private int addArrayElementsTo(System.Collections.ArrayList toAddto, System.String array)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(array);
int i = 0;
while (tokenizer.HasMoreTokens())
{
toAddto.Add(tokenizer.NextToken());
i++;
}
return i;
}
/// <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;
}
/// <summary> Creates a String of the Class name of the <code>IChemObject</code> reader
/// for this file format. The input is read line-by-line
/// until a line containing an identifying string is
/// found.
///
/// <p>The ReaderFactory detects more formats than the CDK
/// has Readers for.
///
/// <p>This method is not able to detect the format of gziped files.
/// Use <code>guessFormat(InputStream)</code> instead for such files.
///
/// </summary>
/// <throws> IOException if an I/O error occurs </throws>
/// <throws> IllegalArgumentException if the input is null </throws>
/// <summary>
/// </summary>
/// <seealso cref="guessFormat(InputStream)">
/// </seealso>
public virtual IChemFormat guessFormat(StreamReader input)
{
if (input == null)
{
throw new System.ArgumentException("input cannot be null");
}
// make a copy of the header
char[] header = new char[this.headerLength];
//UPGRADE_ISSUE: Method 'java.io.BufferedReader.markSupported' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000'"
//if (!input.markSupported())
//{
// //logger.error("Mark not supported");
// throw new System.ArgumentException("input must support mark");
//}
//int pos = this.headerLength;//input.mark(this.headerLength);
input.Read(header, 0, this.headerLength);
input.BaseStream.Seek(0, SeekOrigin.Begin);
//UPGRADE_ISSUE: Constructor 'java.io.BufferedReader.BufferedReader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderBufferedReader_javaioReader'"
System.IO.StringReader buffer = new StringReader(new System.String(header));
/* Search file for a line containing an identifying keyword */
System.String line = null;
int lineNumber = 1;
while ((line = buffer.ReadLine()) != null)
{
//logger.debug(lineNumber + ": ", line);
for (int i = 0; i < formats.Count; i++)
{
IChemFormatMatcher cfMatcher = (IChemFormatMatcher)formats[i];
if (cfMatcher.matches(lineNumber, line))
{
//logger.info("Detected format: ", cfMatcher.FormatName);
return cfMatcher;
}
}
lineNumber++;
}
//logger.warn("Now comes the tricky and more difficult ones....");
//UPGRADE_ISSUE: Constructor 'java.io.BufferedReader.BufferedReader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderBufferedReader_javaioReader'"
buffer = new StringReader(new System.String(header));
line = buffer.ReadLine();
// is it a XYZ file?
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line.Trim());
try
{
int tokenCount = tokenizer.Count;
if (tokenCount == 1)
{
System.Int32.Parse(tokenizer.NextToken());
// if not failed, then it is a XYZ file
return null;// new org.openscience.cdk.io.formats.XYZFormat();
}
else if (tokenCount == 2)
{
System.Int32.Parse(tokenizer.NextToken());
if ("Bohr".ToUpper().Equals(tokenizer.NextToken().ToUpper()))
{
return null;// new org.openscience.cdk.io.formats.XYZFormat();
}
}
}
catch (System.FormatException exception)
{
//logger.info("No, it's not a XYZ file");
}
//logger.warn("File format undetermined");
return null;
}
/// <summary> Private method that actually parses the input to read a ChemFile
/// object. In its current state it is able to read all the molecules
/// (if more than one is present) in the specified HIN file. These are
/// placed in a SetOfMolecules object which in turn is placed in a ChemModel
/// which in turn is placed in a ChemSequence object and which is finally
/// placed in a ChemFile object and returned to the user.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.newChemSequence();
IChemModel chemModel = file.Builder.newChemModel();
ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();
System.String info;
SupportClass.Tokenizer tokenizer;
try
{
System.String line;
// read in header info
while (true)
{
line = input.ReadLine();
if (line.IndexOf("mol ") == 0)
{
info = getMolName(line);
break;
}
}
// start the actual molecule data - may be multiple molecule
line = input.ReadLine();
while (true)
{
if (line == null)
break; // end of file
if (line.IndexOf(';') == 0)
continue; // comment line
if (line.IndexOf("mol ") == 0)
{
info = getMolName(line);
line = input.ReadLine();
}
IMolecule m = file.Builder.newMolecule();
m.setProperty(CDKConstants.TITLE, info);
// Each elemnt of cons is an ArrayList of length 3 which stores
// the start and end indices and bond order of each bond
// found in the HIN file. Before adding bonds we need to reduce
// the number of bonds so as not to count the same bond twice
System.Collections.ArrayList cons = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
// read data for current molecule
int atomSerial = 0;
while (true)
{
if (line.IndexOf("endmol ") >= 0)
{
break;
}
if (line.IndexOf(';') == 0)
continue; // comment line
tokenizer = new SupportClass.Tokenizer(line, " ");
int ntoken = tokenizer.Count;
System.String[] toks = new System.String[ntoken];
for (int i = 0; i < ntoken; i++)
toks[i] = tokenizer.NextToken();
System.String sym = new System.Text.StringBuilder(toks[3]).ToString();
double charge = System.Double.Parse(toks[6]);
double x = System.Double.Parse(toks[7]);
double y = System.Double.Parse(toks[8]);
double z = System.Double.Parse(toks[9]);
int nbond = System.Int32.Parse(toks[10]);
IAtom atom = file.Builder.newAtom(sym, new Point3d(x, y, z));
atom.setCharge(charge);
for (int j = 11; j < (11 + nbond * 2); j += 2)
{
double bo = 1;
int s = System.Int32.Parse(toks[j]) - 1; // since atoms start from 1 in the file
char bt = toks[j + 1][0];
switch (bt)
{
case 's':
bo = 1;
break;
case 'd':
bo = 2;
break;
case 't':
bo = 3;
break;
case 'a':
bo = 1.5;
break;
}
System.Collections.ArrayList ar = new System.Collections.ArrayList(3);
ar.Add((System.Int32)atomSerial);
ar.Add((System.Int32)s);
ar.Add((double)bo);
cons.Add(ar);
}
m.addAtom(atom);
atomSerial++;
line = input.ReadLine();
}
// before storing the molecule lets include the connections
// First we reduce the number of bonds stored, since we have
// stored both, say, C1-H1 and H1-C1.
System.Collections.ArrayList blist = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < cons.Count; i++)
{
System.Collections.ArrayList ar = (System.Collections.ArrayList)cons[i];
// make a reversed list
System.Collections.ArrayList arev = new System.Collections.ArrayList(3);
arev.Add(ar[1]);
arev.Add(ar[0]);
arev.Add(ar[2]);
// Now see if ar or arev are already in blist
if (blist.Contains(ar) || blist.Contains(arev))
continue;
else
blist.Add(ar);
}
// now just store all the bonds we have
for (int i = 0; i < blist.Count; i++)
{
System.Collections.ArrayList ar = (System.Collections.ArrayList)blist[i];
int s = ((System.Int32)ar[0]);
int e = ((System.Int32)ar[1]);
double bo = ((System.Double)ar[2]);
m.addBond(s, e, bo);
}
setOfMolecules.addMolecule(m);
line = input.ReadLine(); // read in the 'mol N'
}
// got all the molecule in the HIN file (hopefully!)
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
file.addChemSequence(chemSequence);
}
catch (System.IO.IOException e)
{
// should make some noise now
file = null;
}
return file;
}
/// <summary> Private method that actually parses the input to read a ChemFile
/// object.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.newChemSequence();
int number_of_atoms = 0;
SupportClass.Tokenizer tokenizer;
try
{
System.String line = input.ReadLine();
while (line.StartsWith("#"))
line = input.ReadLine();
/*while (input.ready() && line != null)
{*/
// System.out.println("lauf");
// parse frame by frame
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
System.String token = tokenizer.NextToken();
number_of_atoms = System.Int32.Parse(token);
System.String info = input.ReadLine();
IChemModel chemModel = file.Builder.newChemModel();
ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();
IMolecule m = file.Builder.newMolecule();
m.setProperty(CDKConstants.TITLE, info);
System.String[] types = new System.String[number_of_atoms];
double[] d = new double[number_of_atoms]; int[] d_atom = new int[number_of_atoms]; // Distances
double[] a = new double[number_of_atoms]; int[] a_atom = new int[number_of_atoms]; // Angles
double[] da = new double[number_of_atoms]; int[] da_atom = new int[number_of_atoms]; // Diederangles
//Point3d[] pos = new Point3d[number_of_atoms]; // calculated positions
int i = 0;
while (i < number_of_atoms)
{
line = input.ReadLine();
// System.out.println("line:\""+line+"\"");
if (line == null)
break;
if (line.StartsWith("#"))
{
// skip comment in file
}
else
{
d[i] = 0d; d_atom[i] = -1;
a[i] = 0d; a_atom[i] = -1;
da[i] = 0d; da_atom[i] = -1;
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
int fields = tokenizer.Count;
if (fields < System.Math.Min(i * 2 + 1, 7))
{
// this is an error but cannot throw exception
}
else if (i == 0)
{
types[i] = tokenizer.NextToken();
i++;
}
else if (i == 1)
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
else if (i == 2)
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
a[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
else
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
a[i] = (System.Double.Parse(tokenizer.NextToken()));
da_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
da[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
}
}
// calculate cartesian coordinates
Point3d[] cartCoords = ZMatrixTools.zmatrixToCartesian(d, d_atom, a, a_atom, da, da_atom);
for (i = 0; i < number_of_atoms; i++)
{
m.addAtom(file.Builder.newAtom(types[i], cartCoords[i]));
}
// System.out.println("molecule:\n"+m);
setOfMolecules.addMolecule(m);
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
line = input.ReadLine();
file.addChemSequence(chemSequence);
}
catch (System.IO.IOException e)
{
// should make some noise now
file = null;
}
return file;
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="smiles"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <exception cref="InvalidSmilesException"> Description of the Exception
/// </exception>
public virtual Reaction parseReactionSmiles(System.String smiles)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(smiles, ">");
System.String reactantSmiles = tokenizer.NextToken();
System.String agentSmiles = "";
System.String productSmiles = tokenizer.NextToken();
if (tokenizer.HasMoreTokens())
{
agentSmiles = productSmiles;
productSmiles = tokenizer.NextToken();
}
Reaction reaction = new Reaction();
// add reactants
IMolecule reactantContainer = parseSmiles(reactantSmiles);
ISetOfMolecules reactantSet = ConnectivityChecker.partitionIntoMolecules(reactantContainer);
IMolecule[] reactants = reactantSet.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
reaction.addReactant(reactants[i]);
}
// add reactants
if (agentSmiles.Length > 0)
{
IMolecule agentContainer = parseSmiles(agentSmiles);
ISetOfMolecules agentSet = ConnectivityChecker.partitionIntoMolecules(agentContainer);
IMolecule[] agents = agentSet.Molecules;
for (int i = 0; i < agents.Length; i++)
{
reaction.addAgent(agents[i]);
}
}
// add products
IMolecule productContainer = parseSmiles(productSmiles);
ISetOfMolecules productSet = ConnectivityChecker.partitionIntoMolecules(productContainer);
IMolecule[] products = productSet.Molecules;
for (int i = 0; i < products.Length; i++)
{
reaction.addProduct(products[i]);
}
return reaction;
}
private IChemModel readChemModel(IChemModel model)
{
int[] atoms = new int[1];
double[] atomxs = new double[1];
double[] atomys = new double[1];
double[] atomzs = new double[1];
double[] atomcharges = new double[1];
int[] bondatomid1 = new int[1];
int[] bondatomid2 = new int[1];
int[] bondorder = new int[1];
int numberOfAtoms = 0;
int numberOfBonds = 0;
try
{
System.String line = input.ReadLine();
while (line != null)
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line);
System.String command = st.NextToken();
if ("!Header".Equals(command))
{
//logger.warn("Ignoring header");
}
else if ("!Info".Equals(command))
{
//logger.warn("Ignoring info");
}
else if ("!Atoms".Equals(command))
{
//logger.info("Reading atom block");
// determine number of atoms to read
try
{
numberOfAtoms = System.Int32.Parse(st.NextToken());
//logger.debug(" #atoms: " + numberOfAtoms);
atoms = new int[numberOfAtoms];
atomxs = new double[numberOfAtoms];
atomys = new double[numberOfAtoms];
atomzs = new double[numberOfAtoms];
atomcharges = new double[numberOfAtoms];
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
atoms[atomID] = System.Int32.Parse(atomInfoFields.NextToken());
//logger.debug("Set atomic number of atom (" + atomID + ") to: " + atoms[atomID]);
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Atoms block");
//logger.debug(exception);
}
}
else if ("!Bonds".Equals(command))
{
//logger.info("Reading bond block");
try
{
// determine number of bonds to read
numberOfBonds = System.Int32.Parse(st.NextToken());
bondatomid1 = new int[numberOfAtoms];
bondatomid2 = new int[numberOfAtoms];
bondorder = new int[numberOfAtoms];
for (int i = 0; i < numberOfBonds; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer bondInfoFields = new SupportClass.Tokenizer(line);
bondatomid1[i] = System.Int32.Parse(bondInfoFields.NextToken());
bondatomid2[i] = System.Int32.Parse(bondInfoFields.NextToken());
System.String order = bondInfoFields.NextToken();
if ("D".Equals(order))
{
bondorder[i] = 2;
}
else if ("S".Equals(order))
{
bondorder[i] = 1;
}
else if ("T".Equals(order))
{
bondorder[i] = 3;
}
else
{
// ignore order, i.e. set to single
//logger.warn("Unrecognized bond order, using single bond instead. Found: " + order);
bondorder[i] = 1;
}
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Bonds block");
//logger.debug(exception);
}
}
else if ("!Coord".Equals(command))
{
//logger.info("Reading coordinate block");
try
{
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
double x = System.Double.Parse(atomInfoFields.NextToken());
double y = System.Double.Parse(atomInfoFields.NextToken());
double z = System.Double.Parse(atomInfoFields.NextToken());
atomxs[atomID] = x;
atomys[atomID] = y;
atomzs[atomID] = z;
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Coord block");
//logger.debug(exception);
}
}
else if ("!Charges".Equals(command))
{
//logger.info("Reading charges block");
try
{
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
double charge = System.Double.Parse(atomInfoFields.NextToken());
atomcharges[atomID] = charge;
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Charges block");
//logger.debug(exception);
}
}
else if ("!End".Equals(command))
{
//logger.info("Found end of file");
// Store atoms
IAtomContainer container = model.Builder.newAtomContainer();
for (int i = 0; i < numberOfAtoms; i++)
{
try
{
IAtom atom = model.Builder.newAtom(IsotopeFactory.getInstance(container.Builder).getElementSymbol(atoms[i]));
atom.AtomicNumber = atoms[i];
atom.setPoint3d(new Point3d(atomxs[i], atomys[i], atomzs[i]));
atom.setCharge(atomcharges[i]);
container.addAtom(atom);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Stored atom: " + atom);
}
catch (System.Exception exception)
{
//logger.error("Cannot create an atom with atomic number: " + atoms[i]);
//logger.debug(exception);
}
}
// Store bonds
for (int i = 0; i < numberOfBonds; i++)
{
container.addBond(bondatomid1[i], bondatomid2[i], bondorder[i]);
}
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addMolecule(model.Builder.newMolecule(container));
model.SetOfMolecules = moleculeSet;
return model;
}
else
{
//logger.warn("Skipping line: " + line);
}
line = input.ReadLine();
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading file");
//logger.debug(exception);
}
// this should not happen, file is lacking !End command
return null;
}
/// <summary> Read a Reaction from a file in MDL RXN format
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IReaction readReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.newReaction();
try
{
input.ReadLine(); // first line should be $RXN
input.ReadLine(); // second line
input.ReadLine(); // third line
input.ReadLine(); // fourth line
}
catch (System.IO.IOException exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try
{
System.String countsLine = input.ReadLine();
/* this line contains the number of reactants
and products */
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(countsLine);
reactantCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + reactantCount + " reactants in file");
productCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + productCount + " products in file");
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try
{
for (int i = 1; i <= reactantCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
input.ReadLine(); // announceMDLFileLine
System.String molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}
while (!molFileLine.Equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
}
catch (CDKException exception)
{
// rethrow exception from MDLReader
throw exception;
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try
{
for (int i = 1; i <= productCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
input.ReadLine(); // String announceMDLFileLine =
System.String molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}
while (!molFileLine.Equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
IMolecule product = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
}
catch (CDKException exception)
{
// rethrow exception from MDLReader
throw exception;
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
//logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
IMolecule[] molecules = reaction.Reactants.Molecules;
for (int i = 0; i < molecules.Length; i++)
{
reactingSide.add(molecules[i]);
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.Products.Molecules;
for (int i = 0; i < molecules.Length; i++)
{
producedSide.add(molecules[i]);
}
// map the atoms
int mappingCount = 0;
IAtom[] reactantAtoms = reactingSide.Atoms;
IAtom[] producedAtoms = producedSide.Atoms;
for (int i = 0; i < reactantAtoms.Length; i++)
{
for (int j = 0; j < producedAtoms.Length; j++)
{
if (reactantAtoms[i].ID != null && reactantAtoms[i].ID.Equals(producedAtoms[j].ID))
{
reaction.addMapping(builder.newMapping(reactantAtoms[i], producedAtoms[j]));
mappingCount++;
break;
}
}
}
//logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
/// <summary> Read a Reaction from a file in MDL RXN format
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IMolecule readMolecule(IMolecule molecule)
{
AtomTypeFactory atFactory = null;
try
{
atFactory = AtomTypeFactory.getInstance("mol2_atomtypes.xml", molecule.Builder);
}
catch (System.Exception exception)
{
System.String error = "Could not instantiate an AtomTypeFactory";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
try
{
System.String line = input.ReadLine();
int atomCount = 0;
int bondCount = 0;
while (line != null)
{
if (line.StartsWith("@<TRIPOS>MOLECULE"))
{
//logger.info("Reading molecule block");
// second line has atom/bond counts?
input.ReadLine(); // disregard the name line
System.String counts = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(counts);
try
{
atomCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom count from MOLECULE block";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
if (tokenizer.HasMoreTokens())
{
try
{
bondCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom and bond counts";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
else
{
bondCount = 0;
}
//logger.info("Reading #atoms: ", atomCount);
//logger.info("Reading #bonds: ", bondCount);
//logger.warn("Not reading molecule qualifiers");
}
else if (line.StartsWith("@<TRIPOS>ATOM"))
{
//logger.info("Reading atom block");
for (int i = 0; i < atomCount; i++)
{
line = input.ReadLine().Trim();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String nameStr = tokenizer.NextToken();
System.String xStr = tokenizer.NextToken();
System.String yStr = tokenizer.NextToken();
System.String zStr = tokenizer.NextToken();
System.String atomTypeStr = tokenizer.NextToken();
IAtomType atomType = atFactory.getAtomType(atomTypeStr);
if (atomType == null)
{
atomType = atFactory.getAtomType("X");
//logger.error("Could not find specified atom type: ", atomTypeStr);
}
IAtom atom = molecule.Builder.newAtom("X");
atom.ID = nameStr;
atom.AtomTypeName = atomTypeStr;
atFactory.configure(atom);
try
{
double x = System.Double.Parse(xStr);
double y = System.Double.Parse(yStr);
double z = System.Double.Parse(zStr);
atom.setPoint3d(new Point3d(x, y, z));
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom coordinates";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
molecule.addAtom(atom);
}
}
else if (line.StartsWith("@<TRIPOS>BOND"))
{
//logger.info("Reading bond block");
for (int i = 0; i < bondCount; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String atom1Str = tokenizer.NextToken();
System.String atom2Str = tokenizer.NextToken();
System.String orderStr = tokenizer.NextToken();
try
{
int atom1 = System.Int32.Parse(atom1Str);
int atom2 = System.Int32.Parse(atom2Str);
double order = 0;
if ("1".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("2".Equals(orderStr))
{
order = CDKConstants.BONDORDER_DOUBLE;
}
else if ("3".Equals(orderStr))
{
order = CDKConstants.BONDORDER_TRIPLE;
}
else if ("am".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("ar".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("du".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("un".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("nc".Equals(orderStr))
{
// not connected
order = 0;
}
if (order != 0)
{
molecule.addBond(atom1 - 1, atom2 - 1, order);
}
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading bond information";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
}
line = input.ReadLine();
}
}
catch (System.IO.IOException exception)
{
System.String error = "Error while reading general structure";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
return molecule;
}
private void processAnnotation(System.String field, System.String value_Renamed, Reaction reaction)
{
//logger.debug("Annote: ", field, "=", value_Renamed);
if (field.Equals("RxnAtts") || field.Equals("RxnType"))
{
// reaction attributes
System.String dictionary = "macie";
if (value_Renamed.Equals("Acid") || value_Renamed.Equals("Base"))
{
dictionary = "chemical";
}
addDictRefedAnnotation(reaction, "Attributes", value_Renamed);
}
else if (field.Equals("ResiduesPresent") || field.Equals("GroupTransferred") || field.Equals("BondFormed") || field.Equals("ReactiveCentres") || field.Equals("BondCleaved") || field.Equals("BondFormed") || field.Equals("Products") || field.Equals("ResiduesPresent"))
{
reaction.setProperty(new DictRef("macie:" + field, value_Renamed), value_Renamed);
}
else if (field.Equals("Reversible"))
{
if (value_Renamed.ToUpper().Equals("yes".ToUpper()))
{
reaction.Direction = IReaction_Fields.BIDIRECTIONAL;
addDictRefedAnnotation(reaction, "ReactionType", "ReversibleReaction");
}
}
else if (field.Equals("OverallReactionType"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed, ",");
int i = 0;
while (tokenizer.HasMoreTokens())
{
System.String token = tokenizer.NextToken();
i++;
reaction.setProperty(DictionaryDatabase.DICTREFPROPERTYNAME + ":field:overallReactionType:" + i, "macie:" + token.ToLower());
}
}
else
{
Match residueLocatorMatcher = residueLocator.Match(field);
if (residueLocatorMatcher.Success)
{
//logger.debug("Found residueLocator: ", field);
IAtom[] atoms = ReactionManipulator.getAllInOneContainer(reaction).Atoms;
bool found = false;
//logger.debug("Searching for given residueLocator through #atom: ", atoms.Length);
//logger.debug("Taken from reaction ", reaction.ID);
for (int i = 0; (i < atoms.Length && !found); i++)
{
if (atoms[i] is PseudoAtom)
{
// that is what we are looking for
PseudoAtom atom = (PseudoAtom)atoms[i];
if (atom.Label.Equals(field))
{
// we have a hit, now mark Atom with dict refs
addDictRefedAnnotation(atom, "ResidueRole", value_Renamed);
found = true;
}
}
}
if (!found)
{
//logger.error("MACiE annotation mentions a residue that does not exist: " + field);
}
}
else
{
//logger.error("Did not parse annotation: ", field);
}
}
}
private void addDictRefedAnnotation(IChemObject object_Renamed, System.String type, System.String values)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(values, ",");
while (tokenizer.HasMoreTokens())
{
System.String token = tokenizer.NextToken();
object_Renamed.setProperty(new DictRef("macie:" + type, token), token);
//logger.debug("Added dict ref ", token, " to ", object_Renamed.GetType().FullName);
}
}
/// <summary> Select the theory and basis set from the first archive line.
///
/// </summary>
/// <param name="line">Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
private System.String parseLevelOfTheory(System.String line)
{
System.Text.StringBuilder summary = new System.Text.StringBuilder();
summary.Append(line);
try
{
do
{
line = input.ReadLine().Trim();
summary.Append(line);
}
while (!(line.IndexOf("@") >= 0));
}
catch (System.Exception exc)
{
//logger.debug("syntax problem while parsing summary of g98 section: ");
//logger.debug(exc);
}
//logger.debug("parseLoT(): " + summary.ToString());
SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(summary.ToString(), "\\");
// Must contain at least 6 tokens
if (st1.Count < 6)
{
return null;
}
// Skip first four tokens
for (int i = 0; i < 4; ++i)
{
st1.NextToken();
}
return st1.NextToken() + "/" + st1.NextToken();
}
/// <summary> Reads a set of vibrations into ChemFrame.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <exception cref="IOException"> if an I/O error occurs
/// </exception>
// private void readFrequencies(IChemModel model) throws IOException
// {
/*
* FIXME: this is yet to be ported
* String line;
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* while ((line != null) && line.startsWith(" Frequencies --")) {
* Vector currentVibs = new Vector();
* StringReader vibValRead = new StringReader(line.substring(15));
* StreamTokenizer token = new StreamTokenizer(vibValRead);
* while (token.nextToken() != StreamTokenizer.TT_EOF) {
* Vibration vib = new Vibration(Double.toString(token.nval));
* currentVibs.addElement(vib);
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* for (int i = 0; i < frame.getAtomCount(); ++i) {
* line = input.readLine();
* StringReader vectorRead = new StringReader(line);
* token = new StreamTokenizer(vectorRead);
* token.nextToken();
* / ignore first token
* token.nextToken();
* / ignore second token
* for (int j = 0; j < currentVibs.size(); ++j) {
* double[] v = new double[3];
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[0] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[1] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[2] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* ((Vibration) currentVibs.elementAt(j)).addAtomVector(v);
* }
* }
* for (int i = 0; i < currentVibs.size(); ++i) {
* frame.addVibration((Vibration) currentVibs.elementAt(i));
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* }
*/
// }
/// <summary> Reads NMR nuclear shieldings.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <param name="labelLine">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
private void readNMRData(IChemModel model, System.String labelLine)
{
IAtomContainer ac = ChemModelManipulator.getAllInOneContainer(model);
// Determine label for properties
System.String label;
if (labelLine.IndexOf("Diamagnetic") >= 0)
{
label = "Diamagnetic Magnetic shielding (Isotropic)";
}
else if (labelLine.IndexOf("Paramagnetic") >= 0)
{
label = "Paramagnetic Magnetic shielding (Isotropic)";
}
else
{
label = "Magnetic shielding (Isotropic)";
}
int atomIndex = 0;
for (int i = 0; i < atomCount; ++i)
{
try
{
System.String line = input.ReadLine().Trim();
while (line.IndexOf("Isotropic") < 0)
{
if (line == null)
{
return;
}
line = input.ReadLine().Trim();
}
SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(line);
// Find Isotropic label
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("Isotropic"))
{
break;
}
}
// Find Isotropic value
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("="))
break;
}
double shielding = System.Double.Parse(st1.NextToken());
//logger.info("Type of shielding: " + label);
ac.getAtomAt(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, (System.Object)shielding);
++atomIndex;
}
catch (System.Exception exc)
{
//logger.debug("failed to read line from gaussian98 file where I expected one.");
}
}
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
System.String s = new System.String(ch, start, length).Trim();
//logger.debug("Start PMP chardata (" + CurrentElement + ") :" + s);
//logger.debug(" ElTitle: " + elementTitle);
if (xpath.ToString().EndsWith("string/") && BUILTIN.Equals("spacegroup"))
{
System.String sg = "P1";
// standardize space group names (see Crystal.java)
if ("P 21 21 21 (1)".Equals(s))
{
sg = "P 2_1 2_1 2_1";
}
cdo.setObjectProperty("Crystal", "spacegroup", sg);
}
else
{
if (xpath.ToString().EndsWith("floatArray/") && (elementTitle.Equals("a") || elementTitle.Equals("b") || elementTitle.Equals("c")))
{
System.String axis = elementTitle + "-axis";
cdo.startObject(axis);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(s);
//logger.debug("Tokens: " + st.Count);
if (st.Count > 2)
{
System.String token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "x", token);
token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "y", token);
token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "z", token);
}
else
{
//logger.debug("PMP Convention error: incorrect number of cell axis fractions!\n");
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("PMP Convention error: " + e.ToString());
}
cdo.endObject(axis);
}
else
{
base.characterData(xpath, ch, start, length);
}
}
//logger.debug("End PMP chardata");
}
public virtual void startElement(CMLStack xpath, System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
System.String name = local;
////logger.debug("StartElement");
currentChars = "";
BUILTIN = "";
DICTREF = "";
for (int i = 0; i < atts.GetLength(); i++)
{
System.String qname = atts.GetFullName(i);
if (qname.Equals("builtin"))
{
BUILTIN = atts.GetValue(i);
////logger.debug(name, "->BUILTIN found: ", atts.GetValue(i));
}
else if (qname.Equals("dictRef"))
{
DICTREF = atts.GetValue(i);
////logger.debug(name, "->DICTREF found: ", atts.GetValue(i));
}
else if (qname.Equals("title"))
{
elementTitle = atts.GetValue(i);
////logger.debug(name, "->TITLE found: ", atts.GetValue(i));
}
else
{
////logger.debug("Qname: ", qname);
}
}
if ("atom".Equals(name))
{
atomCounter++;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
System.String value_Renamed = atts.GetValue(i);
if (att.Equals("id"))
{
// this is supported in CML 1.x
elid.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("elementType"))
{
elsym.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("title"))
{
eltitles.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("x2"))
{
x2.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("xy2"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
x2.Add(tokenizer.NextToken());
y2.Add(tokenizer.NextToken());
}
// this is supported in CML 2.0
else if (att.Equals("xyzFract"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
xfract.Add(tokenizer.NextToken());
yfract.Add(tokenizer.NextToken());
zfract.Add(tokenizer.NextToken());
}
// this is supported in CML 2.0
else if (att.Equals("xyz3"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
x3.Add(tokenizer.NextToken());
y3.Add(tokenizer.NextToken());
z3.Add(tokenizer.NextToken());
}
// this is supported in CML 2.0
else if (att.Equals("y2"))
{
y2.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("x3"))
{
x3.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("y3"))
{
y3.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("z3"))
{
z3.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("xFract"))
{
xfract.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("yFract"))
{
yfract.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("zFract"))
{
zfract.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("formalCharge"))
{
formalCharges.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("hydrogenCount"))
{
hCounts.Add(value_Renamed);
}
else if (att.Equals("isotope"))
{
isotope.Add(value_Renamed);
}
else if (att.Equals("dictRef"))
{
atomDictRefs.Add(value_Renamed);
}
else if (att.Equals("spinMultiplicity"))
{
spinMultiplicities.Add(value_Renamed);
}
else
{
////logger.warn("Unparsed attribute: " + att);
}
}
}
else if ("atomArray".Equals(name))
{
bool atomsCounted = false;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
int count = 0;
if (att.Equals("atomID"))
{
count = addArrayElementsTo(elid, atts.GetValue(i));
}
else if (att.Equals("elementType"))
{
count = addArrayElementsTo(elsym, atts.GetValue(i));
}
else if (att.Equals("x2"))
{
count = addArrayElementsTo(x2, atts.GetValue(i));
}
else if (att.Equals("y2"))
{
count = addArrayElementsTo(y2, atts.GetValue(i));
}
else if (att.Equals("x3"))
{
count = addArrayElementsTo(x3, atts.GetValue(i));
}
else if (att.Equals("y3"))
{
count = addArrayElementsTo(y3, atts.GetValue(i));
}
else if (att.Equals("z3"))
{
count = addArrayElementsTo(z3, atts.GetValue(i));
}
else if (att.Equals("xFract"))
{
count = addArrayElementsTo(xfract, atts.GetValue(i));
}
else if (att.Equals("yFract"))
{
count = addArrayElementsTo(yfract, atts.GetValue(i));
}
else if (att.Equals("zFract"))
{
count = addArrayElementsTo(zfract, atts.GetValue(i));
}
else
{
////logger.warn("Unparsed attribute: " + att);
}
if (!atomsCounted)
{
atomCounter += count;
atomsCounted = true;
}
}
}
else if ("bond".Equals(name))
{
bondCounter++;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
////logger.debug("B2 ", att, "=", atts.GetValue(i));
if (att.Equals("id"))
{
bondid.Add(atts.GetValue(i));
////logger.debug("B3 ", bondid);
}
else if (att.Equals("atomRefs") || att.Equals("atomRefs2"))
{
// this is CML 2.0 support
// expect exactly two references
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(atts.GetValue(i));
bondARef1.Add((System.String)st.NextToken());
bondARef2.Add((System.String)st.NextToken());
}
catch (System.Exception e)
{
//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("Error in CML file: ", e.Message);
////logger.debug(e);
}
}
else if (att.Equals("order"))
{
// this is CML 2.0 support
order.Add(atts.GetValue(i).Trim());
}
else if (att.Equals("dictRef"))
{
bondDictRefs.Add(atts.GetValue(i).Trim());
}
}
stereoGiven = false;
curRef = 0;
}
else if ("bondArray".Equals(name))
{
bool bondsCounted = false;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
int count = 0;
if (att.Equals("bondID"))
{
count = addArrayElementsTo(bondid, atts.GetValue(i));
}
else if (att.Equals("atomRefs1"))
{
count = addArrayElementsTo(bondARef1, atts.GetValue(i));
}
else if (att.Equals("atomRefs2"))
{
count = addArrayElementsTo(bondARef2, atts.GetValue(i));
}
else if (att.Equals("atomRef1"))
{
count = addArrayElementsTo(bondARef1, atts.GetValue(i));
}
else if (att.Equals("atomRef2"))
{
count = addArrayElementsTo(bondARef2, atts.GetValue(i));
}
else if (att.Equals("order"))
{
count = addArrayElementsTo(order, atts.GetValue(i));
}
else
{
////logger.warn("Unparsed attribute: " + att);
}
if (!bondsCounted)
{
bondCounter += count;
bondsCounted = true;
}
}
curRef = 0;
}
else if ("molecule".Equals(name))
{
newMolecule();
BUILTIN = "";
cdo.startObject("Molecule");
for (int i = 0; i < atts.GetLength(); i++)
{
if (atts.GetFullName(i).Equals("id"))
{
cdo.setObjectProperty("Molecule", "id", atts.GetValue(i));
}
else if (atts.GetFullName(i).Equals("dictRef"))
{
cdo.setObjectProperty("Molecule", "dictRef", atts.GetValue(i));
}
}
}
else if ("crystal".Equals(name))
{
newCrystalData();
cdo.startObject("Crystal");
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
if (att.Equals("z"))
{
cdo.setObjectProperty("Crystal", "z", atts.GetValue(i));
}
}
}
else if ("symmetry".Equals(name))
{
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
if (att.Equals("spaceGroup"))
{
cdo.setObjectProperty("Crystal", "spacegroup", atts.GetValue(i));
}
}
}
else if ("scalar".Equals(name))
{
if (xpath.ToString().EndsWith("crystal/scalar/"))
crystalScalar++;
}
else if ("list".Equals(name))
{
cdo.startObject("SetOfMolecules");
}
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
System.String s = new System.String(ch, start, length).Trim();
if (isELSYM)
{
elsym.Add(s);
}
else if (isBond)
{
//logger.debug("CD (bond): " + s);
if (connect_root.Length > 0)
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(s);
while (st.HasMoreTokens())
{
System.String atom = (System.String)st.NextToken();
if (!atom.Equals("0"))
{
//logger.debug("new bond: " + connect_root + "-" + atom);
cdo.startObject("Bond");
int atom1 = System.Int32.Parse(connect_root) - 1;
int atom2 = System.Int32.Parse(atom) - 1;
cdo.setObjectProperty("Bond", "atom1", ((System.Int32)atom1).ToString());
cdo.setObjectProperty("Bond", "atom2", ((System.Int32)atom2).ToString());
cdo.setObjectProperty("Bond", "order", "1");
cdo.endObject("Bond");
}
}
}
}
else
{
base.characterData(xpath, ch, start, length);
}
}
public virtual void endElement(CMLStack xpath, System.String uri, System.String name, System.String raw)
{
////logger.debug("EndElement: ", name);
System.String cData = currentChars;
if ("bond".Equals(name))
{
if (!stereoGiven)
bondStereo.Add("");
if (bondStereo.Count > bondDictRefs.Count)
bondDictRefs.Add(null);
}
else if ("atom".Equals(name))
{
if (atomCounter > eltitles.Count)
{
eltitles.Add(null);
}
if (atomCounter > hCounts.Count)
{
/* while strictly undefined, assume zero
implicit hydrogens when no number is given */
hCounts.Add("0");
}
if (atomCounter > atomDictRefs.Count)
{
atomDictRefs.Add(null);
}
if (atomCounter > isotope.Count)
{
isotope.Add(null);
}
if (atomCounter > spinMultiplicities.Count)
{
spinMultiplicities.Add(null);
}
if (atomCounter > formalCharges.Count)
{
/* while strictly undefined, assume zero
implicit hydrogens when no number is given */
formalCharges.Add("0");
}
/* It may happen that not all atoms have
associated 2D or 3D coordinates. accept that */
if (atomCounter > x2.Count && x2.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
x2.Add(null);
y2.Add(null);
}
if (atomCounter > x3.Count && x3.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
x3.Add(null);
y3.Add(null);
z3.Add(null);
}
if (atomCounter > xfract.Count && xfract.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
xfract.Add(null);
yfract.Add(null);
zfract.Add(null);
}
}
else if ("molecule".Equals(name))
{
storeData();
cdo.endObject("Molecule");
}
else if ("crystal".Equals(name))
{
if (crystalScalar > 0)
{
// convert unit cell parameters to cartesians
Vector3d[] axes = CrystalGeometryTools.notionalToCartesian(unitcellparams[0], unitcellparams[1], unitcellparams[2], unitcellparams[3], unitcellparams[4], unitcellparams[5]);
aAxis = axes[0];
bAxis = axes[1];
cAxis = axes[2];
cartesianAxesSet = true;
cdo.startObject("a-axis");
cdo.setObjectProperty("a-axis", "x", aAxis.x.ToString());
cdo.setObjectProperty("a-axis", "y", aAxis.y.ToString());
cdo.setObjectProperty("a-axis", "z", aAxis.z.ToString());
cdo.endObject("a-axis");
cdo.startObject("b-axis");
cdo.setObjectProperty("b-axis", "x", bAxis.x.ToString());
cdo.setObjectProperty("b-axis", "y", bAxis.y.ToString());
cdo.setObjectProperty("b-axis", "z", bAxis.z.ToString());
cdo.endObject("b-axis");
cdo.startObject("c-axis");
cdo.setObjectProperty("c-axis", "x", cAxis.x.ToString());
cdo.setObjectProperty("c-axis", "y", cAxis.y.ToString());
cdo.setObjectProperty("c-axis", "z", cAxis.z.ToString());
cdo.endObject("c-axis");
}
else
{
////logger.error("Could not find crystal unit cell parameters");
}
cdo.endObject("Crystal");
}
else if ("list".Equals(name))
{
cdo.endObject("SetOfMolecules");
}
else if ("coordinate3".Equals(name))
{
if (BUILTIN.Equals("xyz3"))
{
////logger.debug("New coord3 xyz3 found: ", currentChars);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(currentChars);
x3.Add(st.NextToken());
y3.Add(st.NextToken());
z3.Add(st.NextToken());
////logger.debug("coord3 x3.length: ", x3.Count);
////logger.debug("coord3 y3.length: ", y3.Count);
////logger.debug("coord3 z3.length: ", z3.Count);
}
catch (System.Exception exception)
{
////logger.error("CMLParsing error while setting coordinate3!");
////logger.debug(exception);
}
}
else
{
////logger.warn("Unknown coordinate3 BUILTIN: " + BUILTIN);
}
}
else if ("string".Equals(name))
{
if (BUILTIN.Equals("elementType"))
{
////logger.debug("Element: ", cData.Trim());
elsym.Add(cData);
}
else if (BUILTIN.Equals("atomRef"))
{
curRef++;
////logger.debug("Bond: ref #", curRef);
if (curRef == 1)
{
bondARef1.Add(cData.Trim());
}
else if (curRef == 2)
{
bondARef2.Add(cData.Trim());
}
}
else if (BUILTIN.Equals("order"))
{
////logger.debug("Bond: order ", cData.Trim());
order.Add(cData.Trim());
}
else if (BUILTIN.Equals("formalCharge"))
{
// NOTE: this combination is in violation of the CML DTD!!!
////logger.warn("formalCharge BUILTIN accepted but violating CML DTD");
////logger.debug("Charge: ", cData.Trim());
System.String charge = cData.Trim();
if (charge.StartsWith("+") && charge.Length > 1)
{
charge = charge.Substring(1);
}
formalCharges.Add(charge);
}
}
else if ("float".Equals(name))
{
if (BUILTIN.Equals("x3"))
{
x3.Add(cData.Trim());
}
else if (BUILTIN.Equals("y3"))
{
y3.Add(cData.Trim());
}
else if (BUILTIN.Equals("z3"))
{
z3.Add(cData.Trim());
}
else if (BUILTIN.Equals("x2"))
{
x2.Add(cData.Trim());
}
else if (BUILTIN.Equals("y2"))
{
y2.Add(cData.Trim());
}
else if (BUILTIN.Equals("order"))
{
// NOTE: this combination is in violation of the CML DTD!!!
order.Add(cData.Trim());
}
else if (BUILTIN.Equals("charge") || BUILTIN.Equals("partialCharge"))
{
partialCharges.Add(cData.Trim());
}
}
else if ("integer".Equals(name))
{
if (BUILTIN.Equals("formalCharge"))
{
formalCharges.Add(cData.Trim());
}
}
else if ("coordinate2".Equals(name))
{
if (BUILTIN.Equals("xy2"))
{
////logger.debug("New coord2 xy2 found.", cData);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
x2.Add(st.NextToken());
y2.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 175, 1);
}
}
}
else if ("stringArray".Equals(name))
{
if (BUILTIN.Equals("id") || BUILTIN.Equals("atomId") || BUILTIN.Equals("atomID"))
{
// invalid according to CML1 DTD but found in OpenBabel 1.x output
try
{
bool countAtoms = (atomCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countAtoms)
{
atomCounter++;
}
System.String token = st.NextToken();
////logger.debug("StringArray (Token): ", token);
elid.Add(token);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 186, 1);
}
}
else if (BUILTIN.Equals("elementType"))
{
try
{
bool countAtoms = (atomCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countAtoms)
{
atomCounter++;
}
elsym.Add(st.NextToken());
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("atomRefs"))
{
curRef++;
////logger.debug("New atomRefs found: ", curRef);
try
{
bool countBonds = (bondCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countBonds)
{
bondCounter++;
}
System.String token = st.NextToken();
////logger.debug("Token: ", token);
if (curRef == 1)
{
bondARef1.Add(token);
}
else if (curRef == 2)
{
bondARef2.Add(token);
}
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("atomRef"))
{
curRef++;
////logger.debug("New atomRef found: ", curRef); // this is CML1 stuff, we get things like:
/*
<bondArray>
<stringArray builtin="atomRef">a2 a2 a2 a2 a3 a3 a4 a4 a5 a6 a7 a9</stringArray>
<stringArray builtin="atomRef">a9 a11 a12 a13 a5 a4 a6 a9 a7 a8 a8 a10</stringArray>
<stringArray builtin="order">1 1 1 1 2 1 2 1 1 1 2 2</stringArray>
</bondArray>
*/
try
{
bool countBonds = (bondCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countBonds)
{
bondCounter++;
}
System.String token = st.NextToken();
////logger.debug("Token: ", token);
if (curRef == 1)
{
bondARef1.Add(token);
}
else if (curRef == 2)
{
bondARef2.Add(token);
}
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("order"))
{
////logger.debug("New bond order found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
System.String token = st.NextToken();
////logger.debug("Token: ", token);
order.Add(token);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
}
else if ("integerArray".Equals(name))
{
////logger.debug("IntegerArray: builtin = ", BUILTIN);
if (BUILTIN.Equals("formalCharge"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
System.String token = st.NextToken();
////logger.debug("Charge added: ", token);
formalCharges.Add(token);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
}
else if ("scalar".Equals(name))
{
if (xpath.ToString().EndsWith("crystal/scalar/"))
{
////logger.debug("Going to set a crystal parameter: " + crystalScalar, " to ", cData);
try
{
unitcellparams[crystalScalar - 1] = System.Double.Parse(cData.Trim());
}
catch (System.FormatException exception)
{
////logger.error("Content must a float: " + cData);
}
}
else
{
if (xpath.ToString().EndsWith("bond/scalar/"))
{
if (DICTREF.Equals("mdl:stereo"))
{
bondStereo.Add(cData.Trim());
stereoGiven = true;
}
}
else
{
if (xpath.ToString().EndsWith("atom/scalar/"))
{
if (DICTREF.Equals("cdk:partialCharge"))
{
partialCharges.Add(cData.Trim());
}
}
else
{
if (xpath.ToString().EndsWith("molecule/scalar/"))
{
if (DICTREF.Equals("pdb:id"))
{
cdo.setObjectProperty("Molecule", DICTREF, cData);
}
}
else
{
////logger.warn("Ignoring scalar: " + xpath);
}
}
}
}
}
else if ("floatArray".Equals(name))
{
if (BUILTIN.Equals("x3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
x3.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
else if (BUILTIN.Equals("y3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
y3.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 213, 1);
}
}
else if (BUILTIN.Equals("z3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
z3.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 221, 1);
}
}
else if (BUILTIN.Equals("x2"))
{
////logger.debug("New floatArray found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
x2.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
else if (BUILTIN.Equals("y2"))
{
////logger.debug("New floatArray found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
y2.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 454, 1);
}
}
else if (BUILTIN.Equals("partialCharge"))
{
////logger.debug("New floatArray with partial charges found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
partialCharges.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 462, 1);
}
}
}
else if ("basic".Equals(name))
{
// assuming this is the child element of <identifier>
this.inchi = cData;
}
else if ("name".Equals(name))
{
if (xpath.ToString().EndsWith("molecule/name/"))
{
cdo.setObjectProperty("Molecule", DICTREF, cData);
}
}
else
{
////logger.warn("Skipping element: " + name);
}
currentChars = "";
BUILTIN = "";
elementTitle = "";
}
/// <summary> Reads the atoms, coordinates and charges.
///
/// <p>IMPORTANT: it does not support the atom list and its negation!
/// </summary>
public virtual void readAtomBlock(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END ATOM".Equals(command))
{
// FIXME: should check wether 3D is really 2D
foundEND = true;
}
else
{
//logger.debug("Parsing atom from: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
IAtom atom = readData.Builder.newAtom("C");
// parse the index
try
{
System.String indexString = tokenizer.NextToken();
atom.ID = indexString;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the element
System.String element = tokenizer.NextToken();
bool isElement = false;
try
{
isElement = IsotopeFactory.getInstance(atom.Builder).isElement(element);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine if element exists!", exception);
}
if (isPseudoAtom(element))
{
atom = readData.Builder.newPseudoAtom(atom);
}
else if (isElement)
{
atom.Symbol = element;
}
else
{
System.String error = "Cannot parse element of type: " + element;
//logger.error(error);
throw new CDKException("(Possible CDK bug) " + error);
}
// parse atom coordinates (in Angstrom)
try
{
System.String xString = tokenizer.NextToken();
System.String yString = tokenizer.NextToken();
System.String zString = tokenizer.NextToken();
double x = System.Double.Parse(xString);
double y = System.Double.Parse(yString);
double z = System.Double.Parse(zString);
atom.setPoint3d(new Point3d(x, y, z));
atom.setPoint2d(new Point2d(x, y)); // FIXME: dirty!
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom coordinates";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// atom-atom mapping
System.String mapping = tokenizer.NextToken();
if (!mapping.Equals("0"))
{
//logger.warn("Skipping atom-atom mapping: " + mapping);
} // else: default 0 is no mapping defined
// the rest are key value things
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (keys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CHG"))
{
int charge = System.Int32.Parse(value_Renamed);
if (charge != 0)
{
// zero is no charge specified
atom.setFormalCharge(charge);
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
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'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// store atom
readData.addAtom(atom);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Added atom: " + atom);
}
}
}
private void processAtomLoopBlock(System.String firstLine)
{
int atomLabel = -1; // -1 means not found in this block
int atomSymbol = -1;
int atomFractX = -1;
int atomFractY = -1;
int atomFractZ = -1;
int atomRealX = -1;
int atomRealY = -1;
int atomRealZ = -1;
System.String line = firstLine.Trim();
int headerCount = 0;
bool hasParsableInformation = false;
while (line != null && line[0] == '_')
{
headerCount++;
if (line.Equals("_atom_site_label") || line.Equals("_atom_site_label_atom_id"))
{
atomLabel = headerCount;
hasParsableInformation = true;
//logger.info("label found in col: " + atomLabel);
}
else if (line.StartsWith("_atom_site_fract_x"))
{
atomFractX = headerCount;
hasParsableInformation = true;
//logger.info("frac x found in col: " + atomFractX);
}
else if (line.StartsWith("_atom_site_fract_y"))
{
atomFractY = headerCount;
hasParsableInformation = true;
//logger.info("frac y found in col: " + atomFractY);
}
else if (line.StartsWith("_atom_site_fract_z"))
{
atomFractZ = headerCount;
hasParsableInformation = true;
//logger.info("frac z found in col: " + atomFractZ);
}
else if (line.Equals("_atom_site.Cartn_x"))
{
atomRealX = headerCount;
hasParsableInformation = true;
//logger.info("cart x found in col: " + atomRealX);
}
else if (line.Equals("_atom_site.Cartn_y"))
{
atomRealY = headerCount;
hasParsableInformation = true;
//logger.info("cart y found in col: " + atomRealY);
}
else if (line.Equals("_atom_site.Cartn_z"))
{
atomRealZ = headerCount;
hasParsableInformation = true;
//logger.info("cart z found in col: " + atomRealZ);
}
else if (line.Equals("_atom_site.type_symbol"))
{
atomSymbol = headerCount;
hasParsableInformation = true;
//logger.info("type_symbol found in col: " + atomSymbol);
}
else
{
//logger.warn("Ignoring atom loop block field: " + line);
}
line = input.ReadLine().Trim();
}
if (hasParsableInformation == false)
{
//logger.info("No parsable info found");
skipUntilEmptyOrCommentLine(line);
}
else
{
// now that headers are parsed, read the data
while (line != null && line.Length > 0 && line[0] != '#')
{
//logger.debug("new row");
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
if (tokenizer.Count < headerCount)
{
//logger.warn("Column count mismatch; assuming continued on next line");
//logger.debug("Found #expected, #found: " + headerCount + ", " + tokenizer.Count);
tokenizer = new SupportClass.Tokenizer(line + input.ReadLine());
}
int colIndex = 0;
// process one row
IAtom atom = crystal.Builder.newAtom("C");
Point3d frac = new Point3d();
Point3d real = new Point3d();
bool hasFractional = false;
bool hasCartesian = false;
while (tokenizer.HasMoreTokens())
{
colIndex++;
System.String field = tokenizer.NextToken();
//logger.debug("Parsing col,token: " + colIndex + "=" + field);
if (colIndex == atomLabel)
{
if (atomSymbol == -1)
{
// no atom symbol found, use label
System.String element = extractFirstLetters(field);
atom.Symbol = element;
}
atom.ID = field;
}
else if (colIndex == atomFractX)
{
hasFractional = true;
frac.x = parseIntoDouble(field);
}
else if (colIndex == atomFractY)
{
hasFractional = true;
frac.y = parseIntoDouble(field);
}
else if (colIndex == atomFractZ)
{
hasFractional = true;
frac.z = parseIntoDouble(field);
}
else if (colIndex == atomSymbol)
{
atom.Symbol = field;
}
else if (colIndex == atomRealX)
{
hasCartesian = true;
//logger.debug("Adding x3: " + parseIntoDouble(field));
real.x = parseIntoDouble(field);
}
else if (colIndex == atomRealY)
{
hasCartesian = true;
//logger.debug("Adding y3: " + parseIntoDouble(field));
real.y = parseIntoDouble(field);
}
else if (colIndex == atomRealZ)
{
hasCartesian = true;
//logger.debug("Adding x3: " + parseIntoDouble(field));
real.z = parseIntoDouble(field);
}
}
if (hasCartesian)
{
Vector3d a = crystal.A;
Vector3d b = crystal.B;
Vector3d c = crystal.C;
frac = CrystalGeometryTools.cartesianToFractional(a, b, c, real);
atom.setFractionalPoint3d(frac);
}
if (hasFractional)
{
atom.setFractionalPoint3d(frac);
}
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Adding atom: " + atom);
crystal.addAtom(atom);
// look up next row
line = input.ReadLine().Trim();
}
}
}
/// <summary> Reads the bond atoms, order and stereo configuration.</summary>
public virtual void readBondBlock(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END BOND".Equals(command))
{
foundEND = true;
}
else
{
//logger.debug("Parsing bond from: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
IBond bond = readData.Builder.newBond();
// parse the index
try
{
System.String indexString = tokenizer.NextToken();
bond.ID = indexString;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing bond index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the order
try
{
System.String orderString = tokenizer.NextToken();
int order = System.Int32.Parse(orderString);
if (order >= 4)
{
//logger.warn("Query order types are not supported (yet). File a bug if you need it");
}
else
{
bond.Order = (double)order;
}
}
catch (System.Exception exception)
{
System.String error = "Error while parsing bond index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 1
try
{
System.String indexAtom1String = tokenizer.NextToken();
int indexAtom1 = System.Int32.Parse(indexAtom1String);
IAtom atom1 = readData.getAtomAt(indexAtom1 - 1);
bond.setAtomAt(atom1, 0);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 1 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 2
try
{
System.String indexAtom2String = tokenizer.NextToken();
int indexAtom2 = System.Int32.Parse(indexAtom2String);
IAtom atom2 = readData.getAtomAt(indexAtom2 - 1);
bond.setAtomAt(atom2, 1);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 2 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// the rest are key=value fields
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (keys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CFG"))
{
int configuration = System.Int32.Parse(value_Renamed);
if (configuration == 0)
{
bond.Stereo = CDKConstants.STEREO_BOND_NONE;
}
else if (configuration == 1)
{
bond.Stereo = CDKConstants.STEREO_BOND_UP;
}
else if (configuration == 2)
{
bond.Stereo = CDKConstants.STEREO_BOND_UNDEFINED;
}
else if (configuration == 3)
{
bond.Stereo = CDKConstants.STEREO_BOND_DOWN;
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
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'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// storing bond
readData.addBond(bond);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Added bond: " + bond);
}
}
}
private System.String getMolName(System.String line)
{
if (line == null)
return ("");
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line, " ");
int ntok = st.Count;
System.String[] toks = new System.String[ntok];
for (int j = 0; j < ntok; j++)
{
toks[j] = st.NextToken();
}
if (toks.Length == 3)
return (toks[2]);
else
return ("");
}
/// <summary> Reads labels.</summary>
public virtual void readSGroup(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END SGROUP".Equals(command))
{
foundEND = true;
}
else
{
//logger.debug("Parsing Sgroup line: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
// parse the index
System.String indexString = tokenizer.NextToken();
//logger.warn("Skipping external index: " + indexString);
// parse command type
System.String type = tokenizer.NextToken();
// parse the external index
System.String externalIndexString = tokenizer.NextToken();
//logger.warn("Skipping external index: " + externalIndexString);
// the rest are key=value fields
System.Collections.Hashtable options = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
if (command.IndexOf("=") != -1)
{
options = parseOptions(exhaustStringTokenizer(tokenizer));
}
// now interpret line
if (type.StartsWith("SUP"))
{
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
int atomID = -1;
System.String label = "";
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (keys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("ATOMS"))
{
SupportClass.Tokenizer atomsTokenizer = new SupportClass.Tokenizer(value_Renamed);
System.Int32.Parse(atomsTokenizer.NextToken()); // should be 1, int atomCount =
atomID = System.Int32.Parse(atomsTokenizer.NextToken());
}
else if (key.Equals("LABEL"))
{
label = value_Renamed;
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
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'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
if (atomID != -1 && label.Length > 0)
{
IAtom atom = readData.getAtomAt(atomID - 1);
if (!(atom is IPseudoAtom))
{
atom = readData.Builder.newPseudoAtom(atom);
}
((IPseudoAtom)atom).Label = label;
readData.setAtomAt(atomID - 1, atom);
}
}
}
else
{
//logger.warn("Skipping unrecognized SGROUP type: " + type);
}
}
}
}
// private procedures
/// <summary> Private method that actually parses the input to read a ChemFile
/// object.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.newChemSequence();
int number_of_atoms = 0;
SupportClass.Tokenizer tokenizer;
try
{
System.String line = input.ReadLine();
while (input.Peek() != -1 && line != null)
{
// parse frame by frame
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
System.String token = tokenizer.NextToken();
number_of_atoms = System.Int32.Parse(token);
System.String info = input.ReadLine();
IChemModel chemModel = file.Builder.newChemModel();
ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();
IMolecule m = file.Builder.newMolecule();
m.setProperty(CDKConstants.TITLE, info);
for (int i = 0; i < number_of_atoms; i++)
{
line = input.ReadLine();
if (line == null)
break;
if (line.StartsWith("#") && line.Length > 1)
{
System.Object comment = m.getProperty(CDKConstants.COMMENT);
if (comment == null)
{
comment = "";
}
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
comment = comment.ToString() + line.Substring(1).Trim();
m.setProperty(CDKConstants.COMMENT, comment);
//logger.debug("Found and set comment: ", comment);
}
else
{
double x = 0.0f, y = 0.0f, z = 0.0f;
double charge = 0.0f;
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
int fields = tokenizer.Count;
if (fields < 4)
{
// this is an error but cannot throw exception
}
else
{
System.String atomtype = tokenizer.NextToken();
//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'"
x = (System.Double.Parse(tokenizer.NextToken()));
//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'"
y = (System.Double.Parse(tokenizer.NextToken()));
//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'"
z = (System.Double.Parse(tokenizer.NextToken()));
if (fields == 8)
{
//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'"
charge = (System.Double.Parse(tokenizer.NextToken()));
}
IAtom atom = file.Builder.newAtom(atomtype, new Point3d(x, y, z));
atom.setCharge(charge);
m.addAtom(atom);
}
}
}
setOfMolecules.addMolecule(m);
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
line = input.ReadLine();
}
file.addChemSequence(chemSequence);
}
catch (System.IO.IOException e)
{
// should make some noise now
file = null;
//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("Error while reading file: ", e.Message);
//logger.debug(e);
}
return file;
}
private IReaction readReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.newReaction();
readLine(); // first line should be $RXN
readLine(); // second line
readLine(); // third line
readLine(); // fourth line
int reactantCount = 0;
int productCount = 0;
bool foundCOUNTS = false;
while (Ready && !foundCOUNTS)
{
System.String command = readCommand();
if (command.StartsWith("COUNTS"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
try
{
tokenizer.NextToken();
reactantCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + reactantCount + " reactants in file");
productCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + productCount + " products in file");
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
foundCOUNTS = true;
}
else
{
//logger.warn("Waiting for COUNTS line, but found: " + command);
}
}
// now read the reactants
for (int i = 1; i <= reactantCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
System.String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.Equals("BEGIN REACTANT"))
{
System.String error = "Excepted start of reactant, but found: " + announceMDLFileLine;
//logger.error(error);
throw new CDKException(error);
}
System.String molFileLine = "";
while (!molFileLine.EndsWith("END REACTANT"))
{
molFileLine = readLine();
molFile.Append(molFileLine);
molFile.Append("\n");
};
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
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'"
System.String error = "Error while reading reactant: " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
// now read the products
for (int i = 1; i <= productCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
System.String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.Equals("BEGIN PRODUCT"))
{
System.String error = "Excepted start of product, but found: " + announceMDLFileLine;
//logger.error(error);
throw new CDKException(error);
}
System.String molFileLine = "";
while (!molFileLine.EndsWith("END PRODUCT"))
{
molFileLine = readLine();
molFile.Append(molFileLine);
molFile.Append("\n");
};
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
IMolecule product = (IMolecule)reader.read(builder.newMolecule());
// add product
reaction.addProduct(product);
}
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'"
System.String error = "Error while reading product: " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
return reaction;
}