions.activityCliffs(table, molecules, activities, similarity, methodName, similarityMetric, preprocessingFunction, options, demo);
+}
+
+//name: Encode Sequences
+//tags: dim-red-preprocessing-function
+//input: column col { semType: Macromolecule }
+//input: string metric 
+//input: double gapOpen { default: 1; caption: Gap open penalty; optional: true }
+//input: double gapExtend { default: 0.6; caption: Gap extension penalty; optional: true }
+//input: string fingerprintType { caption: Fingerprint type; default: Morgan; choices: ['Morgan','RDKit','Pattern','AtomPair','MACCS','TopologicalTorsion']; optional: true }
+//output: object result
+//meta.supportedSemTypes: Macromolecule
+//meta.supportedTypes: string
+//meta.supportedDistanceFunctions: Hamming,Levenshtein,Monomer chemical distance,Needlemann-Wunsch
+export async function macromoleculePreprocessingFunction(col: DG.Column, metric: any, gapOpen: number, gapExtend: number, fingerprintType: string) {
+  return PackageFunctions.macromoleculePreprocessingFunction(col, metric, gapOpen, gapExtend, fingerprintType);
+}
+
+//name: Helm Fingerprints
+//input: column col { semType: Macromolecule }
+//input: string _metric 
+//output: object result
+//meta.supportedSemTypes: Macromolecule
+//meta.supportedTypes: string
+//meta.supportedUnits: helm
+//meta.supportedDistanceFunctions: Tanimoto,Asymmetric,Cosine,Sokal
+export async function helmPreprocessingFunction(col: any, _metric: any) {
+  return PackageFunctions.helmPreprocessingFunction(col, _metric);
+}
+
+//name: Sequence Space
+//description: Creates 2D sequence space with projected sequences by pairwise distance
+//input: dataframe table 
+//input: column molecules { semType: Macromolecule }
+//input: string methodName { choices: ['UMAP','t-SNE'] }
+//input: string similarityMetric { choices: ['Hamming','Levenshtein','Monomer chemical distance'] }
+//input: bool plotEmbeddings { default: true }
+//input: func preprocessingFunction { optional: true }
+//input: object options { optional: true }
+//input: bool clusterEmbeddings { optional: true; default: true }
+//input: bool isDemo { optional: true }
+//top-menu: Bio | Analyze | Sequence Space...
+//editor: Bio:SequenceSpaceEditor
+export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Column, methodName: any, similarityMetric: any, plotEmbeddings: boolean, preprocessingFunction?: any, options?: any, clusterEmbeddings?: boolean, isDemo?: boolean) {
+  return PackageFunctions.sequenceSpaceTopMenu(table, molecules, methodName, similarityMetric, plotEmbeddings, preprocessingFunction, options, clusterEmbeddings, isDemo);
+}
+
+//name: To Atomic Level
+//description: Converts sequences to molblocks
+//input: dataframe table { description: Input data table }
+//input: column seqCol { semType: Macromolecule; caption: Sequence }
+//input: bool nonlinear { default: false; caption: Non-linear; description: Slower mode for cycling/branching HELM structures }
+//input: bool highlight { default: false; caption: Highlight monomers; description: Highlight monomers' substructures of the molecule }
+//top-menu: Bio | Transform | To Atomic Level...
+export async function toAtomicLevel(table: DG.DataFrame, seqCol: DG.Column, nonlinear: boolean, highlight: boolean) {
+  return PackageFunctions.toAtomicLevel(table, seqCol, nonlinear, highlight);
+}
+
+//name: To Atomic Level...
+//input: column seqCol { semType: Macromolecule }
+//meta.action: to atomic level
+export async function toAtomicLevelAction(seqCol: DG.Column) {
+  return PackageFunctions.toAtomicLevelAction(seqCol);
+}
+
+//name: Molecular Structure
+//tags: panel, bio, widgets
+//input: semantic_value sequence { semType: Macromolecule }
+//output: widget result
+export async function toAtomicLevelPanel(sequence: DG.SemanticValue) {
+  return PackageFunctions.toAtomicLevelPanel(sequence);
+}
+
+//name: Molecular 3D Structure
+//tags: panel, bio, widgets
+//input: semantic_value sequence { semType: Macromolecule }
+//output: widget result
+export async function sequence3dStructureWidget(sequence: DG.SemanticValue) {
+  return PackageFunctions.sequence3dStructureWidget(sequence);
+}
+
+//name: MSA
+//description: Performs multiple sequence alignment
+//tags: panel, bio
+//top-menu: Bio | Analyze | MSA...
+export function multipleSequenceAlignmentDialog() {
+  return PackageFunctions.multipleSequenceAlignmentDialog();
+}
+
+//name: Multiple Sequence Alignment
+//description: Multiple sequence alignment
+//tags: bio
+//input: column sequenceCol { semType: Macromolecule }
+//input: column clustersCol 
+//input: object options { optional: true }
+//output: column result
+export async function alignSequences(sequenceCol: any, clustersCol: any, options?: any) {
+  return PackageFunctions.alignSequences(sequenceCol, clustersCol, options);
+}
+
+//name: Composition Analysis
+//description: Visualizes sequence composition on a WebLogo plot
+//output: viewer result
+//meta.icon: files/icons/composition-analysis.svg
+//top-menu: Bio | Analyze | Composition
+export async function compositionAnalysis() {
+  return PackageFunctions.compositionAnalysis();
+}
+
+//name: importFasta
+//description: Opens FASTA file
+//tags: file-handler
+//input: string fileContent 
+//output: list<dataframe> result
+//meta.ext: fasta, fna, ffn, faa, frn, fa, fst
+export function importFasta(fileContent: string) {
+  return PackageFunctions.importFasta(fileContent);
+}
+
+//name: importBam
+//description: Opens Bam file
+//tags: file-handler
+//input: string fileContent 
+//output: list<dataframe> result
+//meta.ext: bam, bai
+export function importBam(fileContent: string) {
+  return PackageFunctions.importBam(fileContent);
+}
+
+//name: convertDialog
+//top-menu: Bio | Transform | Convert Notation...
+export function convertDialog() {
+  return PackageFunctions.convertDialog();
+}
+
+//name: Convert Notation...
+//input: column col { semType: Macromolecule }
+//meta.action: Convert Notation...
+export function convertColumnAction(col: DG.Column) {
+  return PackageFunctions.convertColumnAction(col);
+}
+
+//name: monomerCellRenderer
+//tags: cellRenderer
+//output: grid_cell_renderer result
+//meta.cellType: Monomer
+//meta.columnTags: quality=Monomer
+export function monomerCellRenderer() {
+  return PackageFunctions.monomerCellRenderer();
+}
+
+//name: testDetectMacromolecule
+//input: string path { choices: ['Demo:Files/','System:AppData/'] }
+//output: dataframe result
+export async function testDetectMacromolecule(path: string) {
+  return PackageFunctions.testDetectMacromolecule(path);
+}
+
+//name: Split to Monomers
+//input: dataframe table 
+//input: column sequence { semType: Macromolecule }
+//output: dataframe result
+//top-menu: Bio | Transform | Split to Monomers...
+//editor: Bio:SplitToMonomersEditor
+export async function splitToMonomersTopMenu(table: DG.DataFrame, sequence: DG.Column) {
+  return PackageFunctions.splitToMonomersTopMenu(table, sequence);
+}
+
+//name: Bio: getHelmMonomers
+//input: column sequence { semType: Macromolecule }
+//output: object result
+export function getHelmMonomers(sequence: any) {
+  return PackageFunctions.getHelmMonomers(sequence);
+}
+
+//name: Sequence Similarity Search
+//tags: viewer
+//output: viewer result
+//meta.icon: files/icons/sequence-similarity-viewer.svg
+export function similaritySearchViewer() {
+  return PackageFunctions.similaritySearchViewer();
+}
+
+//name: similaritySearch
+//description: Finds similar sequences
+//output: viewer result
+//top-menu: Bio | Search | Similarity Search
+export function similaritySearchTopMenu() {
+  return PackageFunctions.similaritySearchTopMenu();
+}
+
+//name: Sequence Diversity Search
+//tags: viewer
+//output: viewer result
+//meta.icon: files/icons/sequence-diversity-viewer.svg
+export function diversitySearchViewer() {
+  return PackageFunctions.diversitySearchViewer();
+}
+
+//name: diversitySearch
+//description: Finds the most diverse sequences
+//output: viewer result
+//top-menu: Bio | Search | Diversity Search
+export function diversitySearchTopMenu() {
+  return PackageFunctions.diversitySearchTopMenu();
+}
+
+//name: SearchSubsequenceEditor
+//tags: editor
+//input: funccall call 
+export function searchSubsequenceEditor(call: DG.FuncCall) {
+  return PackageFunctions.searchSubsequenceEditor(call);
+}
+
+//name: Subsequence Search
+//input: column macromolecules 
+//top-menu: Bio | Search | Subsequence Search ...
+//editor: Bio:SearchSubsequenceEditor
+export function SubsequenceSearchTopMenu(macromolecules: DG.Column) {
+  return PackageFunctions.SubsequenceSearchTopMenu(macromolecules);
+}
+
+//name: Identity Scoring
+//description: Adds a column with fraction of matching monomers
+//input: dataframe table { description: Table containing Macromolecule column }
+//input: column macromolecule { semType: Macromolecule; description: Sequences to score }
+//input: string reference { description: Sequence,matching column format }
+//output: column result
+//top-menu: Bio | Calculate | Identity...
+export async function sequenceIdentityScoring(table: DG.DataFrame, macromolecule: DG.Column, reference: string) {
+  return PackageFunctions.sequenceIdentityScoring(table, macromolecule, reference);
+}
+
+//name: Similarity Scoring
+//description: Adds a column with similarity scores, calculated as sum of monomer fingerprint similarities
+//input: dataframe table { description: Table containing Macromolecule column }
+//input: column macromolecule { semType: Macromolecule; description: Sequences to score }
+//input: string reference { description: Sequence,matching column format }
+//output: column result
+//top-menu: Bio | Calculate | Similarity...
+export async function sequenceSimilarityScoring(table: DG.DataFrame, macromolecule: DG.Column, reference: string) {
+  return PackageFunctions.sequenceSimilarityScoring(table, macromolecule, reference);
+}
+
+//name: Manage Monomer Libraries
+//description: Manage HELM monomer libraries
+export async function manageMonomerLibraries() {
+  return PackageFunctions.manageMonomerLibraries();
+}
+
+//name: Manage Monomer Libraries View
+//top-menu: Bio | Manage | Monomer Libraries
+export async function manageLibrariesView() {
+  return PackageFunctions.manageLibrariesView();
+}
+
+//name: manageMonomersView
+//description: Edit and create monomers
+//top-menu: Bio | Manage | Monomers
+export async function manageMonomersView() {
+  return PackageFunctions.manageMonomersView();
+}
+
+//name: Manage Monomer Libraries
+//tags: app
+//output: view result
+//meta.browsePath: Peptides
+//meta.icon: files/icons/monomers.png
+export async function manageMonomerLibrariesView() {
+  return PackageFunctions.manageMonomerLibrariesView();
+}
+
+//name: Monomer Manager Tree Browser
+//input: dynamic treeNode 
+//input: dynamic browsePanel 
+export async function manageMonomerLibrariesViewTreeBrowser(treeNode: any, browsePanel: any) {
+  return PackageFunctions.manageMonomerLibrariesViewTreeBrowser(treeNode, browsePanel);
+}
+
+//name: saveAsFasta
+//description: As FASTA...
+//tags: fileExporter
+export function saveAsFasta() {
+  return PackageFunctions.saveAsFasta();
+}
+
+//name: Bio Substructure Filter
+//description: Substructure filter for macromolecules
+//tags: filter
+//output: filter result
+//meta.semType: Macromolecule
+export function bioSubstructureFilter() {
+  return PackageFunctions.bioSubstructureFilter();
+}
+
+//name: Bio Substructure Filter Test
+//description: Substructure filter for Helm package tests
+//output: object result
+export function bioSubstructureFilterTest() {
+  return PackageFunctions.bioSubstructureFilterTest();
+}
+
+//name: webLogoLargeApp
+export async function webLogoLargeApp() {
+  return PackageFunctions.webLogoLargeApp();
+}
+
+//name: webLogoAggApp
+export async function webLogoAggApp() {
+  return PackageFunctions.webLogoAggApp();
+}
+
+//name: getRegionApp
+export async function getRegionApp() {
+  return PackageFunctions.getRegionApp();
+}
+
+//name: getRegionHelmApp
+export async function getRegionHelmApp() {
+  return PackageFunctions.getRegionHelmApp();
+}
+
+//name: longSeqTableSeparator
+export function longSeqTableSeparator() {
+  return PackageFunctions.longSeqTableSeparator();
+}
+
+//name: longSeqTableFasta
+export function longSeqTableFasta() {
+  return PackageFunctions.longSeqTableFasta();
+}
+
+//name: longSeqTableHelm
+export function longSeqTableHelm() {
+  return PackageFunctions.longSeqTableHelm();
+}
+
+//name: addCopyMenu
+//input: object cell 
+//input: object menu 
+export function addCopyMenu(cell: any, menu: any) {
+  return PackageFunctions.addCopyMenu(cell, menu);
+}
+
+//name: demoBioSimilarityDiversity
+//description: Sequence similarity tracking and evaluation dataset diversity
+//meta.demoPath: Bioinformatics | Similarity, Diversity
+//meta.path: /apps/Tutorials/Demo/Bioinformatics/Similarity,%20Diversity
+//meta.demoSkip: GROK-14320
+export async function demoBioSimilarityDiversity() {
+  return PackageFunctions.demoBioSimilarityDiversity();
+}
+
+//name: demoBioSequenceSpace
+//description: Exploring sequence space of Macromolecules, comparison with hierarchical clustering results
+//meta.demoPath: Bioinformatics | Sequence Space
+//meta.path: /apps/Tutorials/Demo/Bioinformatics/Sequence%20Space
+//meta.demoSkip: GROK-14320
+export async function demoBioSequenceSpace() {
+  return PackageFunctions.demoBioSequenceSpace();
+}
+
+//name: demoBioActivityCliffs
+//description: Activity Cliffs analysis on Macromolecules data
+//meta.demoPath: Bioinformatics | Activity Cliffs
+//meta.path: /apps/Tutorials/Demo/Bioinformatics/Activity%20Cliffs
+//meta.demoSkip: GROK-14320
+export async function demoBioActivityCliffs() {
+  return PackageFunctions.demoBioActivityCliffs();
+}
+
+//name: demoBioAtomicLevel
+//description: Atomic level structure of Macromolecules
+//meta.demoPath: Bioinformatics | Atomic Level
+//meta.path: /apps/Tutorials/Demo/Bioinformatics/Atomic%20Level
+//meta.demoSkip: GROK-14320
+export async function demoBioAtomicLevel() {
+  return PackageFunctions.demoBioAtomicLevel();
+}
+
+//name: SDF to JSON Library
+//input: dataframe table 
+export async function sdfToJsonLib(table: DG.DataFrame) {
+  return PackageFunctions.sdfToJsonLib(table);
+}
+
+//name: seq2atomic
+//description: Converts a `Macromolecule` sequence to its atomic level `Molecule` representation
+//input: string seq { semType: Macromolecule }
+//input: bool nonlinear 
+//output: string molfile { semType: Molecule }
+//friendlyName: seq2atomic
+export async function seq2atomic(seq: string, nonlinear: boolean) {
+  return PackageFunctions.seq2atomic(seq, nonlinear);
+}
+
+//name: seqIdentity
+//description: Gets identity to a reference sequence
+//input: string seq { semType: Macromolecule }
+//input: string ref { semType: Macromolecule }
+//output: double result
+//friendlyName: seqIdentity
+export async function seqIdentity(seq: string, ref: string) {
+  return PackageFunctions.seqIdentity(seq, ref);
+}
+
+//name: detectMacromoleculeProbe
+//input: file file 
+//input: string colName 
+//input: double probeCount { default: 100 }
+export async function detectMacromoleculeProbe(file: DG.FileInfo, colName: string, probeCount: number) {
+  return PackageFunctions.detectMacromoleculeProbe(file, colName, probeCount);
+}
+
+//name: getSeqHelper
+//output: object result
+export async function getSeqHelper() {
+  return PackageFunctions.getSeqHelper();
+}
+
+//name: getMolFromHelm
+//input: dataframe df 
+//input: column helmCol 
+//input: bool chiralityEngine { default: true }
+//output: column result
+export async function getMolFromHelm(df: DG.DataFrame, helmCol: any, chiralityEngine: boolean) {
+  return PackageFunctions.getMolFromHelm(df, helmCol, chiralityEngine);
+}