/// <summary>
/// Mass number for a atom with a given atomic number and exact mass.
/// </summary>
/// <param name="atomicNumber">atomic number</param>
/// <param name="exactMass">exact mass</param>
/// <returns>the mass number (or <see langword="null"/>>) if no mass number was found</returns>
/// <exception cref="IOException">isotope configuration could not be loaded</exception>
private static int?MassNumber(int atomicNumber, double exactMass)
{
var symbol = PeriodicTable.GetSymbol(atomicNumber);
var isotope = CDK.IsotopeFactory.GetIsotope(symbol, exactMass, 0.001);
return(isotope?.MassNumber);
}
private BODRIsotopeFactory()
{
string configFile = "NCDK.Config.Data.isotopes.dat";
var ins = ResourceLoader.GetAsStream(configFile);
var buffer = new byte[8];
ins.Read(buffer, 0, 4);
Array.Reverse(buffer, 0, 4);
int isotopeCount = BitConverter.ToInt32(buffer, 0);
for (int i = 0; i < isotopeCount; i++)
{
var atomicNum = ins.ReadByte();
ins.Read(buffer, 0, 2);
Array.Reverse(buffer, 0, 2);
var massNum = BitConverter.ToInt16(buffer, 0);
ins.Read(buffer, 0, 8);
Array.Reverse(buffer, 0, 8);
var exactMass = BitConverter.ToDouble(buffer, 0);
double natAbund;
if (ins.ReadByte() == 1)
{
ins.Read(buffer, 0, 8);
Array.Reverse(buffer, 0, 8);
natAbund = BitConverter.ToDouble(buffer, 0);
}
else
{
natAbund = 0;
}
var isotope = new BODRIsotope(PeriodicTable.GetSymbol(atomicNum), atomicNum, massNum, exactMass, natAbund);
Add(isotope);
}
}
private void ProcessAtomsBlock(int lineCount, IAtomContainer container)
{
for (int i = 0; i < lineCount; i++)
{
string line = input.ReadLine();
int atomicNumber = int.Parse(line.Substring(7, 3).Trim(), NumberFormatInfo.InvariantInfo);
IAtom atom = container.Builder.NewAtom();
atom.AtomicNumber = atomicNumber;
atom.Symbol = PeriodicTable.GetSymbol(atomicNumber);
container.Atoms.Add(atom);
}
}
private static bool ParseAtomSymbol(IAtom atom, string str)
{
int len = str.Length;
int pos = 0;
int mass = -1;
int anum = 0;
int hcnt = 0;
int chg = 0;
// optional mass
if (pos < len && IsDigit(str[pos]))
{
mass = (str[pos++] - '0');
while (pos < len && IsDigit(str[pos]))
{
mass = 10 * mass + (str[pos++] - '0');
}
}
else
{
switch (str)
{
case "R":
atom.AtomicNumber = 0;
atom.Symbol = "R";
return(true);
case "*":
atom.AtomicNumber = 0;
atom.Symbol = "*";
return(true);
case "D":
atom.AtomicNumber = 1;
atom.MassNumber = 2;
atom.Symbol = "H";
return(true);
case "T":
atom.AtomicNumber = 1;
atom.MassNumber = 3;
atom.Symbol = "H";
return(true);
}
}
// atom symbol
if (pos < len && IsUpper(str[pos]))
{
int beg = pos;
pos++;
while (pos < len && IsLower(str[pos]))
{
pos++;
}
anum = ChemicalElement.OfSymbol(str.Substring(beg, pos - beg)).AtomicNumber;
if (anum == AtomicNumbers.Unknown)
{
return(false);
}
// optional fields after atom symbol
while (pos < len)
{
switch (str[pos])
{
case 'H':
pos++;
if (pos < len && IsDigit(str[pos]))
{
while (pos < len && IsDigit(str[pos]))
{
hcnt = 10 * hcnt + (str[pos++] - '0');
}
}
else
{
hcnt = 1;
}
break;
case '+':
pos++;
if (pos < len && IsDigit(str[pos]))
{
chg = (str[pos++] - '0');
while (pos < len && IsDigit(str[pos]))
{
chg = 10 * chg + (str[pos++] - '0');
}
}
else
{
chg = +1;
}
break;
case '-':
pos++;
if (pos < len && IsDigit(str[pos]))
{
chg = (str[pos++] - '0');
while (pos < len && IsDigit(str[pos]))
{
chg = 10 * chg + (str[pos++] - '0');
}
chg *= -1;
}
else
{
chg = -1;
}
break;
default:
return(false);
}
}
}
else
{
return(false);
}
if (mass < 0)
{
atom.MassNumber = null;
}
else
{
atom.MassNumber = mass;
}
atom.AtomicNumber = anum;
atom.Symbol = PeriodicTable.GetSymbol(anum);
atom.ImplicitHydrogenCount = hcnt;
atom.FormalCharge = chg;
return(pos == len && len > 0);
}
/// <summary>
/// Reads a set of coordinates into ChemFrame.
/// </summary>
/// <param name="model"></param>
private void ReadCoordinates(IChemModel model)
{
var moleculeSet = model.Builder.NewAtomContainerSet();
IAtomContainer molecule = model.Builder.NewAtomContainer();
string line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
while (true)
{
line = input.ReadLine();
if ((line == null) || (line.Contains("-----")))
{
break;
}
int atomicNumber;
StringReader sr = new StringReader(line);
StreamTokenizer token = new StreamTokenizer(sr);
token.NextToken();
// ignore first token
if (token.NextToken() == StreamTokenizer.TTypeNumber)
{
atomicNumber = (int)token.NumberValue;
if (atomicNumber == 0)
{
// Skip dummy atoms. Dummy atoms must be skipped
// if frequencies are to be read because Gaussian
// does not report dummy atoms in frequencies, and
// the number of atoms is used for reading frequencies.
continue;
}
}
else
{
throw new CDKException("Error while reading coordinates: expected integer.");
}
token.NextToken();
// ignore third token
double x;
double y;
double z;
if (token.NextToken() == StreamTokenizer.TTypeNumber)
{
x = token.NumberValue;
}
else
{
throw new IOException("Error reading x coordinate");
}
if (token.NextToken() == StreamTokenizer.TTypeNumber)
{
y = token.NumberValue;
}
else
{
throw new IOException("Error reading y coordinate");
}
if (token.NextToken() == StreamTokenizer.TTypeNumber)
{
z = token.NumberValue;
}
else
{
throw new IOException("Error reading z coordinate");
}
string symbol = "Du";
symbol = PeriodicTable.GetSymbol(atomicNumber);
IAtom atom = model.Builder.NewAtom(symbol);
atom.Point3D = new Vector3(x, y, z);
molecule.Atoms.Add(atom);
}
// this is the place where we store the atomcount to be used as a
// counter in the nmr reading
atomCount = molecule.Atoms.Count;
moleculeSet.Add(molecule);
model.MoleculeSet = moleculeSet;
}
