src/structure/structure-builder.js

/**
 * @file Structure Builder
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @private
 */

function StructureBuilder (structure) {
  let currentModelindex = null
  let currentChainid = null
  let currentResname = null
  let currentResno = null
  let currentInscode = null
  let currentHetero = null

  let previousResname
  let previousHetero

  const atomStore = structure.atomStore
  const residueStore = structure.residueStore
  const chainStore = structure.chainStore
  const modelStore = structure.modelStore

  const residueMap = structure.residueMap

  let ai = -1
  let ri = -1
  let ci = -1
  let mi = -1

  function addResidueType (ri) {
    const count = residueStore.atomCount[ ri ]
    const offset = residueStore.atomOffset[ ri ]
    const atomTypeIdList = new Array(count)
    for (let i = 0; i < count; ++i) {
      atomTypeIdList[ i ] = atomStore.atomTypeId[ offset + i ]
    }
    residueStore.residueTypeId[ ri ] = residueMap.add(
      previousResname, atomTypeIdList, previousHetero
    )
  }

  this.addAtom = function (modelindex, chainname, chainid, resname, resno, hetero, sstruc, inscode) {
    let addModel = false
    let addChain = false
    let addResidue = false

    if (currentModelindex !== modelindex) {
      addModel = true
      addChain = true
      addResidue = true
      mi += 1
      ci += 1
      ri += 1
    } else if (currentChainid !== chainid) {
      addChain = true
      addResidue = true
      ci += 1
      ri += 1
    } else if (currentResno !== resno || currentResname !== resname || currentInscode !== inscode) {
      addResidue = true
      ri += 1
    }
    ai += 1

    if (addModel) {
      modelStore.growIfFull()
      modelStore.chainOffset[ mi ] = ci
      modelStore.chainCount[ mi ] = 0
      modelStore.count += 1
      chainStore.modelIndex[ ci ] = mi
    }

    if (addChain) {
      chainStore.growIfFull()
      chainStore.setChainname(ci, chainname)
      chainStore.setChainid(ci, chainid)
      chainStore.residueOffset[ ci ] = ri
      chainStore.residueCount[ ci ] = 0
      chainStore.count += 1
      chainStore.modelIndex[ ci ] = mi
      modelStore.chainCount[ mi ] += 1
      residueStore.chainIndex[ ri ] = ci
    }

    if (addResidue) {
      previousResname = currentResname
      previousHetero = currentHetero
      if (ri > 0) addResidueType(ri - 1)
      residueStore.growIfFull()
      residueStore.resno[ ri ] = resno
      if (sstruc !== undefined) {
        residueStore.sstruc[ ri ] = sstruc.charCodeAt(0)
      }
      if (inscode !== undefined) {
        residueStore.inscode[ ri ] = inscode.charCodeAt(0)
      }
      residueStore.atomOffset[ ri ] = ai
      residueStore.atomCount[ ri ] = 0
      residueStore.count += 1
      residueStore.chainIndex[ ri ] = ci
      chainStore.residueCount[ ci ] += 1
    }

    atomStore.count += 1
    atomStore.residueIndex[ ai ] = ri
    residueStore.atomCount[ ri ] += 1

    currentModelindex = modelindex
    currentChainid = chainid
    currentResname = resname
    currentResno = resno
    currentInscode = inscode
    currentHetero = hetero
  }

  this.finalize = function () {
    previousResname = currentResname
    previousHetero = currentHetero
    if (ri > -1) addResidueType(ri)
  }
}

export default StructureBuilder