message: stub for param integration
diff: @@ -44,9 +44,7 @@ const hbondEnergyCutoff = -0.5
  const hbondEnergyMinimal = -9.9
  interface DSSPContext {
  - /** Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter */
  oldDefinition: boolean,
  - /** alpha-helices are preferred over 3-10 helix */
  oldOrdering: boolean,
  getResidueFlag: (f: DSSPType) => SecondaryStructureType,
  getFlagName: (f: DSSPType) => String,
  @@ -113,12 +111,15 @@ namespace DSSPType {
  }
  }
  +export interface SecondaryStructureComputationParams {
  + oldDefinition: boolean
  + oldOrdering: boolean
  +}
  +
  export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
  conformation: AtomicConformation,
  - oldDefinition = true,
  - oldOrdering = true): SecondaryStructure {
  + params?: Partial<SecondaryStructureComputationParams>): SecondaryStructure {
  // TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
  - // console.log(`calculating secondary structure elements using ${ oldDefinition ? 'old' : 'revised'} definition and ${ oldOrdering ? 'old' : 'revised'} ordering of secondary structure elements`)
  const { lookup3d, proteinResidues } = calcAtomicTraceLookup3D(hierarchy, conformation)
  const backboneIndices = calcBackboneAtomIndices(hierarchy, proteinResidues)
  const hbonds = calcBackboneHbonds(hierarchy, conformation, proteinResidues, backboneIndices, lookup3d)
  @@ -126,12 +127,16 @@ export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
  const residueCount = proteinResidues.length
  const flags = new Uint32Array(residueCount)
  + const oldDefinition: boolean = (params && params.oldDefinition) || true
  + const oldOrdering: boolean = (params && params.oldOrdering) || true
  + console.log(`calculating secondary structure elements using ${ oldDefinition ? 'old' : 'revised'} definition and ${ oldOrdering ? 'old' : 'revised'} ordering of secondary structure elements`)
  +
  const torsionAngles = calculateDihedralAngles(hierarchy, conformation, proteinResidues, backboneIndices)
  const ladders: Ladder[] = []
  const bridges: Bridge[] = []
  - const getResidueFlag = oldOrdering ? getOriginalResidueFlag : getUpdatedResidueFlag
  + const getResidueFlag = oldDefinition ? getOriginalResidueFlag : getUpdatedResidueFlag
  const getFlagName = oldOrdering ? getOriginalFlagName : getUpdatedFlagName
  const ctx: DSSPContext = {
  