public override void write(IChemObject object_Renamed)
{
if (object_Renamed is IMolecule)
{
try
{
ISetOfMolecules som = object_Renamed.Builder.newSetOfMolecules();
som.addMolecule((IMolecule)object_Renamed);
writeMolecule(som);
}
catch (System.Exception ex)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException("Error while writing HIN file: " + ex.Message, ex);
}
}
else if (object_Renamed is ISetOfMolecules)
{
try
{
writeMolecule((ISetOfMolecules)object_Renamed);
}
catch (System.IO.IOException ex)
{
//
}
}
else
{
throw new CDKException("HINWriter only supports output of Molecule or SetOfMolecule classes.");
}
}
public static void removeAtomAndConnectedElectronContainers(IChemModel chemModel, IAtom atom)
{
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
if (crystal.contains(atom))
{
crystal.removeAtomAndConnectedElectronContainers(atom);
}
return;
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
SetOfMoleculesManipulator.removeAtomAndConnectedElectronContainers(moleculeSet, atom);
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
SetOfReactionsManipulator.removeAtomAndConnectedElectronContainers(reactionSet, atom);
}
}
public static void removeElectronContainer(IChemModel chemModel, IElectronContainer electrons)
{
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
if (crystal.contains(electrons))
{
crystal.removeElectronContainer(electrons);
}
return;
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
SetOfMoleculesManipulator.removeElectronContainer(moleculeSet, electrons);
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
SetOfReactionsManipulator.removeElectronContainer(reactionSet, electrons);
}
}
/// <summary> Takes an object which subclasses IChemObject, e.g.Molecule, and will read
/// this from from the Reader. If the specific implementation
/// does not support a specific IChemObject it will throw an Exception.
///
/// </summary>
/// <param name="object">The object that subclasses IChemObject
/// </param>
/// <returns> The IChemObject read
/// </returns>
/// <exception cref="CDKException">
/// </exception>
public override IChemObject read(IChemObject object_Renamed)
{
if (object_Renamed is IChemFile)
{
IChemFile file = (IChemFile)object_Renamed;
IChemSequence sequence = file.Builder.newChemSequence();
IChemModel model = file.Builder.newChemModel();
ISetOfMolecules moleculeSet = file.Builder.newSetOfMolecules();
moleculeSet.addMolecule(readMolecule(model.Builder.newMolecule()));
model.SetOfMolecules = moleculeSet;
sequence.addChemModel(model);
file.addChemSequence(sequence);
return(file);
}
else if (object_Renamed is IChemModel)
{
IChemModel model = (IChemModel)object_Renamed;
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addMolecule(readMolecule(model.Builder.newMolecule()));
model.SetOfMolecules = moleculeSet;
return(model);
}
else
{
throw new CDKException("Only supported is ChemModel, and not " + object_Renamed.GetType().FullName + ".");
}
}
/// <summary> Partitions the atoms in an AtomContainer into covalently connected components.
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be partitioned into connected components, i.e. molecules
/// </param>
/// <returns> A SetOfMolecules.
///
/// </returns>
/// <cdk.dictref> blue-obelisk:graphPartitioning </cdk.dictref>
public static ISetOfMolecules partitionIntoMolecules(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IElectronContainer eContainer = null;
IMolecule molecule = null;
ISetOfMolecules molecules = atomContainer.Builder.newSetOfMolecules();
System.Collections.ArrayList sphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
atom.setFlag(CDKConstants.VISITED, false);
ac.addAtom(atom);
}
IElectronContainer[] eContainers = atomContainer.ElectronContainers;
for (int f = 0; f < eContainers.Length; f++)
{
eContainer = eContainers[f];
eContainer.setFlag(CDKConstants.VISITED, false);
ac.addElectronContainer(eContainer);
}
while (ac.AtomCount > 0)
{
atom = ac.getAtomAt(0);
molecule = atomContainer.Builder.newMolecule();
sphere.Clear();
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
molecules.addMolecule(molecule);
ac.remove(molecule);
}
return(molecules);
}
/// <summary> Writes a SetOfMolecules to an OutputStream for the reaction.
///
/// </summary>
/// <param name="som"> The SetOfMolecules that is written to an OutputStream
/// </param>
private void writeSetOfMolecules(ISetOfMolecules som)
{
for (int i = 0; i < som.MoleculeCount; i++)
{
IMolecule mol = som.getMolecule(i);
for (int j = 0; j < som.getMultiplier(i); j++)
{
//MemoryStream ms = new MemoryStream();
//StreamWriter sw = new StreamWriter(ms);
writer.Write("$MOL\n");
MDLWriter mdlwriter = null;
try
{
mdlwriter = new MDLWriter(writer);
}
catch (System.Exception ex)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error(ex.Message);
//logger.debug(ex);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException("Exception while creating MDLWriter: " + ex.Message, ex);
}
mdlwriter.write(mol);
//writer.Write(sw.ToString());
}
}
}
/// <summary> Constructs an empty, forward reaction.</summary>
public Reaction()
{
this.reactants = new SetOfMolecules();
this.products = new SetOfMolecules();
this.agents = new SetOfMolecules();
this.map = new Mapping[growArraySize];
mappingCount = 0;
reactionDirection = IReaction_Fields.FORWARD;
}
/// <summary> Adds all molecules in the SetOfMolecules to this container.
///
/// </summary>
/// <param name="moleculeSet"> The SetOfMolecules
/// </param>
public virtual void add(ISetOfMolecules moleculeSet)
{
IMolecule[] mols = moleculeSet.Molecules;
for (int i = 0; i < mols.Length; i++)
{
addMolecule(mols[i]);
}
/* notifyChanged() called in super.addAtomContainer() */
}
public static IChemModel newChemModel(IAtomContainer molecule)
{
IChemModel model = molecule.Builder.newChemModel();
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addAtomContainer(molecule);
model.SetOfMolecules = moleculeSet;
return(model);
}
// procedures required by CDOInterface
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void startDocument()
{
//logger.info("New CDO Object");
currentChemSequence = currentChemFile.Builder.newChemSequence();
currentChemModel = currentChemFile.Builder.newChemModel();
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
currentMolecule = currentChemFile.Builder.newMolecule();
atomEnumeration = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
//protected internal LoggingTool logger;
/// <summary> Basic contructor</summary>
public ChemFileCDO(IChemFile file)
{
//logger = new LoggingTool(this);
currentChemFile = file;
currentChemSequence = file.Builder.newChemSequence();
currentChemModel = file.Builder.newChemModel();
currentSetOfMolecules = file.Builder.newSetOfMolecules();
currentSetOfReactions = null;
currentReaction = null;
currentMolecule = file.Builder.newMolecule();
atomEnumeration = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
public static ISetOfMolecules getAllMolecules(ISetOfReactions set_Renamed)
{
ISetOfMolecules moleculeSet = set_Renamed.Builder.newSetOfMolecules();
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
moleculeSet.add(ReactionManipulator.getAllMolecules(reaction));
}
return(moleculeSet);
}
/// <summary> Returns all the AtomContainer's of a ChemModel.</summary>
public static IAtomContainer[] getAllAtomContainers(IChemModel chemModel)
{
ISetOfMolecules moleculeSet = chemModel.Builder.newSetOfMolecules();
if (chemModel.SetOfMolecules != null)
{
moleculeSet.add(chemModel.SetOfMolecules);
}
if (chemModel.SetOfReactions != null)
{
moleculeSet.add(SetOfReactionsManipulator.getAllMolecules(chemModel.SetOfReactions));
}
return(SetOfMoleculesManipulator.getAllAtomContainers(moleculeSet));
}
/// <summary> Writes a list of molecules to an OutputStream
///
/// </summary>
/// <param name="som"> SetOfMolecules that is written to an OutputStream
/// </param>
public virtual void writeSetOfMolecules(ISetOfMolecules som)
{
IMolecule[] molecules = som.Molecules;
writeMolecule(molecules[0]);
for (int i = 1; i <= som.MoleculeCount - 1; i++)
{
try
{
writeMolecule(molecules[i]);
}
catch (System.Exception exc)
{
}
}
}
// private functions
/// <summary> Reads a ChemFile object from input.
///
/// </summary>
/// <returns> ChemFile with the content read from the input
/// </returns>
private IChemFile readChemFile(IChemFile cf)
{
// have to do stuff here
try
{
System.String line = input.ReadLine();
while (line != null)
{
if (line.StartsWith("INChI="))
{
// ok, the fun starts
cf = cf.Builder.newChemFile();
// ok, we need to parse things like:
// INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H
//UPGRADE_NOTE: Final was removed from the declaration of 'INChI '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String INChI = line.Substring(6);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(INChI, "/");
// ok, we expect 4 tokens
//UPGRADE_NOTE: Final was removed from the declaration of 'version '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String version = tokenizer.NextToken(); // 1.12Beta
//UPGRADE_NOTE: Final was removed from the declaration of 'formula '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String formula = tokenizer.NextToken(); // C6H6
//UPGRADE_NOTE: Final was removed from the declaration of 'connections '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String connections = tokenizer.NextToken().Substring(1); // 1-2-4-6-5-3-1
//UPGRADE_NOTE: Final was removed from the declaration of 'hydrogens '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String hydrogens = tokenizer.NextToken().Substring(1); // 1-6H
IAtomContainer parsedContent = inchiTool.processFormula(cf.Builder.newAtomContainer(), formula);
inchiTool.processConnections(connections, parsedContent, -1);
ISetOfMolecules moleculeSet = cf.Builder.newSetOfMolecules();
moleculeSet.addMolecule(cf.Builder.newMolecule(parsedContent));
IChemModel model = cf.Builder.newChemModel();
model.SetOfMolecules = moleculeSet;
IChemSequence sequence = cf.Builder.newChemSequence();
sequence.addChemModel(model);
cf.addChemSequence(sequence);
}
line = input.ReadLine();
}
}
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'"
throw new CDKException("Error while reading INChI file: " + exception.Message, exception);
}
return(cf);
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="smiles"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <exception cref="InvalidSmilesException"> Description of the Exception
/// </exception>
public virtual Reaction parseReactionSmiles(System.String smiles)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(smiles, ">");
System.String reactantSmiles = tokenizer.NextToken();
System.String agentSmiles = "";
System.String productSmiles = tokenizer.NextToken();
if (tokenizer.HasMoreTokens())
{
agentSmiles = productSmiles;
productSmiles = tokenizer.NextToken();
}
Reaction reaction = new Reaction();
// add reactants
IMolecule reactantContainer = parseSmiles(reactantSmiles);
ISetOfMolecules reactantSet = ConnectivityChecker.partitionIntoMolecules(reactantContainer);
IMolecule[] reactants = reactantSet.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
reaction.addReactant(reactants[i]);
}
// add reactants
if (agentSmiles.Length > 0)
{
IMolecule agentContainer = parseSmiles(agentSmiles);
ISetOfMolecules agentSet = ConnectivityChecker.partitionIntoMolecules(agentContainer);
IMolecule[] agents = agentSet.Molecules;
for (int i = 0; i < agents.Length; i++)
{
reaction.addAgent(agents[i]);
}
}
// add products
IMolecule productContainer = parseSmiles(productSmiles);
ISetOfMolecules productSet = ConnectivityChecker.partitionIntoMolecules(productContainer);
IMolecule[] products = productSet.Molecules;
for (int i = 0; i < products.Length; i++)
{
reaction.addProduct(products[i]);
}
return(reaction);
}
public static ISetOfMolecules getAllMolecules(IReaction reaction)
{
ISetOfMolecules moleculeSet = reaction.Builder.newSetOfMolecules();
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
moleculeSet.addMolecule(reactants[i]);
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
moleculeSet.addMolecule(products[i]);
}
return(moleculeSet);
}
private IChemModel readChemModel(IChemModel chemModel)
{
ISetOfMolecules setOfMolecules = chemModel.SetOfMolecules;
if (setOfMolecules == null)
{
setOfMolecules = chemModel.Builder.newSetOfMolecules();
}
IMolecule m = readMolecule(chemModel.Builder.newMolecule());
if (m != null)
{
setOfMolecules.addMolecule(m);
}
chemModel.SetOfMolecules = setOfMolecules;
return(chemModel);
}
public static IAtomContainer createNewMolecule(IChemModel chemModel)
{
// Add a new molecule either the set of molecules
IMolecule molecule = chemModel.Builder.newMolecule();
if (chemModel.SetOfMolecules != null)
{
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
moleculeSet.addMolecule(molecule);
}
else
{
ISetOfMolecules moleculeSet = chemModel.Builder.newSetOfMolecules();
moleculeSet.addMolecule(molecule);
chemModel.SetOfMolecules = moleculeSet;
}
return(molecule);
}
/// <summary> Method that saturates a molecule by adding implicit hydrogens.
///
/// </summary>
/// <param name="container"> Molecule to saturate
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> implicit hydrogen </cdk.keyword>
//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'"
public virtual System.Collections.Hashtable addImplicitHydrogensToSatisfyValency(IAtomContainer container)
{
ISetOfMolecules moleculeSet = ConnectivityChecker.partitionIntoMolecules(container);
IMolecule[] molecules = moleculeSet.Molecules;
//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.Hashtable hydrogenAtomMap = new System.Collections.Hashtable();
for (int k = 0; k < molecules.Length; k++)
{
IMolecule molPart = molecules[k];
IAtom[] atoms = molPart.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
int[] hydrogens = addImplicitHydrogensToSatisfyValency(molPart, atoms[f]);
hydrogenAtomMap[atoms[f]] = hydrogens;
}
}
return(hydrogenAtomMap);
}
/// <summary> Writes an array of Molecules to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="molecules"> Array of Molecules that is written to an OutputStream
/// </param>
private void writeSetOfMolecules(ISetOfMolecules som)
{
IMolecule[] molecules = som.Molecules;
for (int i = 0; i < som.MoleculeCount; i++)
{
try
{
bool[] isVisible = new bool[molecules[i].AtomCount];
for (int k = 0; k < isVisible.Length; k++)
{
isVisible[k] = true;
}
writeMolecule(molecules[i], isVisible);
}
catch (System.Exception exc)
{
}
}
}
/// <summary> Reads partial atomic charges and add the to the given ChemModel.
///
/// </summary>
/// <param name="model">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
/// <throws> IOException Description of the Exception </throws>
private void readPartialCharges(IChemModel model)
{
//logger.info("Reading partial atomic charges");
ISetOfMolecules moleculeSet = model.SetOfMolecules;
IMolecule molecule = moleculeSet.getMolecule(0);
System.String line = input.ReadLine();
// skip first line after "Total atomic charges"
while (input.Peek() != -1)
{
line = input.ReadLine();
//logger.debug("Read charge block line: " + line);
if ((line == null) || (line.IndexOf("Sum of Mulliken charges") >= 0))
{
//logger.debug("End of charge block found");
break;
}
System.IO.StringReader sr = new System.IO.StringReader(line);
SupportClass.StreamTokenizerSupport tokenizer = new SupportClass.StreamTokenizerSupport(sr);
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int atomCounter = (int)tokenizer.nval;
tokenizer.NextToken();
// ignore the symbol
double charge;
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
charge = tokenizer.nval;
//logger.debug("Found charge for atom " + atomCounter + ": " + charge);
}
else
{
throw new CDKException("Error while reading charge: expected double.");
}
IAtom atom = molecule.getAtomAt(atomCounter - 1);
atom.setCharge(charge);
}
}
}
/// <summary> Reads data from the "file system" file through the use of the "input"
/// field, parses data and feeds the ChemFile object with the extracted data.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
///
/// </returns>
/// <throws IOException may> be thrown buy the <code>this.input.readLine()</code> instruction. </throws IOException may>
/// <summary>
/// </summary>
/// <seealso cref="org.openscience.cdk.io.GamessReader.input">
/// </seealso>
//TODO Answer the question : Is this method's name appropriate (given the fact that it do not read a ChemFile object, but return it)?
private IChemFile readChemFile(IChemFile file)
{
IChemSequence sequence = file.Builder.newChemSequence(); // TODO Answer the question : Is this line needed ?
IChemModel model = file.Builder.newChemModel(); // TODO Answer the question : Is this line needed ?
ISetOfMolecules moleculeSet = file.Builder.newSetOfMolecules();
model.SetOfMolecules = moleculeSet; //TODO Answer the question : Should I do this?
sequence.addChemModel(model); //TODO Answer the question : Should I do this?
file.addChemSequence(sequence); //TODO Answer the question : Should I do this?
System.String currentReadLine = this.input.ReadLine();
while (this.input.Peek() != -1 == true && (currentReadLine != null))
{
/*
* There are 2 types of coordinate sets:
* - bohr coordinates sets (if statement)
* - angstr???m coordinates sets (else statement)
*/
if (currentReadLine.IndexOf("COORDINATES (BOHR)") >= 0)
{
/*
* The following line do no contain data, so it is ignored.
*/
this.input.ReadLine();
moleculeSet.addMolecule(this.readCoordinates(file.Builder.newMolecule(), GamessReader.BOHR_UNIT));
//break; //<- stops when the first set of coordinates is found.
}
else if (currentReadLine.IndexOf(" COORDINATES OF ALL ATOMS ARE (ANGS)") >= 0)
{
/*
* The following 2 lines do no contain data, so it are ignored.
*/
this.input.ReadLine();
this.input.ReadLine();
moleculeSet.addMolecule(this.readCoordinates(file.Builder.newMolecule(), GamessReader.ANGSTROM_UNIT));
//break; //<- stops when the first set of coordinates is found.
}
currentReadLine = this.input.ReadLine();
}
return(file);
}
public static IAtomContainer getRelevantAtomContainer(IChemModel chemModel, IBond bond)
{
IAtomContainer result = null;
if (chemModel.SetOfMolecules != null)
{
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
result = SetOfMoleculesManipulator.getRelevantAtomContainer(moleculeSet, bond);
if (result != null)
{
return(result);
}
}
if (chemModel.SetOfReactions != null)
{
ISetOfReactions reactionSet = chemModel.SetOfReactions;
return(SetOfReactionsManipulator.getRelevantAtomContainer(reactionSet, bond));
}
// This should never happen.
return(null);
}
public virtual void createIDs(IChemModel model)
{
ICrystal crystal = model.Crystal;
if (crystal != null)
{
createIDs(crystal);
}
ISetOfMolecules moleculeSet = model.SetOfMolecules;
if (moleculeSet != null)
{
createIDs(moleculeSet);
}
ISetOfReactions reactionSet = model.SetOfReactions;
if (reactionSet != null)
{
createIDs(reactionSet);
}
}
/// <summary> Method that saturates a molecule by adding explicit hydrogens.
/// In order to get coordinates for these Hydrogens, you need to
/// remember the average bondlength of you molecule (coordinates for
/// all atoms should be available) by using
/// double bondLength = GeometryTools.getBondLengthAverage(atomContainer);
/// and then use this method here and then use
/// org.openscience.cdk.HydrogenPlacer(atomContainer, bondLength);
///
/// </summary>
/// <param name="molecule"> Molecule to saturate
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IMolecule molecule)
{
//logger.debug("Start of addExplicitHydrogensToSatisfyValency");
ISetOfMolecules moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule);
IMolecule[] molecules = moleculeSet.Molecules;
IAtomContainer changedAtomsAndBonds = molecule.Builder.newAtomContainer();
IAtomContainer intermediateContainer = null;
for (int k = 0; k < molecules.Length; k++)
{
IMolecule molPart = molecules[k];
IAtom[] atoms = molPart.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
intermediateContainer = addHydrogensToSatisfyValency(molPart, atoms[i], molecule);
changedAtomsAndBonds.add(intermediateContainer);
}
}
//logger.debug("End of addExplicitHydrogensToSatisfyValency");
return(changedAtomsAndBonds);
}
public static int getBondCount(IChemModel chemModel)
{
int count = 0;
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
count += crystal.getBondCount();
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
count += SetOfMoleculesManipulator.getBondCount(moleculeSet);
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
count += SetOfReactionsManipulator.getBondCount(reactionSet);
}
return(count);
}
/// <summary> Puts all the Molecules of this container together in one
/// AtomContainer.
///
/// </summary>
/// <returns> The AtomContainer with all the Molecules of this container
///
/// </returns>
/// <deprecated> This method has a serious performace impact. Try to use
/// other methods.
/// </deprecated>
public static IAtomContainer getAllInOneContainer(IChemModel chemModel)
{
IAtomContainer container = chemModel.Builder.newAtomContainer();
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
container.add(crystal);
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
container.add(SetOfMoleculesManipulator.getAllInOneContainer(moleculeSet));
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
container.add(SetOfReactionsManipulator.getAllInOneContainer(reactionSet));
}
return(container);
}
public static System.Collections.IList getAllChemObjects(IChemModel chemModel)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(chemModel);
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
list.Add(crystal);
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
list.AddRange(SetOfMoleculesManipulator.getAllChemObjects(moleculeSet));
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
list.AddRange(SetOfReactionsManipulator.getAllChemObjects(reactionSet));
}
return(list);
}
/// <summary> Returns the minimum and maximum X and Y coordinates of the molecules in the
/// SetOfMolecules. The output is returned as: <pre>
/// minmax[0] = minX;
/// minmax[1] = minY;
/// minmax[2] = maxX;
/// minmax[3] = maxY;
/// </pre>
/// See comment for center(ISetOfMolecules setOfMolecules, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <returns> An four int array as defined above.
/// </returns>
//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'"
public static double[] getMinMax(ISetOfMolecules setOfMolecules, System.Collections.Hashtable renderingCoordinates)
{
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MIN_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double maxX = System.Double.MinValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MIN_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double maxY = System.Double.MinValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MAX_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double minX = System.Double.MaxValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MAX_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double minY = System.Double.MaxValue;
for (int j = 0; j < setOfMolecules.AtomContainerCount; j++)
{
IAtomContainer container = setOfMolecules.getAtomContainer(j);
for (int i = 0; i < container.AtomCount; i++)
{
IAtom atom = container.getAtomAt(i);
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (renderingCoordinates[atom] != null)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).x > maxX)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
maxX = ((Point2d)renderingCoordinates[atom]).x;
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).x < minX)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
minX = ((Point2d)renderingCoordinates[atom]).x;
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).y > maxY)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
maxY = ((Point2d)renderingCoordinates[atom]).y;
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).y < minY)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
minY = ((Point2d)renderingCoordinates[atom]).y;
}
}
}
}
double[] minmax = new double[4];
minmax[0] = minX;
minmax[1] = minY;
minmax[2] = maxX;
minmax[3] = maxY;
return minmax;
}
/// <summary> Returns the java.awt.Dimension of a SetOfMolecules
/// See comment for center(ISetOfMolecules setOfMolecules, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="setOfMolecules">Of which the dimension should be returned
/// </param>
/// <returns> The java.awt.Dimension of this SetOfMolecules
/// </returns>
//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'"
public static System.Drawing.Size get2DDimension(ISetOfMolecules setOfMolecules, System.Collections.Hashtable renderingCoordinates)
{
double[] minmax = getMinMax(setOfMolecules, renderingCoordinates);
double maxX = minmax[2];
double maxY = minmax[3];
double minX = minmax[0];
double minY = minmax[1];
//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'"
return new System.Drawing.Size((int)(maxX - minX + 1), (int)(maxY - minY + 1));
}
/// <summary> Writes a SetOfMolecules to an OutputStream for the reaction.
///
/// </summary>
/// <param name="som"> The SetOfMolecules that is written to an OutputStream
/// </param>
private void writeSetOfMolecules(ISetOfMolecules som)
{
for (int i = 0; i < som.MoleculeCount; i++)
{
IMolecule mol = som.getMolecule(i);
for (int j = 0; j < som.getMultiplier(i); j++)
{
//MemoryStream ms = new MemoryStream();
//StreamWriter sw = new StreamWriter(ms);
writer.Write("$MOL\n");
MDLWriter mdlwriter = null;
try
{
mdlwriter = new MDLWriter(writer);
}
catch (System.Exception ex)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error(ex.Message);
//logger.debug(ex);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException("Exception while creating MDLWriter: " + ex.Message, ex);
}
mdlwriter.write(mol);
//writer.Write(sw.ToString());
}
}
}
/// <summary> Adds all molecules in the SetOfMolecules to this container.
///
/// </summary>
/// <param name="moleculeSet"> The SetOfMolecules
/// </param>
public virtual void add(ISetOfMolecules moleculeSet)
{
IMolecule[] mols = moleculeSet.Molecules;
for (int i = 0; i < mols.Length; i++)
{
addMolecule(mols[i]);
}
/* notifyChanged() called in super.addAtomContainer() */
}
/// <summary> Constructs an empty, forward reaction.</summary>
public Reaction()
{
this.reactants = new SetOfMolecules();
this.products = new SetOfMolecules();
this.agents = new SetOfMolecules();
this.map = new Mapping[growArraySize];
mappingCount = 0;
reactionDirection = IReaction_Fields.FORWARD;
}
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> writes all the molecules supplied in a SetOfMolecules class to
/// a single HIN file. You can also supply a single Molecule object
/// as well
/// </summary>
/// <param name="mol">the Molecule to write
/// </param>
private void writeMolecule(ISetOfMolecules som)
{
//int na = 0;
//String info = "";
System.String sym = "";
double chrg = 0.0;
//boolean writecharge = true;
for (int molnum = 0; molnum < som.MoleculeCount; molnum++)
{
IMolecule mol = som.getMolecule(molnum);
try
{
int natom = mol.AtomCount;
int nbond = mol.getBondCount();
System.String molname = "mol " + (molnum + 1) + " " + ((System.String)mol.getProperty(CDKConstants.TITLE));
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(molname.ToCharArray(), 0, molname.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
// Loop through the atoms and write them out:
IAtom[] atoms = mol.Atoms;
IBond[] bonds = mol.Bonds;
for (int i = 0; i < natom; i++)
{
System.String line = "atom ";
IAtom a = atoms[i];
sym = a.Symbol;
chrg = a.getCharge();
Point3d p3 = a.getPoint3d();
line = line + ((System.Int32)(i + 1)).ToString() + " - " + sym + " ** - " + ((double)chrg).ToString() + " " + p3.x.ToString() + " " + p3.y.ToString() + " " + p3.z.ToString() + " ";
System.String buf = "";
int ncon = 0;
for (int j = 0; j < nbond; j++)
{
IBond b = bonds[j];
if (b.contains(a))
{
// current atom is in the bond so lets get the connected atom
IAtom ca = b.getConnectedAtom(a);
double bo = b.Order;
int serial = -1;
System.String bt = "";
// get the serial no for this atom
serial = mol.getAtomNumber(ca);
if (bo == 1)
bt = new System.Text.StringBuilder("s").ToString();
else if (bo == 2)
bt = new System.Text.StringBuilder("d").ToString();
else if (bo == 3)
bt = new System.Text.StringBuilder("t").ToString();
else if (bo == 1.5)
bt = new System.Text.StringBuilder("a").ToString();
buf = buf + ((System.Int32)(serial + 1)).ToString() + " " + bt + " ";
ncon++;
}
}
line = line + " " + ((System.Int32)ncon).ToString() + " " + buf;
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(line.ToCharArray(), 0, line.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
System.String buf2 = "endmol " + (molnum + 1);
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(buf2.ToCharArray(), 0, buf2.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
catch (System.IO.IOException e)
{
throw e;
}
}
}
/// <summary> Writes a list of molecules to an OutputStream
///
/// </summary>
/// <param name="som"> SetOfMolecules that is written to an OutputStream
/// </param>
public virtual void writeSetOfMolecules(ISetOfMolecules som)
{
IMolecule[] molecules = som.Molecules;
writeMolecule(molecules[0]);
for (int i = 1; i <= som.MoleculeCount - 1; i++)
{
try
{
writeMolecule(molecules[i]);
}
catch (System.Exception exc)
{
}
}
}
//protected internal LoggingTool logger;
/// <summary> Basic contructor</summary>
public ChemFileCDO(IChemFile file)
{
//logger = new LoggingTool(this);
currentChemFile = file;
currentChemSequence = file.Builder.newChemSequence();
currentChemModel = file.Builder.newChemModel();
currentSetOfMolecules = file.Builder.newSetOfMolecules();
currentSetOfReactions = null;
currentReaction = null;
currentMolecule = file.Builder.newMolecule();
atomEnumeration = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
// procedures required by CDOInterface
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void startDocument()
{
//logger.info("New CDO Object");
currentChemSequence = currentChemFile.Builder.newChemSequence();
currentChemModel = currentChemFile.Builder.newChemModel();
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
currentMolecule = currentChemFile.Builder.newMolecule();
atomEnumeration = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void startObject(System.String objectType)
{
//logger.debug("START:" + objectType);
if (objectType.Equals("Molecule"))
{
if (currentChemModel == null)
currentChemModel = currentChemFile.Builder.newChemModel();
if (currentSetOfMolecules == null)
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Atom"))
{
currentAtom = currentChemFile.Builder.newAtom("H");
//logger.debug("Atom # " + numberOfAtoms);
numberOfAtoms++;
}
else if (objectType.Equals("Bond"))
{
bond_id = null;
bond_stereo = -99;
}
else if (objectType.Equals("Animation"))
{
currentChemSequence = currentChemFile.Builder.newChemSequence();
}
else if (objectType.Equals("Frame"))
{
currentChemModel = currentChemFile.Builder.newChemModel();
}
else if (objectType.Equals("SetOfMolecules"))
{
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Crystal"))
{
currentMolecule = currentChemFile.Builder.newCrystal(currentMolecule);
}
else if (objectType.Equals("a-axis") || objectType.Equals("b-axis") || objectType.Equals("c-axis"))
{
crystal_axis_x = 0.0;
crystal_axis_y = 0.0;
crystal_axis_z = 0.0;
}
else if (objectType.Equals("SetOfReactions"))
{
currentSetOfReactions = currentChemFile.Builder.newSetOfReactions();
}
else if (objectType.Equals("Reaction"))
{
if (currentSetOfReactions == null)
startObject("SetOfReactions");
currentReaction = currentChemFile.Builder.newReaction();
}
else if (objectType.Equals("Reactant"))
{
if (currentReaction == null)
startObject("Reaction");
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Product"))
{
if (currentReaction == null)
startObject("Reaction");
currentMolecule = currentChemFile.Builder.newMolecule();
}
}
public virtual void createIDs(ISetOfMolecules containerSet)
{
createIDs((ISetOfAtomContainers)containerSet);
}
/// <summary> Writes an array of Molecules to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="molecules"> Array of Molecules that is written to an OutputStream
/// </param>
private void writeSetOfMolecules(ISetOfMolecules som)
{
IMolecule[] molecules = som.Molecules;
for (int i = 0; i < som.MoleculeCount; i++)
{
try
{
bool[] isVisible = new bool[molecules[i].AtomCount];
for (int k = 0; k < isVisible.Length; k++)
{
isVisible[k] = true;
}
writeMolecule(molecules[i], isVisible);
}
catch (System.Exception exc)
{
}
}
}
