QUESTDB_website/static/js/data.js

class excitationTypes {
  static get Valence() { return new excitationType(1 << 1, new description("Valence")) }
  static get Rydberg() { return new excitationType(1 << 2, new description("Rydberg")) }
  static get PiPis() { return new excitationType(1 << 3, new description(String.raw`\pi \rightarrow \pi^\star`, true)) }
  static get nPis() { return new excitationType(1 << 4, new description(String.raw`n \rightarrow \pi^\star`, true)) }
  static get Single() { return new excitationType(1 << 5, new description("Single")) }
  static get Double() { return new excitationType(1 << 6, new description("Double")) }
  static get SingletSinglet() { return new excitationType(1 << 7, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Singlet}`, true)) }
  static get SingletTriplet() { return new excitationType(1 << 8, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Triplet}`, true)) }
  static get DoubletDoublet() { return new excitationType(1 << 9, new description(String.raw`\mathrm{Doublet} \rightarrow \mathrm{Doublet}`, true)) }
  // Max bit shifts is 31 because int are int32 So 1 << 31 are -2147483648
  static get Others() { return new excitationType(1 << 31, new description("Others")) }
  static get All() { return EnumUltils.getAll(this, excitationType) }
  static GetFlags(value) { return EnumUltils.GetFlags(value, this, excitationType) }
}

class EnumUltils {
  static getAll(enumClass, valueType) {
    var lst = []
    for (const prop of Object.getOwnPropertyNames(enumClass)) {
      if (prop != "All") {
        const value = enumClass[prop]
        if (trueTypeOf(value) == valueType.name) {
          lst.push([prop, value])
        }
      }
    }
    return lst
  }
  static GetFlags(value, enumClass, valueType) {
    return this.getAll(enumClass, valueType).filter((x) => { value & x[1] })
  }
}

class description {
  constructor(string, isLaTeX = false) {
    this.string = string
    this.isLaTeX = isLaTeX
  }
}
class DescribedValueBase {
  constructor(value, description) {
    this.Value = value;
    this.description = description
  }
  valueOf() {
    return this.Value;
  }
}

class excitationType extends DescribedValueBase {
}
class VertExcitationKind extends DescribedValueBase {

}
class code {
  constructor(name, version) {
    this.name = name;
    this.version = version;
  };
  toString() {
    var str = this.name;
    if (this.version) {
      str = str + ' (' + this.version + ')';
    }
    return str;
  }
  static fromString(str) {
    var vals = str.split(",")
    if (vals.length >= 2) {
      return new code(vals[0], vals[1]);
    } else {
      return new code(vals[0], null);
    }
  }
}
class method {
  constructor(name, basis = null) {
    this.name = name;
    this.basis = basis;
  }
  static fromString(str) {
    var vals = str.split(",")
    if (vals.length == 2) {
      return new method(vals[0], vals[1]);
    }
    else {
      return new method(vals[0], null)
    }
  }
  toString(separator = "/") {
    var str = this.name;
    if (this.basis) {
      str = str + separator + this.basis;
    }
    return str;
  }
  get isTBE() {
    return /^TBE/.test(this.name)
  }
}

class state {
  constructor(number, multiplicity, symetry) {
    this.number = number;
    this.multiplicity = multiplicity;
    this.symetry = symetry;
  };
  toString() {
    var str = this.number + ' ^' + this.multiplicity + this.symetry;
    return str;
  };
  toLaTeX() {
    var tex = String.raw`${this.number}\:^{${this.multiplicity}}\mathrm{${this.symetry}}`;
    return tex;
  };
}
class DOI {
  constructor(doistring, IsSupporting = false) {
    this.string = doistring
    this.IsSupporting = IsSupporting
  };
  static fromString(str) {
    const vals = str.split(",")
    if (vals.length == 1) {
      return new DOI(vals[0].toString())
    }
    else {
      return new DOI(vals[0].toString(), (true ? vals[1] === true.toString() : false))
    }
  }
  toString() {
    var str = this.string;
    if (this.IsSupporting) {
      str += " " + "(SI)"
    }
    return str
  };
  get url() {
    return new URL(this.string, 'https://doi.org').toString()
  }
}

class excitationBase {
  constructor(initial, final, type = '', T1 = null) {
    this.initial = initial;
    this.final = final
    this.type = new excitationType(0, new description(type, true))
    if (type) {
      const tys = type.split(";")
      const arrow = String.raw`\rightarrow`
      for (const ty of tys) {
        if (ty.includes(arrow)) {
          const [initialt, finalt] = ty.split(arrow, 2)
          const initialts = initialt.split(",").map(x => x.trim())
          const finalts = finalt.split(",").map(x => x.trim())
          if (initialts.length == 2 && finalts.length == 2) {
            this.type.Value = this.type | excitationTypes.Double
          }
          else if (initialts.length == 1 && finalts.length == 1) {
            this.type.Value = this.type | excitationTypes.Single
          }
          if (initialts.includes("n") && finalts.includes(String.raw`\pi^\star`)) {
            this.type.Value = this.type | excitationTypes.nPis
          } else if (initialts.includes(String.raw`\pi`) && finalts.includes(String.raw`\pi^\star`)) {
            this.type.Value = this.type | excitationTypes.PiPis
          }
        } else if (ty.includes(String.raw`\mathrm{R}`)) {
          this.type.Value = this.type | excitationTypes.Rydberg
        } else if (ty.includes(String.raw`\mathrm{V}`)) {
          this.type.Value = this.type | excitationTypes.Valence
        } else if (ty.toLowerCase()===excitationTypes.Double.description.string.toLowerCase()){
          this.type.Value = this.type | excitationTypes.Double
        }
      }
    }
    var m = new Map([
      [JSON.stringify([1, 1]), excitationTypes.SingletSinglet],
      [JSON.stringify([2, 2]), excitationTypes.DoubletDoublet],
      [JSON.stringify([1, 3]), excitationTypes.SingletTriplet],
    ])
    const marray = JSON.stringify([initial.multiplicity, final.multiplicity])
    if (m.has(marray)) {
      this.type.Value = this.type.Value | m.get(marray)
    }
    if (this.type.Value == 0) {
      this.type.Value = excitationTypes.Others.Value;
    }
    this.T1 = T1
  }
}
class excitationValue extends excitationBase {
  constructor(initial, final, type, value, oscilatorForces = null, T1 = null, isUnsafe = false) {
    super(initial, final, type, T1)
    this.value = value
    this.oscilatorForces = oscilatorForces
    this.isUnsafe = isUnsafe
  }
}

class excitation extends excitationBase {
  constructor(initial, final, Eabs, Efluo, EZPE) {
    super(initial, final)
    this.Eabs = Eabs
    this.Efluo = Efluo
    this.EZPE = EZPE
  }
  get Eadia() {
    return (this.Eabs + this.Efluo) / 2
  }
  get Ezz() {
    return this.Eadia - this.EZPE
  }
  toString() {
    return this.start + ', ' + this.end + ', ' + noNanPrecision(this.Eabs, 3);
  }
}

class dataFileBase {
  constructor() {
    this.molecule = ''
    this.comment = ""
    this.code = null
    this.method = null
    this.excitations = []
    this.DOI = null
    this.sourceFile = null
  }
  static _GetMetaRexEx() {
    //metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas)
    return /^#\s*([A-Za-z_]+)\s*:\s*(.*)$/;
  }
  CopyExcitationsTypeFrom(data) {
    for (const ex of this.excitations) {
      const ex2 = data.excitations.find((e) => {
        return (JSON.stringify(e.initial) === JSON.stringify(ex.initial)) && (JSON.stringify(e.final) === JSON.stringify(ex.final))
      })
      if (ex2 !== undefined) {
        if (DebugMode.Enabled) {
          console.assert(ex.type == 0 || (ex2.type ^ (excitationTypes.Rydberg | excitationTypes.Valence) == ex.type ^ (excitationTypes.Rydberg | excitationTypes.Valence)), "Excitation type error", [ex, ex2, data.sourceFile])
        }

        ex.type = ex2.type
      }
    }
  }
  static async loadAsync(file, kind = undefined) {
    switch (trueTypeOf(file)) {
      case String.name:
        file = getFullDataPath(file)
        var str = await getTextFromFileUrlAsync(file)
        break;
      case File.name:
        var str = await getTextFromUploadedFileAsync(file)
        break
    }
    var dat = this.loadString(str, kind);
    dat.sourceFile = new websiteFile(file)
    return dat
  }
  _OnReadMetaPair(key, value) {
    switch (key) {
      case "molecule":
        this.molecule = value
        break;
      case "comment":
        this.comment = value
        break;
      case "code":
        this.code = code.fromString(value)
        break;
      case "method":
        this.method = method.fromString(value)
        break;
      case "doi":
        this.DOI = DOI.fromString(value);
        break;
      default:
    }
  }
  _OnReadRow(line) {
    var vals = line.match(/\([^\)]+\)|\S+/g)
    var start = new state(parseInt(vals[0], 10), parseInt(vals[1], 10), vals[2]);
    var end = new state(parseInt(vals[3], 10), parseInt(vals[4], 10), vals[5]);
    var hasType = vals.length >= 7 && isNaN(vals[6])
    var type = ((vals.length >= 7 && hasType) ? vals[6] : null)
    if (type === "_") {
      type = null
    }
    if (type) {
      const m = type.match(/^\(([^\)]*)\)$/)
      if (m) {
        type = m[1]
      }
    }
    var val = ((vals.length >= 7 + hasType) ? new stringNumber(vals[6 + hasType]) : NaN)
    var T1 = ((vals.length >= 8 + hasType) ? new stringNumber(vals[7 + hasType]) : NaN)
    var oscilatorForces = ((vals.length >= 9 + hasType) ? new stringNumber(vals[8 + hasType]) : NaN)
    var isUnsafe = ((vals.length >= 10 + hasType) ? vals[9 + hasType] === true.toString() : false)
    var ex = new excitationValue(start, end, type, val, oscilatorForces, T1, isUnsafe);
    if (this.VertExcitationKind) {
      ex.VertExcitationKind = this.VertExcitationKind
    }
    return ex;
  };
  _OnReadMeta(line) {
    // get key value
    var match = line.match(dataFileBase._GetMetaRexEx())
    // normalize key to lower
    var key = match[1].toLowerCase()
    //if data has value
    if (match.length == 3 && match[2]) {
      var val = match[2]
      this._OnReadMetaPair(key, val)
    }
  }
  static loadString(text, kind = null) {
    // for each line with metadata
    var ismetaArea = true;
    var dat = new VertDataFile()
    for (var line of text.split("\n")) {
      //if it's not empty line
      line = line.trim();
      if (line) {
        //if # may be metadata or comment
        if (line.charAt(0) == "#") {
          //if it's metadata
          if (ismetaArea && dataFileBase._GetMetaRexEx().test(line)) {
            dat._OnReadMeta(line);
          }
        } else { //else its row
          ismetaArea = false;
          dat.excitations.push(dat._OnReadRow(line, kind));
        }
      }
    }
    if (DebugMode.Enabled) {
      var stfy = dat.excitations.map(e => JSON.stringify([e.initial, e.final]))
      var double = []
      stfy.forEach(function (element, i) {
        // Find if there is a duplicate or not
        if (stfy.indexOf(element, i + 1) >= 0) {
          // Find if the element is already in the result array or not
          if (double.indexOf(element) === -1) {
            double.push(dat.excitations[i])
          }
        }
      });
      console.assert(double.length === 0, "Double found", double, dat.molecule, dat.method.toString())
      if (dat.DOI.string !== "10.1021/acs.jctc.8b01205") {
        for (const ex of dat.excitations) {
          console.assert(Number.isNaN(ex.T1.valueOf()) | ex.T1 > 50 | ex.isUnsafe == true, "Must be unsafe", dat, ex)
        }
      }
    }
    return dat
  }
}
class VertExcitationKinds {
  static get Absorbtion() { return new VertExcitationKind(1, new description("Absorption")) }
  static get Fluorescence() { return new VertExcitationKind(1 << 1, new description("Fluorescence")) }
  static get All() { return EnumUltils.getAll(this, VertExcitationKind) }
  static GetFlags(value) { return EnumUltils.GetFlags(value, this, VertExcitationKind) }
}
class VertDataFile extends dataFileBase {
  constructor(VertExcitationKind) {
    super()
    this.VertExcitationKind = VertExcitationKind
    this.geometry = null
  }
  _OnReadMetaPair(key, value) {
    if (key == "geom") {
      this.geometry = method.fromString(value)
    }
    else {
      super._OnReadMetaPair(key, value)
    }
  }
  _OnReadRow(line, kind) {
    var ex = super._OnReadRow(line)
    ex.VertExcitationKind = kind
    return ex
  }
}

class CombinedData {
  constructor() {
    this.Abs = null
    this.Fluo = null
    this.ZPE = null
  }
  get excitations() {
    var exs = []
    var dic = new Map()
    if (this.Abs != null) {
      for (const el of this.Abs.excitations) {
        var key = JSON.stringify([el.initial, el.final])
        if (!dic.has(key)) {
          dic.set(key, {})
        }
        dic.get(key)["abs"] = el.value
      }
      if (this.Fluo != null) {
        for (const el of this.Fluo.excitations) {
          var key = JSON.stringify([el.initial, el.final])
          if (!dic.has(key)) {
            dic.set(key, {})
          }
          dic.get(key)["fluo"] = el.value
        }
      }
      if (this.ZPE != null) {
        for (const el of this.ZPE.excitations) {
          var key = JSON.stringify([el.initial, el.final])
          if (!dic.has(key)) {
            dic.set(key, {})
          }
          dic.get(key)["ZPE"] = el.value
        }
      }
      dic.forEach((value, key) => {
        var eabs = NaN
        var efluo = NaN
        var eZPE = NaN
        var mykey = JSON.parse(key)
        for (var el of mykey) {
          Reflect.setPrototypeOf(el, state.prototype)
        }
        if ("abs" in value) {
          eabs = value["abs"]
        }
        if ("fluo" in value) {
          efluo = value["fluo"]
        }
        if ("ZPE" in value) {
          eZPE = value["ZPE"]
        }
        exs.push(new excitation(mykey[0], mykey[1], eabs, efluo, eZPE))
      })
      return exs
    }
  }
}