/// <summary> Check whether a set of atoms in an atomcontainer is connected
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be check for connectedness
/// </param>
/// <returns> true if the AtomContainer is connected
/// </returns>
public static bool isConnected(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IMolecule molecule = atomContainer.Builder.newMolecule();
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);
atomContainer.getAtomAt(f).setFlag(CDKConstants.VISITED, false);
ac.addAtom(atomContainer.getAtomAt(f));
}
IBond[] bonds = atomContainer.Bonds;
for (int f = 0; f < bonds.Length; f++)
{
bonds[f].setFlag(CDKConstants.VISITED, false);
ac.addBond(bonds[f]);
}
atom = ac.getAtomAt(0);
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
if (molecule.AtomCount == atomContainer.AtomCount)
{
return(true);
}
return(false);
}
/// <summary> Adds a reactant to this reaction.
///
/// </summary>
/// <param name="reactant"> Molecule added as reactant to this reaction
/// </param>
/// <seealso cref="getReactants">
/// </seealso>
public virtual void addReactant(IMolecule reactant)
{
addReactant(reactant, 1.0);
/* notifyChanged() is called by
* addReactant(Molecule reactant, double coefficient) */
}
/// <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> Adds a product to this reaction.
///
/// </summary>
/// <param name="product"> Molecule added as product to this reaction
/// </param>
/// <seealso cref="getProducts">
/// </seealso>
public virtual void addProduct(IMolecule product)
{
this.addProduct(product, 1.0);
/* notifyChanged() is called by
* addProduct(Molecule product, double coefficient)*/
}
/// <summary> Adds a product to this reaction.
///
/// </summary>
/// <param name="product"> Molecule added as product to this reaction
/// </param>
/// <param name="coefficient">Stoichiometry coefficient for this molecule
/// </param>
/// <seealso cref="getProducts">
/// </seealso>
public virtual void addProduct(IMolecule product, double coefficient)
{
products.addAtomContainer(product, coefficient);
/* notifyChanged() is called by
* addReactant(Molecule reactant, double coefficient) */
}
/// <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> 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 addHydrogensToSatisfyValency(IMolecule molecule)
{
//logger.debug("Start of addHydrogensToSatisfyValency");
IAtomContainer changedAtomsAndBonds = addExplicitHydrogensToSatisfyValency(molecule);
//logger.debug("End of addHydrogensToSatisfyValency");
return(changedAtomsAndBonds);
}
/// <summary> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="molecule"> Molecule that is written to an OutputStream
/// </param>
public virtual void writeMolecule(IMolecule molecule)
{
bool[] isVisible = new bool[molecule.AtomCount];
for (int i = 0; i < isVisible.Length; i++)
{
isVisible[i] = true;
}
writeMolecule(molecule, isVisible);
}
private IMolecule readMolecule(IMolecule molecule)
{
JmolAdapter adapter = new SmarterJmolAdapter();
// note that it actually let's the adapter detect the format!
System.Object model = adapter.openBufferedReader("", input);
molecule.add(new Convertor(molecule.Builder).convert(model));
return(molecule);
}
public MainWindow()
{
molecule = new Molecule();
InitializeComponent();
foreach(String s in molecule.FormulasList)
{
formulaCombo.Items.Add(s);
}
}
/// <summary> writes a single frame in XYZ format to the Writer.</summary>
/// <param name="mol">the Molecule to write
/// </param>
public virtual void writeMolecule(IMolecule mol)
{
System.String st = "";
bool writecharge = true;
try
{
System.String s1 = ((System.Int32)mol.AtomCount).ToString();
//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(s1.ToCharArray(), 0, s1.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 s2 = null; // FIXME: add some interesting comment
if (s2 != null)
{
//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(s2.ToCharArray(), 0, s2.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;
for (int i = 0; i < atoms.Length; i++)
{
IAtom a = atoms[i];
st = a.Symbol;
Point3d p3 = a.getPoint3d();
if (p3 != null)
{
st = st + "\t" + p3.x.ToString() + "\t" + p3.y.ToString() + "\t" + p3.z.ToString();
}
if (writecharge)
{
double ct = a.getCharge();
st = st + "\t" + ct;
}
//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(st.ToCharArray(), 0, st.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;
//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 writing file: ", e.Message);
//logger.debug(e);
}
}
public bool AreIsomers(IMolecule molecule)
{
if (!(molecule is ChemicalCompound))
{
return(false);
}
var compound = molecule as ChemicalCompound;
return(AreAtomsCountEqual(compound));
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="smiles"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <exception cref="InvalidSmilesException"> Description of the Exception
/// </exception>
public virtual Reaction parseReactionSmiles(System.String smiles)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(smiles, ">");
System.String reactantSmiles = tokenizer.NextToken();
System.String agentSmiles = "";
System.String productSmiles = tokenizer.NextToken();
if (tokenizer.HasMoreTokens())
{
agentSmiles = productSmiles;
productSmiles = tokenizer.NextToken();
}
Reaction reaction = new Reaction();
// add reactants
IMolecule reactantContainer = parseSmiles(reactantSmiles);
ISetOfMolecules reactantSet = ConnectivityChecker.partitionIntoMolecules(reactantContainer);
IMolecule[] reactants = reactantSet.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
reaction.addReactant(reactants[i]);
}
// add reactants
if (agentSmiles.Length > 0)
{
IMolecule agentContainer = parseSmiles(agentSmiles);
ISetOfMolecules agentSet = ConnectivityChecker.partitionIntoMolecules(agentContainer);
IMolecule[] agents = agentSet.Molecules;
for (int i = 0; i < agents.Length; i++)
{
reaction.addAgent(agents[i]);
}
}
// add products
IMolecule productContainer = parseSmiles(productSmiles);
ISetOfMolecules productSet = ConnectivityChecker.partitionIntoMolecules(productContainer);
IMolecule[] products = productSet.Molecules;
for (int i = 0; i < products.Length; i++)
{
reaction.addProduct(products[i]);
}
return(reaction);
}
private IChemModel readChemModel(IChemModel 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> 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> Returns the atoms which are closest to an atom in an AtomContainer by bonds.
/// If number of atoms in or below sphere x<max andnumber of atoms in or below sphere x+1>max then atoms in or below sphere x+1 are returned.
///
/// </summary>
/// <param name="ac"> The AtomContainer to examine
/// </param>
/// <param name="a"> the atom to start from
/// </param>
/// <param name="max">the number of neighbours to return
/// </param>
/// <returns> the average bond length
/// </returns>
public static IAtom[] findClosestByBond(IAtomContainer ac, IAtom a, int max)
{
IMolecule mol = ac.Builder.newMolecule();
System.Collections.ArrayList v = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
v.Add(a);
breadthFirstSearch(ac, v, mol, max);
IAtom[] returnValue = new IAtom[mol.Atoms.Length - 1];
int k = 0;
for (int i = 0; i < mol.Atoms.Length; i++)
{
if (mol.Atoms[i] != a)
{
returnValue[k] = mol.Atoms[i];
k++;
}
}
return(returnValue);
}
public static System.Collections.ArrayList getAllIDs(IReaction reaction)
{
System.Collections.ArrayList idList = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
if (reaction.ID != null)
{
idList.Add(reaction.ID);
}
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
IMolecule mol = reactants[i];
idList.AddRange(AtomContainerManipulator.getAllIDs(mol));
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
IMolecule mol = products[i];
idList.AddRange(AtomContainerManipulator.getAllIDs(mol));
}
return(idList);
}
public static void removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)
{
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
IMolecule mol = reactants[i];
if (mol.contains(atom))
{
mol.removeAtomAndConnectedElectronContainers(atom);
}
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
IMolecule mol = products[i];
if (mol.contains(atom))
{
mol.removeAtomAndConnectedElectronContainers(atom);
}
}
}
public static void removeElectronContainer(IReaction reaction, IElectronContainer electrons)
{
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
IMolecule mol = reactants[i];
if (mol.contains(electrons))
{
mol.removeElectronContainer(electrons);
}
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
IMolecule mol = products[i];
if (mol.contains(electrons))
{
mol.removeElectronContainer(electrons);
}
}
}
/// <summary> Writes the content from molecule to output.
///
/// </summary>
/// <param name="molecule"> Molecule of which the data is outputted.
/// </param>
public virtual void writeMolecule(IMolecule molecule)
{
SmilesGenerator sg = new SmilesGenerator(molecule.Builder);
System.String smiles = "";
try
{
smiles = sg.createSMILES(molecule);
//logger.debug("Generated SMILES: " + smiles);
writer.Write(smiles);
//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();
writer.Flush();
//logger.debug("file flushed...");
}
catch (System.Exception exc)
{
//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 writing Molecule: ", exc.Message);
//logger.debug(exc);
}
}
/// <deprecated> This method has a serious performace impact. Try to use
/// other methods.
/// </deprecated>
public static IAtomContainer getAllInOneContainer(IReaction reaction)
{
IAtomContainer container = reaction.Builder.newAtomContainer();
if (reaction == null)
{
return(container);
}
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
IMolecule molecule = reactants[i];
container.add(molecule);
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
IMolecule molecule = products[i];
container.add(molecule);
}
return(container);
}
/// <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 virtual void writeMolecule(IMolecule molecule)
{
writer.Write("{\n");
writer.Write(" Molecule mol = new Molecule();\n");
IDCreator idCreator = new IDCreator();
idCreator.createIDs(molecule);
IAtom[] atoms = molecule.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
writeAtom(atom);
writer.Write(" mol.addAtom(" + atom.ID + ");\n");
}
IBond[] bonds = molecule.Bonds;
for (int i = 0; i < bonds.Length; i++)
{
IBond bond = bonds[i];
writeBond(bond);
writer.Write(" mol.addBond(" + bond.ID + ");\n");
}
writer.Write("}\n");
}
/// <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 addHydrogensToSatisfyValency(IMolecule molecule)
{
//logger.debug("Start of addHydrogensToSatisfyValency");
IAtomContainer changedAtomsAndBonds = addExplicitHydrogensToSatisfyValency(molecule);
//logger.debug("End of addHydrogensToSatisfyValency");
return changedAtomsAndBonds;
}
/// <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)
{
// System.out.println("Staring partitioning with this ac: " + ac);
breadthFirstSearch(ac, sphere, molecule, -1);
}
public void ExportMolecule(IMolecule molecule)
{
}
/// <summary> writes a single frame in XYZ format to the Writer.</summary>
/// <param name="mol">the Molecule to write
/// </param>
public virtual void writeMolecule(IMolecule mol)
{
System.String st = "";
bool writecharge = true;
try
{
System.String s1 = ((System.Int32)mol.AtomCount).ToString();
//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(s1.ToCharArray(), 0, s1.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 s2 = null; // FIXME: add some interesting comment
if (s2 != null)
{
//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(s2.ToCharArray(), 0, s2.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;
for (int i = 0; i < atoms.Length; i++)
{
IAtom a = atoms[i];
st = a.Symbol;
Point3d p3 = a.getPoint3d();
if (p3 != null)
{
st = st + "\t" + p3.x.ToString() + "\t" + p3.y.ToString() + "\t" + p3.z.ToString();
}
if (writecharge)
{
double ct = a.getCharge();
st = st + "\t" + ct;
}
//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(st.ToCharArray(), 0, st.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;
//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 writing file: ", e.Message);
//logger.debug(e);
}
}
// 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> Writes a single frame in XYZ format to the Writer.
///
/// </summary>
/// <param name="mol">the Molecule to write
/// </param>
public virtual void writeMolecule(IMolecule mol)
{
try
{
/*
# Name: benzene
# Creating user name: tom
# Creation time: Wed Dec 28 00:18:30 1988
# Modifying user name: tom
# Modification time: Wed Dec 28 00:18:30 1988*/
//logger.debug("Writing header...");
if (mol.getProperty(CDKConstants.TITLE) != null)
{
//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'"
writer.Write("# Name: " + mol.getProperty(CDKConstants.TITLE) + "\n");
}
// FIXME: add other types of meta data
//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();
/*
@<TRIPOS>MOLECULE
benzene
12 12 1 0 0
SMALL
NO_CHARGES */
//logger.debug("Writing molecule block...");
writer.Write("@<TRIPOS>MOLECULE\n");
writer.Write(mol.ID + "\n");
writer.Write(mol.AtomCount + " " + mol.getBondCount() + "\n"); // that's the minimum amount of info required the format
writer.Write("SMALL\n"); // no biopolymer
writer.Write("NO CHARGES\n"); // other options include Gasteiger charges
/*
@<TRIPOS>ATOM
1 C1 1.207 2.091 0.000 C.ar 1 BENZENE 0.000
2 C2 2.414 1.394 0.000 C.ar 1 BENZENE 0.000
3 C3 2.414 0.000 0.000 C.ar 1 BENZENE 0.000
4 C4 1.207 -0.697 0.000 C.ar 1 BENZENE 0.000
5 C5 0.000 0.000 0.000 C.ar 1 BENZENE 0.000
6 C6 0.000 1.394 0.000 C.ar 1 BENZENE 0.000
7 H1 1.207 3.175 0.000 H 1 BENZENE 0.000
8 H2 3.353 1.936 0.000 H 1 BENZENE 0.000
9 H3 3.353 -0.542 0.000 H 1 BENZENE 0.000
10 H4 1.207 -1.781 0.000 H 1 BENZENE 0.000
11 H5 -0.939 -0.542 0.000 H 1 BENZENE 0.000
12 H6 -0.939 1.936 0.000 H 1 BENZENE 0.000 */
// write atom block
//logger.debug("Writing atom block...");
writer.Write("@<TRIPOS>ATOM\n");
IAtom[] atoms = mol.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
writer.Write(i + " " + atoms[i].ID + " ");
if (atoms[i].getPoint3d() != null)
{
writer.Write(atoms[i].X3d + " ");
writer.Write(atoms[i].Y3d + " ");
writer.Write(atoms[i].Z3d + " ");
}
else if (atoms[i].getPoint2d() != null)
{
writer.Write(atoms[i].X2d + " ");
writer.Write(atoms[i].Y2d + " ");
writer.Write(" 0.000 ");
}
else
{
writer.Write("0.000 0.000 0.000 ");
}
writer.Write(atoms[i].Symbol + "\n"); // FIXME: should use perceived Mol2 Atom Types!
}
/*
@<TRIPOS>BOND
1 1 2 ar
2 1 6 ar
3 2 3 ar
4 3 4 ar
5 4 5 ar
6 5 6 ar
7 1 7 1
8 2 8 1
9 3 9 1
10 4 10 1
11 5 11 1
12 6 12 1*/
// write bond block
//logger.debug("Writing bond block...");
writer.Write("@<TRIPOS>BOND\n");
IBond[] bonds = mol.Bonds;
for (int i = 0; i < bonds.Length; i++)
{
//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'"
writer.Write(i + " " + mol.getAtomNumber(bonds[i].getAtomAt(0)) + " " + mol.getAtomNumber(bonds[i].getAtomAt(1)) + " " + ((int)bonds[i].Order) + "\n");
}
}
catch (System.IO.IOException e)
{
throw e;
}
}
/// <summary> Generate canonical SMILES from the <code>molecule</code>. This method
/// canonicaly lables the molecule but dose not perform any checks on the
/// chemical validity of the molecule. Does not care about multiple molecules.
/// IMPORTANT: A precomputed Set of All Rings (SAR) can be passed to this
/// SmilesGenerator in order to avoid recomputing it. Use setRings() to
/// assign the SAR.
///
/// </summary>
/// <param name="molecule"> The molecule to evaluate
/// </param>
/// <param name="chiral"> true=SMILES will be chiral, false=SMILES
/// will not be chiral.
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
/// <returns> Description of the Returned Value
/// </returns>
/// <exception cref="CDKException"> At least one atom has no Point2D;
/// coordinates are needed for creating the chiral smiles. This excpetion
/// can only be thrown if chiral smiles is created, ignore it if you want a
/// non-chiral smiles (createSMILES(AtomContainer) does not throw an
/// exception).
/// </exception>
/// <seealso cref="org.openscience.cdk.graph.invariant.CanonicalLabeler.canonLabel(IAtomContainer)">
/// </seealso>
//UPGRADE_NOTE: Synchronized keyword was removed from method 'createSMILESWithoutCheckForMultipleMolecules'. Lock expression was added. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1027'"
public virtual System.String createSMILESWithoutCheckForMultipleMolecules(IMolecule molecule, bool chiral, bool[] doubleBondConfiguration)
{
lock (this)
{
if (molecule.AtomCount == 0)
{
return "";
}
canLabler.canonLabel(molecule);
brokenBonds.Clear();
ringMarker = 0;
IAtom[] all = molecule.Atoms;
IAtom start = null;
for (int i = 0; i < all.Length; i++)
{
IAtom atom = all[i];
if (chiral && atom.getPoint2d() == null)
{
throw new CDKException("Atom number " + i + " has no 2D coordinates, but 2D coordinates are needed for creating chiral smiles");
}
//System.out.println("Setting all VISITED flags to false");
atom.setFlag(CDKConstants.VISITED, false);
if ((long)((System.Int64)atom.getProperty("CanonicalLable")) == 1)
{
start = atom;
}
}
//detect aromaticity
if (rings == null)
{
if (ringFinder == null)
{
ringFinder = new AllRingsFinder();
}
rings = ringFinder.findAllRings(molecule);
}
HueckelAromaticityDetector.detectAromaticity(molecule, rings, false);
if (chiral && rings.AtomContainerCount > 0)
{
System.Collections.ArrayList v = RingPartitioner.partitionRings(rings);
//System.out.println("RingSystems: " + v.size());
for (int i = 0; i < v.Count; i++)
{
int counter = 0;
IAtomContainer allrings = RingSetManipulator.getAllInOneContainer((IRingSet)v[i]);
for (int k = 0; k < allrings.AtomCount; k++)
{
if (!BondTools.isStereo(molecule, allrings.getAtomAt(k)) && hasWedges(molecule, allrings.getAtomAt(k)) != null)
{
IBond bond = molecule.getBond(allrings.getAtomAt(k), hasWedges(molecule, allrings.getAtomAt(k)));
if (bond.Stereo == CDKConstants.STEREO_BOND_UP)
{
allrings.getAtomAt(k).setProperty(RING_CONFIG, UP);
}
else
{
allrings.getAtomAt(k).setProperty(RING_CONFIG, DOWN);
}
counter++;
}
}
if (counter == 1)
{
for (int k = 0; k < allrings.AtomCount; k++)
{
allrings.getAtomAt(k).setProperty(RING_CONFIG, UP);
}
}
}
}
System.Text.StringBuilder l = new System.Text.StringBuilder();
createSMILES(start, l, molecule, chiral, doubleBondConfiguration);
rings = null;
return l.ToString();
}
}
/// <summary> Sets the coefficient of a a product to a given value.
///
/// </summary>
/// <param name="product"> Product for which the coefficient is set
/// </param>
/// <param name="coefficient">The new coefficient for the given product
/// </param>
/// <returns> true if Molecule has been found and stoichiometry has been set.
/// </returns>
/// <seealso cref="getProductCoefficient">
/// </seealso>
public virtual bool setProductCoefficient(IMolecule product, double coefficient)
{
notifyChanged();
return products.setMultiplier(product, coefficient);
}
/// <summary> Adds an agent to this reaction.
///
/// </summary>
/// <param name="agent"> Molecule added as agent to this reaction
/// </param>
/// <seealso cref="getAgents">
/// </seealso>
public virtual void addAgent(IMolecule agent)
{
agents.addAtomContainer(agent);
notifyChanged();
}
/// <summary> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="molecule"> Molecule that is written to an OutputStream
/// </param>
public virtual void writeMolecule(IMolecule molecule)
{
bool[] isVisible = new bool[molecule.AtomCount];
for (int i = 0; i < isVisible.Length; i++)
{
isVisible[i] = true;
}
writeMolecule(molecule, isVisible);
}
/// <summary> Adds a reactant to this reaction with a stoichiometry coefficient.
///
/// </summary>
/// <param name="reactant"> Molecule added as reactant to this reaction
/// </param>
/// <param name="coefficient">Stoichiometry coefficient for this molecule
/// </param>
/// <seealso cref="getReactants">
/// </seealso>
public virtual void addReactant(IMolecule reactant, double coefficient)
{
reactants.addAtomContainer(reactant, coefficient);
notifyChanged();
}
/// <summary> Returns the stoichiometry coefficient of the given reactant.
///
/// </summary>
/// <param name="reactant">Reactant for which the coefficient is returned.
/// </param>
/// <returns> -1, if the given molecule is not a product in this Reaction
/// </returns>
/// <seealso cref="setReactantCoefficient">
/// </seealso>
public virtual double getReactantCoefficient(IMolecule reactant)
{
return reactants.getMultiplier(reactant);
}
/// <summary> Adds a product to this reaction.
///
/// </summary>
/// <param name="product"> Molecule added as product to this reaction
/// </param>
/// <param name="coefficient">Stoichiometry coefficient for this molecule
/// </param>
/// <seealso cref="getProducts">
/// </seealso>
public virtual void addProduct(IMolecule product, double coefficient)
{
products.addAtomContainer(product, coefficient);
/* notifyChanged() is called by
addReactant(Molecule reactant, double coefficient) */
}
/// <summary> Writes the content from molecule to output.
///
/// </summary>
/// <param name="molecule"> Molecule of which the data is outputted.
/// </param>
public virtual void writeMolecule(IMolecule molecule)
{
SmilesGenerator sg = new SmilesGenerator(molecule.Builder);
System.String smiles = "";
try
{
smiles = sg.createSMILES(molecule);
//logger.debug("Generated SMILES: " + smiles);
writer.Write(smiles);
//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();
writer.Flush();
//logger.debug("file flushed...");
}
catch (System.Exception exc)
{
//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 writing Molecule: ", exc.Message);
//logger.debug(exc);
}
}
/// <summary> Generate canonical SMILES from the <code>molecule</code>. This method
/// canonicaly lables the molecule but dose not perform any checks on the
/// chemical validity of the molecule. This method also takes care of multiple
/// molecules.
/// IMPORTANT: A precomputed Set of All Rings (SAR) can be passed to this
/// SmilesGenerator in order to avoid recomputing it. Use setRings() to
/// assign the SAR.
///
/// </summary>
/// <param name="molecule"> The molecule to evaluate
/// </param>
/// <param name="chiral"> true=SMILES will be chiral, false=SMILES
/// will not be chiral.
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
/// <returns> Description of the Returned Value
/// </returns>
/// <exception cref="CDKException"> At least one atom has no Point2D;
/// coordinates are needed for crating the chiral smiles. This excpetion
/// can only be thrown if chiral smiles is created, ignore it if you want a
/// non-chiral smiles (createSMILES(AtomContainer) does not throw an
/// exception).
/// </exception>
/// <seealso cref="org.openscience.cdk.graph.invariant.CanonicalLabeler.canonLabel(IAtomContainer)">
/// </seealso>
//UPGRADE_NOTE: Synchronized keyword was removed from method 'createSMILES'. Lock expression was added. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1027'"
public virtual System.String createSMILES(IMolecule molecule, bool chiral, bool[] doubleBondConfiguration)
{
lock (this)
{
ISetOfMolecules moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule);
if (moleculeSet.MoleculeCount > 1)
{
System.Text.StringBuilder fullSMILES = new System.Text.StringBuilder();
IMolecule[] molecules = moleculeSet.Molecules;
for (int i = 0; i < molecules.Length; i++)
{
IMolecule molPart = molecules[i];
fullSMILES.Append(createSMILESWithoutCheckForMultipleMolecules(molPart, chiral, doubleBondConfiguration));
if (i < (molecules.Length - 1))
{
// are there more molecules?
fullSMILES.Append('.');
}
}
return fullSMILES.ToString();
}
else
{
return (createSMILESWithoutCheckForMultipleMolecules(molecule, chiral, doubleBondConfiguration));
}
}
}
/// <summary> Adds a reactant to this reaction.
///
/// </summary>
/// <param name="reactant"> Molecule added as reactant to this reaction
/// </param>
/// <seealso cref="getReactants">
/// </seealso>
public virtual void addReactant(IMolecule reactant)
{
addReactant(reactant, 1.0);
/* notifyChanged() is called by
addReactant(Molecule reactant, double coefficient) */
}
/// <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> Adds an molecule to this container.
///
/// </summary>
/// <param name="molecule"> The molecule to be added to this container
/// </param>
public virtual void addMolecule(IMolecule molecule)
{
base.addAtomContainer(molecule);
/* notifyChanged() called in super.addAtomContainer() */
}
/// <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 static void ProcessChemModel(IChemModel chemModel, ISettings settings, FileUsage usage,
MoleculeLoadingResults results, MoleculeProcessingProgress progress,
float sectionSz)
{
//if (ChemModelManipulator.getAllInOneContainer(chemModel).getBondCount() == 0)
//{
// return;
//}
// check for coordinates
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))//
{
results.Num2DCoords++;
}
// usage == FileUsage.TwoD)
//{
// throw new UserLevelException("File has no 2D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))// &&
{
results.Num3DCoords++;
}
// usage == FileUsage.ThreeD)
//{
// throw new UserLevelException("File has no 3D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
ElementPTFactory elements = ElementPTFactory.Instance;
// calc item sz
int numItems = 0;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
numItems += chemModel.SetOfMolecules.Molecules[mol].Atoms.Length;
//numItems += chemModel.SetOfMolecules.Molecules[mol].Bonds.Length;
}
}
float itemSz = sectionSz / (float)numItems;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
IMolecule molecule = chemModel.SetOfMolecules.Molecules[mol];
results.NumAtoms += molecule.Atoms.Length;
results.NumBonds += molecule.Bonds.Length;
foreach (IAtom atom in molecule.Atoms)
{
PeriodicTableElement pe = elements.getElement(atom.Symbol);
if (pe != null)
{
atom.AtomicNumber = pe.AtomicNumber;
atom.Properties["PeriodicTableElement"] = pe;
atom.Properties["Period"] = int.Parse(pe.Period);
}
else
{
progress.Log(string.Format("Failed to find periodic element: {0}", atom.Symbol), LogItem.ItemLevel.Failure);
}
progress.UpdateProgress(itemSz);
}
progress.Log(string.Format("Processed {0} atoms", molecule.Atoms.Length), LogItem.ItemLevel.Info);
}
}
progress.Log("Processed Model", LogItem.ItemLevel.Success);
}
/// <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> 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> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="container"> Molecule that is written to an OutputStream
/// </param>
/// <param name="isVisible">Should a certain atom be written to mdl?
/// </param>
public virtual void writeMolecule(IMolecule container, bool[] isVisible)
{
System.String line = "";
// taking care of the $$$$ signs:
// we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
if (moleculeNumber == 2)
{
writer.Write("$$$$");
//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();
}
// write header block
// lines get shortened to 80 chars, that's in the spec
System.String title = (System.String)container.getProperty(CDKConstants.TITLE);
if (title == null)
{
title = "";
}
if (title.Length > 80)
{
title = title.Substring(0, (80) - (0));
}
writer.Write(title + "\n");
/* From CTX spec
* This line has the format:
* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
* (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
* User's first and last initials (l), program name (P),
* date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input, internal registry number (R)
* if input through MDL form.
* A blank line can be substituted for line 2.
*/
writer.Write(" CDK ");
//UPGRADE_ISSUE: Constructor 'java.text.SimpleDateFormat.SimpleDateFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextSimpleDateFormat'"
//UPGRADE_TODO: The equivalent in .NET for method 'java.util.Calendar.getTime' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.TimeZone generatedAux3 = System.TimeZone.CurrentTimeZone;
//writer.Write(SupportClass.FormatDateTime(new SimpleDateFormat("M/d/y,H:m", new System.Globalization.CultureInfo("en-US")), SupportClass.CalendarManager.manager.GetDateTime(new System.Globalization.GregorianCalendar())));
writer.Write('\n');
System.String comment = (System.String)container.getProperty(CDKConstants.REMARK);
if (comment == null)
{
comment = "";
}
if (comment.Length > 80)
{
comment = comment.Substring(0, (80) - (0));
}
writer.Write(comment + "\n");
// write Counts line
int upToWhichAtom = 0;
for (int i = 0; i < isVisible.Length; i++)
{
if (isVisible[i])
{
upToWhichAtom++;
}
}
line += formatMDLInt(upToWhichAtom, 3);
int numberOfBonds = 0;
if (upToWhichAtom < container.AtomCount)
{
for (int i = 0; i < container.getBondCount(); i++)
{
if (isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[1])])
{
numberOfBonds++;
}
}
}
else
{
numberOfBonds = container.getBondCount();
}
line += formatMDLInt(numberOfBonds, 3);
line += " 0 0 0 0 0 0 0 0999 V2000\n";
writer.Write(line);
// write Atom block
IAtom[] atoms = container.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
if (isVisible[f])
{
IAtom atom = atoms[f];
line = "";
if (atom.getPoint3d() != null)
{
//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'"
line += formatMDLFloat((float)atom.X3d);
//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'"
line += formatMDLFloat((float)atom.Y3d);
//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'"
line += (formatMDLFloat((float)atom.Z3d) + " ");
}
else if (atom.getPoint2d() != null)
{
//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'"
line += formatMDLFloat((float)atom.X2d);
//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'"
line += formatMDLFloat((float)atom.Y2d);
line += " 0.0000 ";
}
else
{
// if no coordinates available, then output a number
// of zeros
line += formatMDLFloat((float)0.0);
line += formatMDLFloat((float)0.0);
line += (formatMDLFloat((float)0.0) + " ");
}
if (container.getAtomAt(f) is IPseudoAtom)
{
line += formatMDLString(((IPseudoAtom)container.getAtomAt(f)).Label, 3);
}
else
{
line += formatMDLString(container.getAtomAt(f).Symbol, 3);
}
line += " 0 0 0 0 0 0 0 0 0 0 0 0";
writer.Write(line);
//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();
}
}
// write Bond block
IBond[] bonds = container.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
if (upToWhichAtom == container.AtomCount || (isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[1])]))
{
IBond bond = bonds[g];
if (bond.getAtoms().Length != 2)
{
//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.warn("Skipping bond with more/less than two atoms: " + bond);
}
else
{
if (bond.Stereo == CDKConstants.STEREO_BOND_UP_INV || bond.Stereo == CDKConstants.STEREO_BOND_DOWN_INV)
{
// turn around atom coding to correct for inv stereo
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
}
else
{
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
}
//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'"
line += formatMDLInt((int)bond.Order, 3);
line += " ";
switch (bond.Stereo)
{
case CDKConstants.STEREO_BOND_UP:
line += "1";
break;
case CDKConstants.STEREO_BOND_UP_INV:
line += "1";
break;
case CDKConstants.STEREO_BOND_DOWN:
line += "6";
break;
case CDKConstants.STEREO_BOND_DOWN_INV:
line += "6";
break;
default:
line += "0";
break;
}
line += " 0 0 0 ";
writer.Write(line);
//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();
}
}
}
// write formal atomic charges
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
int charge = atom.getFormalCharge();
if (charge != 0)
{
writer.Write("M CHG 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(charge, 3));
//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();
}
}
// write formal isotope information
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
if (!(atom is IPseudoAtom))
{
int atomicMass = atom.MassNumber;
int majorMass = IsotopeFactory.getInstance(atom.Builder).getMajorIsotope(atom.Symbol).MassNumber;
if (atomicMass != 0 && atomicMass != majorMass)
{
writer.Write("M ISO 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(atomicMass, 3));
//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();
}
}
}
// close molecule
writer.Write("M END");
//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();
//write sdfields, if any
if (sdFields != null)
{
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
CSGraphT.SupportClass.SetSupport set_Renamed = new CSGraphT.SupportClass.HashSetSupport(sdFields.Keys);
System.Collections.IEnumerator iterator = set_Renamed.GetEnumerator();
//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'"
while (iterator.MoveNext())
{
//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'"
System.Object element = iterator.Current;
writer.Write("> <" + ((System.String)element) + ">");
//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();
//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'"
writer.Write(sdFields[element].ToString());
//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();
//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();
}
}
// taking care of the $$$$ signs:
// we write such a sign at the end of all except the first molecule
if (moleculeNumber != 1)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
moleculeNumber++;
writer.Flush();
}
public virtual void writeMolecule(IMolecule molecule)
{
writer.Write("{\n");
writer.Write(" Molecule mol = new Molecule();\n");
IDCreator idCreator = new IDCreator();
idCreator.createIDs(molecule);
IAtom[] atoms = molecule.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
writeAtom(atom);
writer.Write(" mol.addAtom(" + atom.ID + ");\n");
}
IBond[] bonds = molecule.Bonds;
for (int i = 0; i < bonds.Length; i++)
{
IBond bond = bonds[i];
writeBond(bond);
writer.Write(" mol.addBond(" + bond.ID + ");\n");
}
writer.Write("}\n");
}
/// <summary> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="container"> Molecule that is written to an OutputStream
/// </param>
/// <param name="isVisible">Should a certain atom be written to mdl?
/// </param>
public virtual void writeMolecule(IMolecule container, bool[] isVisible)
{
System.String line = "";
// taking care of the $$$$ signs:
// we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
if (moleculeNumber == 2)
{
writer.Write("$$$$");
//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();
}
// write header block
// lines get shortened to 80 chars, that's in the spec
System.String title = (System.String)container.getProperty(CDKConstants.TITLE);
if (title == null)
title = "";
if (title.Length > 80)
title = title.Substring(0, (80) - (0));
writer.Write(title + "\n");
/* From CTX spec
* This line has the format:
* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
* (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
* User's first and last initials (l), program name (P),
* date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input, internal registry number (R)
* if input through MDL form.
* A blank line can be substituted for line 2.
*/
writer.Write(" CDK ");
//UPGRADE_ISSUE: Constructor 'java.text.SimpleDateFormat.SimpleDateFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextSimpleDateFormat'"
//UPGRADE_TODO: The equivalent in .NET for method 'java.util.Calendar.getTime' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.TimeZone generatedAux3 = System.TimeZone.CurrentTimeZone;
//writer.Write(SupportClass.FormatDateTime(new SimpleDateFormat("M/d/y,H:m", new System.Globalization.CultureInfo("en-US")), SupportClass.CalendarManager.manager.GetDateTime(new System.Globalization.GregorianCalendar())));
writer.Write('\n');
System.String comment = (System.String)container.getProperty(CDKConstants.REMARK);
if (comment == null)
comment = "";
if (comment.Length > 80)
comment = comment.Substring(0, (80) - (0));
writer.Write(comment + "\n");
// write Counts line
int upToWhichAtom = 0;
for (int i = 0; i < isVisible.Length; i++)
{
if (isVisible[i])
upToWhichAtom++;
}
line += formatMDLInt(upToWhichAtom, 3);
int numberOfBonds = 0;
if (upToWhichAtom < container.AtomCount)
{
for (int i = 0; i < container.getBondCount(); i++)
{
if (isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[1])])
numberOfBonds++;
}
}
else
{
numberOfBonds = container.getBondCount();
}
line += formatMDLInt(numberOfBonds, 3);
line += " 0 0 0 0 0 0 0 0999 V2000\n";
writer.Write(line);
// write Atom block
IAtom[] atoms = container.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
if (isVisible[f])
{
IAtom atom = atoms[f];
line = "";
if (atom.getPoint3d() != null)
{
//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'"
line += formatMDLFloat((float)atom.X3d);
//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'"
line += formatMDLFloat((float)atom.Y3d);
//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'"
line += (formatMDLFloat((float)atom.Z3d) + " ");
}
else if (atom.getPoint2d() != null)
{
//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'"
line += formatMDLFloat((float)atom.X2d);
//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'"
line += formatMDLFloat((float)atom.Y2d);
line += " 0.0000 ";
}
else
{
// if no coordinates available, then output a number
// of zeros
line += formatMDLFloat((float)0.0);
line += formatMDLFloat((float)0.0);
line += (formatMDLFloat((float)0.0) + " ");
}
if (container.getAtomAt(f) is IPseudoAtom)
line += formatMDLString(((IPseudoAtom)container.getAtomAt(f)).Label, 3);
else
line += formatMDLString(container.getAtomAt(f).Symbol, 3);
line += " 0 0 0 0 0 0 0 0 0 0 0 0";
writer.Write(line);
//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();
}
}
// write Bond block
IBond[] bonds = container.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
if (upToWhichAtom == container.AtomCount || (isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[1])]))
{
IBond bond = bonds[g];
if (bond.getAtoms().Length != 2)
{
//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.warn("Skipping bond with more/less than two atoms: " + bond);
}
else
{
if (bond.Stereo == CDKConstants.STEREO_BOND_UP_INV || bond.Stereo == CDKConstants.STEREO_BOND_DOWN_INV)
{
// turn around atom coding to correct for inv stereo
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
}
else
{
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
}
//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'"
line += formatMDLInt((int)bond.Order, 3);
line += " ";
switch (bond.Stereo)
{
case CDKConstants.STEREO_BOND_UP:
line += "1";
break;
case CDKConstants.STEREO_BOND_UP_INV:
line += "1";
break;
case CDKConstants.STEREO_BOND_DOWN:
line += "6";
break;
case CDKConstants.STEREO_BOND_DOWN_INV:
line += "6";
break;
default:
line += "0";
break;
}
line += " 0 0 0 ";
writer.Write(line);
//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();
}
}
}
// write formal atomic charges
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
int charge = atom.getFormalCharge();
if (charge != 0)
{
writer.Write("M CHG 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(charge, 3));
//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();
}
}
// write formal isotope information
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
if (!(atom is IPseudoAtom))
{
int atomicMass = atom.MassNumber;
int majorMass = IsotopeFactory.getInstance(atom.Builder).getMajorIsotope(atom.Symbol).MassNumber;
if (atomicMass != 0 && atomicMass != majorMass)
{
writer.Write("M ISO 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(atomicMass, 3));
//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();
}
}
}
// close molecule
writer.Write("M END");
//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();
//write sdfields, if any
if (sdFields != null)
{
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
CSGraphT.SupportClass.SetSupport set_Renamed = new CSGraphT.SupportClass.HashSetSupport(sdFields.Keys);
System.Collections.IEnumerator iterator = set_Renamed.GetEnumerator();
//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'"
while (iterator.MoveNext())
{
//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'"
System.Object element = iterator.Current;
writer.Write("> <" + ((System.String)element) + ">");
//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();
//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'"
writer.Write(sdFields[element].ToString());
//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();
//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();
}
}
// taking care of the $$$$ signs:
// we write such a sign at the end of all except the first molecule
if (moleculeNumber != 1)
{
writer.Write("$$$$");
//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();
}
moleculeNumber++;
writer.Flush();
}
/// <summary> Generate canonical SMILES from the <code>molecule</code>. This method
/// canonicaly lables the molecule but does not perform any checks on the
/// chemical validity of the molecule.
/// IMPORTANT: A precomputed Set of All Rings (SAR) can be passed to this
/// SmilesGenerator in order to avoid recomputing it. Use setRings() to
/// assign the SAR.
///
/// </summary>
/// <param name="molecule"> The molecule to evaluate
/// </param>
/// <returns> Description of the Returned Value
/// </returns>
/// <seealso cref="org.openscience.cdk.graph.invariant.CanonicalLabeler.canonLabel(IAtomContainer)">
/// </seealso>
//UPGRADE_NOTE: Synchronized keyword was removed from method 'createSMILES'. Lock expression was added. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1027'"
public virtual System.String createSMILES(IMolecule molecule)
{
lock (this)
{
try
{
return (createSMILES(molecule, false, new bool[molecule.getBondCount()]));
}
catch (CDKException exception)
{
// This exception can only happen if a chiral smiles is requested
return ("");
}
}
}
/// <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;
}
/// <summary> Generate canonical and chiral SMILES from the <code>molecule</code>. This
/// method canonicaly lables the molecule but dose not perform any checks on
/// the chemical validity of the molecule. The chiral smiles is done like in
/// the <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">
/// daylight theory manual</a> . I did not find rules for canonical and chiral
/// smiles, therefore there is no guarantee that the smiles complies to any
/// externeal rules, but it is canonical compared to other smiles produced by
/// this method. The method checks if there are 2D coordinates but does not
/// check if coordinates make sense. Invalid stereo configurations are ignored;
/// if there are no valid stereo configuration the smiles will be the same as
/// the non-chiral one. Note that often stereo configurations are only complete
/// and can be converted to a smiles if explicit Hs are given.
/// IMPORTANT: A precomputed Set of All Rings (SAR) can be passed to this
/// SmilesGenerator in order to avoid recomputing it. Use setRings() to
/// assign the SAR.
///
/// </summary>
/// <param name="molecule"> The molecule to evaluate
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
/// <returns> Description of the Returned Value
/// </returns>
/// <exception cref="CDKException"> At least one atom has no Point2D;
/// coordinates are needed for creating the chiral smiles.
/// </exception>
/// <seealso cref="org.openscience.cdk.graph.invariant.CanonicalLabeler.canonLabel(IAtomContainer)">
/// </seealso>
//UPGRADE_NOTE: Synchronized keyword was removed from method 'createChiralSMILES'. Lock expression was added. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1027'"
public virtual System.String createChiralSMILES(IMolecule molecule, bool[] doubleBondConfiguration)
{
lock (this)
{
return (createSMILES(molecule, true, doubleBondConfiguration));
}
}
/// <summary> Returns the stoichiometry coefficient of the given product.
///
/// </summary>
/// <param name="product">Product for which the coefficient is returned.
/// </param>
/// <returns> -1, if the given molecule is not a product in this Reaction
/// </returns>
/// <seealso cref="setProductCoefficient">
/// </seealso>
public virtual double getProductCoefficient(IMolecule product)
{
return products.getMultiplier(product);
}
/// <summary> Adds a product to this reaction.
///
/// </summary>
/// <param name="product"> Molecule added as product to this reaction
/// </param>
/// <seealso cref="getProducts">
/// </seealso>
public virtual void addProduct(IMolecule product)
{
this.addProduct(product, 1.0);
/* notifyChanged() is called by
addProduct(Molecule product, double coefficient)*/
}
/// <summary> Sets the coefficient of a a reactant to a given value.
///
/// </summary>
/// <param name="reactant"> Reactant for which the coefficient is set
/// </param>
/// <param name="coefficient">The new coefficient for the given reactant
/// </param>
/// <returns> true if Molecule has been found and stoichiometry has been set.
/// </returns>
/// <seealso cref="getReactantCoefficient">
/// </seealso>
public virtual bool setReactantCoefficient(IMolecule reactant, double coefficient)
{
notifyChanged();
return reactants.setMultiplier(reactant, coefficient);
}
private IMolecule readMolecule(IMolecule molecule)
{
JmolAdapter adapter = new SmarterJmolAdapter();
// note that it actually let's the adapter detect the format!
System.Object model = adapter.openBufferedReader("", input);
molecule.add(new Convertor(molecule.Builder).convert(model));
return molecule;
}
