@datagrok/helm 3.0.1 → 3.0.3

package/dist/323.js.map

@@ -1 +0,0 @@
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The string\n// values match the canonical Pistoia HELM Web Editor, except `NUCLEOTIDE` which\n// uses the corrected spelling `HELM_NUCLEOTIDE` (was `HELM_NUCLETIDE`).\nimport {HelmTypes, MonomerTypes, PolymerTypes} from '@datagrok-libraries/hwe';\n\nexport {HelmTypes, MonomerTypes, PolymerTypes};\n\n// hwe migration: these two small enums are not part of the hwe value vocabulary.\n// They are defined here locally (replicating the legacy HELM Web Editor values)\n// so `@datagrok-libraries/bio` no longer depends on\n// `@datagrok-libraries/helm-web-editor`.\nexport enum MonomerNumberingTypes {\n  default = 0,\n  continuous = 1,\n}\n\nexport enum HelmTabKeys {\n  Sequence = 'sequence',\n  Helm = 'notation',\n  Properties = 'properties',\n  StructureView = 'structureview',\n}\n","import {PolymerTypes} from '../helm/consts';\n\nexport 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: 10_000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n  // symbols for the corresponding monomers in HELM library\n\n  DEOXYRIBOSE: {polymerType: PolymerTypes.RNA, symbol: 'd'},\n  RIBOSE: {polymerType: PolymerTypes.RNA, symbol: 'r'},\n  PHOSPHATE: {polymerType: PolymerTypes.RNA, symbol: 'p'},\n\n  OXYGEN: 'O',\n  HYDROGEN: 'H',\n} as const;\n\n","// interface for typed arrays, like Float32Array and Uint32Array\nimport {ALPHABET} from '../utils/macromolecule';\nimport {HELM_POLYMER_TYPE} from '../utils/const';\nimport {HelmType, ISeqMonomer} from '../helm/types';\n\nexport interface ITypedArray {\n  length: number;\n  [key: number]: any;\n}\n\n/** Type for user settings of monomer library set to use. */\nexport type UserLibSettings = {\n  exclude: string[],\n  explicit: string[],\n  /** Libraries might contain different monomers for same symbol. Object for monomer symbol to library name of choice*/\n  duplicateMonomerPreferences: {[polymerType: string]: {[monomerSymbol: string]: string}}\n}\n\n/** Stores necessary data about atoms of a monomer parsed from Molfile */\nexport type Atoms = {\n    /** Element symbols for monomer's atoms */\n    atomTypes: string[],\n    /** Cartesian coordiantes of monomer's atoms */\n    x: Float32Array,\n    y: Float32Array,\n    /** V3K atom line may contain keyword args */\n    kwargs: string[],\n  }\n\n/** Stores necessary data about bonds of a monomer parsed from Molfile */\nexport type Bonds = {\n    /** bond types for all lines of Molfile bond block */\n    bondTypes: Uint32Array,\n    /** Indices of all atom pairs, indexing starting from 1  */\n    atomPairs: number[][],\n    /** If a bond has CFG=... keyword argument, it is parsed and sotred as a\n     * value of the map, with the key being the bond's index  */\n    bondConfiguration: Map<number, number>,\n    /** V3K bond line may contain keyword args */\n    kwargs: Map<number, string>,\n}\n\n/** Metadata associated with the monomer necessary to restore the resulting molfile */\nexport type MonomerMetadata = {\n    /** terminal nodes: 0-th corresponds to the \"leftmost\" one, 1st, to the \"rightmost\",\n     * e.g. N-terminus and C-terminus in peptides */\n    terminalNodes: number[],\n    /** r-group nodes: 0-th corresponds to the \"leftmost\" one, 1st, to the \"rightmost\" */\n    rNodes: number[],\n    /** shift from the origin to the next backbone, null for branch monomers */\n    backboneShift: number[] | null,\n    /** shift from the origin to the next branch, null for branch monomers */\n    branchShift: number[] | null\n}\n\nexport type MolGraph = {\n    atoms: Atoms,\n    bonds: Bonds,\n    meta: MonomerMetadata,\n    stereoAtoms?: number[],\n    terminalR2Atom?: string, // for peptides, store the removed R2 Atom type, if any\n}\n\nexport type MonomerMolGraphMap = { [polymerType: string]: { [symbol: string]: MolGraph } };\n\nexport type LibMonomerKey = { polymerType: string, symbol: string }\n\nexport function getMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey): MolGraph | undefined {\n  return dict[libKey.polymerType]?.[libKey.symbol];\n}\n\nexport function hasMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey): boolean {\n  return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\n\nexport function setMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey, value: MolGraph): void {\n  let pt = dict[libKey.polymerType];\n  if (!pt)\n    pt = dict[libKey.polymerType] = {};\n  pt[libKey.symbol] = value;\n}\n\n// export function getMolGraph(\n//   dict: MonomerMolGraphMap, polymerType: PolymerType, symbol: string\n// ): MolGraph | undefined {\n//   return dict[polymerType]?.[symbol];\n// }\n\nexport type Point = {\n    x: number,\n    y: number\n}\n\n/** Helper structure wrapping common arguments to several functions */\nexport type LoopVariables = {\n    i: number,\n    nodeShift: number,\n    bondShift: number,\n    backbonePositionShift: number[],\n    backboneAttachNode: number; // node to which the next backbone is attached\n    branchPositionShift: number[],\n    branchAttachNode: number,\n    flipFactor: number,\n    // todo: should we consider representations other than planar?\n}\n\n/** Helper structure wrapping common arguments to several functions */\nexport type LoopConstants = {\n    sugar: MolGraph | null,\n    phosphate: MolGraph | null,\n    seqLength: number,\n    atomCount: number,\n    bondCount: number,\n}\n\n/** Helper structure to simulate pointer to number  */\nexport type NumberWrapper = {\n  value: number | null // null if there is no branch attach node\n}\n\n/** Role of an entry in a HELM RNA splitted sequence.\n * SUGAR/BASE/PHOSPHATE are the standard triple positions.\n * TERMINAL_5P marks a 5'-end terminal modifier (e.g. Chol) — a monomer\n * with R2 only that takes the place of the leading sugar.\n * TERMINAL_3P marks a 3'-end terminal modifier (e.g. GalNAc) — a monomer\n * with R1 only that takes the place of the trailing phosphate. The OH cap\n * MUST be omitted when a TERMINAL_3P is present. */\nexport enum NucleotideRole {\n  SUGAR = 0,\n  BASE = 1,\n  PHOSPHATE = 2,\n  TERMINAL_5P = 3,\n  TERMINAL_3P = 4,\n}\n\nexport type MonomerMapValue = { biotype: HelmType, symbol: string, atoms: number[], bonds: number[] };\n\nexport class MonomerMap extends Map<number, MonomerMapValue> {\n  constructor(entries?: [number, MonomerMapValue][] | null) {\n    super(entries);\n  }\n}\n\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n  constructor(\n    public readonly molfile: string,\n    public readonly monomers: MonomerMap,\n  ) {}\n\n  static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n\n/** Only simple types allowed for worker data, avoid classes with methods */\nexport type SeqToMolfileWorkerData = {\n  seqList: ISeqMonomer[][],\n  /** Per-row parallel array of NucleotideRole tags (only set for rows in\n   * \"HELM RNA triples\" mode, where each nucleotide contributes 3 entries\n   * sugar/base/phosphate). undefined for legacy bases-only rows. */\n  rolesList?: (NucleotideRole[] | undefined)[],\n  monomersDict: MonomerMolGraphMap,\n  alphabet: ALPHABET,\n  polymerType: HELM_POLYMER_TYPE,\n  start: number,\n  end: number,\n}\n\nexport type SeqToMolfileWorkerRes = {\n  molfiles: MolfileWithMap[];\n  warnings: string[]\n}\n","import {MonomerType, PolymerType} from '../helm/types';\nimport {MonomerTypes, PolymerTypes} from '../helm/consts';\nimport {RGroup} from '../types/monomer-library';\n\n// hwe exports the HELM type vocabulary as `as const` objects (value-only), not\n// TS enums, so we re-create the value+type duality the old `import X = Enum`\n// aliases provided — consumers use these both as a value (`.RNA`) and as a type.\nconst HELM_POLYMER_TYPE = PolymerTypes;\ntype HELM_POLYMER_TYPE = PolymerType;\nconst HELM_MONOMER_TYPE = MonomerTypes;\ntype HELM_MONOMER_TYPE = MonomerType;\n\nexport {HELM_POLYMER_TYPE, HELM_MONOMER_TYPE};\n\n/** Required HELM library monomer fields:\n * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */\nexport const enum HELM_REQUIRED_FIELD {\n  SYMBOL = 'symbol',\n  NAME = 'name',\n  MOLFILE = 'molfile',\n  AUTHOR = 'author',\n  ID = 'id',\n  RGROUPS = 'rgroups',\n  SMILES = 'smiles',\n  POLYMER_TYPE = 'polymerType',\n  MONOMER_TYPE = 'monomerType',\n  CREATE_DATE = 'createDate',\n}\n\n// fields of \"rgroups\" sub-object in HELM library\nexport const enum HELM_RGROUP_FIELDS {\n  CAP_GROUP_SMILES = 'capGroupSmiles',\n  // WARNING: both capitalization variants coexist\n  CAP_GROUP_SMILES_UPPERCASE = 'capGroupSMILES',\n  ALTERNATE_ID = 'alternateId',\n  CAP_GROUP_NAME = 'capGroupName',\n  LABEL = 'label',\n}\n\nexport const enum HELM_OPTIONAL_FIELDS {\n  NATURAL_ANALOG = 'naturalAnalog',\n  META = 'meta', // for SequenceTranslator\n}\n\n// todo: remove\nexport const enum HELM_FIELDS {\n  MONOMER_TYPE = 'monomerType',\n  SMILES = 'smiles',\n  NAME = 'name',\n  AUTHOR = 'author',\n  MOLFILE = 'molfile',\n  NATURAL_ANALOG = 'naturalAnalog',\n  RGROUPS = 'rgroups',\n  CREATE_DATE = 'createDate',\n  ID = 'id',\n  POLYMER_TYPE = 'polymerType',\n  SYMBOL = 'symbol'\n}\n\n// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n  HELM_FIELDS.SYMBOL,\n  HELM_FIELDS.MOLFILE,\n  HELM_FIELDS.RGROUPS,\n  HELM_FIELDS.NAME,\n  // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n  // supported\n];\n\nexport const SDF_MONOMER_NAME = 'MonomerName';\n\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};\n\nexport const DUMMY_MONOMER = {\n  'monomerType': 'Backbone' as MonomerType,\n  'smiles': '',\n  'name': '',\n  'author': 'Datagrok',\n  'molfile': '',\n  'naturalAnalog': '',\n  'rgroups': [] as RGroup[],\n  'createDate': null,\n  'id': 0,\n  'polymerType': 'PEPTIDE' as PolymerType,\n  'symbol': ''\n} as const;\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;\n\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(\n  `[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`,\n  'g'\n);\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 {CellRendererBackBase} from '../cell-renderer-back-base';\nimport {ISeqHandler} from './seq-handler';\nimport {PolymerType} from '../../helm/types';\nimport {NOTATION_PROVIDER_CONSTRUCTOR_ROLE} from './consts';\n\nexport type SeqSplittedBase = ArrayLike<string> & Iterable<string>;\n\nexport interface ISeqConnection {\n  seq1Type: PolymerType;\n  seq2Type: PolymerType;\n  seqIndex1: number;\n  seqIndex2: number;\n  monomerIndex1: number;\n  monomerIndex2: number;\n  rGroup1: number;\n  rGroup2: number;\n}\n\nexport interface ISeqGraphInfo {\n  /**  Connections between monomers with numbers - note that monomer numbers are 0-based*/\n  connections: ISeqConnection[];\n  /** Start positions of disjoint sequence parts in the original sequence */\n  disjointSeqStarts: number[];\n  /** Polimer types same as the indexes. only applicapble to helm */\n  polymerTypes?: PolymerType[];\n}\n\nexport interface ISeqSplitted {\n\n  graphInfo?: ISeqGraphInfo;\n\n  isGap(posIdx: number): boolean;\n\n  /** */\n  getCanonical(posIdx: number): string;\n\n  /** For fasta and Helm must not be enclosed to square brackets [meA].*/\n  getOriginal(posIdx: number): string;\n\n  // TODO: Get ISeqMonomer for seq position\n  // get(posIdx: number): ISeqMonomer;\n\n  length: number;\n\n  /** Returns list of canonical monomers in the region specified */\n  getCanonicalRegion(start: number, end: number): string[];\n\n  /** Returns the list of original monomers in the region specified */\n  getOriginalRegion(start: number, end: number): string[];\n\n  get gapOriginal(): string;\n}\n\n/**\n * Extracts displayable monomer symbol(s) from a raw position value.\n * Used by the Monomer cell renderer when a notation provider needs custom\n * interpretation of split-to-monomer position values.\n *\n * For example, a Parabilis position `[VHL1379]*dLys` contains two monomers\n * (`VHL1379` and `dLys`). The canonicalizer separates them with\n * {@link MONOMER_MOTIF_SPLITTER} so the renderer can display/tooltip each one.\n */\nexport interface IMonomerCanonicalizer {\n  /** Convert a raw position value to a displayable monomer string.\n   *  If the position contains multiple monomers, join them with\n   *  {@link MONOMER_MOTIF_SPLITTER} (` , `). */\n  canonicalize(original: string): string;\n\n  /** Returns true if the raw position value represents a gap in this notation. */\n  isGap(original: string): boolean;\n}\n\nexport interface INotationProvider {\n  get defaultGapOriginal(): string;\n\n  /** Adjust {@link seqHandler} units, {@link seqHandler.column.tags} by {@link seqHandler} constructor */\n  setUnits(seqHandler: ISeqHandler): void;\n\n  get splitter(): SplitterFunc;\n\n  /** Any Macromolecule can be presented as Helm notation */\n  getHelm(seq: string, options: any): string;\n\n  createCellRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;\n\n  /** nqName of a registered function that returns an {@link IMonomerCanonicalizer} instance.\n   *  When set, split-to-monomers will tag Monomer columns with this function name so the\n   *  monomer cell renderer can resolve display symbols from raw position values.\n   *  Return null/undefined if no custom canonicalization is needed. */\n  readonly monomerCanonicalizerFuncName?: string | null;\n}\n\nexport abstract class NotationProviderBase {\n  /** Name of the custom notation */\n  static get notationName(): string {\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(): boolean {\n    return false;\n  };\n\n  /** Method for converting HELM to this notation */\n  static convertFromHelm(helm: string, options: any): string {\n    throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n  };\n\n  static async getProviderConstructors(): Promise<typeof NotationProviderBase[]> {\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: any[] = 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\nexport type SeqColStats = { freq: MonomerFreqs, sameLength: boolean }\nexport type SplitterFunc = (seq: string) => ISeqSplitted;\nexport type MonomerFreqs = { [m: string]: number };\n\n/** Alphabet candidate type */\nexport class CandidateType {\n  name: string;\n  alphabet: Set<string>;\n  cutoff: number;\n\n  constructor(name: string, alphabet: Set<string>, cutoff: number) {\n    this.name = name;\n    this.alphabet = alphabet;\n    this.cutoff = cutoff;\n  }\n}\n\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n  freq: MonomerFreqs;\n  /** Cos, max = 1, min = 0 */\n  similarity: number;\n\n  constructor(candidate: CandidateType, freq: MonomerFreqs, similarity: number) {\n    super(candidate.name, candidate.alphabet, candidate.cutoff);\n    this.freq = freq;\n    this.similarity = similarity;\n  }\n}\n","import {CandidateType} from './types';\n\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport enum NOTATION {\n  FASTA = 'fasta',\n  SEPARATOR = 'separator',\n  HELM = 'helm',\n  /* Requires notation handler */ CUSTOM = 'custom',\n  /* Requires notation handler */ BILN = 'biln',\n}\n\nexport const enum ALIGNMENT {\n  SEQ_MSA = 'SEQ.MSA',\n  SEQ = 'SEQ',\n}\n\nexport enum ALPHABET {\n  DNA = 'DNA',\n  RNA = 'RNA',\n  PT = 'PT',\n  /** Unknown */\n  UN = 'UN',\n}\n\nexport enum TAGS {\n  aligned = 'aligned',\n  alphabet = 'alphabet',\n  alphabetSize = '.alphabetSize',\n  alphabetIsMultichar = '.alphabetIsMultichar',\n  separator = 'separator',\n  isHelmCompatible = '.isHelmCompatible',\n  positionNames = '.positionNames',\n  positionLabels = '.positionLabels',\n  regions = '.regions',\n  positionShift = '.positionShift',\n  selectedPosition = '.selectedPosition',\n  polymerTypeColumnName = '.polymerTypeColumnName',\n  annotations = '.annotations',\n  numberingScheme = '.numberingScheme',\n  annotationColumnName = '.annotationColumnName',\n}\n\nexport {TAGS as BioTags};\n\nexport const positionSeparator: string = ', ';\n\nexport const monomerRe: RegExp = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\n\nexport const helmRe: RegExp = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re: RegExp = /\\[([^\\[\\]]+)]/g;\n\nexport const Alphabets = new class {\n  fasta = {\n    peptide: new Set<string>([\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<string>(['A', 'C', 'G', 'T']),\n    rna: new Set<string>(['A', 'C', 'G', 'U']),\n  };\n}();\n\nexport const candidateAlphabets: CandidateType[] = [\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\n/** Canonical gap symbol */\nexport const GAP_SYMBOL: string = '' as const;\n\nexport const GapOriginals: {\n  [units: string]: string\n} = {\n  [NOTATION.FASTA]: '-',\n  [NOTATION.SEPARATOR]: '',\n  [NOTATION.HELM]: '*',\n  [NOTATION.BILN]: '',\n};\n\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\n\n/** Tag on Monomer columns storing the nqName of a function that returns an IMonomerCanonicalizer.\n *  The `.%` prefix ensures this tag is persisted with projects. */\nexport const MONOMER_CANONICALIZER_FUNC_TAG = '.%monomer-canonicalizer-func';\n\n/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n","import * as grok from 'datagrok-api/grok';\nimport * as ui from 'datagrok-api/ui';\nimport * as DG from 'datagrok-api/dg';\n\nimport {IMonomerLibBase} from '../types/monomer-library';\nimport {HelmType, PolymerType} from '../helm/types';\nimport {HelmTypes, PolymerTypes} from '../helm/consts';\n\n/** Hypothetical interface to convert mol block notation.\n * It should be placed in the chem-meta package, and have an implementation in the Chem package.\n * So dependency of MonomerWorks on molfile conversion operation becomes explicit.\n */\nexport interface IMolfileConverter {\n  convertV2000toV3000(src: string): string;\n\n  convertV3000toV2000(src: string): string;\n}\n\nexport class MonomerWorks {\n  private monomerLib: IMonomerLibBase;\n\n  //private molfileConverter: IMolfileConverter;\n\n  constructor(monomerLib: IMonomerLibBase/*, molfileConverter: IMolfileConverter*/) {\n    this.monomerLib = monomerLib;\n    //this.molfileConverter = molfileConverter;\n  }\n\n  //types according to Monomer possible\n  public getCappedRotatedMonomer(monomerType: PolymerType, monomerName: string): string | null {\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\n    return null;\n  }\n}\n\nexport function helmTypeToPolymerType(helmType: HelmType): PolymerType {\n  let polymerType: PolymerType | undefined = 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 = PolymerTypes.RNA;\n    break;\n  case HelmTypes.AA:\n    polymerType = PolymerTypes.PEPTIDE;\n    break;\n  case HelmTypes.CHEM:\n    polymerType = PolymerTypes.CHEM;\n    break;\n  case HelmTypes.BLOB:\n    polymerType = PolymerTypes.BLOB;\n    break;\n  default:\n    polymerType = PolymerTypes.PEPTIDE;\n    console.warn(`Unexpected HelmType '${helmType}'`);\n  }\n  return polymerType;\n}\n","/* eslint-disable max-len */\nimport {monomerWorksConsts as C} from './consts';\nimport {getMolGraph, LoopConstants, LoopVariables, MolfileWithMap, MolGraph, MonomerMap, MonomerMolGraphMap,\n  NucleotideRole} from './types';\nimport {HELM_FIELDS, HELM_CORE_FIELDS, HELM_POLYMER_TYPE, HELM_MONOMER_TYPE,} from '../utils/const';\nimport {ALPHABET, GAP_SYMBOL} from '../utils/macromolecule/consts';\nimport {IMonomerLibBase, Monomer} from '../types/monomer-library';\nimport {ISeqMonomer, PolymerType} from '../helm/types';\nimport {helmTypeToPolymerType} from './monomer-works';\n\n\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(\n  monomerLib: IMonomerLibBase, polymerType: PolymerType, alphabet: ALPHABET\n): Map<string, any> {\n  const map = new Map<string, any>();\n  for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n    const it: Monomer = monomerLib.getMonomer(polymerType, monomerSymbol)!;\n    if (\n      // RNA: all branch monomers (bases) and all backbone monomers (sugars +\n      // phosphates, including modified ones). Modifications are looked up by\n      // symbol at assembly time, so they MUST be present in the formatted lib.\n      polymerType === HELM_POLYMER_TYPE.RNA || (\n        polymerType === HELM_POLYMER_TYPE.PEPTIDE &&\n      it[HELM_FIELDS.MONOMER_TYPE] !== HELM_MONOMER_TYPE.BRANCH\n      )) {\n      const monomerObject: { [key: string]: any } = {};\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\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly\n *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).\n * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */\nexport function monomerSeqToMolfile(\n  monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap,\n  alphabet: ALPHABET, polymerType: PolymerType,\n  roles?: NucleotideRole[]\n): MolfileWithMap {\n  if (monomerSeq.length === 0) {\n    // throw new Error('monomerSeq is empty');\n    return MolfileWithMap.createEmpty();\n  }\n\n  // Triples mode is on only when the caller flagged the row with roles\n  // (built and validated by `buildRolesForHelmRna` in to-atomic-level.ts).\n  // The roles array carries the per-position semantics — including\n  // TERMINAL_5P / TERMINAL_3P for non-canonical chain ends — so we don't\n  // re-validate the length here.\n  const triplesMode = polymerType === HELM_POLYMER_TYPE.RNA && !!roles &&\n    roles.length === monomerSeq.length;\n\n  // define atom and bond counts, taking into account the bond type\n  const {atomCount, bondCount, needsCapping} =\n    getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles);\n\n  // create arrays to store lines of the resulting molfile\n  const molfileAtomBlock = new Array<string>(atomCount);\n  const molfileBondBlock = new Array<string>(bondCount);\n\n  let addMonomerToMolblock: (monomer: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables, LC: LoopConstants) => void;\n\n  let sugar = null;\n  let phosphate = null;\n\n  if (polymerType === HELM_POLYMER_TYPE.PEPTIDE)\n    addMonomerToMolblock = addAminoAcidToMolblock;\n  else { // nucleotides\n    addMonomerToMolblock = addNucleotideToMolblock;\n    // Default sugar/phosphate are only consulted in bases-only mode. In\n    // triples mode, every nucleotide carries its own.\n    if (!triplesMode) {\n      sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n      phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n    }\n  }\n  const v: LoopVariables = {\n    i: 0,\n    nodeShift: 0,\n    bondShift: 0,\n    backbonePositionShift: new Array<number>(2).fill(0),\n    branchPositionShift: new Array<number>(2).fill(0),\n    backboneAttachNode: 0,\n    branchAttachNode: 0,\n    flipFactor: 1,\n  };\n\n  const LC: LoopConstants = {\n    sugar: sugar!,\n    phosphate: phosphate!,\n    // In triples mode, the \"logical\" sequence length is the nucleotide count.\n    seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : monomerSeq.length,\n    atomCount: atomCount,\n    bondCount: bondCount,\n  };\n\n  const monomers: MonomerMap = new MonomerMap();\n  const steabsCollection: number [] = [];\n  let nAtoms = 0;\n  let lastMonomerCappingAtom: string | undefined = undefined;\n\n  if (triplesMode) {\n    runTriplesAssembly(\n      monomerSeq, roles!, monomersDict, molfileAtomBlock, molfileBondBlock,\n      v, LC, monomers, steabsCollection,\n      (a) => { nAtoms += a; }, () => nAtoms);\n  } else {\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n      const seqMonomer = monomerSeq[v.i];\n      if (seqMonomer.symbol === GAP_SYMBOL) 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\n      const mAtomCount = v.nodeShift - mAtomFirst;\n      const mAtomList: number[] = new Array<number>(mAtomCount);\n      for (let maI = 0; maI < mAtomCount; ++maI) mAtomList[maI] = mAtomFirst + maI;\n\n      const mBondCount = v.bondShift - mBondFirst;\n      const mBondList: number[] = new Array<number>(mBondCount);\n      for (let mbI = 0; mbI < mBondCount; ++mbI) mBondList[mbI] = mBondFirst + mbI;\n\n      monomers.set(v.i, {\n        biotype: seqMonomer.biotype,\n        symbol: seqMonomer.symbol,\n        atoms: mAtomList, bonds: mBondList\n      });\n    }\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\n  const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n\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\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\n  // return molfileParts.join('');\n  return {molfile: result, monomers: monomers};\n}\n\n\nfunction getCollectionBlock(collection: number[]): string {\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\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 ${collection[i]}`;\n    } else\n      newCollectionRow = updatedRow;\n    //in case last atom was added - close the block\n    if (i === collection.length - 1)\n      rowsArray.push(`${newCollectionRow})\\n`);\n  }\n  return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n\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(\n  molfileAtomBlock: string[], molfileBondBlock: string[],\n  v: LoopVariables, LC: LoopConstants, cappingAtomType: string = C.OXYGEN\n): void {\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\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}\n\nfunction addAminoAcidToMolblock(monomer: MolGraph, molfileAtomBlock: string[],\n  molfileBondBlock: string[], v: LoopVariables\n): void {\n  v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n  addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\n\nfunction addBackboneMonomerToMolblock(\n  monomer: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables\n): void {\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\n  // construct the lines of V3K molfile bond block\n  fillBondLines(monomer, molfileBondBlock, v);\n\n  // peptide bond\n  fillChainExtendingBond(monomer, molfileBondBlock, v);\n\n  // update branch variables if necessary\n  if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n    updateBranchVariables(monomer, v);\n\n  // update loop variables\n  updateChainExtendingVariables(monomer, v);\n}\n\nfunction addNucleotideToMolblock(\n  nucleobase: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables, LC: LoopConstants\n): void {\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\n  addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\n\nfunction addBranchMonomerToMolblock(\n  monomer: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables\n): void {\n  fillBranchAtomLines(monomer, molfileAtomBlock, v);\n  fillBondLines(monomer, molfileBondBlock, v);\n  fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n\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\n  // update loop variables\n  v.bondShift += monomer.bonds.atomPairs.length + 1;\n  v.nodeShift += monomer.atoms.atomTypes.length;\n}\n\nfunction updateChainExtendingVariables(monomer: MolGraph, v: LoopVariables): void {\n  v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n  v.bondShift += monomer.bonds.atomPairs.length + 1;\n\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}\n\nfunction updateBranchVariables(monomer: MolGraph, v: LoopVariables): void {\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}\n\nfunction fillAtomLines(monomer: MolGraph, molfileAtomBlock: string[], v: LoopVariables): void {\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\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer: MolGraph, molfileAtomBlock: string[], v: LoopVariables): void {\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}\n\nfunction fillBondLines(monomer: MolGraph, molfileBondBlock: string[], v: LoopVariables): void {\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}\n\nfunction fillChainExtendingBond(monomer: MolGraph, molfileBondBlock: string[], v: LoopVariables): void {\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\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer: MolGraph, molfileBondBlock: string[], v: LoopVariables): void {\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\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {ISeqMonomer[]} monomerSeq - the sequence of monomers\n * @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers\n * @param {ALPHABET} alphabet - the alphabet of the monomers\n * @param {PolymerType} polymerType - the type of polymer\n * @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples\n * @param {Array} roles - per-position role tags (only meaningful when triplesMode is true)\n * @return {Object} the atom/bond counts plus needsCapping flag */\nfunction getResultingAtomBondCounts(\n  monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap,\n  alphabet: ALPHABET, polymerType: PolymerType,\n  triplesMode: boolean, roles?: NucleotideRole[]\n): { atomCount: number, bondCount: number, needsCapping: boolean } {\n  let atomCount = 0;\n  let bondCount = 0;\n\n  let monomerCount: number = 0;\n  let needsCapping = true;\n  let lastMonomerGraph: MolGraph | null = null;\n  let lastPhosphateGraph: MolGraph | null = null;\n  // sum up all the atoms/nodes provided by the sequence\n  for (let i = 0; i < monomerSeq.length; ++i) {\n    const seqMonomer = monomerSeq[i];\n    if (seqMonomer.symbol === GAP_SYMBOL) 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    // In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track\n    // the LAST one — its atoms/bonds are dropped at the 3'-terminus.\n    if (triplesMode && i % 3 === 2) lastPhosphateGraph = lastMonomerGraph;\n  }\n\n  // add extra values depending on the polymer type\n  if (polymerType === 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  } else if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)\n    void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it\n\n    // Per-monomer-loop already summed sugars + bases + phosphates for every\n    // entry in monomerSeq (terminals included). Reservation: each backbone\n    // emit (sugar / phosphate / terminal) reserves +1 bond slot for the\n    // chain-extending bond, each branch (base) reserves +1 for its branch\n    // bond. Total reservations = monomerCount.\n    bondCount += monomerCount;\n\n    // OH cap atom rides on the 3'-end. Skip it when HELM specified a\n    // 3'-terminal modifier (e.g. GalNAc) that IS the chain end.\n    const has3pTerm = !!roles && roles.length > 0 &&\n      roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;\n    if (has3pTerm) {\n      needsCapping = false;\n      // Mirror the peptide branch (which does both atomCount-- and bondCount--\n      // when it skips the terminal cap). `bondCount += monomerCount` above\n      // reserves one chain-extending slot per monomer; the LAST monomer's slot\n      // is normally filled by the terminal OH cap bond. With a 3'-terminal\n      // modifier there is no cap, so that last reserved slot stays empty —\n      // leaving the declared bond count one higher than the emitted bond\n      // lines. Drop it so the V3000 COUNTS line matches the bond block exactly\n      // (otherwise the pre-OCL molfile is malformed and only survives because\n      // the OCL chirality pass re-derives the counts).\n      bondCount -= 1;\n    } else\n      atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)\n  } else { // nucleotides — bases-only legacy path with default sugar/phosphate\n    const sugar = (alphabet === ALPHABET.DNA) ?\n      getMolGraph(monomersDict, C.DEOXYRIBOSE)! : getMolGraph(monomersDict, C.RIBOSE)!;\n    const phosphate = getMolGraph(monomersDict, C.PHOSPHATE)!;\n\n    // add phosphate per each pair of nucleobase symbols\n    atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n\n    // add sugar per each nucleobase symbol\n    atomCount += monomerSeq.length * sugar.atoms.x.length;\n\n    // add the leftmost cap group 'OH' (i.e. 'O')\n    atomCount += 1;\n\n    // add bonds from phosphate monomers\n    bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n\n    // add bonds from sugar monomers\n    bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n\n    // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n    bondCount -= 1;\n\n    // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n    bondCount += monomerSeq.length * 3;\n  }\n\n  return {atomCount, bondCount, needsCapping};\n}\n\n// Role-driven RNA assembly. Walks the monomers in chain order and emits\n// each one according to its NucleotideRole (assigned by `buildRolesForHelmRna`\n// from the library, not from a fixed triple index):\n//   - BASE                                  → branch monomer, attached to the\n//                                             branch point of the sugar most\n//                                             recently emitted.\n//   - SUGAR / PHOSPHATE / TERMINAL_5P / 3P  → backbone monomer, chained to the\n//                                             previous backbone unit.\n//\n// Because the role comes from chemistry, this transparently handles every\n// backbone layout — standard [sugar, base, phosphate] triples, a 5'-leading\n// phosphate, several phosphates / linkers in a row, a linker dropped in the\n// middle of the chain, missing trailing phosphate, and 5'/3' terminal\n// modifiers — without any index arithmetic. The first backbone monomer\n// naturally has no incoming chain bond (v.backboneAttachNode starts at 0),\n// and the trailing OH cap is added by the caller via needsCapping (skipped\n// when a TERMINAL_3P ends the chain).\nfunction runTriplesAssembly(\n  monomerSeq: ISeqMonomer[], roles: NucleotideRole[],\n  monomersDict: MonomerMolGraphMap,\n  molfileAtomBlock: string[], molfileBondBlock: string[],\n  v: LoopVariables, LC: LoopConstants,\n  monomers: MonomerMap, steabsCollection: number[],\n  addAtoms: (n: number) => void, getAtoms: () => number\n): void {\n  void LC; // assembly is driven by per-monomer roles, not by LC.seqLength\n  for (let i = 0; i < monomerSeq.length; ++i) {\n    const sm = monomerSeq[i];\n    if (sm.symbol === GAP_SYMBOL) continue;\n    const role = roles[i];\n    const mG = getMolGraph(monomersDict,\n      {symbol: sm.symbol, polymerType: helmTypeToPolymerType(sm.biotype)})!;\n\n    const aFirst = v.nodeShift;\n    const bFirst = v.bondShift;\n    v.i = i; // keep loop counter monotone (unused by nucleotide geometry)\n    if (role === NucleotideRole.BASE)\n      // Branch: attaches to v.branchAttachNode, set when the preceding sugar\n      // was emitted. Does not advance the backbone, so the next backbone unit\n      // still chains from that sugar's 3' side.\n      addBranchMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n    else\n      // Backbone: sugar / phosphate / linker / terminal modifier. Chains from\n      // the previous backbone unit (none for the very first one) and, for a\n      // sugar, sets up the branch attach point for the next base.\n      addBackboneMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n\n    mG.stereoAtoms?.forEach((s) => steabsCollection.push(s + getAtoms()));\n    addAtoms(mG.atoms.x.length);\n\n    const aList: number[] = [];\n    for (let a = aFirst; a < v.nodeShift; ++a) aList.push(a);\n    const bList: number[] = [];\n    for (let b = bFirst; b < v.bondShift; ++b) bList.push(b);\n    monomers.set(i, {biotype: sm.biotype, symbol: sm.symbol, atoms: aList, bonds: bList});\n  }\n}\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: number): number {\n  return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n\n","import 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package/dist/455.js

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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}\n/** Role of an entry in a HELM RNA splitted sequence.\n * SUGAR/BASE/PHOSPHATE are the standard triple positions.\n * TERMINAL_5P marks a 5'-end terminal modifier (e.g. Chol) — a monomer\n * with R2 only that takes the place of the leading sugar.\n * TERMINAL_3P marks a 3'-end terminal modifier (e.g. GalNAc) — a monomer\n * with R1 only that takes the place of the trailing phosphate. The OH cap\n * MUST be omitted when a TERMINAL_3P is present. */\nexport var NucleotideRole;\n(function (NucleotideRole) {\n    NucleotideRole[NucleotideRole[\"SUGAR\"] = 0] = \"SUGAR\";\n    NucleotideRole[NucleotideRole[\"BASE\"] = 1] = \"BASE\";\n    NucleotideRole[NucleotideRole[\"PHOSPHATE\"] = 2] = \"PHOSPHATE\";\n    NucleotideRole[NucleotideRole[\"TERMINAL_5P\"] = 3] = \"TERMINAL_5P\";\n    NucleotideRole[NucleotideRole[\"TERMINAL_3P\"] = 4] = \"TERMINAL_3P\";\n})(NucleotideRole || (NucleotideRole = {}));\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 = ' , ';\n/** Tag on Monomer columns storing the nqName of a function that returns an IMonomerCanonicalizer.\n *  The `.%` prefix ensures this tag is persisted with projects. */\nexport const MONOMER_CANONICALIZER_FUNC_TAG = '.%monomer-canonicalizer-func';\n/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\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, NucleotideRole } 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 (\n        // RNA: all branch monomers (bases) and all backbone monomers (sugars +\n        // phosphates, including modified ones). Modifications are looked up by\n        // symbol at assembly time, so they MUST be present in the formatted lib.\n        polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ || (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 {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly\n *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).\n * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // Triples mode is on only when the caller flagged the row with roles\n    // (built and validated by `buildRolesForHelmRna` in to-atomic-level.ts).\n    // The roles array carries the per-position semantics — including\n    // TERMINAL_5P / TERMINAL_3P for non-canonical chain ends — so we don't\n    // re-validate the length here.\n    const triplesMode = polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ && !!roles &&\n        roles.length === monomerSeq.length;\n    // define atom and bond counts, taking into account the bond type\n    const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles);\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        // Default sugar/phosphate are only consulted in bases-only mode. In\n        // triples mode, every nucleotide carries its own.\n        if (!triplesMode) {\n            sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n            phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        }\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        // In triples mode, the \"logical\" sequence length is the nucleotide count.\n        seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : 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    if (triplesMode) {\n        runTriplesAssembly(monomerSeq, roles, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, (a) => { nAtoms += a; }, () => nAtoms);\n    }\n    else {\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    }\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 {ISeqMonomer[]} monomerSeq - the sequence of monomers\n * @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers\n * @param {ALPHABET} alphabet - the alphabet of the monomers\n * @param {PolymerType} polymerType - the type of polymer\n * @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples\n * @param {Array} roles - per-position role tags (only meaningful when triplesMode is true)\n * @return {Object} the atom/bond counts plus needsCapping flag */\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    let lastPhosphateGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (let i = 0; i < monomerSeq.length; ++i) {\n        const seqMonomer = monomerSeq[i];\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        // In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track\n        // the LAST one — its atoms/bonds are dropped at the 3'-terminus.\n        if (triplesMode && i % 3 === 2)\n            lastPhosphateGraph = lastMonomerGraph;\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 if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)\n        void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it\n        // Per-monomer-loop already summed sugars + bases + phosphates for every\n        // entry in monomerSeq (terminals included). Reservation: each backbone\n        // emit (sugar / phosphate / terminal) reserves +1 bond slot for the\n        // chain-extending bond, each branch (base) reserves +1 for its branch\n        // bond. Total reservations = monomerCount.\n        bondCount += monomerCount;\n        // OH cap atom rides on the 3'-end. Skip it when HELM specified a\n        // 3'-terminal modifier (e.g. GalNAc) that IS the chain end.\n        const has3pTerm = !!roles && roles.length > 0 &&\n            roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;\n        if (has3pTerm)\n            needsCapping = false;\n        else\n            atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)\n    }\n    else { // nucleotides — bases-only legacy path with default sugar/phosphate\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// Triples-mode RNA assembly. Iterates by NUCLEOTIDE over the row's \"core\"\n// positions (those tagged SUGAR/BASE/PHOSPHATE), and emits at most one\n// TERMINAL_5P at the head and one TERMINAL_3P at the tail.\n//\n// Layout permutations the function handles:\n//   roles = [SUGAR, BASE, PHOSPHATE, ...]                     // standard RNA\n//   roles = [..., SUGAR, BASE]                                // no trailing P\n//   roles = [TERMINAL_5P, SUGAR, BASE, PHOSPHATE, ...]        // 5' modifier\n//   roles = [..., SUGAR, BASE, TERMINAL_3P]                   // 3' modifier (replaces last P)\n//   roles = [TERMINAL_5P, ..., TERMINAL_3P]                   // both\n//\n// When a TERMINAL_3P is present the OH cap MUST be skipped (the last\n// monomer is the chain end, period); the caller takes responsibility for\n// needsCapping=false in `getResultingAtomBondCounts`.\nfunction runTriplesAssembly(monomerSeq, roles, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, addAtoms, getAtoms) {\n    const has5pTerm = roles.length > 0 && roles[0] === NucleotideRole.TERMINAL_5P;\n    const has3pTerm = roles.length > 0 && roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;\n    const coreStart = has5pTerm ? 1 : 0;\n    const coreEnd = has3pTerm ? roles.length - 1 : roles.length;\n    const coreLen = coreEnd - coreStart;\n    const N = Math.ceil(coreLen / 3); // nucleotide count in the core\n    // coreLen === 3N → trailing P present.  coreLen === 3N - 1 → no trailing P.\n    const hasTrailingP = coreLen === 3 * N;\n    // Helper: emit one monomer as a backbone unit and record its atom/bond\n    // ranges in the per-row monomer map.\n    const emitBackbone = (sm, mapKey) => {\n        const mG = getMolGraph(monomersDict, { symbol: sm.symbol, polymerType: helmTypeToPolymerType(sm.biotype) });\n        const aFirst = v.nodeShift;\n        const bFirst = v.bondShift;\n        addBackboneMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n        mG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(mG.atoms.x.length);\n        const aList = [];\n        for (let a = aFirst; a < v.nodeShift; ++a)\n            aList.push(a);\n        const bList = [];\n        for (let b = bFirst; b < v.bondShift; ++b)\n            bList.push(b);\n        monomers.set(mapKey, { biotype: sm.biotype, symbol: sm.symbol, atoms: aList, bonds: bList });\n    };\n    // 1. 5'-end terminal modifier (e.g. Chol).\n    if (has5pTerm) {\n        v.i = 0;\n        emitBackbone(monomerSeq[0], 0);\n    }\n    // 2. Core triples loop: each iteration emits [prev-P (if n>=1)] + sugar + base.\n    for (let n = 0; n < N; ++n) {\n        v.i = n + (has5pTerm ? 1 : 0); // keep v.i monotone across emits\n        const sugarSeqIdx = coreStart + 3 * n;\n        const baseSeqIdx = sugarSeqIdx + 1;\n        const sugarSm = monomerSeq[sugarSeqIdx];\n        const baseSm = monomerSeq[baseSeqIdx];\n        const sugarG = getMolGraph(monomersDict, { symbol: sugarSm.symbol, polymerType: helmTypeToPolymerType(sugarSm.biotype) });\n        const baseG = getMolGraph(monomersDict, { symbol: baseSm.symbol, polymerType: helmTypeToPolymerType(baseSm.biotype) });\n        // Inter-nucleotide phosphate sits at coreStart + 3*(n-1) + 2 for n >= 1.\n        if (n >= 1) {\n            const prevPhosKey = coreStart + 3 * (n - 1) + 2;\n            emitBackbone(monomerSeq[prevPhosKey], prevPhosKey);\n        }\n        // Sugar (backbone)\n        const sugarAtomFirst = v.nodeShift;\n        const sugarBondFirst = v.bondShift;\n        addBackboneMonomerToMolblock(sugarG, molfileAtomBlock, molfileBondBlock, v);\n        sugarG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(sugarG.atoms.x.length);\n        const sAList = [];\n        for (let a = sugarAtomFirst; a < v.nodeShift; ++a)\n            sAList.push(a);\n        const sBList = [];\n        for (let b = sugarBondFirst; b < v.bondShift; ++b)\n            sBList.push(b);\n        monomers.set(sugarSeqIdx, {\n            biotype: sugarSm.biotype, symbol: sugarSm.symbol,\n            atoms: sAList, bonds: sBList,\n        });\n        // Base (branch)\n        const baseAtomFirst = v.nodeShift;\n        const baseBondFirst = v.bondShift;\n        addBranchMonomerToMolblock(baseG, molfileAtomBlock, molfileBondBlock, v);\n        baseG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(baseG.atoms.x.length);\n        const bAList = [];\n        for (let a = baseAtomFirst; a < v.nodeShift; ++a)\n            bAList.push(a);\n        const bBList = [];\n        for (let b = baseBondFirst; b < v.bondShift; ++b)\n            bBList.push(b);\n        monomers.set(baseSeqIdx, {\n            biotype: baseSm.biotype, symbol: baseSm.symbol,\n            atoms: bAList, bonds: bBList,\n        });\n    }\n    // 3. Trailing phosphate (the LAST nucleotide's P) — only if HELM wrote\n    // one AND there is no 3'-terminal modifier replacing it.\n    if (hasTrailingP) {\n        const lastPhosKey = coreStart + 3 * (N - 1) + 2;\n        emitBackbone(monomerSeq[lastPhosKey], lastPhosKey);\n    }\n    // 4. 3'-end terminal modifier (e.g. GalNAc).\n    if (has3pTerm) {\n        v.i = N + (has5pTerm ? 1 : 0);\n        emitBackbone(monomerSeq[roles.length - 1], roles.length - 1);\n    }\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, rolesList, 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            const roles = rolesList ? rolesList[rowI] : undefined;\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles);\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","NucleotideRole","NOTATION","ALPHABET","TAGS","MonomerMap","Map","constructor","entries","super","MolfileWithMap","molfile","monomers","this","createEmpty","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","roles","length","triplesMode","atomCount","bondCount","needsCapping","monomerCount","lastMonomerGraph","lastPhosphateGraph","i","seqMonomer","Error","biotype","atoms","x","bonds","bondTypes","meta","rNodes","terminalR2Atom","toLowerCase","TERMINAL_3P","sugar","DNA","phosphate","getResultingAtomBondCounts","molfileAtomBlock","Array","molfileBondBlock","addMonomerToMolblock","addAminoAcidToMolblock","addNucleotideToMolblock","v","nodeShift","bondShift","backbonePositionShift","fill","branchPositionShift","backboneAttachNode","branchAttachNode","flipFactor","LC","seqLength","Math","ceil","steabsCollection","lastMonomerCappingAtom","nAtoms","addAtoms","getAtoms","has5pTerm","TERMINAL_5P","has3pTerm","coreStart","coreLen","N","hasTrailingP","emitBackbone","sm","mapKey","mG","aFirst","bFirst","addBackboneMonomerToMolblock","stereoAtoms","forEach","push","aList","a","bList","b","set","n","sugarSeqIdx","baseSeqIdx","sugarSm","baseSm","sugarG","baseG","prevPhosKey","sugarAtomFirst","sugarBondFirst","sAList","sBList","baseAtomFirst","baseBondFirst","addBranchMonomerToMolblock","bAList","bBList","lastPhosKey","runTriplesAssembly","monomer","mAtomFirst","mBondFirst","mAtomCount","mAtomList","maI","mBondCount","mBondList","mbI","cappingAtomType","atomIdx","keepPrecision","firstAtom","secondAtom","capResultingMolblock","molfileCountsLine","result","join","collection","rowsArray","newCollectionRow","updatedRow","getCollectionBlock","j","atomTypes","y","kwargs","fillAtomLines","fillBondLines","bondIdx","terminalNodes","fillChainExtendingBond","branchShift","updateBranchVariables","atomPairs","backboneShift","updateChainExtendingVariables","nucleobase","fillBranchAtomLines","branchMonomer","fillBackboneToBranchBond","bondCfg","bondConfiguration","has","orientation","get","round","PT","RNA","FASTA","SEPARATOR","HELM","BILN","onmessage","event","seqList","rolesList","start","end","data","resMolList","molfileWarningList","rowI","seq","undefined","err","msg","message","toString","postMessage","molfiles","warnings"],"sourceRoot":""}

package/dist/657.js

@@ -1,2 +0,0 @@
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Set),selectionLayer:Z(t,i,r)}}(t,{theme:this._currentTheme(),selectedAtomIds:e.atoms,highlightedAtomIds:this._editorHighlights()});this._spliceLayer("hw-highlights",i.highlightLayer),this._spliceLayer("hw-selections",i.selectionLayer)}_spliceLayer(t,e){let i=this._svgRoot.querySelector(`.${t}`);if(null===i||null===i.parentNode)return;let r=this._doc.createElementNS("http://www.w3.org/2000/svg","svg");r.innerHTML=e;let l=r.querySelector(`.${t}`);null!==l&&i.parentNode.replaceChild(l,i)}_editorHighlights(){let t=this._editor;return"function"==typeof t._currentHighlights?t._currentHighlights():new Set}_currentTheme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyResize(t,e){this._width=t,this._height=e,this._pinnedBbox=null,this._renderFresh()}_applyViewport(t){let e=this._svgRoot.querySelector(".hw-content");if(null===e)return;let i=`translate(${t.offset.x} ${t.offset.y}) scale(${t.scale})`,r=""===this._baseTransform?i:`${i} ${this._baseTransform}`;e.setAttribute("transform",r)}_showTooltip(t,e,i){let r=this._tooltip;if(null===r)return;let l=""===t.symbol?"?":t.symbol,s=t.monomer?.name??"",o=t.bio.positionInChain,n=""===t.bio.chainId?"?":t.bio.chainId,a=""!==s&&s!==l?`${s} @ ${n}:${o}`:`${l} @ ${n}:${o}`,h=this._renderRdkitTooltipSvg(t);rt(this._doc,r,{symbol:l,name:a,rdkitSvg:h,rdkitTestid:"atom-tooltip-rdkit-svg"});let d=""!==s&&s!==l?`${l} — ${s}  @ ${n}:${o}`:`${l}  @ ${n}:${o}`,u=this._doc.createElement("div");u.setAttribute("class","hw-atom-tooltip__text"),u.style.display="none",u.appendChild(this._doc.createTextNode(d)),r.appendChild(u),lt(r,e,i)}_renderRdkitTooltipSvg(e){let i=this._editor.getService().options.rdkitModule;if(null==i)return null;let r=e.monomer;if(null===r)return null;let l=r.smiles;if(void 0===l||""===l)return null;let s=`${r.polymerType}:${r.symbol}`;if(this._rdkitSvgCache.has(s))return this._rdkitSvgCache.get(s)??null;let o=et(i,l,220,140);if(this._rdkitSvgCache.size>=t._RDKIT_CACHE_LIMIT){let t=this._rdkitSvgCache.keys().next().value;void 0!==t&&this._rdkitSvgCache.delete(t)}return this._rdkitSvgCache.set(s,o),o}_hideTooltip(){st(this._tooltip)}_showBondTooltip(t,e,i){let r=this._bondTooltip;if(null===r)return;let l=at(t.r1),s=at(t.r2),o=`${t.a1.symbol}@${t.a1.bio.chainId}:${t.a1.bio.positionInChain}`,n=`${t.a2.symbol}@${t.a2.bio.chainId}:${t.a2.bio.positionInChain}`;rt(this._doc,r,{symbol:`${l}-${s} (${t.kind})`,name:`${o} ↔ ${n}`}),lt(r,e,i)}_hideBondTooltip(){st(this._bondTooltip)}_paintBondPreview(t,e,i){let r=this._svgRoot.querySelector(".hw-content");if(null===r)return;let l=r.querySelector(".hw-bond-preview");null===l&&(l=this._doc.createElementNS("http://www.w3.org/2000/svg","line"),l.setAttribute("class","hw-bond-preview"),l.setAttribute("data-testid","bond-preview"),l.setAttribute("stroke-dasharray","6 4"),l.setAttribute("stroke-width","2"),l.setAttribute("fill","none"),l.setAttribute("pointer-events","none"),r.appendChild(l)),l.setAttribute("x1",String(t.x)),l.setAttribute("y1",String(t.y)),l.setAttribute("x2",String(e.x)),l.setAttribute("y2",String(e.y)),l.setAttribute("stroke",i?"#1f5fcd":"#999999")}_clearBondPreview(){let t=this._svgRoot.querySelector(".hw-bond-preview");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t)}_paintSelectionRect(t,e){let i=Math.min(t.x,e.x),r=Math.min(t.y,e.y),l=Math.abs(t.x-e.x),s=Math.abs(t.y-e.y);this._paintSelectionRectAt(i,r,l,s)}_paintSelectionRectFromRect(t){this._paintSelectionRectAt(t.x,t.y,t.width,t.height)}_paintSelectionRectAt(t,e,i,r){let l=this._svgRoot.querySelector(".hw-content");if(null===l)return;let s=l.querySelector(".hw-selection-rect");null===s&&(s=this._doc.createElementNS("http://www.w3.org/2000/svg","rect"),s.setAttribute("class","hw-selection-rect"),s.setAttribute("data-testid","selection-rect"),s.setAttribute("fill","rgba(31, 95, 205, 0.08)"),s.setAttribute("stroke","#1f5fcd"),s.setAttribute("stroke-width","1"),s.setAttribute("stroke-dasharray","4 3"),s.setAttribute("pointer-events","none"),l.appendChild(s)),s.setAttribute("x",String(t)),s.setAttribute("y",String(e)),s.setAttribute("width",String(i)),s.setAttribute("height",String(r))}_clearSelectionRect(){let t=this._svgRoot.querySelector(".hw-selection-rect");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t)}};nt._RDKIT_CACHE_LIMIT=256;function at(t){switch(t.kind){case"numeric":return`R${t.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${t.position}pos:R${t.r}`}}var ht=class t{constructor(t,e){this._onClose=null,this._primaryAction=null,this._host=t,this._doc=e.documentImpl??Q(t);let i=this._doc,r={class:"hw-modal-backdrop",role:"presentation"};void 0!==e.testId&&(r["data-testid"]=`dialog-${e.testId}`);let l=tt(i,"div",r),s={class:"hw-modal",role:"dialog","aria-modal":"true","aria-label":e.title};void 0!==e.testId&&(s["data-testid"]=`dialog-${e.testId}-frame`);let o=tt(i,"div",s),n=tt(i,"div",{class:"hw-modal__header"},[e.title]),a=tt(i,"div",{class:"hw-modal__body"});o.appendChild(n),o.appendChild(a),l.appendChild(o);let h=t=>{t.stopPropagation()};for(let t of["mousedown","mousemove","mouseup","mouseover","mouseenter","mouseleave","wheel","contextmenu","dblclick","keydown","keyup","keypress"])l.addEventListener(t,h);o.addEventListener("keydown",t=>{let e=t;if("Enter"!==e.key||"TEXTAREA"===e.target?.tagName)return;let i=this._primaryAction;null!==i&&(e.preventDefault?.(),e.stopImmediatePropagation?.(),i())}),l.addEventListener("click",t=>{t.target!==l?t.stopPropagation():this.close()}),this.root=l,this.body=a}static anyOpen(){return t._openStack.length>0}static closeTopmost(){let e=t._openStack[t._openStack.length-1];return void 0!==e&&(e.close(),!0)}open(e){this._onClose=e??null,null===this.root.parentNode&&this._host.appendChild(this.root),t._openStack.includes(this)||t._openStack.push(this),ot(this._doc)}close(){let e=t._openStack.indexOf(this);e>=0&&t._openStack.splice(e,1),null!==this.root.parentNode&&this.root.parentNode.removeChild(this.root);let i=this._onClose;this._onClose=null,null!==i&&i()}setPrimaryAction(t){this._primaryAction=t}get isOpen(){return null!==this.root.parentNode}};ht._openStack=[];Object.freeze(new Set);function dt(t){return t.startsWith("[")&&t.endsWith("]")||1===t.length&&/^[A-Za-z]$/.test(t)?t:`[${t}]`}function ut(t,e,i){return`${dt(t)}(${dt(e)})${dt(i)}`}var pt="http://www.w3.org/2000/svg",ct={sugar:r.SUGAR,base:r.BASE,linker:r.LINKER},_t={sugar:["r","R"],base:["A"],linker:["p","P"]},bt={x:70,y:60},ft={x:140,y:60},gt={x:70,y:130},vt=class t{constructor(t,e,i){this.onValueSet=new s,this.onPickModeChange=new s,this._slots=new Map,this._favStar=null,this._pickMode=null,this._destroyed=!1,this._builderRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??Q(t),this._hooks=i?.paletteHooks??null,this._favHooks=i?.favoriteHooks??null,this.element=tt(this._doc,"div",{class:"hw-rna-builder","data-testid":"rna-builder"});let r=tt(this._doc,"div",{class:"hw-rna-builder__header"});if(r.appendChild(tt(this._doc,"div",{class:"hw-rna-builder__title"},["RNA builder"])),null!==this._favHooks){let t=tt(this._doc,"span",{class:"hw-rna-builder__fav hw-rna-builder__fav--disabled",role:"button",tabindex:"0","data-testid":"rna-builder-fav-star",title:"Favorite this triplet","aria-pressed":"false","aria-disabled":"true"},["☆"]),e=t=>{t.stopPropagation();let e=this.getSelection();""===e.preview||null===this._favHooks||this._favHooks.toggleFavoriteTriplet(e.sugar,e.base,e.linker)};t.addEventListener("click",e),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&e(t)}),this._favStar=t,r.appendChild(t)}this.element.appendChild(r),this._hintEl=tt(this._doc,"div",{class:"hw-rna-builder__hint","data-testid":"rna-builder-hint",hidden:!0}),this.element.appendChild(this._hintEl);let l=this._buildSvg();this.element.appendChild(l),this._preview=tt(this._doc,"div",{class:"hw-rna-builder__preview","data-testid":"rna-builder-preview"}),this.element.appendChild(this._preview),this._addBtn=tt(this._doc,"button",{class:"hw-rna-builder__add",type:"button","data-testid":"rna-builder-add-btn"},["Add triplet"]),this._addBtn.addEventListener("click",()=>this._onAddClicked()),this.element.appendChild(this._addBtn),t.appendChild(this.element);let o=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),n=e.on("theme:change",()=>{this._destroyed||this._repaintSlotColors()});this._libUnsub=()=>{try{o()}catch{}try{n()}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}getSelection(){let t=this._slots.get("sugar")?.value??"",e=this._slots.get("base")?.value??"",i=this._slots.get("linker")?.value??"";return{sugar:t,base:e,linker:i,preview:""!==t&&""!==e&&""!==i?ut(t,e,i):""}}setField(t,e){let i=this._slots.get(t);void 0!==i&&(i.value=e,this._setLabelText(i.labelEl,e),this._repaintSlot(i),this._updatePreview(),this.onValueSet.next({field:t,symbol:e}))}startPickMode(t){this._pickMode!==t?(null!==this._pickMode&&this._setSlotPressed(this._pickMode,!1),this._pickMode=t,this._setSlotPressed(t,!0),this._setHintActive(t),this.onPickModeChange.next({field:t}),null!==this._hooks&&this._hooks.beginBiotypeFilter(ct[t],e=>{this.setField(t,e),this._exitPickMode()},()=>{this._exitPickMode()})):this.cancelPickMode()}cancelPickMode(){null!==this._pickMode&&(null!==this._hooks&&this._hooks.endBiotypeFilter(),this._exitPickMode())}getPickMode(){return this._pickMode}triggerAdd(){this._onAddClicked()}destroy(){this._destroyed||(this._destroyed=!0,null!==this._pickMode&&null!==this._hooks&&this._hooks.endBiotypeFilter(),this._libUnsub(),this.onValueSet.complete(),this.onPickModeChange.complete(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}_buildSvg(){let t=this._doc.createElementNS(pt,"svg");t.setAttribute("class","hw-rna-builder__triplet"),t.setAttribute("viewBox","0 0 200 180"),t.setAttribute("data-testid","rna-builder-triplet-svg"),t.setAttribute("role","group"),t.setAttribute("aria-label","Triplet preview");let e=this._doc.createElementNS(pt,"line");e.setAttribute("class","hw-rna-builder__bond"),e.setAttribute("x1",String(bt.x+18)),e.setAttribute("y1",String(bt.y)),e.setAttribute("x2",String(ft.x-18)),e.setAttribute("y2",String(ft.y)),t.appendChild(e);let i=this._doc.createElementNS(pt,"line");i.setAttribute("class","hw-rna-builder__bond"),i.setAttribute("x1",String(bt.x)),i.setAttribute("y1",String(bt.y+18)),i.setAttribute("x2",String(gt.x)),i.setAttribute("y2",String(gt.y-22)),t.appendChild(i);let r=this._doc.createElementNS(pt,"rect");r.setAttribute("class","hw-rna-builder__slot-shape"),r.setAttribute("x",String(-18)),r.setAttribute("y",String(-18)),r.setAttribute("width",String(36)),r.setAttribute("height",String(36)),r.setAttribute("rx","8"),r.setAttribute("ry","8");let l=this._buildSlot("sugar","Pick sugar (backbone)",bt,r),s=this._doc.createElementNS(pt,"circle");s.setAttribute("class","hw-rna-builder__slot-shape"),s.setAttribute("cx","0"),s.setAttribute("cy","0"),s.setAttribute("r",String(18));let o=this._buildSlot("linker","Pick linker",ft,s),n=this._doc.createElementNS(pt,"path");n.setAttribute("class","hw-rna-builder__slot-shape"),n.setAttribute("d","M -22 0 L 0 -22 L 22 0 L 0 22 Z");let a=this._buildSlot("base","Pick base",gt,n);return t.appendChild(o.groupEl),t.appendChild(l.groupEl),t.appendChild(a.groupEl),this._slots.set("sugar",l),this._slots.set("linker",o),this._slots.set("base",a),t}_buildSlot(t,e,i,r){let l=this._doc.createElementNS(pt,"g");l.setAttribute("class","hw-rna-builder__slot"),l.setAttribute("data-slot",t),l.setAttribute("data-testid",`rna-builder-slot-${t}`),l.setAttribute("role","button"),l.setAttribute("tabindex","0"),l.setAttribute("aria-label",e),l.setAttribute("aria-pressed","false"),l.setAttribute("transform",`translate(${i.x} ${i.y})`),l.appendChild(r);let s=this._doc.createElementNS(pt,"text");s.setAttribute("class","hw-rna-builder__slot-label"),s.setAttribute("data-testid",`rna-builder-${t}-value`),s.setAttribute("x","0"),s.setAttribute("y","0"),s.setAttribute("text-anchor","middle"),s.setAttribute("dominant-baseline","central"),l.appendChild(s);let o=e=>{e.stopPropagation(),this.startPickMode(t)};return l.addEventListener("click",o),l.addEventListener("keydown",t=>{let e=t;("Enter"===e.key||" "===e.key)&&o(t)}),l.addEventListener("mouseenter",e=>this._showSlotTooltip(t,e)),l.addEventListener("mouseleave",()=>this._hideSlotTooltip()),l.addEventListener("focus",()=>this._showSlotTooltip(t,null)),l.addEventListener("blur",()=>this._hideSlotTooltip()),{id:t,biotype:ct[t],groupEl:l,shapeEl:r,labelEl:s,value:""}}_setLabelText(t,e){let i=[];for(let e=t.firstChild;null!==e;e=e.nextSibling)"title"===e.nodeName||"TITLE"===e.nodeName||i.push(e);for(let e of i)t.removeChild(e);let r=function(t){let e=t.length;return e<=2?16:e<=4?11:e<=7?8:e<=10?6:5}(e);t.setAttribute("font-size",String(r)),t.setAttribute("text-anchor","middle"),t.setAttribute("dominant-baseline","central");let l=e.length>10?`${e.slice(0,9)}…`:e;t.appendChild(this._doc.createTextNode(l));let s=t.parentNode;if(null!==s){let t=null;for(let e=s.firstChild;null!==e;e=e.nextSibling)if("title"===e.nodeName||"TITLE"===e.nodeName){t=e;break}for(null===t&&(t=this._doc.createElementNS(pt,"title"),s.insertBefore(t,s.firstChild));null!==t.firstChild;)t.removeChild(t.firstChild);t.appendChild(this._doc.createTextNode(e))}}_repaintSlotColors(){for(let t of this._slots.values())this._repaintSlot(t)}_repaintSlot(t){let e=this._editor.getService().monomerLib,i=this._theme(),r=""===t.value?null:function(t,e,i){return t.getMonomerSet(e).get(i)??null}(e,t.biotype,t.value),l=M(r,t.biotype,i.colorTheme);t.shapeEl.style.fill=l.background,t.shapeEl.style.stroke=l.line,t.labelEl.style.fill=l.text}_populateDefaults(){let t=this._editor.getService().monomerLib;for(let[e,i]of this._slots.entries()){let r=yt(t,i.biotype),l=wt(r,_t[e]),s=""!==i.value&&r.some(t=>t.symbol===i.value)?i.value:l??r[0]?.symbol??"";i.value=s,this._setLabelText(i.labelEl,s)}}_updatePreview(){let t=this.getSelection();for(;null!==this._preview.firstChild;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(""===t.preview?"-":t.preview)),this._updateFavStar(t)}_updateFavStar(t){if(null===this._favStar||null===this._favHooks)return;let e=""!==t.preview,i=e&&this._favHooks.isFavoriteTriplet(t.sugar,t.base,t.linker);for(;null!==this._favStar.firstChild;)this._favStar.removeChild(this._favStar.firstChild);this._favStar.appendChild(this._doc.createTextNode(i?"★":"☆")),this._favStar.setAttribute("aria-pressed",i?"true":"false"),e?this._favStar.removeAttribute("aria-disabled"):this._favStar.setAttribute("aria-disabled","true");let r="hw-rna-builder__fav"+(i?" hw-rna-builder__fav--active":"")+(e?"":" hw-rna-builder__fav--disabled");this._favStar.setAttribute("class",r)}_onAddClicked(){let t=this.getSelection();""!==t.preview&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)}_exitPickMode(){if(null===this._pickMode)return;let t=this._pickMode;this._setSlotPressed(t,!1),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null})}_setHintActive(t){let e=this._hintEl;for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(null===t)return void e.setAttribute("hidden","");e.removeAttribute("hidden");let i="sugar"===t?"sugar":"base"===t?"base":"linker";e.appendChild(this._doc.createTextNode(`Pick ${i} from palette`))}_setSlotPressed(t,e){let i=this._slots.get(t);if(void 0===i)return;i.groupEl.setAttribute("aria-pressed",e?"true":"false");let r=(i.groupEl.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-rna-builder__slot--active"!==t).join(" ");i.groupEl.setAttribute("class",e?`${r} hw-rna-builder__slot--active`:r)}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_builderRdkitSvgFor(e){if(null===e)return null;let i=e.smiles;if(void 0===i||""===i)return null;let r=this._rdkit();if(null===r)return null;let l=`${e.polymerType}:${e.symbol}`;if(this._builderRdkitCache.has(l))return this._builderRdkitCache.get(l)??null;let s=et(r,i,220,140);if(this._builderRdkitCache.size>=t._BUILDER_RDKIT_CACHE_LIMIT){let t=this._builderRdkitCache.keys().next().value;void 0!==t&&this._builderRdkitCache.delete(t)}return this._builderRdkitCache.set(l,s),s}_slotHint(t){switch(t){case"sugar":return"Click to choose a different sugar";case"base":return"Click to choose a different base";case"linker":return"Click to choose a different linker"}}_slotTitle(t,e){let i=""===e?"?":e;switch(t){case"sugar":return`Sugar: ${i}`;case"base":return`Base: ${i}`;case"linker":return`Linker: ${i}`}}_showSlotTooltip(t,e){let i=this._slots.get(t);if(void 0===i)return;let r=this._editor.getService().monomerLib.getMonomerSet(i.biotype),l=""===i.value?null:r.get(i.value)??null,s=it(this._doc,"builder-tooltip","hw-builder-tooltip");rt(this._doc,s,{symbol:this._slotTitle(t,i.value),name:l?.name??"",rdkitSvg:this._builderRdkitSvgFor(l),rdkitTestid:"builder-tooltip-rdkit-svg",hint:this._slotHint(t)});let o=e;if(null!==o&&"number"==typeof o.clientX&&"number"==typeof o.clientY)lt(s,o.clientX,o.clientY);else{let t=i.groupEl,e="function"==typeof t.getBoundingClientRect?t.getBoundingClientRect():null;null!==e?lt(s,e.left+e.width/2,e.top+e.height/2):lt(s,0,0)}}_hideSlotTooltip(){st(this._doc.body.querySelector('[data-testid="builder-tooltip"]'))}};vt._BUILDER_RDKIT_CACHE_LIMIT=256;var mt=vt;function yt(t,e){let i=t.getMonomerSet(e),r=[];for(let t of i.values())r.push(t);return r.sort((t,e)=>t.symbol.localeCompare(e.symbol)),r}function wt(t,e){let i=new Set;for(let e of t)i.add(e.symbol);for(let t of e)if(i.has(t))return t;return null}var kt="Favorites",At={[kt]:"★ Favorites",[l.PEPTIDE]:"Peptides",[l.RNA]:"RNA",[l.CHEM]:"CHEM",[l.BLOB]:"BLOB",G:"G"},St=[kt,l.PEPTIDE,l.RNA,l.CHEM,l.BLOB,"G"],Ct="hwe:palette:favorites",Tt="hwe:palette:active-tab";function Et(t){return`${t.sugar}|${t.base}|${t.linker}`}var xt=class t{constructor(t,e,i){this.favoritesChanged=new s,this._nextAddUnsub=()=>{},this._favorites=new Set,this._favoriteTriplets=[],this._pendingRnaSelection=null,this._visibleTabs=[kt],this._activeTab=kt,this._searchInput=null,this._filter="",this._destroyed=!1,this._rnaBuilder=null,this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,this._pickEscapeListener=null,this._pickOutsideClickListener=null,this._paletteRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??Q(t),this._opts={documentImpl:this._doc,groupByNaturalAnalog:i?.groupByNaturalAnalog??!0,allowFavorites:i?.allowFavorites??!0},this._loadFavorites(),this._activeTab=this._resolveInitialTab(i?.initialTab),this.element=tt(this._doc,"div",{class:"hw-palette","data-testid":"palette"}),t.appendChild(this.element),this._render(),this._libUnsub=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),this._themeUnsub=e.on("theme:change",()=>{this._destroyed||this.refresh()}),this._nextAddUnsub=e.on("option:change",t=>{this._destroyed||"nextAdd"===t.key&&this._updatePrimedClasses()})}refresh(){this._render()}setFilter(t){this._filter=t.trim().toLowerCase(),null!==this._searchInput&&this._searchInput.value!==t&&(this._searchInput.value=t),this._applyFilter()}setActiveTab(t){this._visibleTabs.includes(t)&&(this._activeTab=t,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter())}getActiveTab(){return this._activeTab}getFavorites(){let t=this._editor.getService().monomerLib,e=[];for(let i of this._favorites)null!==this._findMonomer(t,i)&&e.push(i);return e}setFavorite(t,e){e!==this._favorites.has(t)&&(e?this._favorites.add(t):this._favorites.delete(t),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}clearFavorites(){0===this._favorites.size&&0===this._favoriteTriplets.length||(this._favorites.clear(),this._favoriteTriplets.length=0,this._saveFavorites(),this._render(),this._emitFavoritesChanged())}getFavoriteTriplets(){return this._favoriteTriplets.map(t=>({...t}))}isFavoriteTriplet(t,e,i){let r=Et({sugar:t,base:e,linker:i});return this._favoriteTriplets.some(t=>Et(t)===r)}setFavoriteTriplet(t,e,i,r){let l=Et({sugar:t,base:e,linker:i}),s=this._favoriteTriplets.findIndex(t=>Et(t)===l);r!==s>=0&&(r?this._favoriteTriplets.push({sugar:t,base:e,linker:i}):this._favoriteTriplets.splice(s,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}_hidePaletteTooltips(){let t=this._doc.body;st(t.querySelector('[data-testid="palette-tooltip"]')),st(t.querySelector('[data-testid="palette-triplet-tooltip"]'))}_emitFavoritesChanged(){this.favoritesChanged.next({favorites:this.getFavorites(),triplets:this.getFavoriteTriplets()})}destroy(){this._destroyed||(this._destroyed=!0,null!==this._rnaBuilder&&(this._rnaBuilder.destroy(),this._rnaBuilder=null),this._libUnsub(),this._themeUnsub(),this._nextAddUnsub(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}getRnaBuilder(){return this._rnaBuilder}hasActiveBiotypeFilter(){return null!==this._activeBiotypeFilter}getActiveBiotypeFilter(){return this._activeBiotypeFilter}cancelBiotypeFilter(){if(null===this._activeBiotypeFilter)return;let t=this._pickCanceller;this._teardownPickMode(),t?.()}_buildPaletteFilterHooks(){return{beginBiotypeFilter:(t,e,i)=>{null!==this._activeBiotypeFilter&&this._teardownPickMode(),this._activeBiotypeFilter=t,this._pickResolver=e,this._pickCanceller=i,this._applyFilter();let r=t=>{"Escape"===t.key&&this.cancelBiotypeFilter()};this._pickEscapeListener=r,this._doc.defaultView?.addEventListener("keydown",r);let l=t=>{if(null===this._activeBiotypeFilter)return;let e=t.target;if(null==e)return;let i=this._activeBiotypeFilter,r=e;for(;null!==r;){let t=void 0===r.getAttribute?null:r.getAttribute("class");if(null!==t){let e=t.split(/\s+/);if(e.includes("hw-palette__tile")){if((r.getAttribute("data-biotype")??"")===i)return;break}if(e.includes("hw-rna-builder__slot")){if(this._isInsideOwnPalette(r))return;break}}r=r.parentElement}this.cancelBiotypeFilter()};this._pickOutsideClickListener=l,this._doc.addEventListener("mousedown",l,!0)},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let t=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`);if(null===t)return;let e=t;try{if("function"==typeof e.scrollTo)return void e.scrollTo({top:0,behavior:"smooth"})}catch{}"number"==typeof e.scrollTop&&(e.scrollTop=0)}_isInsideOwnPalette(t){let e=t;for(;null!==e;){if(e===this.element)return!0;e=e.parentElement}return!1}_teardownPickMode(){null!==this._activeBiotypeFilter&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,null!==this._pickEscapeListener&&(this._doc.defaultView?.removeEventListener("keydown",this._pickEscapeListener),this._pickEscapeListener=null),null!==this._pickOutsideClickListener&&(this._doc.removeEventListener("mousedown",this._pickOutsideClickListener,!0),this._pickOutsideClickListener=null),this._applyFilter())}_render(){for(null!==this._rnaBuilder&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);null!==this.element.firstChild;)this.element.removeChild(this.element.firstChild);let t=this._doc.createElement("input");t.setAttribute("type","search"),t.setAttribute("class","hw-palette__search"),t.setAttribute("placeholder","Search monomers..."),t.setAttribute("data-testid","palette-search"),""!==this._filter&&(t.value=this._filter),t.addEventListener("input",()=>this.setFilter(t.value)),this._searchInput=t,this.element.appendChild(t),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=kt);let e=tt(this._doc,"div",{class:"hw-palette__tabs",role:"tablist","data-testid":"palette-tabs"});for(let t of this._visibleTabs){let i=t===this._activeTab,r=tt(this._doc,"button",{class:"hw-palette__tab",type:"button",role:"tab","aria-controls":`hw-palette-pane-${t}`,"aria-selected":i?"true":"false","data-testid":`palette-tab-${t}`,"data-tab":t,title:At[t]},[At[t]]);r.addEventListener("click",()=>this.setActiveTab(t)),e.appendChild(r)}this.element.appendChild(e);let i=tt(this._doc,"div",{class:"hw-palette__panes"}),r=this._theme(),l=this._editor.getService().monomerLib;for(let t of this._visibleTabs){let e=t===this._activeTab,s=tt(this._doc,"div",{class:"hw-palette__pane",id:`hw-palette-pane-${t}`,role:"tabpanel","data-testid":`palette-pane-${t}`,"data-tab":t,hidden:!e});t===kt?this._buildFavoritesPane(s,l,r):this._buildPolymerPane(s,t,l,r),i.appendChild(s)}this.element.appendChild(i),this._applyFilter()}_computeVisibleTabs(){let t=this._editor.getService().monomerLib,e=new Set;for(let i of t.getPolymerTypes())e.add(i);let i=[];i.push(kt);for(let t of St)t!==kt&&e.has(t)&&i.push(t);return i}_buildFavoritesPane(t,e,i){let r=this._resolveFavoriteMonomers(e),l=this._favoriteTriplets;if(0===r.length&&0===l.length){let e=tt(this._doc,"div",{class:"hw-palette__placeholder","data-testid":"palette-favorites-empty"},["No favorites yet — click the ☆ on any tile to add one."]);return void t.appendChild(e)}for(let[e,i]of this._groupByPolymerAndType(r))t.appendChild(this._renderGroup(e,i));l.length>0&&t.appendChild(this._renderTripletGroup("RNA · Triplets",l,e))}_groupByPolymerAndType(t){let e=new Map;for(let i of t){let t=i.polymerType,r=i.monomerType??"Undefined",l=`${t}|${r}`,s=e.get(l);void 0===s&&(s={pt:t,mt:r,list:[]},e.set(l,s)),s.list.push(i)}let i=t=>{let e=St.indexOf(t);return e<0?99:e},r={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(e.values()).sort((t,e)=>i(t.pt)-i(e.pt)||(r[t.mt]??9)-(r[e.mt]??9)||t.mt.localeCompare(e.mt)).map(t=>[`${this._polymerLabel(t.pt)} · ${t.mt}`,t.list])}_polymerLabel(t){return At[t]??t}_renderTripletGroup(t,e,i){let r=tt(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),l=tt(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),s=tt(this._doc,"div",{class:"hw-triplet-chips","data-testid":"palette-triplet-favorites"});for(let t of e)s.appendChild(this._renderTripletChip(t,i));return r.appendChild(l),r.appendChild(s),r}_renderTripletChip(t,e){let i=ut(t.sugar,t.base,t.linker),l=e.getMonomerSet(r.BASE).get(t.base)??null,s=M(l,r.BASE,this._theme().colorTheme),o=this.isFavoriteTriplet(t.sugar,t.base,t.linker),n=void 0!==l?.name&&""!==l.name?`${i} — ${l.name}`:i,{root:a}=function(t,e){let i=!1!==e.showStar,r=tt(t,"span",{class:"hw-triplet-chip__star"},[e.favorite?"★":"☆"]),l=tt(t,"span",{class:"hw-triplet-chip__label"},[e.label]),s=["hw-triplet-chip"];e.favorite&&s.push("hw-triplet-chip--favorite");let o=i?[r,l]:[l];return{root:tt(t,"div",{class:s.join(" "),role:"button",tabindex:"0","aria-label":e.title,"data-sugar":e.sugar,"data-base":e.base,"data-linker":e.linker,"data-triplet":e.label,"data-testid":`palette-triplet-${e.label}`,title:e.title,style:`background:${e.background};color:${e.textColor};`},o),star:r}}(this._doc,{sugar:t.sugar,base:t.base,linker:t.linker,label:i,title:n,background:_(s.background),textColor:s.text,favorite:o,showStar:this._opts.allowFavorites});return this._wireTripletChip(a,t),a}_wireTripletChip(t,e){t.addEventListener("mouseenter",t=>{let i=t,r=it(this._doc,"palette-triplet-tooltip","hw-palette-tooltip hw-triplet-tooltip");(function(t,e,i){for(;null!==e.firstChild;)e.removeChild(e.firstChild);e.appendChild(tt(t,"div",{class:"hw-tooltip__symbol"},[i.title]));let r=tt(t,"div",{class:"hw-tooltip__triplet"});for(let e of i.parts){let l=tt(t,"div",{class:"hw-tooltip__triplet-part"});if(l.appendChild(tt(t,"div",{class:"hw-tooltip__triplet-role"},[`${e.role}: ${e.symbol}`])),void 0!==e.name&&""!==e.name&&e.name!==e.symbol&&l.appendChild(tt(t,"div",{class:"hw-tooltip__name"},[e.name])),void 0!==e.rdkitSvg&&null!==e.rdkitSvg&&""!==e.rdkitSvg){let r={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(r["data-testid"]=i.rdkitTestid);let s=tt(t,"div",r);s.innerHTML=e.rdkitSvg,l.appendChild(s)}r.appendChild(l)}e.appendChild(r),void 0!==i.hint&&""!==i.hint&&e.appendChild(tt(t,"div",{class:"hw-tooltip__hint"},[i.hint]))})(this._doc,r,{title:ut(e.sugar,e.base,e.linker),parts:this._tripletTooltipParts(e),hint:"Click to add this triplet",rdkitTestid:"palette-triplet-tooltip-rdkit-svg"}),lt(r,"number"==typeof i.clientX?i.clientX:0,"number"==typeof i.clientY?i.clientY:0)}),t.addEventListener("mouseleave",()=>{st(this._doc.body.querySelector('[data-testid="palette-triplet-tooltip"]'))}),t.addEventListener("click",t=>{let i=t.target;if(this._opts.allowFavorites&&!0===i?.classList?.contains("hw-triplet-chip__star"))return this.setFavoriteTriplet(e.sugar,e.base,e.linker,!this.isFavoriteTriplet(e.sugar,e.base,e.linker)),void t.stopPropagation();this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)}),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)})}_buildRnaDefaultChips(e){let i=this._pickSymbol(e.getMonomerSet(r.SUGAR),["r","R"]),l=this._pickSymbol(e.getMonomerSet(r.LINKER),["p","P"]),s=e.getMonomerSet(r.BASE);if(null===i||null===l)return null;let o=t._DEFAULT_TRIPLET_BASES.filter(t=>s.has(t));if(0===o.length)return null;let n=tt(this._doc,"div",{class:"hw-triplet-chips hw-triplet-chips--defaults","data-testid":"rna-default-triplets"});for(let t of o)n.appendChild(this._renderTripletChip({sugar:i,base:t,linker:l},e));return n}_tripletTooltipParts(t){let e=this._editor.getService().monomerLib,i=(t,i,r)=>{let l=e.getMonomerSet(i).get(r)??null;return{role:t,symbol:r,...void 0!==l?.name?{name:l.name}:{},rdkitSvg:null===l?null:this._paletteRdkitSvg(l)}};return[i("Sugar",r.SUGAR,t.sugar),i("Base",r.BASE,t.base),i("Linker",r.LINKER,t.linker)]}_pickSymbol(t,e){for(let i of e)if(t.has(i))return i;let i=t.keys().next();return!0===i.done?null:i.value}_restoreRnaSelection(){let t=this._pendingRnaSelection;if(this._pendingRnaSelection=null,null===t||null===this._rnaBuilder)return;let e=this._editor.getService().monomerLib;""!==t.sugar&&e.getMonomerSet(r.SUGAR).has(t.sugar)&&this._rnaBuilder.setField("sugar",t.sugar),""!==t.base&&e.getMonomerSet(r.BASE).has(t.base)&&this._rnaBuilder.setField("base",t.base),""!==t.linker&&e.getMonomerSet(r.LINKER).has(t.linker)&&this._rnaBuilder.setField("linker",t.linker)}_resolveFavoriteMonomers(t){let e=[];for(let i of this._favorites){let r=this._findMonomer(t,i);null!==r&&e.push(r)}return e}_findMonomer(t,e){for(let i of t.getPolymerTypes()){let r=t.getMonomer(i,e);if(null!==r)return r}return null}_buildPolymerPane(t,e,i,r){let s=e,o=this._monomersForPolymer(s,i);if(0===o.length)return;if(s===l.RNA){this._rnaBuilder=new mt(t,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(t,e,i)=>this.isFavoriteTriplet(t,e,i),toggleFavoriteTriplet:(t,e,i)=>this.setFavoriteTriplet(t,e,i,!this.isFavoriteTriplet(t,e,i))}:null}),this._restoreRnaSelection();let e=this._buildRnaDefaultChips(i);null!==e&&t.appendChild(e);let r=this._groupRna(o);for(let[e,i]of r)0!==i.length&&t.appendChild(this._renderGroup(e,i));return}if(s===l.PEPTIDE&&this._opts.groupByNaturalAnalog){let e=this._groupByAnalog(o);for(let[i,r]of e){let e=""===i?"Other":i;t.appendChild(this._renderGroup(e,r))}return}let n=tt(this._doc,"div",{class:"hw-palette__group-tiles"}),a=this._editor.getNextAddSymbol(),h=this._sortByColor(o);for(let t of h){let e=this._biotype(t,s);n.appendChild(this._renderTile(t,e,a))}t.appendChild(n)}_renderGroup(t,e){let i=tt(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),r=tt(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),l=tt(this._doc,"div",{class:"hw-palette__group-tiles"}),s=this._editor.getNextAddSymbol(),o=this._sortByColor(e);for(let t of o){let e=this._biotype(t,t.polymerType);l.appendChild(this._renderTile(t,e,s))}return i.appendChild(r),i.appendChild(l),i}_sortByColor(t){let e=this._theme(),i=t.map((t,i)=>{let r=function(t){let e=a(t);if(null===e)return{h:0,s:0,l:0};let[i,r,l]=u(e[0],e[1],e[2]);return{h:i,s:r,l}}(M(t,this._biotype(t,t.polymerType),e.colorTheme).background),l=0===r.s?1:0;return{m:t,idx:i,h:r.h,s:r.s,l:r.l,isGrey:l}});return i.sort((t,e)=>t.isGrey!==e.isGrey?t.isGrey-e.isGrey:t.h!==e.h?t.h-e.h:t.s!==e.s?t.s-e.s:t.l!==e.l?t.l-e.l:t.idx-e.idx),i.map(t=>t.m)}_monomersForPolymer(t,e){let i=e.getMonomerSymbolsByType(t),r=[];for(let l of i){let i=e.getMonomer(t,l);null!==i&&r.push(i)}return r.sort((t,e)=>t.symbol.localeCompare(e.symbol)),r}_groupByAnalog(t){let e=new Map;for(let i of t){let t=i.naturalAnalog??"",r=e.get(t);void 0===r&&(r=[],e.set(t,r)),r.push(i)}let i=[],r=Array.from(e.keys()).sort((t,e)=>""===t&&""!==e?1:""===e&&""!==t?-1:t.localeCompare(e));for(let t of r)i.push([t,e.get(t)]);return new Map(i)}_groupRna(t){let e=[],i=[],l=[],s=[];for(let o of t){let t=$(o);t===r.SUGAR?e.push(o):t===r.BASE?i.push(o):t===r.LINKER?l.push(o):s.push(o)}let o=new Map;return o.set("Backbones",e),o.set("Bases",i),o.set("Linkers",l),s.length>0&&o.set("Other",s),o}_renderTile(t,e,i){let r=this._favorites.has(t.symbol),l=null!==i&&i.symbol===t.symbol&&i.biotype===e,{root:s,star:o}=function(t,e){let i=M(e.monomer,e.biotype,e.theme.colorTheme),r=_(i.background),l=i.text,s=function(t,e){let i=b(t),r=b(e);return(Math.max(i,r)+.05)/(Math.min(i,r)+.05)}(l,r)<5,o=e.monomer.symbol,n=function(t){return t<=3?14:t<=6?11:t<=9?9:8}(o.length),a=`font-size:${n}px;${o.length>=10?"line-height:1.1;letter-spacing:-0.02em;":""}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:80px;display:inline-block;`,h=tt(t,"span",{class:"hw-palette__star"},[e.favorite?"★":"☆"]),d=tt(t,"span",{class:"hw-palette__label",style:a},[o]),u=["hw-palette__tile"];e.primed&&u.push("hw-palette__tile--primed"),e.favorite&&u.push("hw-palette__tile--favorite"),s&&u.push("hw-palette__tile--low-contrast");let p=void 0!==e.monomer.name?`${o} — ${e.monomer.name}`:o,c=`background:${r};color:${l};width:100%;min-width:48px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return{root:tt(t,"div",{class:u.join(" "),draggable:"true",role:"button","aria-pressed":e.primed?"true":"false","aria-label":p,"data-symbol":o,"data-biotype":e.biotype,"data-bg":r,"data-raw-bg":i.background,"data-testid":`palette-tile-${o}`,title:p,style:c},[h,d]),star:h}}(this._doc,{monomer:t,biotype:e,theme:this._theme(),favorite:r,primed:l});return this._wireTile(s,o,t,e),s}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_paletteRdkitSvg(e){let i=e.smiles;if(void 0===i||""===i)return null;let r=this._rdkit();if(null===r)return null;let l=`${e.polymerType}:${e.symbol}`;if(this._paletteRdkitCache.has(l))return this._paletteRdkitCache.get(l)??null;let s=et(r,i,220,140);if(this._paletteRdkitCache.size>=t._PALETTE_RDKIT_CACHE_LIMIT){let t=this._paletteRdkitCache.keys().next().value;void 0!==t&&this._paletteRdkitCache.delete(t)}return this._paletteRdkitCache.set(l,s),s}_wireTile(t,e,i,r){t.addEventListener("mouseenter",t=>{let e=t,r=it(this._doc,"palette-tooltip","hw-palette-tooltip");rt(this._doc,r,{symbol:i.symbol,name:i.name??"",rdkitSvg:this._paletteRdkitSvg(i),rdkitTestid:"palette-tooltip-rdkit-svg"}),lt(r,"number"==typeof e.clientX?e.clientX:0,"number"==typeof e.clientY?e.clientY:0)}),t.addEventListener("mouseleave",()=>{st(this._doc.body.querySelector('[data-testid="palette-tooltip"]'))}),t.addEventListener("click",t=>{let e=t.target;if(this._opts.allowFavorites&&void 0!==e&&!0===e?.classList?.contains("hw-palette__star"))return this.setFavorite(i.symbol,!this._favorites.has(i.symbol)),void t.stopPropagation();if(null!==this._activeBiotypeFilter&&this._activeBiotypeFilter===r){let e=this._pickResolver;return this._teardownPickMode(),e?.(i.symbol),this._scrollActivePaneToTop(),void t.stopPropagation()}let l=this._editor.getSelection();if(l.atoms.size>0){let e=this._editor.getMol(),s=[];for(let t of l.atoms){let i=e.atoms.find(e=>e.id===t);void 0!==i&&s.push(i)}return s.length>0&&s.every(t=>t.biotype===r)?(this._editor.replaceMonomers(s,i.symbol),void t.stopPropagation()):(this._editor.fire("editor:status",{message:`Cannot bulk-replace ${s.length} selected atom(s) with ${i.symbol}: selection contains incompatible biotypes for ${r}.`,severity:"warn",durationMs:3e3}),void t.stopPropagation())}let s=this._editor.getNextAddSymbol();if(null!==s&&s.symbol===i.symbol&&s.biotype===r)return this._editor.setNextAddSymbol(null),void this._updatePrimedClasses();this._editor.setNextAddSymbol(i.symbol,r),this._updatePrimedClasses()}),t.addEventListener("dragstart",t=>{let e=t.dataTransfer;if(null!=e)try{e.setData("application/x-hwe-monomer",JSON.stringify({symbol:i.symbol,biotype:r})),e.effectAllowed="copy"}catch{}st(this._doc.body.querySelector('[data-testid="palette-tooltip"]')),this._editor.startPaletteDrag(i.symbol,r)})}_biotype(t,e){let i=$(t);if(null!==i)return i;switch(e){case l.PEPTIDE:return r.AA;case l.RNA:return r.SUGAR;case l.CHEM:return r.CHEM;case l.BLOB:return r.BLOB;default:return r.CHEM}}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyFilter(){let t=this._filter,e=this._activeBiotypeFilter,i=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`),r=(i??this.element).querySelectorAll(".hw-palette__tile");for(let i=0;i<r.length;i++){let l=r[i],s=(l.getAttribute("data-symbol")??"").toLowerCase(),o=(l.getAttribute("title")??"").toLowerCase(),n=l.getAttribute("data-biotype")??"",a=(""===t||s.indexOf(t)>=0||o.indexOf(t)>=0)&&(null===e||n===e);l.style.display=a?"":"none"}let l=(i??this.element).querySelectorAll(".hw-triplet-chip");for(let i=0;i<l.length;i++){let r=l[i],s=[r.getAttribute("data-triplet")??"",r.getAttribute("data-sugar")??"",r.getAttribute("data-base")??"",r.getAttribute("data-linker")??""].join(" ").toLowerCase(),o=(""===t||s.indexOf(t)>=0)&&null===e;r.style.display=o?"":"none"}let s=(i??this.element).querySelectorAll(".hw-palette__group");for(let t=0;t<s.length;t++){let e=s[t],i=e.querySelectorAll(".hw-palette__tile, .hw-triplet-chip"),r=!1;for(let t=0;t<i.length;t++)if("none"!==i[t].style.display){r=!0;break}r?(e.removeAttribute("hidden"),e.removeAttribute("data-section-empty")):(e.setAttribute("hidden",""),e.setAttribute("data-section-empty","true"))}}_updatePrimedClasses(){let t=this._editor.getNextAddSymbol(),e=this.element.querySelectorAll(".hw-palette__tile");for(let i=0;i<e.length;i++){let r=e[i],l=r.getAttribute("data-symbol")??"",s=r.getAttribute("data-biotype")??"",o=null!==t&&t.symbol===l&&t.biotype===s,n=(r.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-palette__tile--primed"!==t).join(" ");r.setAttribute("class",o?`${n} hw-palette__tile--primed`:n),r.setAttribute("aria-pressed",o?"true":"false")}}_applyActiveTabClasses(){let t=this.element.querySelectorAll(".hw-palette__tab");for(let e=0;e<t.length;e++){let i=t[e],r=i.getAttribute("data-tab")??"";i.setAttribute("aria-selected",r===this._activeTab?"true":"false")}let e=this.element.querySelectorAll(".hw-palette__pane");for(let t=0;t<e.length;t++){let i=e[t];(i.getAttribute("data-tab")??"")===this._activeTab?i.removeAttribute("hidden"):i.setAttribute("hidden","")}}_localStorage(){if(!this._opts.allowFavorites)return null;let t=this._doc.defaultView;if(null==t)return null;try{return t.localStorage??null}catch{return null}}_resolveInitialTab(t){if(void 0!==t&&St.includes(t))return t;let e=this._localStorage();if(null!==e)try{let t=e.getItem(Tt);if(null!==t&&St.includes(t))return t}catch{}return kt}_persistActiveTab(){let t=this._localStorage();if(null!==t)try{t.setItem(Tt,this._activeTab)}catch{}}_loadFavorites(){let t=this._localStorage();if(null!==t){try{let e=t.getItem(Ct);if(null!==e&&""!==e){let t=JSON.parse(e),i=this._extractSymbols(t);for(let t of i)this._favorites.add(t);for(let e of this._extractTriplets(t))this._favoriteTriplets.push(e);return}}catch{}try{let e=t.getItem("hwe.palette.favorites");if(null===e||""===e)return;let i=JSON.parse(e);if(Array.isArray(i)){for(let t of i){if("string"!=typeof t)continue;let e=t.indexOf("|"),i=e>=0?t.slice(e+1):t;""!==i&&this._favorites.add(i)}this._saveFavorites()}}catch{}}}_extractSymbols(t){if(Array.isArray(t)){let e=[];for(let i of t)"string"==typeof i&&e.push(i);return e}if(null!==t&&"object"==typeof t){let e=t;if(Array.isArray(e.symbols)){let t=[];for(let i of e.symbols)"string"==typeof i&&t.push(i);return t}}return[]}_extractTriplets(t){if(null===t||"object"!=typeof t)return[];let e=t;if(!Array.isArray(e.triplets))return[];let i=[];for(let t of e.triplets){if(null===t||"object"!=typeof t)continue;let e=t;"string"==typeof e.sugar&&"string"==typeof e.base&&"string"==typeof e.linker&&i.push({sugar:e.sugar,base:e.base,linker:e.linker})}return i}_saveFavorites(){let t=this._localStorage();if(null!==t)try{let e={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(e.triplets=this._favoriteTriplets.map(t=>({...t}))),t.setItem(Ct,JSON.stringify(e))}catch{}}};xt._DEFAULT_TRIPLET_BASES=["A","C","G","U","T"],xt._PALETTE_RDKIT_CACHE_LIMIT=256;new Set([l.PEPTIDE,l.RNA,l.CHEM,l.BLOB]),new Set(["Backbone","Branch","Terminal","Undefined"])}}]);
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