/// <summary> Method that assign properties to an atom given a particular atomType.
///
/// </summary>
/// <param name="atom"> Atom to configure
/// </param>
/// <param name="atomType"> AtomType
/// </param>
public static void configure(IAtom atom, IAtomType atomType)
{
atom.AtomTypeName = atomType.AtomTypeName;
atom.MaxBondOrder = atomType.MaxBondOrder;
atom.BondOrderSum = atomType.BondOrderSum;
atom.VanderwaalsRadius = atomType.VanderwaalsRadius;
atom.CovalentRadius = atomType.CovalentRadius;
atom.Valency = atomType.Valency;
atom.setFormalCharge(atomType.getFormalCharge());
atom.Hybridization = atomType.Hybridization;
atom.FormalNeighbourCount = atomType.FormalNeighbourCount;
atom.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
atom.setFlag(CDKConstants.IS_HYDROGENBOND_DONOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_DONOR));
System.Object constant = atomType.getProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT);
if (constant != null)
{
atom.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, constant);
}
atom.setFlag(CDKConstants.ISAROMATIC, atomType.getFlag(CDKConstants.ISAROMATIC));
System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color");
if (color != null)
{
atom.setProperty("org.openscience.cdk.renderer.color", color);
}
if (atomType.AtomicNumber != 0)
{
atom.AtomicNumber = atomType.AtomicNumber;
}
if (atomType.getExactMass() > 0.0)
{
atom.setExactMass(atomType.getExactMass());
}
}
/// <summary> Method that assign properties to an atom given a particular atomType.
///
/// </summary>
/// <param name="atom"> Atom to configure
/// </param>
/// <param name="atomType"> AtomType
/// </param>
public static void configure(IAtom atom, IAtomType atomType)
{
atom.AtomTypeName = atomType.AtomTypeName;
atom.MaxBondOrder = atomType.MaxBondOrder;
atom.BondOrderSum = atomType.BondOrderSum;
atom.VanderwaalsRadius = atomType.VanderwaalsRadius;
atom.CovalentRadius = atomType.CovalentRadius;
atom.Valency = atomType.Valency;
atom.setFormalCharge(atomType.getFormalCharge());
atom.Hybridization = atomType.Hybridization;
atom.FormalNeighbourCount = atomType.FormalNeighbourCount;
atom.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
atom.setFlag(CDKConstants.IS_HYDROGENBOND_DONOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_DONOR));
System.Object constant = atomType.getProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT);
if (constant != null)
{
atom.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, constant);
}
atom.setFlag(CDKConstants.ISAROMATIC, atomType.getFlag(CDKConstants.ISAROMATIC));
System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color");
if (color != null)
{
atom.setProperty("org.openscience.cdk.renderer.color", color);
}
if (atomType.AtomicNumber != 0)
{
atom.AtomicNumber = atomType.AtomicNumber;
}
if (atomType.getExactMass() > 0.0)
{
atom.setExactMass(atomType.getExactMass());
}
}
/// <summary>
/// Set integer FormalCharge for an atom
/// </summary>
/// <param name="atom"></param>
/// <param name="charge"></param>
public static void SetFormalCharge(
IAtom atom,
int charge)
{
atom.setFormalCharge(new java.lang.Integer(charge));
return;
}
/// <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...");
}
/// <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);
}
}
}