@datagrok/bio 2.25.17 → 2.26.1

package/CHANGELOG.md

@@ -1,5 +1,9 @@
 # Bio changelog
 
+## 2.26.0 (2026-03-04)
+
+* Antibodies support: Numbering schemes, highlighting, allignment, liabilities detection, extracting regions, and more.
+
 ## 2.25.15 (2026-02-26)
 
 * Monomer collections

package/dist/282.js

@@ -0,0 +1,2 @@
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Static antibody numbering scheme region definitions.\n *\n * Contains FR/CDR boundaries for IMGT, Kabat, Chothia, and AHo schemes.\n * These are the canonical position ranges used after a numbering tool\n * (e.g. ANARCI) has assigned scheme-specific position names.\n */\nexport var NumberingScheme;\n(function (NumberingScheme) {\n    NumberingScheme[\"IMGT\"] = \"IMGT\";\n    NumberingScheme[\"Kabat\"] = \"Kabat\";\n    NumberingScheme[\"Chothia\"] = \"Chothia\";\n    NumberingScheme[\"AHo\"] = \"AHo\";\n})(NumberingScheme || (NumberingScheme = {}));\nexport var ChainType;\n(function (ChainType) {\n    ChainType[\"Heavy\"] = \"Heavy\";\n    ChainType[\"Light_Kappa\"] = \"Light_Kappa\";\n    ChainType[\"Light_Lambda\"] = \"Light_Lambda\";\n})(ChainType || (ChainType = {}));\n/** IMGT region boundaries — the reference numbering scheme.\n * @see https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html\n */\nexport const IMGT_REGIONS = {\n    [ChainType.Heavy]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '26', chainType: ChainType.Heavy },\n        { name: 'CDR1', type: 'CDR', startPosition: '27', endPosition: '38', chainType: ChainType.Heavy },\n        { name: 'FR2', type: 'FR', startPosition: '39', endPosition: '55', chainType: ChainType.Heavy },\n        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '65', chainType: ChainType.Heavy },\n        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '104', chainType: ChainType.Heavy },\n        { name: 'CDR3', type: 'CDR', startPosition: '105', endPosition: '117', chainType: ChainType.Heavy },\n        { name: 'FR4', type: 'FR', startPosition: '118', endPosition: '128', chainType: ChainType.Heavy },\n    ],\n    [ChainType.Light_Kappa]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '26', chainType: ChainType.Light_Kappa },\n        { name: 'CDR1', type: 'CDR', startPosition: '27', endPosition: '38', chainType: ChainType.Light_Kappa },\n        { name: 'FR2', type: 'FR', startPosition: '39', endPosition: '55', chainType: ChainType.Light_Kappa },\n        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '65', chainType: ChainType.Light_Kappa },\n        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '104', chainType: ChainType.Light_Kappa },\n        { name: 'CDR3', type: 'CDR', startPosition: '105', endPosition: '117', chainType: ChainType.Light_Kappa },\n        { name: 'FR4', type: 'FR', startPosition: '118', endPosition: '127', chainType: ChainType.Light_Kappa },\n    ],\n    [ChainType.Light_Lambda]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '26', chainType: ChainType.Light_Lambda },\n        { name: 'CDR1', type: 'CDR', startPosition: '27', endPosition: '38', chainType: ChainType.Light_Lambda },\n        { name: 'FR2', type: 'FR', startPosition: '39', endPosition: '55', chainType: ChainType.Light_Lambda },\n        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '65', chainType: ChainType.Light_Lambda },\n        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '104', chainType: ChainType.Light_Lambda },\n        { name: 'CDR3', type: 'CDR', startPosition: '105', endPosition: '117', chainType: ChainType.Light_Lambda },\n        { name: 'FR4', type: 'FR', startPosition: '118', endPosition: '127', chainType: ChainType.Light_Lambda },\n    ],\n};\n/** Kabat region boundaries (differ mainly in CDR definitions). */\nexport const KABAT_REGIONS = {\n    [ChainType.Heavy]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '30', chainType: ChainType.Heavy },\n        { name: 'CDR1', type: 'CDR', startPosition: '31', endPosition: '35', chainType: ChainType.Heavy },\n        { name: 'FR2', type: 'FR', startPosition: '36', endPosition: '49', chainType: ChainType.Heavy },\n        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '65', chainType: ChainType.Heavy },\n        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '94', chainType: ChainType.Heavy },\n        { name: 'CDR3', type: 'CDR', startPosition: '95', endPosition: '102', chainType: ChainType.Heavy },\n        { name: 'FR4', type: 'FR', startPosition: '103', endPosition: '113', chainType: ChainType.Heavy },\n    ],\n    [ChainType.Light_Kappa]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '23', chainType: ChainType.Light_Kappa },\n        { name: 'CDR1', type: 'CDR', startPosition: '24', endPosition: '34', chainType: ChainType.Light_Kappa },\n        { name: 'FR2', type: 'FR', startPosition: '35', endPosition: '49', chainType: ChainType.Light_Kappa },\n        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '56', chainType: ChainType.Light_Kappa },\n        { name: 'FR3', type: 'FR', startPosition: '57', endPosition: '88', chainType: ChainType.Light_Kappa },\n        { name: 'CDR3', type: 'CDR', startPosition: '89', endPosition: '97', chainType: ChainType.Light_Kappa },\n        { name: 'FR4', type: 'FR', startPosition: '98', endPosition: '107', chainType: ChainType.Light_Kappa },\n    ],\n    [ChainType.Light_Lambda]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '23', chainType: ChainType.Light_Lambda },\n        { name: 'CDR1', type: 'CDR', startPosition: '24', endPosition: '34', chainType: ChainType.Light_Lambda },\n        { name: 'FR2', type: 'FR', startPosition: '35', endPosition: '49', chainType: ChainType.Light_Lambda },\n        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '56', chainType: ChainType.Light_Lambda },\n        { name: 'FR3', type: 'FR', startPosition: '57', endPosition: '88', chainType: ChainType.Light_Lambda },\n        { name: 'CDR3', type: 'CDR', startPosition: '89', endPosition: '97', chainType: ChainType.Light_Lambda },\n        { name: 'FR4', type: 'FR', startPosition: '98', endPosition: '107', chainType: ChainType.Light_Lambda },\n    ],\n};\n/** Chothia region boundaries. */\nexport const CHOTHIA_REGIONS = {\n    [ChainType.Heavy]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '25', chainType: ChainType.Heavy },\n        { name: 'CDR1', type: 'CDR', startPosition: '26', endPosition: '32', chainType: ChainType.Heavy },\n        { name: 'FR2', type: 'FR', startPosition: '33', endPosition: '51', chainType: ChainType.Heavy },\n        { name: 'CDR2', type: 'CDR', startPosition: '52', endPosition: '56', chainType: ChainType.Heavy },\n        { name: 'FR3', type: 'FR', startPosition: '57', endPosition: '94', chainType: ChainType.Heavy },\n        { name: 'CDR3', type: 'CDR', startPosition: '95', endPosition: '102', chainType: ChainType.Heavy },\n        { name: 'FR4', type: 'FR', startPosition: '103', endPosition: '113', chainType: ChainType.Heavy },\n    ],\n    [ChainType.Light_Kappa]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '25', chainType: ChainType.Light_Kappa },\n        { name: 'CDR1', type: 'CDR', startPosition: '26', endPosition: '32', chainType: ChainType.Light_Kappa },\n        { name: 'FR2', type: 'FR', startPosition: '33', endPosition: '49', chainType: ChainType.Light_Kappa },\n        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '52', chainType: ChainType.Light_Kappa },\n        { name: 'FR3', type: 'FR', startPosition: '53', endPosition: '90', chainType: ChainType.Light_Kappa },\n        { name: 'CDR3', type: 'CDR', startPosition: '91', endPosition: '96', chainType: ChainType.Light_Kappa },\n        { name: 'FR4', type: 'FR', startPosition: '97', endPosition: '107', chainType: ChainType.Light_Kappa },\n    ],\n    [ChainType.Light_Lambda]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '25', chainType: ChainType.Light_Lambda },\n        { name: 'CDR1', type: 'CDR', startPosition: '26', endPosition: '32', chainType: ChainType.Light_Lambda },\n        { name: 'FR2', type: 'FR', startPosition: '33', endPosition: '49', chainType: ChainType.Light_Lambda },\n        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '52', chainType: ChainType.Light_Lambda },\n        { name: 'FR3', type: 'FR', startPosition: '53', endPosition: '90', chainType: ChainType.Light_Lambda },\n        { name: 'CDR3', type: 'CDR', startPosition: '91', endPosition: '96', chainType: ChainType.Light_Lambda },\n        { name: 'FR4', type: 'FR', startPosition: '97', endPosition: '107', chainType: ChainType.Light_Lambda },\n    ],\n};\n/** AHo region boundaries. */\nexport const AHO_REGIONS = {\n    [ChainType.Heavy]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '24', chainType: ChainType.Heavy },\n        { name: 'CDR1', type: 'CDR', startPosition: '25', endPosition: '40', chainType: ChainType.Heavy },\n        { name: 'FR2', type: 'FR', startPosition: '41', endPosition: '55', chainType: ChainType.Heavy },\n        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '78', chainType: ChainType.Heavy },\n        { name: 'FR3', type: 'FR', startPosition: '79', endPosition: '108', chainType: ChainType.Heavy },\n        { name: 'CDR3', type: 'CDR', startPosition: '109', endPosition: '138', chainType: ChainType.Heavy },\n        { name: 'FR4', type: 'FR', startPosition: '139', endPosition: '149', chainType: ChainType.Heavy },\n    ],\n    [ChainType.Light_Kappa]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '24', chainType: ChainType.Light_Kappa },\n        { name: 'CDR1', type: 'CDR', startPosition: '25', endPosition: '40', chainType: ChainType.Light_Kappa },\n        { name: 'FR2', type: 'FR', startPosition: '41', endPosition: '55', chainType: ChainType.Light_Kappa },\n        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '78', chainType: ChainType.Light_Kappa },\n        { name: 'FR3', type: 'FR', startPosition: '79', endPosition: '108', chainType: ChainType.Light_Kappa },\n        { name: 'CDR3', type: 'CDR', startPosition: '109', endPosition: '138', chainType: ChainType.Light_Kappa },\n        { name: 'FR4', type: 'FR', startPosition: '139', endPosition: '149', chainType: ChainType.Light_Kappa },\n    ],\n    [ChainType.Light_Lambda]: [\n        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '24', chainType: ChainType.Light_Lambda },\n        { name: 'CDR1', type: 'CDR', startPosition: '25', endPosition: '40', chainType: ChainType.Light_Lambda },\n        { name: 'FR2', type: 'FR', startPosition: '41', endPosition: '55', chainType: ChainType.Light_Lambda },\n        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '78', chainType: ChainType.Light_Lambda },\n        { name: 'FR3', type: 'FR', startPosition: '79', endPosition: '108', chainType: ChainType.Light_Lambda },\n        { name: 'CDR3', type: 'CDR', startPosition: '109', endPosition: '138', chainType: ChainType.Light_Lambda },\n        { name: 'FR4', type: 'FR', startPosition: '139', endPosition: '149', chainType: ChainType.Light_Lambda },\n    ],\n};\n/** Lookup table: scheme → chain type → region defs */\nexport const SCHEME_REGIONS = {\n    [NumberingScheme.IMGT]: IMGT_REGIONS,\n    [NumberingScheme.Kabat]: KABAT_REGIONS,\n    [NumberingScheme.Chothia]: CHOTHIA_REGIONS,\n    [NumberingScheme.AHo]: AHO_REGIONS,\n};\n//# sourceMappingURL=numbering-schemes.js.map","/* eslint-disable max-len */\nimport * as grok from 'datagrok-api/grok';\nimport * as ui from 'datagrok-api/ui';\nimport * as DG from 'datagrok-api/dg';\n\nimport {TAGS as bioTAGS, ALIGNMENT, ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';\nimport {\n  SeqAnnotation, SeqAnnotationHit, AnnotationCategory,\n} from '@datagrok-libraries/bio/src/utils/macromolecule/annotations';\nimport {NumberingScheme} from '@datagrok-libraries/bio/src/utils/macromolecule/numbering-schemes';\nimport {\n  setColumnAnnotations, getColumnAnnotations,\n  getOrCreateAnnotationColumn, getRowAnnotations, setRowAnnotations, mergeRowHits,\n} from './annotation-manager';\nimport {_package} from '../../package';\nimport type {NumberingResult, Scheme} from '../antibody-numbering (WIP)';\nimport {VdRegionsViewer} from '../../viewers/vd-regions-viewer';\nimport { VdRegion, VdRegionType } from '@datagrok-libraries/bio/src/viewers/vd-regions';\n\nconst BUILTIN_ENGINE_KEY = '__builtin__';\nconst BUILTIN_ENGINE_LABEL = 'Built-in (TypeScript)';\n\n/** An engine entry: either a dynamically discovered DG.Func or the built-in TS engine. */\ninterface NumberingEngine {\n  /** Display label for the dropdown */\n  label: string;\n  /** Unique key — nqName for DG.Func engines, BUILTIN_ENGINE_KEY for built-in */\n  key: string;\n  /** The DG.Func to call, or null for the built-in engine */\n  func: DG.Func | null;\n}\n\n/** Discovers all registered antibody numbering engines + the built-in TS engine.\n *  Dynamic engines (meta.role = 'antibodyNumbering') come first; built-in is last. */\nfunction discoverEngines(): NumberingEngine[] {\n  const engines: NumberingEngine[] = [];\n\n  const funcs = DG.Func.find({meta: {role: 'antibodyNumbering'}});\n  if (funcs.length === 0) {\n    grok.shell.error('No antibody numbering engines found. Make sure that Proteomics plugin is installed and up to date.');\n    throw new Error('No external antibody numbering engines found. Make sure that Proteomics plugin is installed and up to date.');\n  }\n  for (const f of funcs) {\n    const pkgName = f.package?.name ?? '';\n    const label = f.friendlyName || f.name;\n    engines.push({\n      label: label,\n      key: pkgName ? `${pkgName}:${f.name}` : f.name,\n      func: f,\n    });\n  }\n\n  // Built-in TS engine is always last\n  engines.push({label: BUILTIN_ENGINE_LABEL, key: BUILTIN_ENGINE_KEY, func: null});\n  return engines;\n}\n\n/** Converts TS NumberingResult[] to a DG.DataFrame matching the expected output shape.\n *  Columns: position_names, chain_type, annotations_json, numbering_detail, numbering_map. */\nexport function numberingResultsToDataFrame(results: NumberingResult[]): DG.DataFrame {\n  const n = results.length;\n  const posNames = DG.Column.fromType(DG.COLUMN_TYPE.STRING, 'position_names', n);\n  const chainTypes = DG.Column.fromType(DG.COLUMN_TYPE.STRING, 'chain_type', n);\n  const annotJson = DG.Column.fromType(DG.COLUMN_TYPE.STRING, 'annotations_json', n);\n  const numDetail = DG.Column.fromType(DG.COLUMN_TYPE.STRING, 'numbering_detail', n);\n  const numMap = DG.Column.fromType(DG.COLUMN_TYPE.STRING, 'numbering_map', n);\n\n  for (let i = 0; i < n; i++) {\n    const r = results[i];\n    if (r.error && r.percentIdentity < 0.3) {\n      posNames.set(i, '');\n      chainTypes.set(i, '');\n      annotJson.set(i, '[]');\n      numDetail.set(i, '');\n      numMap.set(i, '');\n    } else {\n      posNames.set(i, r.positionNames);\n      chainTypes.set(i, r.chainType);\n      annotJson.set(i, JSON.stringify(r.annotations));\n      numDetail.set(i, JSON.stringify(r.numberingDetail));\n      numMap.set(i, JSON.stringify(r.numberingMap));\n    }\n  }\n\n  return DG.DataFrame.fromColumns([posNames, chainTypes, annotJson, numDetail, numMap]);\n}\n\n/** Runs the built-in TS numbering engine on all rows of a sequence column. */\nasync function runBuiltinNumbering(\n  seqCol: DG.Column<string>, schemeName: string,\n): Promise<DG.DataFrame> {\n  const {numberSequences, extractSequence} = await import('../antibody-numbering (WIP)');\n  const scheme = schemeName.toLowerCase() as Scheme;\n\n  const sequences: string[] = [];\n  for (let i = 0; i < seqCol.length; i++) {\n    const raw = seqCol.get(i);\n    sequences.push(extractSequence(raw ?? ''));\n  }\n\n  const results = numberSequences(sequences, scheme);\n  return numberingResultsToDataFrame(results);\n}\n\nexport function showNumberingSchemeDialog(): void {\n  const df = grok.shell.tv?.dataFrame;\n  if (!df) {\n    grok.shell.warning('No table open');\n    return;\n  }\n\n  const seqCols = df.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);\n  if (seqCols.length === 0) {\n    grok.shell.warning('No macromolecule columns found');\n    return;\n  }\n\n  const engines = discoverEngines();\n  const engineLabels = engines.map((e) => e.label);\n  const schemeChoices = Object.values(NumberingScheme);\n\n  const tableInput = ui.input.table('Table', {value: df});\n  const seqInput = ui.input.column('Sequence', {\n    table: df, value: seqCols[0],\n    filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE,\n  });\n  const schemeInput = ui.input.choice('Scheme', {value: NumberingScheme.IMGT, items: schemeChoices});\n  const engineInput = ui.input.choice('Engine', {\n    value: engineLabels[0], items: engineLabels,\n  });\n  // const populateRegions = ui.input.bool('Populate FR/CDR regions', {value: true});\n  // const openVdRegions = ui.input.bool('Open VD Regions viewer', {value: true});\n\n  const dialog = ui.dialog({title: 'Apply Antibody Numbering'})\n    .add(ui.inputs([tableInput, seqInput, schemeInput, engineInput]))\n    .onOK(async () => {\n      const seqCol = seqInput.value!;\n      const schemeName = schemeInput.value!;\n      const selectedLabel = engineInput.value!;\n      const engine = engines.find((e) => e.label === selectedLabel) ?? engines[engines.length - 1];\n      const pi = DG.TaskBarProgressIndicator.create(`Applying ${schemeName} numbering...`);\n      try {\n        let result: DG.DataFrame;\n        if (engine.func)\n          result = await engine.func.apply({df: df, seqCol: seqCol, scheme: schemeName.toLowerCase()});\n        else\n          result = await runBuiltinNumbering(seqCol, schemeName);\n\n        applyNumberingResults(df, seqCol, result, schemeName, true, engine.label);\n\n        // // Open VD Regions viewer\n        // if (openVdRegions.value && grok.shell.tv) {\n        //   try {\n        //     await grok.shell.tv.dataFrame.plot.fromType('VdRegions', {});\n        //   } catch (err) {\n        //     console.warn('Could not open VD Regions viewer:', err);\n        //   }\n        // }\n      } catch (err: any) {\n        grok.shell.error(`Numbering failed: ${err.message ?? err}`);\n        console.error(err);\n      } finally {\n        pi.close();\n      }\n    });\n\n  dialog.show();\n}\n\n/** Builds a map from ungapped character index to gapped character index.\n *  Used when the source column is already aligned (MSA) — numbering engines strip gaps,\n *  so their output indices refer to the ungapped sequence, not the gapped original. */\nfunction buildUngappedToGappedMap(gappedSeq: string): number[] {\n  const map: number[] = [];\n  for (let g = 0; g < gappedSeq.length; g++) {\n    if (gappedSeq[g] !== '-' && gappedSeq[g] !== '.')\n      map.push(g);\n  }\n  return map;\n}\n\n/** Parses a position code into [numericPart, insertionLetter] for sorting.\n *  E.g. \"27\" → [27, \"\"], \"111A\" → [111, \"A\"], \"27B\" → [27, \"B\"]. */\nfunction parsePositionCode(code: string): [number, string] {\n  const match = code.match(/^(\\d+)([A-Z]?)$/);\n  if (!match) return [Infinity, code];\n  return [parseInt(match[1], 10), match[2]];\n}\n\n/** Sorts position codes in scheme order: numeric ascending, then insertion letter. */\nfunction sortPositionCodes(codes: string[]): string[] {\n  return codes.slice().sort((a, b) => {\n    const [numA, insA] = parsePositionCode(a);\n    const [numB, insB] = parsePositionCode(b);\n    if (numA !== numB) return numA - numB;\n    return insA.localeCompare(insB);\n  });\n}\n\n/** Builds unified position list from all rows and creates an aligned sequence column.\n *  Includes flanking residues (before/after the numbered region) padded with gaps.\n *  Layout: [pre-region gaps+residues] [scheme-aligned region] [post-region residues+gaps]\n *  @returns aligned column, full position list (including flanking), and the pre-region offset. */\nfunction createAlignedColumn(\n  df: DG.DataFrame, seqCol: DG.Column<string>, result: DG.DataFrame,\n): {alignedCol: DG.Column<string>; unifiedPositions: string[]; preOffset: number} | null {\n  const numberingMapCol = result.col('numbering_map');\n  if (!numberingMapCol) return null;\n\n  // Pass 1: collect all scheme position codes and per-row flanking lengths\n  const allCodes = new Set<string>();\n  const rowMaps: (Record<string, number> | null)[] = [];\n  const rowPreLens: number[] = []; // chars before first numbered position\n  const rowPostLens: number[] = []; // chars after last numbered position\n\n  for (let i = 0; i < result.rowCount; i++) {\n    const mapStr = numberingMapCol.get(i);\n    const rawSeq = seqCol.get(i) ?? '';\n    if (!mapStr) {\n      rowMaps.push(null);\n      rowPreLens.push(0);\n      rowPostLens.push(0);\n      continue;\n    }\n    try {\n      const posToCharIdx: Record<string, number> = JSON.parse(mapStr);\n      rowMaps.push(posToCharIdx);\n      for (const code of Object.keys(posToCharIdx))\n        allCodes.add(code);\n\n      // Find min/max char indices that were numbered\n      const charIndices = Object.values(posToCharIdx);\n      const minChar = Math.min(...charIndices);\n      const maxChar = Math.max(...charIndices);\n      rowPreLens.push(minChar); // chars before first numbered\n      rowPostLens.push(Math.max(0, rawSeq.length - maxChar - 1)); // chars after last numbered\n    } catch {\n      rowMaps.push(null);\n      rowPreLens.push(0);\n      rowPostLens.push(0);\n    }\n  }\n\n  if (allCodes.size === 0) return null;\n\n  const maxPreLen = Math.max(0, ...rowPreLens);\n  const maxPostLen = Math.max(0, ...rowPostLens);\n\n  // Build position names: [pre-flanking] + [scheme positions] + [post-flanking]\n  const schemePositions = sortPositionCodes(Array.from(allCodes));\n  const preNames: string[] = [];\n  for (let p = maxPreLen; p > 0; p--)\n    preNames.push(`N-${p}`);\n  const postNames: string[] = [];\n  for (let p = 1; p <= maxPostLen; p++)\n    postNames.push(`C+${p}`);\n\n  const unifiedPositions = [...preNames, ...schemePositions, ...postNames];\n  const totalLen = unifiedPositions.length;\n  const preOffset = maxPreLen; // scheme region starts at this index in the aligned string\n\n  // Map scheme position codes → index in the full unified list\n  const posToUnifiedIdx = new Map<string, number>();\n  for (let s = 0; s < schemePositions.length; s++)\n    posToUnifiedIdx.set(schemePositions[s], preOffset + s);\n\n  // Pass 2: build aligned sequences\n  const colName = df.columns.getUnusedName(`${seqCol.name} (aligned)`);\n  const alignedCol = DG.Column.fromType(DG.COLUMN_TYPE.STRING, colName, df.rowCount);\n\n  for (let i = 0; i < df.rowCount; i++) {\n    const map = i < rowMaps.length ? rowMaps[i] : null;\n    const rawSeq = seqCol.get(i) ?? '';\n\n    if (!map) {\n      alignedCol.set(i, '-'.repeat(totalLen));\n      continue;\n    }\n\n    const aligned = new Array<string>(totalLen).fill('-');\n\n    // Place scheme-numbered residues\n    for (const [posCode, charIdx] of Object.entries(map)) {\n      const uIdx = posToUnifiedIdx.get(posCode);\n      if (uIdx != null && charIdx < rawSeq.length)\n        aligned[uIdx] = rawSeq[charIdx];\n    }\n\n    // Place pre-region flanking residues (right-aligned within the pre-region block)\n    const preLen = rowPreLens[i];\n    const charIndices = Object.values(map);\n    const minChar = Math.min(...charIndices);\n    for (let p = 0; p < preLen; p++)\n      aligned[preOffset - preLen + p] = rawSeq[minChar - preLen + p];\n\n    // Place post-region flanking residues (left-aligned within the post-region block)\n    const postLen = rowPostLens[i];\n    const maxChar = Math.max(...charIndices);\n    const postStart = preOffset + schemePositions.length;\n    for (let p = 0; p < postLen; p++)\n      aligned[postStart + p] = rawSeq[maxChar + 1 + p];\n\n    alignedCol.set(i, aligned.join(''));\n  }\n\n  // Set macromolecule tags on the aligned column\n  alignedCol.semType = DG.SEMTYPE.MACROMOLECULE;\n  alignedCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);\n  alignedCol.setTag(bioTAGS.alphabet, ALPHABET.PT);\n  alignedCol.meta.units = NOTATION.FASTA;\n  alignedCol.setTag(DG.Tags.CellRenderer, 'sequence');\n  alignedCol.setTag(bioTAGS.positionNames, unifiedPositions.join(', '));\n\n  return {alignedCol, unifiedPositions, preOffset};\n}\n\n/** Applies numbering results (from either engine) to the sequence column and dataframe.\n *\n *  Annotation strategy:\n *  - Original column: row-level region spans only (char indices from numbering_map).\n *    No column-level position names (they differ per row).\n *  - Aligned column: column-level annotations only (all rows share unified positions).\n *    Position names tag set to the unified list. */\nfunction applyNumberingResults(\n  df: DG.DataFrame, seqCol: DG.Column<string>, result: DG.DataFrame,\n  schemeName: string, populateRegions: boolean, engineLabel: string,\n): void {\n  if (!result || result.rowCount === 0) {\n    grok.shell.warning('No numbering results returned');\n    return;\n  }\n\n  const posNamesCol = result.getCol('position_names');\n  const chainTypeCol = result.getCol('chain_type');\n  const annotJsonCol = result.getCol('annotations_json');\n  const numberingMapCol = result.col('numbering_map');\n\n  // If the source column is already aligned (MSA), remap numbering_map indices\n  // from ungapped to gapped, since numbering engines strip gaps before processing.\n  const isAligned = true; // always treat as aligned to handle remapping\n  if (isAligned && numberingMapCol) {\n    for (let i = 0; i < result.rowCount; i++) {\n      const mapStr = numberingMapCol.get(i);\n      if (!mapStr) continue;\n      try {\n        const posToCharIdx: Record<string, number> = JSON.parse(mapStr);\n        const rawSeq = seqCol.get(i) ?? 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'') : '';\n  const annotationsJson = bestRowIdx >= 0 ? (annotJsonCol.get(bestRowIdx) ?? '[]') : '[]';\n\n  if (bestRowIdx < 0) {\n    grok.shell.warning(`${engineLabel} could not number the sequences. Check that they are valid antibody variable region sequences.`);\n    return;\n  }\n\n  // Mark scheme on original column (no position names — they differ per row)\n  seqCol.setTag(bioTAGS.numberingScheme, schemeName);\n\n  // --- Original column: column-level annotation definitions (needed for renderer\n  // to resolve annotation IDs → colors/names) + row-level region spans ---\n  if (populateRegions) {\n    try {\n      const regionAnnotations: SeqAnnotation[] = JSON.parse(annotationsJson);\n      const existing = getColumnAnnotations(seqCol).filter((a) => a.category !== AnnotationCategory.Structure);\n      setColumnAnnotations(seqCol, [...existing, ...regionAnnotations]);\n    } catch (err) {\n      console.warn('Failed to set annotation definitions on original column:', err);\n    }\n  }\n\n  if (populateRegions && numberingMapCol) {\n    try {\n      const annotCol = getOrCreateAnnotationColumn(df, seqCol);\n      for (let i = 0; i < result.rowCount; i++) {\n        const mapStr = numberingMapCol.get(i);\n        const rowAnnotJson = annotJsonCol.get(i);\n        if (!mapStr || !rowAnnotJson) continue;\n        const posToCharIdx: Record<string, number> = JSON.parse(mapStr);\n        const rowRegions: SeqAnnotation[] = JSON.parse(rowAnnotJson);\n\n        const regionHits: SeqAnnotationHit[] = [];\n        for (const region of rowRegions) {\n          if (region.start == null || region.end == null) continue;\n          const startCharIdx = posToCharIdx[region.start];\n          const endCharIdx = posToCharIdx[region.end];\n          if (startCharIdx == null || endCharIdx == null) continue;\n          regionHits.push({\n            annotationId: region.id,\n            positionIndex: startCharIdx,\n            endPositionIndex: endCharIdx,\n            positionName: region.start,\n            matchedMonomers: '',\n          });\n        }\n\n        const existingHits = getRowAnnotations(annotCol, i) ?? 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package/dist/287.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=287.js.map

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package/dist/288.js

@@ -0,0 +1,2 @@
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Run liability scanning first.');\n    return;\n  }\n\n  const rowData = cacheAllRowAnnotations(annotCol);\n  const bs = DG.BitSet.create(df.rowCount);\n  for (let i = 0; i < df.rowCount; i++) {\n    if (rowData[i] && rowData[i]!.length > 0)\n      bs.set(i, true);\n  }\n\n  df.filter.copyFrom(bs);\n  grok.shell.info(`Filtered to ${bs.trueCount} rows with liability hits`);\n}\n\n/** Selects all rows that contain a specific annotation hit. */\nexport function selectRowsWithAnnotation(df: DG.DataFrame, seqCol: DG.Column<string>, annotationId: string): void {\n  const annotColName = getAnnotationColumnName(seqCol.name);\n  let annotCol: DG.Column<string> | null = null;\n  try {\n    annotCol = df.columns.byName(annotColName) as DG.Column<string>;\n  } catch { /* not found */ }\n\n  if (!annotCol) {\n    grok.shell.warning('No annotation data found.');\n    return;\n  }\n\n  const rowData = cacheAllRowAnnotations(annotCol);\n  const bs = DG.BitSet.create(df.rowCount);\n  for (let i = 0; i < df.rowCount; i++) {\n    if (rowData[i]?.some((h) => h.annotationId === annotationId))\n      bs.set(i, true);\n  }\n\n  df.selection.copyFrom(bs);\n  grok.shell.info(`Selected ${bs.trueCount} rows with ${annotationId} hits`);\n}\n\n/** Extracts a named region annotation as a new column.\n *  Uses per-row region spans from the companion column when available (unaligned data),\n *  falls back to column-level position names (aligned/MSA data). */\nexport function extractAnnotatedRegion(\n  df: DG.DataFrame,\n  seqCol: DG.Column<string>,\n  annotationName: string,\n  seqHelper: ISeqHelper,\n): DG.Column<string> | null {\n  const annotations = getColumnAnnotations(seqCol);\n  const annot = annotations.find((a) =>\n    a.name === annotationName && a.category === AnnotationCategory.Structure);\n\n  if (!annot) {\n    grok.shell.warning(`Region annotation \"${annotationName}\" not found.`);\n    return null;\n  }\n\n  const sh = seqHelper.getSeqHandler(seqCol);\n  const colName = `${seqCol.name}(${annotationName})`;\n\n  // Try per-row extraction using companion column region spans\n  const annotColName = getAnnotationColumnName(seqCol.name);\n  let annotCol: DG.Column<string> | null = null;\n  try { annotCol = df.columns.byName(annotColName) as DG.Column<string>; } catch { /* not found */ }\n\n  if (annotCol) {\n    const allRowData = cacheAllRowAnnotations(annotCol);\n    const hasPerRowRegions = allRowData.some((rd) =>\n      rd?.some((h: SeqAnnotationHit) => h.annotationId === annot.id && h.endPositionIndex != null));\n\n    if (hasPerRowRegions) {\n      const regCol = DG.Column.fromType(DG.COLUMN_TYPE.STRING, colName, df.rowCount);\n      for (let i = 0; i < df.rowCount; i++) {\n        const rowHits = allRowData[i];\n        const regionHit = rowHits?.find((h: SeqAnnotationHit) =>\n          h.annotationId === annot.id && h.endPositionIndex != null);\n        if (regionHit) {\n          const splitted = sh.getSplitted(i);\n          const parts: string[] = [];\n          for (let p = regionHit.positionIndex; p <= regionHit.endPositionIndex!; p++) {\n            if (p < splitted.length)\n              parts.push(splitted.getOriginal(p));\n          }\n          regCol.set(i, parts.join(sh.separator || ''));\n        } else\n          regCol.set(i, '');\n      }\n      df.columns.add(regCol);\n      grok.data.detectSemanticTypes(df);\n      grok.shell.info(`Extracted region ${annotationName} as column \"${colName}\"`);\n      return regCol;\n    }\n  }\n\n  // Fall back to column-level position names (aligned/MSA data)\n  if (annot.start == null || annot.end == null) {\n    grok.shell.warning(`Region annotation \"${annotationName}\" has no position range.`);\n    return null;\n  }\n\n  const startIdx = sh.posList.indexOf(annot.start);\n  const endIdx = sh.posList.indexOf(annot.end);\n\n  if (startIdx < 0 || endIdx < 0) {\n    grok.shell.warning(`Position names \"${annot.start}\" or \"${annot.end}\" not found in position list.`);\n    return null;\n  }\n\n  const regCol = sh.getRegion(startIdx, endIdx, colName);\n  df.columns.add(regCol);\n  grok.data.detectSemanticTypes(df);\n  grok.shell.info(`Extracted region ${annotationName} as column \"${colName}\"`);\n  return regCol;\n}\n"],"names":["filterByLiabilityHits","df","seqCol","annotColName","name","annotCol","columns","byName","warning","rowData","bs","create","rowCount","i","length","set","filter","copyFrom","info","trueCount","extractAnnotatedRegion","annotationName","seqHelper","annot","find","a","category","Structure","sh","getSeqHandler","colName","allRowData","some","rd","h","annotationId","id","endPositionIndex","regCol","fromType","STRING","rowHits","regionHit","splitted","getSplitted","parts","p","positionIndex","push","getOriginal","join","separator","add","detectSemanticTypes","start","end","startIdx","posList","indexOf","endIdx","getRegion"],"sourceRoot":""}

package/dist/422.js

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+//# sourceMappingURL=422.js.map

package/dist/422.js.map

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eslint-disable max-len */\nimport * as DG from 'datagrok-api/dg';\n\nimport {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';\nimport {\n  SeqAnnotation, SeqAnnotationHit, RowAnnotationData,\n  AnnotationVisualType, AnnotationCategory, LiabilitySeverity,\n  ANNOTATION_COLORS,\n} from '@datagrok-libraries/bio/src/utils/macromolecule/annotations';\nimport {\n  getOrCreateAnnotationColumn, setColumnAnnotations, setRowAnnotations,\n  getColumnAnnotations, getRowAnnotations, mergeRowHits,\n} from './annotation-manager';\n\n/** A single liability scanning rule. */\nexport interface LiabilityRule {\n  id: string;\n  name: string;\n  pattern: RegExp;\n  length: number;\n  severity: LiabilitySeverity;\n  /** Sub-category for grouping (e.g. \"deamidation\", \"oxidation\") */\n  ruleCategory: string;\n  color: string;\n  enabled: boolean;\n}\n\n/** Built-in liability rules for antibody engineering. */\nexport const BUILTIN_LIABILITY_RULES: LiabilityRule[] = [\n  {id: 'deamid-ng', name: 'Deamidation (NG)', pattern: /NG/g, length: 2, severity: LiabilitySeverity.High, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-ns', name: 'Deamidation (NS)', pattern: /NS/g, length: 2, severity: LiabilitySeverity.Medium, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-na', name: 'Deamidation (NA)', pattern: /NA/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-nd', name: 'Deamidation (ND)', pattern: /ND/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-nt', name: 'Deamidation (NT)', pattern: /NT/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'isom-dg', name: 'Isomerization (DG)', pattern: /DG/g, length: 2, severity: LiabilitySeverity.High, ruleCategory: 'isomerization', color: ANNOTATION_COLORS.liability.isomerization, enabled: true},\n  {id: 'isom-ds', name: 'Isomerization (DS)', pattern: /DS/g, length: 2, severity: LiabilitySeverity.Medium, ruleCategory: 'isomerization', color: ANNOTATION_COLORS.liability.isomerization, enabled: true},\n  {id: 'oxid-m', name: 'Oxidation (Met)', pattern: /M/g, length: 1, severity: LiabilitySeverity.Medium, ruleCategory: 'oxidation', color: ANNOTATION_COLORS.liability.oxidation, enabled: true},\n  {id: 'oxid-w', name: 'Oxidation (Trp)', pattern: /W/g, length: 1, severity: LiabilitySeverity.Low, ruleCategory: 'oxidation', color: ANNOTATION_COLORS.liability.oxidation, enabled: true},\n  {id: 'glyco-nxst', name: 'N-glycosylation', pattern: /N[^P][ST]/g, length: 3, severity: LiabilitySeverity.High, ruleCategory: 'glycosylation', color: ANNOTATION_COLORS.liability.glycosylation, enabled: true},\n  {id: 'free-cys', name: 'Free Cysteine', pattern: /C/g, length: 1, severity: LiabilitySeverity.Info, ruleCategory: 'freeCysteine', color: ANNOTATION_COLORS.liability.freeCysteine, enabled: false},\n];\n\n/** Extracts a canonical single-letter string from a sequence handler for a given row. */\nfunction getCanonicalString(sh: ISeqHandler, rowIdx: number): string {\n  const splitted = sh.getSplitted(rowIdx);\n  const chars: string[] = new Array(splitted.length);\n  for (let i = 0; i < splitted.length; i++)\n    chars[i] = splitted.getOriginal(i);\n  return chars.join('');\n}\n\nexport interface ScanLiabilitiesResult {\n  annotations: SeqAnnotation[];\n  rowData: RowAnnotationData[];\n  totalHits: number;\n}\n\n/** Scans all rows of a macromolecule column for liability motifs.\n *  Returns column-level SeqAnnotation entries + per-row SeqAnnotationHit arrays. */\nexport function scanLiabilities(\n  col: DG.Column<string>,\n  sh: ISeqHandler,\n  rules: LiabilityRule[],\n): ScanLiabilitiesResult {\n  const enabledRules = rules.filter((r) => r.enabled);\n  const posList = sh.posList;\n\n  // Track which rules had hits\n  const ruleHitCounts = new Map<string, number>();\n\n  const rowData: RowAnnotationData[] = new Array(col.length);\n  let totalHits = 0;\n\n  for (let rowIdx = 0; rowIdx < col.length; rowIdx++) {\n    const seq = getCanonicalString(sh, rowIdx);\n    const hits: SeqAnnotationHit[] = [];\n\n    for (const rule of enabledRules) {\n      // Reset regex lastIndex for global patterns\n      rule.pattern.lastIndex = 0;\n      let match: RegExpExecArray | null;\n      while ((match = rule.pattern.exec(seq)) !== null) {\n        hits.push({\n          annotationId: rule.id,\n          positionIndex: match.index,\n          positionName: match.index < posList.length ? posList[match.index] : undefined,\n          matchedMonomers: match[0],\n        });\n        ruleHitCounts.set(rule.id, (ruleHitCounts.get(rule.id) ?? 0) + 1);\n        totalHits++;\n      }\n    }\n    rowData[rowIdx] = hits;\n  }\n\n  // Build column-level annotations only for rules that had hits\n  const annotations: SeqAnnotation[] = enabledRules\n    .filter((r) => ruleHitCounts.has(r.id))\n    .map((r) => ({\n      id: r.id,\n      name: r.name,\n      description: `${r.ruleCategory} liability pattern (${ruleHitCounts.get(r.id)} hits)`,\n      start: null,\n      end: null,\n      visualType: r.length === 1 ? AnnotationVisualType.Point : AnnotationVisualType.Motif,\n      category: AnnotationCategory.Liability,\n      color: r.color,\n      severity: r.severity,\n      motifPattern: r.pattern.source,\n      autoGenerated: true,\n    }));\n\n  return {annotations, rowData, totalHits};\n}\n\n/** Applies liability scan results to the DataFrame (writes tags + companion column). */\nexport function applyLiabilityScanResults(\n  df: DG.DataFrame,\n  seqCol: DG.Column<string>,\n  result: ScanLiabilitiesResult,\n): void {\n  // Merge with existing annotations, removing old liability entries\n  const existing = getColumnAnnotations(seqCol)\n    .filter((a) => a.category !== AnnotationCategory.Liability);\n  setColumnAnnotations(seqCol, [...existing, ...result.annotations]);\n\n  // Write per-row data to hidden companion column, preserving region hits from numbering\n  const annotCol = getOrCreateAnnotationColumn(df, seqCol);\n  for (let i = 0; i < result.rowData.length; i++) {\n    const existingHits = getRowAnnotations(annotCol, i) ?? [];\n    setRowAnnotations(annotCol, i, mergeRowHits(existingHits, result.rowData[i], false, true));\n  }\n}\n\n/** Creates a liability summary count column (total hits per row). */\nexport function createLiabilitySummaryColumn(\n  df: DG.DataFrame,\n  seqCol: DG.Column<string>,\n  result: ScanLiabilitiesResult,\n): DG.Column<number> {\n  const colName = `${seqCol.name}_liability_count`;\n  const counts = result.rowData.map((hits) => hits.length);\n  const col = df.columns.addNewInt(colName);\n  for (let i = 0; i < counts.length; i++)\n    col.set(i, counts[i]);\n  return col;\n}\n","import * as grok from 'datagrok-api/grok';\nimport * as ui from 'datagrok-api/ui';\nimport * as DG from 'datagrok-api/dg';\n\nimport {_package} from '../../package';\nimport {\n  BUILTIN_LIABILITY_RULES, LiabilityRule, scanLiabilities,\n  applyLiabilityScanResults, createLiabilitySummaryColumn,\n} from './liability-scanner';\nimport {LiabilitySeverity} from '@datagrok-libraries/bio/src/utils/macromolecule/annotations';\n\nconst severityLabels: Record<string, string> = {\n  [LiabilitySeverity.High]: 'High',\n  [LiabilitySeverity.Medium]: 'Medium',\n  [LiabilitySeverity.Low]: 'Low',\n  [LiabilitySeverity.Info]: 'Info',\n};\n\nexport function showLiabilityScannerDialog(): void {\n  const df = grok.shell.tv?.dataFrame;\n  if (!df) {\n    grok.shell.warning('No table open');\n    return;\n  }\n\n  const seqCols = df.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);\n  if (seqCols.length === 0) {\n    grok.shell.warning('No macromolecule columns found');\n    return;\n  }\n\n  const rules = BUILTIN_LIABILITY_RULES.map((r) => ({...r, pattern: new RegExp(r.pattern.source, 'g')}));\n\n  const tableInput = ui.input.table('Table', {value: df});\n  const seqInput = ui.input.column('Sequence', {\n    table: df, value: seqCols[0],\n    filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE,\n  });\n\n  // Rule checkboxes\n  const ruleChecks: {rule: LiabilityRule; input: DG.InputBase<boolean>}[] = [];\n  const rulesDiv = ui.divV([]);\n  for (const rule of rules) {\n    const check = ui.input.bool(rule.name, {\n      value: rule.enabled,\n      tooltipText: `Severity: ${severityLabels[rule.severity] ?? rule.severity}`,\n    });\n    ruleChecks.push({rule, input: check});\n    rulesDiv.append(check.root);\n  }\n\n  const highlightInput = ui.input.bool('Highlight in cell renderer', {value: true});\n  const annotColInput = ui.input.bool('Create annotation column', {value: true});\n  const summaryInput = ui.input.bool('Create summary count column', {value: false});\n\n  const dialog = ui.dialog({title: 'Scan Sequence Liabilities'})\n    .add(ui.inputs([tableInput, seqInput]))\n    .add(ui.h3('Rules'))\n    .add(rulesDiv)\n    .add(ui.h3('Output'))\n    .add(ui.inputs([highlightInput, annotColInput, summaryInput]))\n    .onOK(() => {\n      try {\n        const seqCol = seqInput.value!;\n        const sh = _package.seqHelper.getSeqHandler(seqCol);\n\n        // Apply checkbox state\n        for (const {rule, input} of ruleChecks)\n          rule.enabled = input.value;\n\n        const result = scanLiabilities(seqCol, sh, rules);\n\n        if (annotColInput.value || highlightInput.value)\n          applyLiabilityScanResults(df, seqCol, result);\n\n        if (summaryInput.value)\n          createLiabilitySummaryColumn(df, seqCol, result);\n\n        grok.shell.info(`Liability scan: ${result.totalHits} hits found across ${result.annotations.length} rules`);\n        df.fireValuesChanged();\n      } catch (err: any) {\n        grok.shell.error(`Liability scan failed: ${err.message ?? err}`);\n        console.error(err);\n      }\n    });\n\n  dialog.show();\n}\n"],"names":["BUILTIN_LIABILITY_RULES","id","name","pattern","length","severity","High","ruleCategory","color","liability","deamidation","enabled","Medium","Low","isomerization","oxidation","glycosylation","Info","freeCysteine","getCanonicalString","sh","rowIdx","splitted","getSplitted","chars","Array","i","getOriginal","join","severityLabels","showLiabilityScannerDialog","df","tv","dataFrame","warning","seqCols","columns","bySemTypeAll","MACROMOLECULE","rules","map","r","RegExp","source","tableInput","table","value","seqInput","column","filter","col","semType","ruleChecks","rulesDiv","rule","check","bool","tooltipText","push","input","append","root","highlightInput","annotColInput","summaryInput","dialog","title","add","onOK","seqCol","_package","seqHelper","getSeqHandler","result","enabledRules","posList","ruleHitCounts","Map","rowData","totalHits","seq","hits","match","lastIndex","exec","annotationId","positionIndex","index","positionName","undefined","matchedMonomers","set","get","annotations","has","description","start","end","visualType","Point","Motif","category","Liability","motifPattern","autoGenerated","scanLiabilities","existing","a","annotCol","existingHits","applyLiabilityScanResults","colName","counts","addNewInt","createLiabilitySummaryColumn","info","fireValuesChanged","err","error","message","console","show"],"sourceRoot":""}

package/dist/455.js

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e("",new n(null))}}var a,s,i;new RegExp("[rd]\\((\\w)\\)p?","g");class r{constructor(t,o,n){this.name=t,this.alphabet=o,this.cutoff=n}}!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(a||(a={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(s||(s={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName"}(i||(i={}));const l=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};var c;function E(t){let o;switch(t){case c.BASE:case c.SUGAR:case c.LINKER:case c.NUCLEOTIDE:case"nucleotide":o="RNA";break;case c.AA:o="PEPTIDE";break;case c.CHEM:o="CHEM";break;case c.BLOB:o="BLOB";break;default:o="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return o}function h(a,i,r,l){if(0===a.length)return e.createEmpty();const c=m,{atomCount:h,bondCount:f,needsCapping:_}=c(a,i,r,l),S=new Array(h),d=new Array(f);let p,T=null,I=null;"PEPTIDE"===l?p=N:(p=b,T=r===s.DNA?o(i,t.DEOXYRIBOSE):o(i,t.RIBOSE),I=o(i,t.PHOSPHATE));const O={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},u={sugar:T,phosphate:I,seqLength:a.length,atomCount:h,bondCount:f},C=new n,B=[];let L,y=0;for(O.i=0;O.i<u.seqLength;++O.i){const t=a[O.i];if(""===t.symbol)continue;const n=o(i,{symbol:t.symbol,polymerType:E(t.biotype)});L=n.terminalR2Atom;const e=O.nodeShift,s=O.bondShift;p(n,S,d,O,u),n.stereoAtoms?.forEach(t=>B.push(t+y)),y+=n.atoms.x.length;const r=O.nodeShift-e,l=new Array(r);for(let t=0;t<r;++t)l[t]=e+t;const c=O.bondShift-s,h=new Array(c);for(let t=0;t<c;++t)h[t]=s+t;C.set(O.i,{biotype:t.biotype,symbol:t.symbol,atoms:l,bonds:h})}_&&function(o,n,e,a,s=t.OXYGEN){const i=e.nodeShift+1;o[a.atomCount]=t.V3K_BEGIN_DATA_LINE+i+" "+(s??t.OXYGEN)+" "+A(e.backbonePositionShift[0])+" "+e.flipFactor*A(e.backbonePositionShift[1])+" 0.000000 0\n";const r=e.backboneAttachNode,l=i;n[a.bondCount]=t.V3K_BEGIN_DATA_LINE+e.bondShift+" 1 "+r+" "+l+"\n"}(S,d,O,u,L??t.OXYGEN);const D=t.V3K_BEGIN_COUNTS_LINE+h+" "+f+t.V3K_COUNTS_LINE_ENDING;let g="";return g+=t.V3K_HEADER_FIRST_LINE,g+=t.V3K_HEADER_SECOND_LINE,g+=t.V3K_BEGIN_CTAB_BLOCK,g+=D,g+=t.V3K_BEGIN_ATOM_BLOCK,g+=S.join(""),g+=t.V3K_END_ATOM_BLOCK,g+=t.V3K_BEGIN_BOND_BLOCK,g+=d.join(""),g+=t.V3K_END_BOND_BLOCK,B.length>0&&(g+=function(t){const o=[];let n=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let e=0;e<t.length;e++){const a=`${n} ${t[e]}`;a.length>76?(o.push(`${n} -\n`),n=`M  V30 ${t[e]}`):n=a,e===t.length-1&&o.push(`${n})\n`)}return`M  V30 BEGIN COLLECTION\n${o.join("")}M  V30 END COLLECTION\n`}(B)),g+=t.V3K_END_CTAB_BLOCK,g+=t.V3K_END,{molfile:g,monomers:C}}function N(t,o,n,e){e.flipFactor=(-1)**(e.i%2),f(t,o,n,e)}function f(o,n,e,a){!function(o,n,e){for(let a=0;a<o.atoms.atomTypes.length;++a){const s=e.nodeShift+a+1;n[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+o.atoms.atomTypes[a]+" "+A(e.backbonePositionShift[0]+o.atoms.x[a])+" "+A(e.backbonePositionShift[1]+e.flipFactor*o.atoms.y[a])+" "+o.atoms.kwargs[a]}}(o,n,a),_(o,e,a),function(o,n,e){if(0!==e.backboneAttachNode){const a=e.bondShift,s=e.backboneAttachNode,i=o.meta.terminalNodes[0]+e.nodeShift;n[e.bondShift-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+s+" "+i+"\n"}}(o,e,a),null!==o.meta.branchShift&&o.meta.terminalNodes.length>2&&function(t,o){o.branchAttachNode=o.nodeShift+t.meta.terminalNodes[2];for(let n=0;n<2;++n)o.branchPositionShift[n]=o.backbonePositionShift[n]+t.meta.branchShift[n]}(o,a),function(t,o){o.backboneAttachNode=o.nodeShift+t.meta.terminalNodes[1],o.bondShift+=t.bonds.atomPairs.length+1,o.nodeShift+=t.atoms.atomTypes.length,o.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,o.backbonePositionShift[1]+=o.flipFactor*(t.meta.backboneShift?.[1]??0)}(o,a)}function b(o,n,e,a,s){if(0===a.i)f(s.sugar,n,e,a);else for(const t of[s.phosphate,s.sugar])f(t,n,e,a);!function(o,n,e,a){(function(o,n,e){for(let a=0;a<o.atoms.atomTypes.length;++a){const s=e.nodeShift+a+1;n[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+o.atoms.atomTypes[a]+" "+A(e.branchPositionShift[0]+o.atoms.x[a])+" "+A(e.branchPositionShift[1]+e.flipFactor*o.atoms.y[a])+" "+o.atoms.kwargs[a]}})(o,n,a),_(o,e,a),function(o,n,e){const a=e.bondShift,s=e.branchAttachNode,i=o.meta.terminalNodes[0]+e.nodeShift;n[a-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+s+" "+i+"\n"}(o,e,a);const s=a.bondShift,i=a.branchAttachNode,r=o.meta.terminalNodes[0]+a.nodeShift;e[s-1]=t.V3K_BEGIN_DATA_LINE+s+" 1 "+i+" "+r+"\n",a.bondShift+=o.bonds.atomPairs.length+1,a.nodeShift+=o.atoms.atomTypes.length}(o,n,e,a)}function _(o,n,e){for(let a=0;a<o.bonds.atomPairs.length;++a){const s=e.bondShift+a+1,i=o.bonds.atomPairs[a][0]+e.nodeShift,r=o.bonds.atomPairs[a][1]+e.nodeShift;let l="";if(o.bonds.bondConfiguration.has(a)){let t=o.bonds.bondConfiguration.get(a);e.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=o.bonds.kwargs.has(a)?" "+o.bonds.kwargs.get(a):"";n[e.bondShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+o.bonds.bondTypes[a]+" "+i+" "+r+l+c+"\n"}}function m(n,e,a,i){let r=0,l=0,c=0,h=!0,N=null;for(const t of n)if(""!==t.symbol){if("*"==t.symbol)throw new Error("Gap canonical symbol is '', not '*");N=o(e,{symbol:t.symbol,polymerType:E(t.biotype)}),r+=N.atoms.x.length,l+=N.bonds.bondTypes.length,c++}if("PEPTIDE"===i)r+=1,l+=c,c>0&&((N?.meta?.rNodes?.length??0)<2||N?.terminalR2Atom?.toLowerCase()===t.HYDROGEN.toLowerCase())&&(h=!1,r-=1,l-=1);else{const i=a===s.DNA?o(e,t.DEOXYRIBOSE):o(e,t.RIBOSE),c=o(e,t.PHOSPHATE);r+=(n.length-1)*c.atoms.x.length,r+=n.length*i.atoms.x.length,r+=1,l+=(n.length-1)*c.bonds.bondTypes.length,l+=n.length*i.bonds.bondTypes.length,l-=1,l+=3*n.length}return{atomCount:r,bondCount:l,needsCapping:h}}function A(o){return Math.round(t.PRECISION_FACTOR*o)/t.PRECISION_FACTOR}new r(s.PT,l.fasta.peptide,.5),new r(s.DNA,l.fasta.dna,.55),new r(s.RNA,l.fasta.rna,.55),a.FASTA,a.SEPARATOR,a.HELM,a.BILN,function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(c||(c={})),onmessage=t=>{const{seqList:o,monomersDict:n,alphabet:e,polymerType:a,start:s,end:i}=t.data,r=new Array(i-s),l=new Array(0);for(let t=s;t<i;++t)try{const i=o[t];r[t-s]=h(i,n,e,a)}catch(o){const n=`Cannot get molfile of row #${t}: ${o instanceof Error?o.message:o.toString()}.`;l.push(n)}postMessage({molfiles:r,warnings:l})},bio={}})();
+var bio;(()=>{"use strict";const t={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M  RGP",V2K_A_LINE:"A  ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:"  0  0  0  0  0  0            999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M  V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M  V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M  V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M  V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M  V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M  V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M  V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M  V30 ",V3K_END:"M  END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"};function o(t,o){return t[o.polymerType]?.[o.symbol]}class n extends Map{constructor(t){super(t)}}class e{constructor(t,o){this.molfile=t,this.monomers=o}static createEmpty(){return new e("",new n(null))}}var a,s,i;new RegExp("[rd]\\((\\w)\\)p?","g");class r{constructor(t,o,n){this.name=t,this.alphabet=o,this.cutoff=n}}!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(a||(a={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(s||(s={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName",t.annotations=".annotations",t.numberingScheme=".numberingScheme",t.annotationColumnName=".annotationColumnName"}(i||(i={}));const l=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};var c;function h(t){let o;switch(t){case c.BASE:case c.SUGAR:case c.LINKER:case c.NUCLEOTIDE:case"nucleotide":o="RNA";break;case c.AA:o="PEPTIDE";break;case c.CHEM:o="CHEM";break;case c.BLOB:o="BLOB";break;default:o="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return o}function E(a,i,r,l){if(0===a.length)return e.createEmpty();const c=_,{atomCount:E,bondCount:f,needsCapping:m}=c(a,i,r,l),S=new Array(E),d=new Array(f);let p,T=null,I=null;"PEPTIDE"===l?p=N:(p=b,T=r===s.DNA?o(i,t.DEOXYRIBOSE):o(i,t.RIBOSE),I=o(i,t.PHOSPHATE));const u={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},O={sugar:T,phosphate:I,seqLength:a.length,atomCount:E,bondCount:f},C=new n,B=[];let L,y=0;for(u.i=0;u.i<O.seqLength;++u.i){const t=a[u.i];if(""===t.symbol)continue;const n=o(i,{symbol:t.symbol,polymerType:h(t.biotype)});L=n.terminalR2Atom;const e=u.nodeShift,s=u.bondShift;p(n,S,d,u,O),n.stereoAtoms?.forEach(t=>B.push(t+y)),y+=n.atoms.x.length;const r=u.nodeShift-e,l=new Array(r);for(let t=0;t<r;++t)l[t]=e+t;const c=u.bondShift-s,E=new Array(c);for(let t=0;t<c;++t)E[t]=s+t;C.set(u.i,{biotype:t.biotype,symbol:t.symbol,atoms:l,bonds:E})}m&&function(o,n,e,a,s=t.OXYGEN){const i=e.nodeShift+1;o[a.atomCount]=t.V3K_BEGIN_DATA_LINE+i+" "+(s??t.OXYGEN)+" "+A(e.backbonePositionShift[0])+" "+e.flipFactor*A(e.backbonePositionShift[1])+" 0.000000 0\n";const r=e.backboneAttachNode,l=i;n[a.bondCount]=t.V3K_BEGIN_DATA_LINE+e.bondShift+" 1 "+r+" "+l+"\n"}(S,d,u,O,L??t.OXYGEN);const D=t.V3K_BEGIN_COUNTS_LINE+E+" "+f+t.V3K_COUNTS_LINE_ENDING;let g="";return g+=t.V3K_HEADER_FIRST_LINE,g+=t.V3K_HEADER_SECOND_LINE,g+=t.V3K_BEGIN_CTAB_BLOCK,g+=D,g+=t.V3K_BEGIN_ATOM_BLOCK,g+=S.join(""),g+=t.V3K_END_ATOM_BLOCK,g+=t.V3K_BEGIN_BOND_BLOCK,g+=d.join(""),g+=t.V3K_END_BOND_BLOCK,B.length>0&&(g+=function(t){const o=[];let n=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let e=0;e<t.length;e++){const a=`${n} ${t[e]}`;a.length>76?(o.push(`${n} -\n`),n=`M  V30 ${t[e]}`):n=a,e===t.length-1&&o.push(`${n})\n`)}return`M  V30 BEGIN COLLECTION\n${o.join("")}M  V30 END COLLECTION\n`}(B)),g+=t.V3K_END_CTAB_BLOCK,g+=t.V3K_END,{molfile:g,monomers:C}}function N(t,o,n,e){e.flipFactor=(-1)**(e.i%2),f(t,o,n,e)}function f(o,n,e,a){!function(o,n,e){for(let a=0;a<o.atoms.atomTypes.length;++a){const s=e.nodeShift+a+1;n[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+o.atoms.atomTypes[a]+" "+A(e.backbonePositionShift[0]+o.atoms.x[a])+" "+A(e.backbonePositionShift[1]+e.flipFactor*o.atoms.y[a])+" "+o.atoms.kwargs[a]}}(o,n,a),m(o,e,a),function(o,n,e){if(0!==e.backboneAttachNode){const a=e.bondShift,s=e.backboneAttachNode,i=o.meta.terminalNodes[0]+e.nodeShift;n[e.bondShift-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+s+" "+i+"\n"}}(o,e,a),null!==o.meta.branchShift&&o.meta.terminalNodes.length>2&&function(t,o){o.branchAttachNode=o.nodeShift+t.meta.terminalNodes[2];for(let n=0;n<2;++n)o.branchPositionShift[n]=o.backbonePositionShift[n]+t.meta.branchShift[n]}(o,a),function(t,o){o.backboneAttachNode=o.nodeShift+t.meta.terminalNodes[1],o.bondShift+=t.bonds.atomPairs.length+1,o.nodeShift+=t.atoms.atomTypes.length,o.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,o.backbonePositionShift[1]+=o.flipFactor*(t.meta.backboneShift?.[1]??0)}(o,a)}function b(o,n,e,a,s){if(0===a.i)f(s.sugar,n,e,a);else for(const t of[s.phosphate,s.sugar])f(t,n,e,a);!function(o,n,e,a){(function(o,n,e){for(let a=0;a<o.atoms.atomTypes.length;++a){const s=e.nodeShift+a+1;n[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+o.atoms.atomTypes[a]+" "+A(e.branchPositionShift[0]+o.atoms.x[a])+" "+A(e.branchPositionShift[1]+e.flipFactor*o.atoms.y[a])+" "+o.atoms.kwargs[a]}})(o,n,a),m(o,e,a),function(o,n,e){const a=e.bondShift,s=e.branchAttachNode,i=o.meta.terminalNodes[0]+e.nodeShift;n[a-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+s+" "+i+"\n"}(o,e,a);const s=a.bondShift,i=a.branchAttachNode,r=o.meta.terminalNodes[0]+a.nodeShift;e[s-1]=t.V3K_BEGIN_DATA_LINE+s+" 1 "+i+" "+r+"\n",a.bondShift+=o.bonds.atomPairs.length+1,a.nodeShift+=o.atoms.atomTypes.length}(o,n,e,a)}function m(o,n,e){for(let a=0;a<o.bonds.atomPairs.length;++a){const s=e.bondShift+a+1,i=o.bonds.atomPairs[a][0]+e.nodeShift,r=o.bonds.atomPairs[a][1]+e.nodeShift;let l="";if(o.bonds.bondConfiguration.has(a)){let t=o.bonds.bondConfiguration.get(a);e.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=o.bonds.kwargs.has(a)?" "+o.bonds.kwargs.get(a):"";n[e.bondShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+o.bonds.bondTypes[a]+" "+i+" "+r+l+c+"\n"}}function _(n,e,a,i){let r=0,l=0,c=0,E=!0,N=null;for(const t of n)if(""!==t.symbol){if("*"==t.symbol)throw new Error("Gap canonical symbol is '', not '*");N=o(e,{symbol:t.symbol,polymerType:h(t.biotype)}),r+=N.atoms.x.length,l+=N.bonds.bondTypes.length,c++}if("PEPTIDE"===i)r+=1,l+=c,c>0&&((N?.meta?.rNodes?.length??0)<2||N?.terminalR2Atom?.toLowerCase()===t.HYDROGEN.toLowerCase())&&(E=!1,r-=1,l-=1);else{const i=a===s.DNA?o(e,t.DEOXYRIBOSE):o(e,t.RIBOSE),c=o(e,t.PHOSPHATE);r+=(n.length-1)*c.atoms.x.length,r+=n.length*i.atoms.x.length,r+=1,l+=(n.length-1)*c.bonds.bondTypes.length,l+=n.length*i.bonds.bondTypes.length,l-=1,l+=3*n.length}return{atomCount:r,bondCount:l,needsCapping:E}}function A(o){return Math.round(t.PRECISION_FACTOR*o)/t.PRECISION_FACTOR}new r(s.PT,l.fasta.peptide,.5),new r(s.DNA,l.fasta.dna,.55),new r(s.RNA,l.fasta.rna,.55),a.FASTA,a.SEPARATOR,a.HELM,a.BILN,function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(c||(c={})),onmessage=t=>{const{seqList:o,monomersDict:n,alphabet:e,polymerType:a,start:s,end:i}=t.data,r=new Array(i-s),l=new Array(0);for(let t=s;t<i;++t)try{const i=o[t];r[t-s]=E(i,n,e,a)}catch(o){const n=`Cannot get molfile of row #${t}: ${o instanceof Error?o.message:o.toString()}.`;l.push(n)}postMessage({molfiles:r,warnings:l})},bio={}})();
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package/dist/455.js.map

@@ -1 +1 @@
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/@datagrok-libraries/bio/src/utils/const.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js","webpack://bio/./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/seq-to-molfile-worker.js"],"sourcesContent":["export const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\n        return 'Custom';\n    }\n    ;\n    /** flag to let bio know if this provider implements method for converting helm to it */\n    static get implementsFromHelm() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\n        // this is terrible, I know, but otherwise this gets put in webworkers and fails due to DG resolution)))\n        // @ts-ignore\n        if (window?.DG) {\n            // @ts-ignore\n            const constFuncs = window.DG.Func.find({ meta: { role: NOTATION_PROVIDER_CONSTRUCTOR_ROLE } });\n            return Promise.all(constFuncs.map((f) => f.apply({})));\n        }\n        return [];\n    }\n}\n/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\n        // TODO: Check type of monomerType arg\n        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n        if (monomer)\n            return monomer.molfile; //TODO cap\n        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = undefined;\n    switch (helmType) {\n        case HelmTypes.BASE:\n        case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n        case HelmTypes.LINKER: // p - phosphate\n        case HelmTypes.NUCLEOTIDE:\n        // @ts-ignore\n        case 'nucleotide':\n            polymerType = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === ALPHABET.DNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE.symbol ||\n                alphabet === ALPHABET.RNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(monomerSymbol, monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const seqMonomer = monomerSeq[v.i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue;\n        const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        lastMonomerCappingAtom = monomer.terminalR2Atom;\n        const mAtomFirst = v.nodeShift;\n        const mBondFirst = v.bondShift;\n        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n        //adding stereo atoms to array for further STEABS block generation\n        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n        nAtoms += monomer.atoms.x.length;\n        const mAtomCount = v.nodeShift - mAtomFirst;\n        const mAtomList = new Array(mAtomCount);\n        for (let maI = 0; maI < mAtomCount; ++maI)\n            mAtomList[maI] = mAtomFirst + maI;\n        const mBondCount = v.bondShift - mBondFirst;\n        const mBondList = new Array(mBondCount);\n        for (let mbI = 0; mbI < mBondCount; ++mbI)\n            mBondList[mbI] = mBondFirst + mbI;\n        monomers.set(v.i, {\n            biotype: seqMonomer.biotype,\n            symbol: seqMonomer.symbol,\n            atoms: mAtomList, bonds: mBondList\n        });\n    }\n    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n    if (needsCapping)\n        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0)\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {string[]}monomerSeq - the sequence of monomers\n * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n * @param {ALPHABET}alphabet - the alphabet of the monomers\n * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const seqMonomer of monomerSeq) {\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue; // Skip for gap/empty monomer in MSA\n        if (seqMonomer.symbol == '*')\n            throw new Error(`Gap canonical symbol is '', not '*`);\n        lastMonomerGraph = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        atomCount += lastMonomerGraph.atoms.x.length;\n        bondCount += lastMonomerGraph.bonds.bondTypes.length;\n        monomerCount++;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerCount;\n        // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n        if (monomerCount > 0) {\n            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n                needsCapping = false;\n                atomCount -= 1; // remove the last atom (the terminal 'O')\n                bondCount -= 1; // remove the last bond (the terminal C-OH)\n            }\n        }\n    }\n    else { // nucleotides\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? 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utils/macromolecule/consts.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/const.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js","webpack://bio/./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/seq-to-molfile-worker.js"],"sourcesContent":["export const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n    TAGS[\"annotations\"] = \".annotations\";\n    TAGS[\"numberingScheme\"] = \".numberingScheme\";\n    TAGS[\"annotationColumnName\"] = \".annotationColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\n        return 'Custom';\n    }\n    ;\n    /** flag to let bio know if this provider implements method for converting helm to it */\n    static get implementsFromHelm() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\n        // this is terrible, I know, but otherwise this gets put in webworkers and fails due to DG resolution)))\n        // @ts-ignore\n        if (window?.DG) {\n            // @ts-ignore\n            const constFuncs = window.DG.Func.find({ meta: { role: NOTATION_PROVIDER_CONSTRUCTOR_ROLE } });\n            return Promise.all(constFuncs.map((f) => f.apply({})));\n        }\n        return [];\n    }\n}\n/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\n        // TODO: Check type of monomerType arg\n        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n        if (monomer)\n            return monomer.molfile; //TODO cap\n        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = undefined;\n    switch (helmType) {\n        case HelmTypes.BASE:\n        case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n        case HelmTypes.LINKER: // p - phosphate\n        case HelmTypes.NUCLEOTIDE:\n        // @ts-ignore\n        case 'nucleotide':\n            polymerType = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === ALPHABET.DNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE.symbol ||\n                alphabet === ALPHABET.RNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(monomerSymbol, monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const seqMonomer = monomerSeq[v.i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue;\n        const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        lastMonomerCappingAtom = monomer.terminalR2Atom;\n        const mAtomFirst = v.nodeShift;\n        const mBondFirst = v.bondShift;\n        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n        //adding stereo atoms to array for further STEABS block generation\n        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n        nAtoms += monomer.atoms.x.length;\n        const mAtomCount = v.nodeShift - mAtomFirst;\n        const mAtomList = new Array(mAtomCount);\n        for (let maI = 0; maI < mAtomCount; ++maI)\n            mAtomList[maI] = mAtomFirst + maI;\n        const mBondCount = v.bondShift - mBondFirst;\n        const mBondList = new Array(mBondCount);\n        for (let mbI = 0; mbI < mBondCount; ++mbI)\n            mBondList[mbI] = mBondFirst + mbI;\n        monomers.set(v.i, {\n            biotype: seqMonomer.biotype,\n            symbol: seqMonomer.symbol,\n            atoms: mAtomList, bonds: mBondList\n        });\n    }\n    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n    if (needsCapping)\n        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0)\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {string[]}monomerSeq - the sequence of monomers\n * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n * @param {ALPHABET}alphabet - the alphabet of the monomers\n * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const seqMonomer of monomerSeq) {\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue; // Skip for gap/empty monomer in MSA\n        if (seqMonomer.symbol == '*')\n            throw new Error(`Gap canonical symbol is '', not '*`);\n        lastMonomerGraph = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        atomCount += lastMonomerGraph.atoms.x.length;\n        bondCount += lastMonomerGraph.bonds.bondTypes.length;\n        monomerCount++;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerCount;\n        // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n        if (monomerCount > 0) {\n            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n                needsCapping = false;\n                atomCount -= 1; // remove the last atom (the terminal 'O')\n                bondCount -= 1; // remove the last bond (the terminal C-OH)\n            }\n        }\n    }\n    else { // nucleotides\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? err.message : err.toString();\n            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n            molfileWarningList.push(msg);\n        }\n    }\n    postMessage({ molfiles: resMolList, warnings: molfileWarningList });\n};\n//# sourceMappingURL=seq-to-molfile-worker.js.map"],"names":["monomerWorksConsts","V2K_RGP_SHIFT","V2K_RGP_LINE","V2K_A_LINE","V3K_COUNTS_SHIFT","V3K_IDX_SHIFT","V3K_HEADER_FIRST_LINE","V3K_HEADER_SECOND_LINE","V3K_BEGIN_CTAB_BLOCK","V3K_END_CTAB_BLOCK","V3K_BEGIN_COUNTS_LINE","V3K_COUNTS_LINE_ENDING","V3K_BEGIN_ATOM_BLOCK","V3K_END_ATOM_BLOCK","V3K_BEGIN_BOND_BLOCK","V3K_END_BOND_BLOCK","V3K_BOND_CONFIG","V3K_BEGIN_DATA_LINE","V3K_END","PRECISION_FACTOR","DEOXYRIBOSE","polymerType","symbol","RIBOSE","PHOSPHATE","OXYGEN","HYDROGEN","getMolGraph","dict","libKey","MonomerMap","Map","constructor","entries","super","MolfileWithMap","molfile","monomers","this","createEmpty","NOTATION","ALPHABET","TAGS","RegExp","CandidateType","name","alphabet","cutoff","Alphabets","fasta","peptide","Set","dna","rna","HelmTypes","helmTypeToPolymerType","helmType","BASE","SUGAR","LINKER","NUCLEOTIDE","AA","CHEM","BLOB","console","warn","monomerSeqToMolfile","monomerSeq","monomersDict","length","getAtomAndBondCounts","getResultingAtomBondCounts","atomCount","bondCount","needsCapping","molfileAtomBlock","Array","molfileBondBlock","addMonomerToMolblock","sugar","phosphate","addAminoAcidToMolblock","addNucleotideToMolblock","DNA","v","i","nodeShift","bondShift","backbonePositionShift","fill","branchPositionShift","backboneAttachNode","branchAttachNode","flipFactor","LC","seqLength","steabsCollection","lastMonomerCappingAtom","nAtoms","seqMonomer","monomer","biotype","terminalR2Atom","mAtomFirst","mBondFirst","stereoAtoms","forEach","push","atoms","x","mAtomCount","mAtomList","maI","mBondCount","mBondList","mbI","set","bonds","cappingAtomType","atomIdx","keepPrecision","firstAtom","secondAtom","capResultingMolblock","molfileCountsLine","result","join","collection","rowsArray","newCollectionRow","updatedRow","getCollectionBlock","addBackboneMonomerToMolblock","j","atomTypes","y","kwargs","fillAtomLines","fillBondLines","bondIdx","meta","terminalNodes","fillChainExtendingBond","branchShift","updateBranchVariables","atomPairs","backboneShift","updateChainExtendingVariables","nucleobase","fillBranchAtomLines","branchMonomer","fillBackboneToBranchBond","addBranchMonomerToMolblock","bondCfg","bondConfiguration","has","orientation","get","bondTypes","monomerCount","lastMonomerGraph","Error","rNodes","toLowerCase","Math","round","PT","RNA","FASTA","SEPARATOR","HELM","BILN","onmessage","event","seqList","start","end","data","resMolList","molfileWarningList","rowI","seq","err","msg","message","toString","postMessage","molfiles","warnings"],"sourceRoot":""}