/// <summary> Reads a text based configuration file.
///
/// </summary>
/// <param name="builder">IChemObjectBuilder used to construct the IAtomType's.
/// </param>
/// <throws> IOException when a problem occured with reading from the InputStream </throws>
/// <returns> A Vector with read IAtomType's.
/// </returns>
public virtual System.Collections.ArrayList readAtomTypes(IChemObjectBuilder builder)
{
System.Collections.ArrayList atomTypes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
if (ins == null)
{
// trying the default
//System.out.println("readAtomTypes getResourceAsStream:"
// + configFile);
//UPGRADE_ISSUE: Method 'java.lang.ClassLoader.getResourceAsStream' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassLoader'"
//UPGRADE_ISSUE: Method 'java.lang.Class.getClassLoader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassgetClassLoader'"
ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + configFile);
}
if (ins == null)
{
throw new System.IO.IOException("There was a problem getting the default stream: " + configFile);
}
// read the contents from file
//UPGRADE_TODO: The differences in the expected value of parameters for constructor 'java.io.BufferedReader.BufferedReader' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
System.IO.StreamReader reader = new System.IO.StreamReader(new System.IO.StreamReader(ins, System.Text.Encoding.Default).BaseStream, new System.IO.StreamReader(ins, System.Text.Encoding.Default).CurrentEncoding, false, 1024);
SupportClass.Tokenizer tokenizer;
System.String string_Renamed;
while (true)
{
string_Renamed = reader.ReadLine();
if (string_Renamed == null)
{
break;
}
if (!string_Renamed.StartsWith("#"))
{
System.String name = "";
System.String rootType = "";
int atomicNumber = 0, colorR = 0, colorG = 0, colorB = 0;
double mass = 0.0, vdwaals = 0.0, covalent = 0.0;
tokenizer = new SupportClass.Tokenizer(string_Renamed, "\t ,;");
int tokenCount = tokenizer.Count;
if (tokenCount == 9)
{
name = tokenizer.NextToken();
rootType = tokenizer.NextToken();
System.String san = tokenizer.NextToken();
System.String sam = tokenizer.NextToken();
System.String svdwaals = tokenizer.NextToken();
System.String scovalent = tokenizer.NextToken();
System.String sColorR = tokenizer.NextToken();
System.String sColorG = tokenizer.NextToken();
System.String sColorB = tokenizer.NextToken();
try
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
mass = System.Double.Parse(sam);
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
vdwaals = System.Double.Parse(svdwaals);
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
covalent = System.Double.Parse(scovalent);
atomicNumber = System.Int32.Parse(san);
colorR = System.Int32.Parse(sColorR);
colorG = System.Int32.Parse(sColorG);
colorB = System.Int32.Parse(sColorB);
}
catch (System.FormatException nfe)
{
throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Malformed Number");
}
IAtomType atomType = builder.newAtomType(name, rootType);
atomType.AtomicNumber = atomicNumber;
atomType.setExactMass(mass);
atomType.VanderwaalsRadius = vdwaals;
atomType.CovalentRadius = covalent;
System.Drawing.Color color = System.Drawing.Color.FromArgb(colorR, colorG, colorB);
atomType.setProperty("org.openscience.cdk.renderer.color", color);
atomTypes.Add(atomType);
}
else
{
throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Wrong Number of fields");
}
}
} // end while
ins.Close();
return(atomTypes);
}
public override void endElement(System.String uri, System.String local, System.String raw)
{
//NOPMD
//logger.debug("END Element: ", raw);
//logger.debug(" uri: ", uri);
//logger.debug(" local: ", local);
//logger.debug(" raw: ", raw);
//logger.debug(" chars: ", currentChars.Trim());
if ("atomType".Equals(local))
{
atomTypes.Add(atomType);
}
else if ("scalar".Equals(local))
{
currentChars.Trim();
try
{
if (scalarType == SCALAR_BONDORDERSUM)
{
atomType.BondOrderSum = System.Double.Parse(currentChars);
}
else if (scalarType == SCALAR_MAXBONDORDER)
{
atomType.MaxBondOrder = System.Double.Parse(currentChars);
}
else if (scalarType == SCALAR_FORMALNEIGHBOURCOUNT)
{
atomType.FormalNeighbourCount = System.Int32.Parse(currentChars);
}
else if (scalarType == SCALAR_VALENCY)
{
atomType.Valency = System.Int32.Parse(currentChars);
}
else if (scalarType == SCALAR_FORMALCHARGE)
{
atomType.setFormalCharge(System.Int32.Parse(currentChars));
}
else if (scalarType == SCALAR_HYBRIDIZATION)
{
if ("sp1".Equals(currentChars))
{
atomType.Hybridization = CDKConstants.HYBRIDIZATION_SP1;
}
else if ("sp2".Equals(currentChars))
{
atomType.Hybridization = CDKConstants.HYBRIDIZATION_SP2;
}
else if ("sp3".Equals(currentChars))
{
atomType.Hybridization = CDKConstants.HYBRIDIZATION_SP3;
}
else
{
//logger.warn("Unrecognized hybridization in config file: ", currentChars);
}
}
else if (scalarType == SCALAR_DA)
{
if ("A".Equals(currentChars))
{
atomType.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, true);
}
else if ("D".Equals(currentChars))
{
atomType.setFlag(CDKConstants.IS_HYDROGENBOND_DONOR, true);
}
else
{
//logger.warn("Unrecognized H-bond donor/acceptor pattern in config file: ", currentChars);
}
}
else if (scalarType == SCALAR_SPHERICALMATCHER)
{
atomType.setProperty(CDKConstants.SPHERICAL_MATCHER, currentChars);
}
else if (scalarType == SCALAR_RINGSIZE)
{
atomType.setProperty(CDKConstants.PART_OF_RING_OF_SIZE, (System.Object)System.Int32.Parse(currentChars));
}
else if (scalarType == SCALAR_CHEMICALGROUPCONSTANT)
{
atomType.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, (System.Object)System.Int32.Parse(currentChars));
}
else if (scalarType == SCALAR_ISAROMATIC)
{
atomType.setFlag(CDKConstants.ISAROMATIC, true);
}
else if (scalarType == SCALAR_VANDERWAALSRADIUS)
{
atomType.VanderwaalsRadius = System.Double.Parse(currentChars);
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Value (", currentChars, ") is not off the expected type: ", exception.Message);
//logger.debug(exception);
}
scalarType = SCALAR_UNSET;
}
currentChars = "";
}