/// <summary>
/// Reads a text based configuration file.
/// </summary>
/// <returns>A <see cref="IEnumerable{IAtomType}"/> with read <see cref="IAtomType"/>'s.</returns>
/// <exception cref="IOException">when a problem occurred with reading from the <see cref="GetStream()"/></exception>
public IEnumerable <IAtomType> ReadAtomTypes()
{
if (GetStream() == null)
{
SetStream(ResourceLoader.GetAsStream(configFile));
}
using (var reader = new StreamReader(GetStream()))
{
string line;
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWithChar('#'))
{
continue;
}
var tokens = line.Split("\t ,;".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
if (tokens.Length != 9)
{
throw new IOException("AtomTypeTable.ReadAtypes: " + "Wrong Number of fields");
}
IAtomType atomType;
try
{
var name = tokens[0];
var rootType = tokens[1];
var san = tokens[2];
var sam = tokens[3];
// skip the vdw radius value
var scovalent = tokens[5];
var sColorR = tokens[6];
var sColorG = tokens[7];
var sColorB = tokens[8];
var mass = double.Parse(sam, NumberFormatInfo.InvariantInfo);
var covalent = double.Parse(scovalent, NumberFormatInfo.InvariantInfo);
var atomicNumber = int.Parse(san, NumberFormatInfo.InvariantInfo);
var colorR = int.Parse(sColorR, NumberFormatInfo.InvariantInfo);
var colorG = int.Parse(sColorG, NumberFormatInfo.InvariantInfo);
var colorB = int.Parse(sColorB, NumberFormatInfo.InvariantInfo);
atomType = builder.NewAtomType(name, rootType);
atomType.AtomicNumber = atomicNumber;
atomType.ExactMass = mass;
atomType.CovalentRadius = covalent;
atomType.SetProperty(CDKPropertyName.Color, CDKPropertyName.RGB2Int(colorR, colorG, colorB));
}
catch (FormatException)
{
throw new IOException("AtomTypeTable.ReadAtypes: " + "Malformed Number");
}
yield return(atomType);
}
}
yield break;
}
/// <summary>
/// Read and stores the atom types in a vector
/// </summary>
/// <exception cref="Exception">Description of the Exception</exception>
private void SetAtomTypes()
{
string name = "";
string rootType = "";
//int an = 0;
int rl = 255;
int gl = 20;
int bl = 147;
int maxbond = 0;
int atomNr = 0;
double mass = 0.0;
st.MoveNext();
string sid = st.Current; st.MoveNext();
rootType = st.Current; st.MoveNext();
string smaxbond = st.Current; st.MoveNext();
string satomNr = st.Current; st.MoveNext();
string smass = st.Current; st.MoveNext();
name = st.Current; st.MoveNext();
try
{
maxbond = int.Parse(smaxbond, NumberFormatInfo.InvariantInfo);
mass = double.Parse(smass, NumberFormatInfo.InvariantInfo);
atomNr = int.Parse(satomNr, NumberFormatInfo.InvariantInfo);
}
catch (FormatException)
{
throw new IOException("AtomTypeTable.ReadAtypes: " + "Malformed Number");
}
IAtomType atomType = builder.NewAtomType(name, rootType);
atomType.AtomicNumber = atomNr;
atomType.ExactMass = mass;
atomType.MassNumber = MassNumber(atomNr, mass);
atomType.FormalNeighbourCount = maxbond;
atomType.Symbol = rootType;
var co = CDKPropertyName.RGB2Int(rl, gl, bl);
atomType.SetProperty(CDKPropertyName.Color, co);
atomType.AtomTypeName = sid;
atomTypes.Add(atomType);
}
