/// <summary> Reads partial atomic charges and add the to the given ChemModel.
///
/// </summary>
/// <param name="model">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
/// <throws> IOException Description of the Exception </throws>
private void readPartialCharges(IChemModel model)
{
//logger.info("Reading partial atomic charges");
ISetOfMolecules moleculeSet = model.SetOfMolecules;
IMolecule molecule = moleculeSet.getMolecule(0);
System.String line = input.ReadLine();
// skip first line after "Total atomic charges"
while (input.Peek() != -1)
{
line = input.ReadLine();
//logger.debug("Read charge block line: " + line);
if ((line == null) || (line.IndexOf("Sum of Mulliken charges") >= 0))
{
//logger.debug("End of charge block found");
break;
}
System.IO.StringReader sr = new System.IO.StringReader(line);
SupportClass.StreamTokenizerSupport tokenizer = new SupportClass.StreamTokenizerSupport(sr);
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int atomCounter = (int)tokenizer.nval;
tokenizer.NextToken();
// ignore the symbol
double charge;
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
charge = tokenizer.nval;
//logger.debug("Found charge for atom " + atomCounter + ": " + charge);
}
else
{
throw new CDKException("Error while reading charge: expected double.");
}
IAtom atom = molecule.getAtomAt(atomCounter - 1);
atom.setCharge(charge);
}
}
}
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> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void setObjectProperty(System.String objectType, System.String propertyType, System.String propertyValue)
{
//logger.debug("objectType: " + objectType);
//logger.debug("propType: " + propertyType);
//logger.debug("property: " + propertyValue);
if (objectType == null)
{
//logger.error("Cannot add property for null object");
return;
}
if (propertyType == null)
{
//logger.error("Cannot add property for null property type");
return;
}
if (propertyValue == null)
{
//logger.warn("Will not add null property");
return;
}
if (objectType.Equals("Molecule"))
{
if (propertyType.Equals("id"))
{
currentMolecule.ID = propertyValue;
}
else if (propertyType.Equals("inchi"))
{
currentMolecule.setProperty("iupac.nist.chemical.identifier", propertyValue);
}
else if (propertyType.Equals("pdb:residueName"))
{
currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue);
}
else if (propertyType.Equals("pdb:oneLetterCode"))
{
currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue);
}
else if (propertyType.Equals("pdb:id"))
{
currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue);
}
else
{
//logger.warn("Not adding molecule property!");
}
}
else if (objectType.Equals("PseudoAtom"))
{
if (propertyType.Equals("label"))
{
if (!(currentAtom is IPseudoAtom))
{
currentAtom = currentChemFile.Builder.newPseudoAtom(currentAtom);
}
((IPseudoAtom)currentAtom).Label = propertyValue;
}
}
else if (objectType.Equals("Atom"))
{
if (propertyType.Equals("type"))
{
if (propertyValue.Equals("R") && !(currentAtom is IPseudoAtom))
{
currentAtom = currentChemFile.Builder.newPseudoAtom(currentAtom);
}
currentAtom.Symbol = propertyValue;
}
else if (propertyType.Equals("x2"))
{
//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'"
currentAtom.X2d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("y2"))
{
//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'"
currentAtom.Y2d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("x3"))
{
//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'"
currentAtom.X3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("y3"))
{
//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'"
currentAtom.Y3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("z3"))
{
//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'"
currentAtom.Z3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("xFract"))
{
//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'"
currentAtom.FractX3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("yFract"))
{
//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'"
currentAtom.FractY3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("zFract"))
{
//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'"
currentAtom.FractZ3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("formalCharge"))
{
currentAtom.setFormalCharge(System.Int32.Parse(propertyValue));
}
else if (propertyType.Equals("charge") || propertyType.Equals("partialCharge"))
{
//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'"
currentAtom.setCharge(System.Double.Parse(propertyValue));
}
else if (propertyType.Equals("hydrogenCount"))
{
currentAtom.setHydrogenCount(System.Int32.Parse(propertyValue));
}
else if (propertyType.Equals("dictRef"))
{
currentAtom.setProperty("org.openscience.cdk.dict", propertyValue);
}
else if (propertyType.Equals("atomicNumber"))
{
currentAtom.AtomicNumber = System.Int32.Parse(propertyValue);
}
else if (propertyType.Equals("massNumber"))
{
//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'"
currentAtom.MassNumber = (int)(System.Double.Parse(propertyValue));
}
else if (propertyType.Equals("spinMultiplicity"))
{
int unpairedElectrons = System.Int32.Parse(propertyValue) - 1;
for (int i = 0; i < unpairedElectrons; i++)
{
currentMolecule.addElectronContainer(currentChemFile.Builder.newSingleElectron(currentAtom));
}
}
else if (propertyType.Equals("id"))
{
//logger.debug("id: ", propertyValue);
currentAtom.ID = propertyValue;
atomEnumeration[propertyValue] = (System.Int32)numberOfAtoms;
}
}
else if (objectType.Equals("Bond"))
{
if (propertyType.Equals("atom1"))
{
bond_a1 = System.Int32.Parse(propertyValue);
}
else if (propertyType.Equals("atom2"))
{
bond_a2 = System.Int32.Parse(propertyValue);
}
else if (propertyType.Equals("id"))
{
//logger.debug("id: " + propertyValue);
bond_id = propertyValue;
}
else if (propertyType.Equals("order"))
{
try
{
bond_order = System.Double.Parse(propertyValue);
}
catch (System.Exception e)
{
//logger.error("Cannot convert to double: " + propertyValue);
bond_order = 1.0;
}
}
else if (propertyType.Equals("stereo"))
{
if (propertyValue.Equals("H"))
{
bond_stereo = CDKConstants.STEREO_BOND_DOWN;
}
else if (propertyValue.Equals("W"))
{
bond_stereo = CDKConstants.STEREO_BOND_UP;
}
}
}
else if (objectType.Equals("Reaction"))
{
if (propertyType.Equals("id"))
{
currentReaction.ID = propertyValue;
}
}
else if (objectType.Equals("SetOfReactions"))
{
if (propertyType.Equals("id"))
{
currentSetOfReactions.ID = propertyValue;
}
}
else if (objectType.Equals("Reactant"))
{
if (propertyType.Equals("id"))
{
currentMolecule.ID = propertyValue;
}
}
else if (objectType.Equals("Product"))
{
if (propertyType.Equals("id"))
{
currentMolecule.ID = propertyValue;
}
}
else if (objectType.Equals("Crystal"))
{
// set these variables
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
if (propertyType.Equals("spacegroup"))
{
//logger.debug("Setting crystal spacegroup to: " + propertyValue);
current.SpaceGroup = propertyValue;
}
else if (propertyType.Equals("z"))
{
try
{
//logger.debug("Setting z to: " + propertyValue);
current.Z = System.Int32.Parse(propertyValue);
}
catch (System.FormatException exception)
{
//logger.error("Error in format of Z value");
}
}
}
else
{
//logger.warn("Cannot add crystal cell parameters to a non " + "Crystal class!");
}
}
else if (objectType.Equals("a-axis") || objectType.Equals("b-axis") || objectType.Equals("c-axis"))
{
// set these variables
if (currentMolecule is ICrystal)
{
//logger.debug("Setting axis (" + objectType + "): " + propertyValue);
if (propertyType.Equals("x"))
{
crystal_axis_x = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("y"))
{
crystal_axis_y = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("z"))
{
crystal_axis_z = System.Double.Parse(propertyValue);
}
}
else
{
//logger.warn("Cannot add crystal cell parameters to a non " + "Crystal class!");
}
}
//logger.debug("Object property set...");
}
// 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 IChemFile readChemFile(IChemFile file)
{
IChemSequence seq = file.Builder.newChemSequence();
IChemModel model = file.Builder.newChemModel();
ICrystal crystal = null;
int lineNumber = 0;
Vector3d a, b, c;
try
{
System.String line = input.ReadLine();
while (input.Peek() != -1 && line != null)
{
//logger.debug((lineNumber++) + ": ", line);
if (line.StartsWith("frame:"))
{
//logger.debug("found new frame");
model = file.Builder.newChemModel();
crystal = file.Builder.newCrystal();
// assume the file format is correct
//logger.debug("reading spacegroup");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
crystal.SpaceGroup = line;
//logger.debug("reading unit cell axes");
Vector3d axis = new Vector3d();
//logger.debug("parsing A: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.A = axis;
axis = new Vector3d();
//logger.debug("parsing B: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.B = axis;
axis = new Vector3d();
//logger.debug("parsing C: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.C = axis;
//logger.debug("Crystal: ", crystal);
a = crystal.A;
b = crystal.B;
c = crystal.C;
//logger.debug("Reading number of atoms");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int atomsToRead = System.Int32.Parse(line);
//logger.debug("Reading no molecules in assym unit cell");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int Z = System.Int32.Parse(line);
crystal.Z = Z;
System.String symbol;
double charge;
Point3d cart;
for (int i = 1; i <= atomsToRead; i++)
{
cart = new Point3d();
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
symbol = line.Substring(0, (line.IndexOf(":")) - (0));
charge = System.Double.Parse(line.Substring(line.IndexOf(":") + 1));
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.x = System.Double.Parse(line); // x
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.y = System.Double.Parse(line); // y
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.z = System.Double.Parse(line); // z
IAtom atom = file.Builder.newAtom(symbol);
atom.setCharge(charge);
// convert cartesian coords to fractional
Point3d frac = CrystalGeometryTools.cartesianToFractional(a, b, c, cart);
atom.setFractionalPoint3d(frac);
crystal.addAtom(atom);
//logger.debug("Added atom: ", atom);
}
model.Crystal = crystal;
seq.addChemModel(model);
}
else
{
//logger.debug("Format seems broken. Skipping these lines:");
while (!line.StartsWith("frame:") && input.Peek() != -1 && line != null)
{
line = input.ReadLine();
//logger.debug(lineNumber++ + ": ", line);
}
//logger.debug("Ok, resynched: found new frame");
}
}
file.addChemSequence(seq);
}
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 message = "Error while parsing CrystClust file: " + exception.Message;
//logger.error(message);
//logger.debug(exception);
throw new CDKException(message, exception);
}
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);
}
