/// <summary> Performs a breadthFirstSearch in an AtomContainer starting with a
/// particular sphere, which usually consists of one start atom. While
/// searching the graph, the method marks each visited atom. It then puts all
/// the atoms connected to the atoms in the given sphere into a new vector
/// which forms the sphere to search for the next recursive method call. All
/// atoms that have been visited are put into a molecule container. This
/// breadthFirstSearch does thus find the connected graph for a given start
/// atom.
///
/// </summary>
/// <param name="ac"> The AtomContainer to be searched
/// </param>
/// <param name="sphere"> A sphere of atoms to start the search with
/// </param>
/// <param name="molecule">A molecule into which all the atoms and bonds are stored
/// that are found during search
/// </param>
public static void breadthFirstSearch(IAtomContainer ac, System.Collections.ArrayList sphere, IMolecule molecule, int max)
{
IAtom atom;
IAtom nextAtom;
System.Collections.ArrayList newSphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < sphere.Count; f++)
{
atom = (IAtom)sphere[f];
//System.out.println("atoms "+ atom + f);
//System.out.println("sphere size "+ sphere.size());
molecule.addAtom(atom);
// first copy LonePair's and SingleElectron's of this Atom as they need
// to be copied too
IElectronContainer[] eContainers = ac.getConnectedElectronContainers(atom);
//System.out.println("found #ec's: " + eContainers.length);
for (int i = 0; i < eContainers.Length; i++)
{
if (!(eContainers[i] is IBond))
{
// ok, no bond, thus LonePair or SingleElectron
// System.out.println("adding non bond " + eContainers[i]);
molecule.addElectronContainer(eContainers[i]);
}
}
// now look at bonds
IBond[] bonds = ac.getConnectedBonds(atom);
for (int g = 0; g < bonds.Length; g++)
{
if (!bonds[g].getFlag(CDKConstants.VISITED))
{
molecule.addBond(bonds[g]);
bonds[g].setFlag(CDKConstants.VISITED, true);
}
nextAtom = bonds[g].getConnectedAtom(atom);
if (!nextAtom.getFlag(CDKConstants.VISITED))
{
// System.out.println("wie oft???");
newSphere.Add(nextAtom);
nextAtom.setFlag(CDKConstants.VISITED, true);
}
}
if (max > -1 && molecule.AtomCount > max)
{
return;
}
}
if (newSphere.Count > 0)
{
breadthFirstSearch(ac, newSphere, molecule, max);
}
}
/// <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 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);
}
/// <summary> Reads a set of coordinates from the "file system" file through the use of
/// the "input" field, scales coordinate to angstr???m unit, builds each atom with
/// the right associated coordinates, builds a new molecule with these atoms
/// and returns the complete molecule.
///
/// <p><b>Implementation</b>:
/// <br>Dummy atoms are ignored.
///
/// </summary>
/// <param name="coordinatesUnits The">unit in which coordinates are given.
///
/// </param>
/// <throws IOException may> be thrown by the "input" object. </throws IOException may>
/// <summary>
/// </summary>
/// <seealso cref="org.openscience.cdk.io.GamessReader.input">
/// </seealso>
//TODO Update method comments with appropriate information.
private IMolecule readCoordinates(IMolecule molecule, bool coordinatesUnits)
{
/*
* Coordinates must all be given in angstr???ms.
*/
double unitScaling = GamessReader.scalesCoordinatesUnits(coordinatesUnits);
System.String retrievedLineFromFile;
while (this.input.Peek() != -1 == true)
{
retrievedLineFromFile = this.input.ReadLine();
/*
* A coordinate set is followed by an empty line, so when this line
* is reached, there are no more coordinates to add to the current set.
*/
if ((retrievedLineFromFile == null) || (retrievedLineFromFile.Trim().Length == 0))
{
break;
}
int atomicNumber;
System.String atomicSymbol;
//StringReader sr = new StringReader(retrievedLineFromFile);
SupportClass.StreamTokenizerSupport token = new SupportClass.StreamTokenizerSupport(new System.IO.StringReader(retrievedLineFromFile));
/*
* The first token is ignored. It contains the atomic symbol and may
* be concatenated with a number.
*/
token.NextToken();
if (token.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'"
atomicNumber = (int)token.nval;
atomicSymbol = this.identifyAtomicSymbol(atomicNumber);
/*
* Dummy atoms are assumed to be given with an atomic number set
* to zero. We will do not add them to the molecule.
*/
if (atomicNumber == 0)
{
continue;
}
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
/*
* Atom's coordinates are stored in an array.
*/
double[] coordinates = new double[3];
for (int i = 0; i < coordinates.Length; i++)
{
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
coordinates[i] = token.nval * unitScaling;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
}
IAtom atom = molecule.Builder.newAtom(atomicSymbol, new Point3d(coordinates[0], coordinates[1], coordinates[2]));
molecule.addAtom(atom);
}
return molecule;
}
/// <summary> Reads a set of coordinates into ChemFrame.
///
/// </summary>
/// <param name="model">Description of the Parameter
/// </param>
/// <throws> IOException if an I/O error occurs </throws>
/// <throws> CDKException Description of the Exception </throws>
private void readCoordinates(IChemModel model)
{
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
IMolecule molecule = model.Builder.newMolecule();
System.String line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
while (input.Peek() != -1)
{
line = input.ReadLine();
if ((line == null) || (line.IndexOf("-----") >= 0))
{
break;
}
int atomicNumber;
System.IO.StringReader sr = new System.IO.StringReader(line);
SupportClass.StreamTokenizerSupport token = new SupportClass.StreamTokenizerSupport(sr);
token.NextToken();
// ignore first token
if (token.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'"
atomicNumber = (int)token.nval;
if (atomicNumber == 0)
{
// Skip dummy atoms. Dummy atoms must be skipped
// if frequencies are to be read because Gaussian
// does not report dummy atoms in frequencies, and
// the number of atoms is used for reading frequencies.
continue;
}
}
else
{
throw new CDKException("Error while reading coordinates: expected integer.");
}
token.NextToken();
// ignore third token
double x;
double y;
double z;
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
x = token.nval;
}
else
{
throw new System.IO.IOException("Error reading x coordinate");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
y = token.nval;
}
else
{
throw new System.IO.IOException("Error reading y coordinate");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
z = token.nval;
}
else
{
throw new System.IO.IOException("Error reading z coordinate");
}
System.String symbol = "Du";
try
{
symbol = IsotopeFactory.getInstance(model.Builder).getElementSymbol(atomicNumber);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine element symbol!", exception);
}
IAtom atom = model.Builder.newAtom(symbol);
atom.setPoint3d(new Point3d(x, y, z));
molecule.addAtom(atom);
}
/*
* this is the place where we store the atomcount to
* be used as a counter in the nmr reading
*/
atomCount = molecule.AtomCount;
moleculeSet.addMolecule(molecule);
model.SetOfMolecules = moleculeSet;
}
/// <summary> Read a Molecule from a file in MDL sd format
///
/// </summary>
/// <returns> The Molecule that was read from the MDL file.
/// </returns>
private IMolecule readMolecule(IMolecule molecule)
{
//logger.debug("Reading new molecule");
int linecount = 0;
int atoms = 0;
int bonds = 0;
int atom1 = 0;
int atom2 = 0;
int order = 0;
int stereo = 0;
int RGroupCounter = 1;
int Rnumber = 0;
System.String[] rGroup = null;
double x = 0.0;
double y = 0.0;
double z = 0.0;
double totalZ = 0.0;
//int[][] conMat = new int[0][0];
//String help;
IBond bond;
IAtom atom;
System.String line = "";
try
{
//logger.info("Reading header");
line = input.ReadLine(); linecount++;
if (line == null)
{
return(null);
}
//logger.debug("Line " + linecount + ": " + line);
if (line.StartsWith("$$$$"))
{
//logger.debug("File is empty, returning empty molecule");
return(molecule);
}
if (line.Length > 0)
{
molecule.setProperty(CDKConstants.TITLE, line);
}
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
if (line.Length > 0)
{
molecule.setProperty(CDKConstants.REMARK, line);
}
//logger.info("Reading rest of file");
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
atoms = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
//logger.debug("Atomcount: " + atoms);
bonds = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
//logger.debug("Bondcount: " + bonds);
// read ATOM block
//logger.info("Reading atom block");
for (int f = 0; f < atoms; f++)
{
line = input.ReadLine(); linecount++;
//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(line.Substring(0, (10) - (0)).Trim());
//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(line.Substring(10, (20) - (10)).Trim());
//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(line.Substring(20, (30) - (20)).Trim());
totalZ += System.Math.Abs(z); // *all* values should be zero, not just the sum
//logger.debug("Coordinates: " + x + "; " + y + "; " + z);
System.String element = line.Substring(31, (34) - (31)).Trim();
//logger.debug("Atom type: ", element);
if (IsotopeFactory.getInstance(molecule.Builder).isElement(element))
{
atom = IsotopeFactory.getInstance(molecule.Builder).configure(molecule.Builder.newAtom(element));
}
else
{
//logger.debug("Atom ", element, " is not an regular element. Creating a PseudoAtom.");
//check if the element is R
rGroup = element.Split(new char[] { '^', 'R' }); // ????
if (rGroup.Length > 1)
{
try
{
Rnumber = System.Int32.Parse(rGroup[(rGroup.Length - 1)]);
RGroupCounter = Rnumber;
}
catch (System.Exception ex)
{
Rnumber = RGroupCounter;
RGroupCounter++;
}
element = "R" + Rnumber;
}
atom = molecule.Builder.newPseudoAtom(element);
}
// store as 3D for now, convert to 2D (if totalZ == 0.0) later
atom.setPoint3d(new Point3d(x, y, z));
// parse further fields
System.String massDiffString = line.Substring(34, (36) - (34)).Trim();
//logger.debug("Mass difference: ", massDiffString);
if (!(atom is IPseudoAtom))
{
try
{
int massDiff = System.Int32.Parse(massDiffString);
if (massDiff != 0)
{
IIsotope major = IsotopeFactory.getInstance(molecule.Builder).getMajorIsotope(element);
atom.AtomicNumber = major.AtomicNumber + massDiff;
}
}
catch (System.Exception exception)
{
//logger.error("Could not parse mass difference field");
}
}
else
{
//logger.error("Cannot set mass difference for a non-element!");
}
System.String chargeCodeString = line.Substring(36, (39) - (36)).Trim();
//logger.debug("Atom charge code: ", chargeCodeString);
int chargeCode = System.Int32.Parse(chargeCodeString);
if (chargeCode == 0)
{
// uncharged species
}
else if (chargeCode == 1)
{
atom.setFormalCharge(+3);
}
else if (chargeCode == 2)
{
atom.setFormalCharge(+2);
}
else if (chargeCode == 3)
{
atom.setFormalCharge(+1);
}
else if (chargeCode == 4)
{
}
else if (chargeCode == 5)
{
atom.setFormalCharge(-1);
}
else if (chargeCode == 6)
{
atom.setFormalCharge(-2);
}
else if (chargeCode == 7)
{
atom.setFormalCharge(-3);
}
try
{
// read the mmm field as position 61-63
System.String reactionAtomIDString = line.Substring(60, (63) - (60)).Trim();
//logger.debug("Parsing mapping id: ", reactionAtomIDString);
try
{
int reactionAtomID = System.Int32.Parse(reactionAtomIDString);
if (reactionAtomID != 0)
{
atom.ID = reactionAtomIDString;
}
}
catch (System.Exception exception)
{
//logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");
//logger.debug(exception);
}
}
catch (System.Exception exception)
{
// older mol files don't have all these fields...
//logger.warn("A few fields are missing. Older MDL MOL file?");
}
molecule.addAtom(atom);
}
// convert to 2D, if totalZ == 0
if (totalZ == 0.0 && !forceReadAs3DCoords.Set)
{
//logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");
IAtom[] atomsToUpdate = molecule.Atoms;
for (int f = 0; f < atomsToUpdate.Length; f++)
{
IAtom atomToUpdate = atomsToUpdate[f];
Point3d p3d = atomToUpdate.getPoint3d();
atomToUpdate.setPoint2d(new Point2d(p3d.x, p3d.y));
atomToUpdate.setPoint3d(null);
}
}
// read BOND block
//logger.info("Reading bond block");
for (int f = 0; f < bonds; f++)
{
line = input.ReadLine(); linecount++;
atom1 = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
atom2 = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
order = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
if (line.Length > 12)
{
stereo = System.Int32.Parse(line.Substring(9, (12) - (9)).Trim());
}
else
{
//logger.warn("Missing expected stereo field at line: " + line);
}
//if (//logger.DebugEnabled)
//{
// //logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order);
//}
if (stereo == 1)
{
// MDL up bond
stereo = CDKConstants.STEREO_BOND_UP;
}
else if (stereo == 6)
{
// MDL down bond
stereo = CDKConstants.STEREO_BOND_DOWN;
}
else if (stereo == 4)
{
//MDL bond undefined
stereo = CDKConstants.STEREO_BOND_UNDEFINED;
}
// interpret CTfile's special bond orders
IAtom a1 = molecule.getAtomAt(atom1 - 1);
IAtom a2 = molecule.getAtomAt(atom2 - 1);
if (order == 4)
{
// aromatic bond
bond = molecule.Builder.newBond(a1, a2, CDKConstants.BONDORDER_AROMATIC, stereo);
// mark both atoms and the bond as aromatic
bond.setFlag(CDKConstants.ISAROMATIC, true);
a1.setFlag(CDKConstants.ISAROMATIC, true);
a2.setFlag(CDKConstants.ISAROMATIC, true);
molecule.addBond(bond);
}
else
{
bond = molecule.Builder.newBond(a1, a2, (double)order, stereo);
molecule.addBond(bond);
}
}
// read PROPERTY block
//logger.info("Reading property block");
while (true)
{
line = input.ReadLine(); linecount++;
if (line == null)
{
throw new CDKException("The expected property block is missing!");
}
if (line.StartsWith("M END"))
{
break;
}
bool lineRead = false;
if (line.StartsWith("M CHG"))
{
// FIXME: if this is encountered for the first time, all
// atom charges should be set to zero first!
int infoCount = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
System.String token = st.NextToken();
int atomNumber = System.Int32.Parse(token.Trim());
token = st.NextToken();
int charge = System.Int32.Parse(token.Trim());
molecule.getAtomAt(atomNumber - 1).setFormalCharge(charge);
}
}
else if (line.StartsWith("M ISO"))
{
try
{
System.String countString = line.Substring(6, (9) - (6)).Trim();
int infoCount = System.Int32.Parse(countString);
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
int atomNumber = System.Int32.Parse(st.NextToken().Trim());
int absMass = System.Int32.Parse(st.NextToken().Trim());
if (absMass != 0)
{
IAtom isotope = molecule.getAtomAt(atomNumber - 1);
isotope.MassNumber = absMass;
}
}
}
catch (System.FormatException 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 (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in isotope information on line: " + line, exception);
}
}
else if (line.StartsWith("M RAD"))
{
try
{
System.String countString = line.Substring(6, (9) - (6)).Trim();
int infoCount = System.Int32.Parse(countString);
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
int atomNumber = System.Int32.Parse(st.NextToken().Trim());
int spinMultiplicity = System.Int32.Parse(st.NextToken().Trim());
if (spinMultiplicity > 1)
{
IAtom radical = molecule.getAtomAt(atomNumber - 1);
for (int j = 2; j <= spinMultiplicity; j++)
{
// 2 means doublet -> one unpaired electron
// 3 means triplet -> two unpaired electron
molecule.addElectronContainer(molecule.Builder.newSingleElectron(radical));
}
}
}
}
catch (System.FormatException 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 (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in radical information on line: " + line, exception);
}
}
else if (line.StartsWith("G "))
{
try
{
System.String atomNumberString = line.Substring(3, (6) - (3)).Trim();
int atomNumber = System.Int32.Parse(atomNumberString);
//String whatIsThisString = line.substring(6,9).trim();
System.String atomName = input.ReadLine();
// convert Atom into a PseudoAtom
IAtom prevAtom = molecule.getAtomAt(atomNumber - 1);
IPseudoAtom pseudoAtom = molecule.Builder.newPseudoAtom(atomName);
if (prevAtom.getPoint2d() != null)
{
pseudoAtom.setPoint2d(prevAtom.getPoint2d());
}
if (prevAtom.getPoint3d() != null)
{
pseudoAtom.setPoint3d(prevAtom.getPoint3d());
}
AtomContainerManipulator.replaceAtomByAtom(molecule, prevAtom, pseudoAtom);
}
catch (System.FormatException exception)
{
//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'"
System.String error = "Error (" + exception.ToString() + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in group information on line: " + line, exception);
}
}
if (!lineRead)
{
//logger.warn("Skipping line in property block: ", line);
}
}
}
catch (CDKException 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 line " + linecount + ": " + line + " -> " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw exception;
}
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 line " + linecount + ": " + line + " -> " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
return(molecule);
}
/// <summary> Reads a set of coordinates from the "file system" file through the use of
/// the "input" field, scales coordinate to angstr???m unit, builds each atom with
/// the right associated coordinates, builds a new molecule with these atoms
/// and returns the complete molecule.
///
/// <p><b>Implementation</b>:
/// <br>Dummy atoms are ignored.
///
/// </summary>
/// <param name="coordinatesUnits The">unit in which coordinates are given.
///
/// </param>
/// <throws IOException may> be thrown by the "input" object. </throws IOException may>
/// <summary>
/// </summary>
/// <seealso cref="org.openscience.cdk.io.GamessReader.input">
/// </seealso>
//TODO Update method comments with appropriate information.
private IMolecule readCoordinates(IMolecule molecule, bool coordinatesUnits)
{
/*
* Coordinates must all be given in angstr???ms.
*/
double unitScaling = GamessReader.scalesCoordinatesUnits(coordinatesUnits);
System.String retrievedLineFromFile;
while (this.input.Peek() != -1 == true)
{
retrievedLineFromFile = this.input.ReadLine();
/*
* A coordinate set is followed by an empty line, so when this line
* is reached, there are no more coordinates to add to the current set.
*/
if ((retrievedLineFromFile == null) || (retrievedLineFromFile.Trim().Length == 0))
{
break;
}
int atomicNumber;
System.String atomicSymbol;
//StringReader sr = new StringReader(retrievedLineFromFile);
SupportClass.StreamTokenizerSupport token = new SupportClass.StreamTokenizerSupport(new System.IO.StringReader(retrievedLineFromFile));
/*
* The first token is ignored. It contains the atomic symbol and may
* be concatenated with a number.
*/
token.NextToken();
if (token.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'"
atomicNumber = (int)token.nval;
atomicSymbol = this.identifyAtomicSymbol(atomicNumber);
/*
* Dummy atoms are assumed to be given with an atomic number set
* to zero. We will do not add them to the molecule.
*/
if (atomicNumber == 0)
{
continue;
}
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
/*
* Atom's coordinates are stored in an array.
*/
double[] coordinates = new double[3];
for (int i = 0; i < coordinates.Length; i++)
{
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
coordinates[i] = token.nval * unitScaling;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
}
IAtom atom = molecule.Builder.newAtom(atomicSymbol, new Point3d(coordinates[0], coordinates[1], coordinates[2]));
molecule.addAtom(atom);
}
return(molecule);
}
/// <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;
}
/// <summary> Performs a breadthFirstSearch in an AtomContainer starting with a
/// particular sphere, which usually consists of one start atom. While
/// searching the graph, the method marks each visited atom. It then puts all
/// the atoms connected to the atoms in the given sphere into a new vector
/// which forms the sphere to search for the next recursive method call. All
/// atoms that have been visited are put into a molecule container. This
/// breadthFirstSearch does thus find the connected graph for a given start
/// atom.
///
/// </summary>
/// <param name="ac"> The AtomContainer to be searched
/// </param>
/// <param name="sphere"> A sphere of atoms to start the search with
/// </param>
/// <param name="molecule">A molecule into which all the atoms and bonds are stored
/// that are found during search
/// </param>
public static void breadthFirstSearch(IAtomContainer ac, System.Collections.ArrayList sphere, IMolecule molecule, int max)
{
IAtom atom;
IAtom nextAtom;
System.Collections.ArrayList newSphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < sphere.Count; f++)
{
atom = (IAtom)sphere[f];
//System.out.println("atoms "+ atom + f);
//System.out.println("sphere size "+ sphere.size());
molecule.addAtom(atom);
// first copy LonePair's and SingleElectron's of this Atom as they need
// to be copied too
IElectronContainer[] eContainers = ac.getConnectedElectronContainers(atom);
//System.out.println("found #ec's: " + eContainers.length);
for (int i = 0; i < eContainers.Length; i++)
{
if (!(eContainers[i] is IBond))
{
// ok, no bond, thus LonePair or SingleElectron
// System.out.println("adding non bond " + eContainers[i]);
molecule.addElectronContainer(eContainers[i]);
}
}
// now look at bonds
IBond[] bonds = ac.getConnectedBonds(atom);
for (int g = 0; g < bonds.Length; g++)
{
if (!bonds[g].getFlag(CDKConstants.VISITED))
{
molecule.addBond(bonds[g]);
bonds[g].setFlag(CDKConstants.VISITED, true);
}
nextAtom = bonds[g].getConnectedAtom(atom);
if (!nextAtom.getFlag(CDKConstants.VISITED))
{
// System.out.println("wie oft???");
newSphere.Add(nextAtom);
nextAtom.setFlag(CDKConstants.VISITED, true);
}
}
if (max > -1 && molecule.AtomCount > max)
return;
}
if (newSphere.Count > 0)
{
breadthFirstSearch(ac, newSphere, molecule, max);
}
}
/// <summary> Produces an AtomContainer without explicit Hs but with H count from one with Hs.
/// The new molecule is a deep copy.
///
/// </summary>
/// <param name="atomContainer">The AtomContainer from which to remove the hydrogens
/// </param>
/// <returns> The molecule without Hs.
/// </returns>
/// <cdk.keyword> hydrogen, removal </cdk.keyword>
public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
{
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
System.Collections.IDictionary map = new System.Collections.Hashtable(); // maps original atoms to clones.
System.Collections.IList remove = new System.Collections.ArrayList(); // lists removed Hs.
// Clone atoms except those to be removed.
IMolecule mol = atomContainer.Builder.newMolecule();
int count = atomContainer.AtomCount;
for (int i = 0; i < count; i++)
{
// Clone/remove this atom?
IAtom atom = atomContainer.getAtomAt(i);
if (!atom.Symbol.Equals("H"))
{
IAtom clonedAtom = null;
try
{
clonedAtom = (IAtom)atom.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clonedAtom.setHydrogenCount(0);
mol.addAtom(clonedAtom);
map[atom] = clonedAtom;
}
else
{
remove.Add(atom); // maintain list of removed H.
}
}
// Clone bonds except those involving removed atoms.
count = atomContainer.getBondCount();
for (int i = 0; i < count; i++)
{
// Check bond.
//UPGRADE_NOTE: Final was removed from the declaration of 'bond '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
IBond bond = atomContainer.getBondAt(i);
IAtom[] atoms = bond.getAtoms();
bool removedBond = false;
//UPGRADE_NOTE: Final was removed from the declaration of 'length '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
int length = atoms.Length;
for (int k = 0; k < length; k++)
{
if (remove.Contains(atoms[k]))
{
removedBond = true;
break;
}
}
// Clone/remove this bond?
if (!removedBond)
// if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
{
IBond clone = null;
try
{
clone = (IBond)atomContainer.getBondAt(i).Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clone.setAtoms(new IAtom[] { (IAtom)map[atoms[0]], (IAtom)map[atoms[1]] });
mol.addBond(clone);
}
}
// Recompute hydrogen counts of neighbours of removed Hydrogens.
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' 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_javautilIteratorhasNext'"
for (System.Collections.IEnumerator i = remove.GetEnumerator(); i.MoveNext();)
{
// Process neighbours.
//UPGRADE_TODO: Method 'java.util.Iterator.next' 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_javautilIteratornext'"
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' 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_javautilIteratorhasNext'"
for (System.Collections.IEnumerator n = atomContainer.getConnectedAtomsVector((IAtom)i.Current).GetEnumerator(); n.MoveNext();)
{
//UPGRADE_NOTE: Final was removed from the declaration of 'neighb '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
//UPGRADE_TODO: Method 'java.util.Iterator.next' 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_javautilIteratornext'"
IAtom neighb = (IAtom)map[n.Current];
neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
}
}
mol.Properties = atomContainer.Properties;
mol.Flags = atomContainer.Flags;
return(mol);
}
/// <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> 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);
}