/// <summary> Writes a SetOfMolecules to an OutputStream for the reaction.
///
/// </summary>
/// <param name="som"> The SetOfMolecules that is written to an OutputStream
/// </param>
private void writeSetOfMolecules(ISetOfMolecules som)
{
for (int i = 0; i < som.MoleculeCount; i++)
{
IMolecule mol = som.getMolecule(i);
for (int j = 0; j < som.getMultiplier(i); j++)
{
//MemoryStream ms = new MemoryStream();
//StreamWriter sw = new StreamWriter(ms);
writer.Write("$MOL\n");
MDLWriter mdlwriter = null;
try
{
mdlwriter = new MDLWriter(writer);
}
catch (System.Exception ex)
{
//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(ex.Message);
//logger.debug(ex);
//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'"
throw new CDKException("Exception while creating MDLWriter: " + ex.Message, ex);
}
mdlwriter.write(mol);
//writer.Write(sw.ToString());
}
}
}
/// <summary> Reads partial atomic charges and add the to the given ChemModel.
///
/// </summary>
/// <param name="model">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
/// <throws> IOException Description of the Exception </throws>
private void readPartialCharges(IChemModel model)
{
//logger.info("Reading partial atomic charges");
ISetOfMolecules moleculeSet = model.SetOfMolecules;
IMolecule molecule = moleculeSet.getMolecule(0);
System.String line = input.ReadLine();
// skip first line after "Total atomic charges"
while (input.Peek() != -1)
{
line = input.ReadLine();
//logger.debug("Read charge block line: " + line);
if ((line == null) || (line.IndexOf("Sum of Mulliken charges") >= 0))
{
//logger.debug("End of charge block found");
break;
}
System.IO.StringReader sr = new System.IO.StringReader(line);
SupportClass.StreamTokenizerSupport tokenizer = new SupportClass.StreamTokenizerSupport(sr);
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int atomCounter = (int)tokenizer.nval;
tokenizer.NextToken();
// ignore the symbol
double charge;
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
charge = tokenizer.nval;
//logger.debug("Found charge for atom " + atomCounter + ": " + charge);
}
else
{
throw new CDKException("Error while reading charge: expected double.");
}
IAtom atom = molecule.getAtomAt(atomCounter - 1);
atom.setCharge(charge);
}
}
}
/// <summary> writes all the molecules supplied in a SetOfMolecules class to
/// a single HIN file. You can also supply a single Molecule object
/// as well
/// </summary>
/// <param name="mol">the Molecule to write
/// </param>
private void writeMolecule(ISetOfMolecules som)
{
//int na = 0;
//String info = "";
System.String sym = "";
double chrg = 0.0;
//boolean writecharge = true;
for (int molnum = 0; molnum < som.MoleculeCount; molnum++)
{
IMolecule mol = som.getMolecule(molnum);
try
{
int natom = mol.AtomCount;
int nbond = mol.getBondCount();
System.String molname = "mol " + (molnum + 1) + " " + ((System.String)mol.getProperty(CDKConstants.TITLE));
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(molname.ToCharArray(), 0, molname.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
// Loop through the atoms and write them out:
IAtom[] atoms = mol.Atoms;
IBond[] bonds = mol.Bonds;
for (int i = 0; i < natom; i++)
{
System.String line = "atom ";
IAtom a = atoms[i];
sym = a.Symbol;
chrg = a.getCharge();
Point3d p3 = a.getPoint3d();
line = line + ((System.Int32)(i + 1)).ToString() + " - " + sym + " ** - " + ((double)chrg).ToString() + " " + p3.x.ToString() + " " + p3.y.ToString() + " " + p3.z.ToString() + " ";
System.String buf = "";
int ncon = 0;
for (int j = 0; j < nbond; j++)
{
IBond b = bonds[j];
if (b.contains(a))
{
// current atom is in the bond so lets get the connected atom
IAtom ca = b.getConnectedAtom(a);
double bo = b.Order;
int serial = -1;
System.String bt = "";
// get the serial no for this atom
serial = mol.getAtomNumber(ca);
if (bo == 1)
bt = new System.Text.StringBuilder("s").ToString();
else if (bo == 2)
bt = new System.Text.StringBuilder("d").ToString();
else if (bo == 3)
bt = new System.Text.StringBuilder("t").ToString();
else if (bo == 1.5)
bt = new System.Text.StringBuilder("a").ToString();
buf = buf + ((System.Int32)(serial + 1)).ToString() + " " + bt + " ";
ncon++;
}
}
line = line + " " + ((System.Int32)ncon).ToString() + " " + buf;
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(line.ToCharArray(), 0, line.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
System.String buf2 = "endmol " + (molnum + 1);
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(buf2.ToCharArray(), 0, buf2.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
catch (System.IO.IOException e)
{
throw e;
}
}
}
/// <summary> Writes a SetOfMolecules to an OutputStream for the reaction.
///
/// </summary>
/// <param name="som"> The SetOfMolecules that is written to an OutputStream
/// </param>
private void writeSetOfMolecules(ISetOfMolecules som)
{
for (int i = 0; i < som.MoleculeCount; i++)
{
IMolecule mol = som.getMolecule(i);
for (int j = 0; j < som.getMultiplier(i); j++)
{
//MemoryStream ms = new MemoryStream();
//StreamWriter sw = new StreamWriter(ms);
writer.Write("$MOL\n");
MDLWriter mdlwriter = null;
try
{
mdlwriter = new MDLWriter(writer);
}
catch (System.Exception ex)
{
//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(ex.Message);
//logger.debug(ex);
//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'"
throw new CDKException("Exception while creating MDLWriter: " + ex.Message, ex);
}
mdlwriter.write(mol);
//writer.Write(sw.ToString());
}
}
}
/// <summary> writes all the molecules supplied in a SetOfMolecules class to
/// a single HIN file. You can also supply a single Molecule object
/// as well
/// </summary>
/// <param name="mol">the Molecule to write
/// </param>
private void writeMolecule(ISetOfMolecules som)
{
//int na = 0;
//String info = "";
System.String sym = "";
double chrg = 0.0;
//boolean writecharge = true;
for (int molnum = 0; molnum < som.MoleculeCount; molnum++)
{
IMolecule mol = som.getMolecule(molnum);
try
{
int natom = mol.AtomCount;
int nbond = mol.getBondCount();
System.String molname = "mol " + (molnum + 1) + " " + ((System.String)mol.getProperty(CDKConstants.TITLE));
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(molname.ToCharArray(), 0, molname.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
// Loop through the atoms and write them out:
IAtom[] atoms = mol.Atoms;
IBond[] bonds = mol.Bonds;
for (int i = 0; i < natom; i++)
{
System.String line = "atom ";
IAtom a = atoms[i];
sym = a.Symbol;
chrg = a.getCharge();
Point3d p3 = a.getPoint3d();
line = line + ((System.Int32)(i + 1)).ToString() + " - " + sym + " ** - " + ((double)chrg).ToString() + " " + p3.x.ToString() + " " + p3.y.ToString() + " " + p3.z.ToString() + " ";
System.String buf = "";
int ncon = 0;
for (int j = 0; j < nbond; j++)
{
IBond b = bonds[j];
if (b.contains(a))
{
// current atom is in the bond so lets get the connected atom
IAtom ca = b.getConnectedAtom(a);
double bo = b.Order;
int serial = -1;
System.String bt = "";
// get the serial no for this atom
serial = mol.getAtomNumber(ca);
if (bo == 1)
{
bt = new System.Text.StringBuilder("s").ToString();
}
else if (bo == 2)
{
bt = new System.Text.StringBuilder("d").ToString();
}
else if (bo == 3)
{
bt = new System.Text.StringBuilder("t").ToString();
}
else if (bo == 1.5)
{
bt = new System.Text.StringBuilder("a").ToString();
}
buf = buf + ((System.Int32)(serial + 1)).ToString() + " " + bt + " ";
ncon++;
}
}
line = line + " " + ((System.Int32)ncon).ToString() + " " + buf;
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(line.ToCharArray(), 0, line.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
System.String buf2 = "endmol " + (molnum + 1);
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(buf2.ToCharArray(), 0, buf2.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
catch (System.IO.IOException e)
{
throw e;
}
}
}