Class TopicMolecule

constructor

• new TopicMolecule(
      molecule: Molecule,
      options?: TopicMoleculeOptions,
  ): TopicMolecule

  Parameters

  • molecule: Molecule
  • options: TopicMoleculeOptions = {}

  Returns TopicMolecule

idCode

molecule

options

atomsPaths

• get atomsPaths(): AtomPath[][][]

  Returns AtomPath[][][]

diaIDs

• get diaIDs(): string[]

  This is related to the current moleculeWithH. The order is NOT canonized

  Returns string[]

diaIDsAndInfo

• get diaIDsAndInfo(): DiaIDAndInfo[]

  Returns DiaIDAndInfo[]

distanceMatrix

• get distanceMatrix(): any[]

  Returns the distance matrix for the current moleculeWithH

  Returns any[]

finalRanks

• get finalRanks(): any

  Returns finalRanks for all the atoms including hydrogens. Those ranks deals with topicity and is related to the current moleculeWithH. All the atoms have a unique identifier.j In order to calculate the ranks we replace all the hydrogens with a X atom.

  Returns any

heterotopicSymmetryRanks

• get heterotopicSymmetryRanks(): number[]

  Returns symmetryRanks for all the atoms including hydrogens. Those ranks deals with topicity and is related to the current moleculeWithH. In order to calculate the ranks we replace all the hydrogens with a X atom.

  Returns number[]

hoseCodes

• get hoseCodes(): any

  This is related to the current moleculeWithH. The order is NOT canonized

  Returns any

moleculeWithH

• get moleculeWithH(): Molecule

  Returns a molecule with all the hydrogens added. The order is NOT canonized

  Returns Molecule

ensureMapNo

• ensureMapNo(): void

  This method ensures that all the atoms have a mapNo in the molecule (and not the moleculeWithH! )

  Returns void

fromMolecule

• fromMolecule(molecule: Molecule): TopicMolecule

  Returns a new TopicMolecule but will copy precalculated information if possible (same idCode). This is very practical when expanding hydrogens for example.

  Parameters

  • molecule: Molecule

  Returns TopicMolecule

getAtomPaths

• getAtomPaths(
      atom1: number,
      atom2: number,
      options?: GetAtomPathOptions,
  ): number[][]

  Parameters

  • atom1: number
  • atom2: number
  • options: GetAtomPathOptions = {}

  Returns number[][]

getAtomPathsFrom

• getAtomPathsFrom(atom: number, options?: GetAtomPathFromOptions): number[][]

  Parameters

  • atom: number
  • options: GetAtomPathFromOptions = {}

  Returns number[][]

getDiaIDsMapping

• getDiaIDsMapping(molecule: Molecule): Record<string, undefined | string>

  This method returns a mapping between the diaIDs of the current molecule. It expects that the initial molfile and the final molfile contains atomMapNo in order to track which atom becomes which one.

  Parameters

  • molecule: Molecule

  Returns Record<string, undefined | string>

getDiaIDsObject

• getDiaIDsObject(): Record<string, GroupedDiaID>

  We return the atomIDs corresponding to the specified diaID as well has the attached hydrogens or heavy atoms

  Returns Record<string, GroupedDiaID>

getGroupedDiastereotopicAtomIDs

• getGroupedDiastereotopicAtomIDs(
      options?: GroupedDiaIDsOptions,
  ): undefined | GroupedDiaID[]

  Returns an array of objects containing the oclID and the corresponding hydrogens and atoms for the specified atomLabel (if any) This always applied to the molecule with expanded hydrogens and chirality

  Parameters

  • options: GroupedDiaIDsOptions = {}

  Returns undefined | GroupedDiaID[]

getHoseFragment

• getHoseFragment(rootAtoms: number[], options?: GetHoseFragmentOptions): Molecule

  Parameters

  • rootAtoms: number[]
  • options: GetHoseFragmentOptions = {}

  Returns Molecule

getMolecule

• getMolecule(): Molecule

  Returns Molecule

setAtomNoInMapNo

• setAtomNoInMapNo(): void

  This method ensures that all the atoms have a mapNo corresponding to the atom number. It will enforce mapNo in molecule and moleculeWithH We start numbering the atoms at 1

  Returns void

toMolfile

• toMolfile(options?: ToMolfileOptions): string

  Parameters

  • options: ToMolfileOptions = {}

  Returns string

toMolfileWithH

• toMolfileWithH(options?: ToMolfileOptions): string

  Parameters

  • options: ToMolfileOptions = {}

  Returns string

toMolfileWithoutH

• toMolfileWithoutH(options?: ToMolfileOptions): string

  Parameters

  • options: ToMolfileOptions = {}

  Returns string