/// <summary> Converts a RingSet to an AtomContainer.
///
/// </summary>
/// <param name="ringSet"> The RingSet to be converted.
/// </param>
/// <returns> The AtomContainer containing the bonds and atoms of the ringSet.
/// </returns>
public static IAtomContainer convertToAtomContainer(IRingSet ringSet)
{
IRing ring = (IRing)ringSet.getAtomContainer(0);
if (ring == null)
{
return(null);
}
IAtomContainer ac = ring.Builder.newAtomContainer();
for (int i = 0; i < ringSet.AtomContainerCount; i++)
{
ring = (IRing)ringSet.getAtomContainer(i);
for (int r = 0; r < ring.getBondCount(); r++)
{
IBond bond = ring.getBondAt(r);
if (!ac.contains(bond))
{
for (int j = 0; j < bond.AtomCount; j++)
{
ac.addAtom(bond.getAtomAt(j));
}
ac.addBond(bond);
}
}
}
return(ac);
}
/// <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> 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> Recursivly perfoms a depth first search in a molecular graphs contained in
/// the AtomContainer molecule, starting at the root atom and returning when it
/// hits the target atom.
/// CAUTION: This recursive method sets the VISITED flag of each atom
/// does not reset it after finishing the search. If you want to do the
/// operation on the same collection of atoms more than once, you have
/// to set all the VISITED flags to false before each operation
/// by looping of the atoms and doing a
/// "atom.setFlag((CDKConstants.VISITED, false));"
///
/// </summary>
/// <param name="molecule">The
/// AtomContainer to be searched
/// </param>
/// <param name="root"> The root atom
/// to start the search at
/// </param>
/// <param name="target"> The target
/// </param>
/// <param name="path"> An
/// AtomContainer to be filled with the path
/// </param>
/// <returns> true if the
/// target atom was found during this function call
/// </returns>
public static bool depthFirstTargetSearch(IAtomContainer molecule, IAtom root, IAtom target, IAtomContainer path)
{
IBond[] bonds = molecule.getConnectedBonds(root);
IAtom nextAtom;
root.setFlag(CDKConstants.VISITED, true);
for (int f = 0; f < bonds.Length; f++)
{
nextAtom = bonds[f].getConnectedAtom(root);
if (!nextAtom.getFlag(CDKConstants.VISITED))
{
path.addAtom(nextAtom);
path.addBond(bonds[f]);
if (nextAtom == target)
{
return(true);
}
else
{
if (!depthFirstTargetSearch(molecule, nextAtom, target, path))
{
// we did not find the target
path.removeAtom(nextAtom);
path.removeElectronContainer(bonds[f]);
}
else
{
return(true);
}
}
}
}
return(false);
}
/// <summary> Converts a Jmol <i>model</i> to a CDK AtomContainer.
///
/// </summary>
/// <param name="model">A Jmol model as returned by the method ModelAdapter.openBufferedReader()
/// </param>
public virtual IAtomContainer convert(System.Object model)
{
IAtomContainer atomContainer = builder.newAtomContainer();
SmarterJmolAdapter adapter = new SmarterJmolAdapter();
// use this hashtable to map the ModelAdapter Unique IDs to
// our CDK Atom's
System.Collections.Hashtable htMapUidsToAtoms = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
Org.Jmol.Api.JmolAdapter.AtomIterator atomIterator = adapter.getAtomIterator(model);
while (atomIterator.hasNext())
{
IAtom atom = builder.newAtom(atomIterator.ElementSymbol);
atom.X3d = atomIterator.X;
atom.Y3d = atomIterator.Y;
atom.Z3d = atomIterator.Z;
htMapUidsToAtoms[atomIterator.UniqueID] = atom;
atomContainer.addAtom(atom);
}
Org.Jmol.Api.JmolAdapter.BondIterator bondIterator = adapter.getBondIterator(model);
while (bondIterator.hasNext())
{
System.Object uid1 = bondIterator.AtomUniqueID1;
System.Object uid2 = bondIterator.AtomUniqueID2;
int order = bondIterator.EncodedOrder;
// now, look up the uids in our atom map.
IAtom atom1 = (IAtom)htMapUidsToAtoms[uid1];
IAtom atom2 = (IAtom)htMapUidsToAtoms[uid2];
IBond bond = builder.newBond(atom1, atom2, (double)order);
atomContainer.addBond(bond);
}
return(atomContainer);
}
public virtual IAtomContainer getPath(IAtomContainer spt, IAtom a1, IAtom a2)
{
IAtomContainer path = spt.Builder.newAtomContainer();
PathTools.resetFlags(spt);
path.addAtom(a1);
PathTools.depthFirstTargetSearch(spt, a1, a2, path);
return(path);
}
/// <summary> Processes the content from the formula field of the INChI.
/// Typical values look like C6H6, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H.
/// </summary>
public virtual IAtomContainer processFormula(IAtomContainer parsedContent, System.String atomsEncoding)
{
//logger.debug("Parsing atom data: ", atomsEncoding);
Regex pattern = new Regex("([A-Z][a-z]?)(\\d+)?(.*)");
//Pattern pattern = Pattern.compile("([A-Z][a-z]?)(\\d+)?(.*)");
System.String remainder = atomsEncoding;
while (remainder.Length > 0)
{
//logger.debug("Remaining: ", remainder);
Match matcher = pattern.Match(remainder);
//Matcher matcher = pattern.matcher(remainder);
//if (matcher.matches())
if (matcher != null && matcher.Success)
{
System.String symbol = matcher.Groups[1].Value;
//logger.debug("Atom symbol: ", symbol);
if (symbol.Equals("H"))
{
// don't add explicit hydrogens
}
else
{
System.String occurenceStr = matcher.Groups[2].Value;
int occurence = 1;
if (occurenceStr != null)
{
occurence = System.Int32.Parse(occurenceStr);
}
//logger.debug(" occurence: ", occurence);
for (int i = 1; i <= occurence; i++)
{
parsedContent.addAtom(parsedContent.Builder.newAtom(symbol));
}
}
remainder = matcher.Groups[3].Value;
if (remainder == null)
{
remainder = "";
}
//logger.debug(" Remaining: ", remainder);
}
else
{
//logger.error("No match found!");
remainder = "";
}
//logger.debug("NO atoms: ", parsedContent.AtomCount);
}
return(parsedContent);
}
/// <summary> Processes the content from the formula field of the INChI.
/// Typical values look like C6H6, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H.
/// </summary>
public virtual IAtomContainer processFormula(IAtomContainer parsedContent, System.String atomsEncoding)
{
//logger.debug("Parsing atom data: ", atomsEncoding);
Regex pattern = new Regex("([A-Z][a-z]?)(\\d+)?(.*)");
//Pattern pattern = Pattern.compile("([A-Z][a-z]?)(\\d+)?(.*)");
System.String remainder = atomsEncoding;
while (remainder.Length > 0)
{
//logger.debug("Remaining: ", remainder);
Match matcher = pattern.Match(remainder);
//Matcher matcher = pattern.matcher(remainder);
//if (matcher.matches())
if (matcher != null && matcher.Success)
{
System.String symbol = matcher.Groups[1].Value;
//logger.debug("Atom symbol: ", symbol);
if (symbol.Equals("H"))
{
// don't add explicit hydrogens
}
else
{
System.String occurenceStr = matcher.Groups[2].Value;
int occurence = 1;
if (occurenceStr != null)
{
occurence = System.Int32.Parse(occurenceStr);
}
//logger.debug(" occurence: ", occurence);
for (int i = 1; i <= occurence; i++)
{
parsedContent.addAtom(parsedContent.Builder.newAtom(symbol));
}
}
remainder = matcher.Groups[3].Value;
if (remainder == null)
remainder = "";
//logger.debug(" Remaining: ", remainder);
}
else
{
//logger.error("No match found!");
remainder = "";
}
//logger.debug("NO atoms: ", parsedContent.AtomCount);
}
return parsedContent;
}
public virtual IAtomContainer getSpanningTree()
{
IAtomContainer ac = molecule.Builder.newAtomContainer();
for (int a = 0; a < V; a++)
{
ac.addAtom(molecule.getAtomAt(a));
}
for (int b = 0; b < E; b++)
{
if (bondsInTree[b])
{
ac.addBond(molecule.getBondAt(b));
}
}
return(ac);
}
/// <summary> Method that saturates an atom in a molecule by adding explicit hydrogens.
///
/// </summary>
/// <param name="atom"> Atom to saturate
/// </param>
/// <param name="container">AtomContainer containing the atom
/// </param>
/// <param name="count"> Number of hydrogens to add
/// </param>
/// <param name="totalContainer">In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
///
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, int count, IAtomContainer totalContainer)
{
//boolean create2DCoordinates = GeometryTools.has2DCoordinates(container);
IIsotope isotope = IsotopeFactory.getInstance(container.Builder).getMajorIsotope("H");
atom.setHydrogenCount(0);
IAtomContainer changedAtomsAndBonds = container.Builder.newAtomContainer();
for (int i = 1; i <= count; i++)
{
IAtom hydrogen = container.Builder.newAtom("H");
IsotopeFactory.getInstance(container.Builder).configure(hydrogen, isotope);
totalContainer.addAtom(hydrogen);
IBond newBond = container.Builder.newBond((IAtom)atom, hydrogen, 1.0);
totalContainer.addBond(newBond);
changedAtomsAndBonds.addAtom(hydrogen);
changedAtomsAndBonds.addBond(newBond);
}
return(changedAtomsAndBonds);
}
private IChemModel readChemModel(IChemModel model)
{
int[] atoms = new int[1];
double[] atomxs = new double[1];
double[] atomys = new double[1];
double[] atomzs = new double[1];
double[] atomcharges = new double[1];
int[] bondatomid1 = new int[1];
int[] bondatomid2 = new int[1];
int[] bondorder = new int[1];
int numberOfAtoms = 0;
int numberOfBonds = 0;
try
{
System.String line = input.ReadLine();
while (line != null)
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line);
System.String command = st.NextToken();
if ("!Header".Equals(command))
{
//logger.warn("Ignoring header");
}
else if ("!Info".Equals(command))
{
//logger.warn("Ignoring info");
}
else if ("!Atoms".Equals(command))
{
//logger.info("Reading atom block");
// determine number of atoms to read
try
{
numberOfAtoms = System.Int32.Parse(st.NextToken());
//logger.debug(" #atoms: " + numberOfAtoms);
atoms = new int[numberOfAtoms];
atomxs = new double[numberOfAtoms];
atomys = new double[numberOfAtoms];
atomzs = new double[numberOfAtoms];
atomcharges = new double[numberOfAtoms];
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
atoms[atomID] = System.Int32.Parse(atomInfoFields.NextToken());
//logger.debug("Set atomic number of atom (" + atomID + ") to: " + atoms[atomID]);
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Atoms block");
//logger.debug(exception);
}
}
else if ("!Bonds".Equals(command))
{
//logger.info("Reading bond block");
try
{
// determine number of bonds to read
numberOfBonds = System.Int32.Parse(st.NextToken());
bondatomid1 = new int[numberOfAtoms];
bondatomid2 = new int[numberOfAtoms];
bondorder = new int[numberOfAtoms];
for (int i = 0; i < numberOfBonds; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer bondInfoFields = new SupportClass.Tokenizer(line);
bondatomid1[i] = System.Int32.Parse(bondInfoFields.NextToken());
bondatomid2[i] = System.Int32.Parse(bondInfoFields.NextToken());
System.String order = bondInfoFields.NextToken();
if ("D".Equals(order))
{
bondorder[i] = 2;
}
else if ("S".Equals(order))
{
bondorder[i] = 1;
}
else if ("T".Equals(order))
{
bondorder[i] = 3;
}
else
{
// ignore order, i.e. set to single
//logger.warn("Unrecognized bond order, using single bond instead. Found: " + order);
bondorder[i] = 1;
}
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Bonds block");
//logger.debug(exception);
}
}
else if ("!Coord".Equals(command))
{
//logger.info("Reading coordinate block");
try
{
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
double x = System.Double.Parse(atomInfoFields.NextToken());
double y = System.Double.Parse(atomInfoFields.NextToken());
double z = System.Double.Parse(atomInfoFields.NextToken());
atomxs[atomID] = x;
atomys[atomID] = y;
atomzs[atomID] = z;
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Coord block");
//logger.debug(exception);
}
}
else if ("!Charges".Equals(command))
{
//logger.info("Reading charges block");
try
{
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
double charge = System.Double.Parse(atomInfoFields.NextToken());
atomcharges[atomID] = charge;
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Charges block");
//logger.debug(exception);
}
}
else if ("!End".Equals(command))
{
//logger.info("Found end of file");
// Store atoms
IAtomContainer container = model.Builder.newAtomContainer();
for (int i = 0; i < numberOfAtoms; i++)
{
try
{
IAtom atom = model.Builder.newAtom(IsotopeFactory.getInstance(container.Builder).getElementSymbol(atoms[i]));
atom.AtomicNumber = atoms[i];
atom.setPoint3d(new Point3d(atomxs[i], atomys[i], atomzs[i]));
atom.setCharge(atomcharges[i]);
container.addAtom(atom);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Stored atom: " + atom);
}
catch (System.Exception exception)
{
//logger.error("Cannot create an atom with atomic number: " + atoms[i]);
//logger.debug(exception);
}
}
// Store bonds
for (int i = 0; i < numberOfBonds; i++)
{
container.addBond(bondatomid1[i], bondatomid2[i], bondorder[i]);
}
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addMolecule(model.Builder.newMolecule(container));
model.SetOfMolecules = moleculeSet;
return(model);
}
else
{
//logger.warn("Skipping line: " + line);
}
line = input.ReadLine();
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading file");
//logger.debug(exception);
}
// this should not happen, file is lacking !End command
return(null);
}
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void endObject(System.String objectType)
{
//logger.debug("END: " + objectType);
if (objectType.Equals("Molecule"))
{
if (currentMolecule is IMolecule)
{
//logger.debug("Adding molecule to set");
currentSetOfMolecules.addMolecule((IMolecule)currentMolecule);
//logger.debug("#mols in set: " + currentSetOfMolecules.MoleculeCount);
}
else if (currentMolecule is ICrystal)
{
//logger.debug("Adding crystal to chemModel");
currentChemModel.Crystal = (ICrystal)currentMolecule;
currentChemSequence.addChemModel(currentChemModel);
}
}
else if (objectType.Equals("SetOfMolecules"))
{
currentChemModel.SetOfMolecules = currentSetOfMolecules;
currentChemSequence.addChemModel(currentChemModel);
}
else if (objectType.Equals("Frame"))
{
// endObject("Molecule");
}
else if (objectType.Equals("Animation"))
{
addChemSequence(currentChemSequence);
//logger.info("This file has " + ChemSequenceCount + " sequence(s).");
}
else if (objectType.Equals("Atom"))
{
currentMolecule.addAtom(currentAtom);
}
else if (objectType.Equals("Bond"))
{
//logger.debug("Bond(" + bond_id + "): " + bond_a1 + ", " + bond_a2 + ", " + bond_order);
if (bond_a1 > currentMolecule.AtomCount || bond_a2 > currentMolecule.AtomCount)
{
//logger.error("Cannot add bond between at least one non-existant atom: " + bond_a1 + " and " + bond_a2);
}
else
{
IAtom a1 = currentMolecule.getAtomAt(bond_a1);
IAtom a2 = currentMolecule.getAtomAt(bond_a2);
IBond b = currentChemFile.Builder.newBond(a1, a2, bond_order);
if (bond_id != null)
{
b.ID = bond_id;
}
if (bond_stereo != -99)
{
b.Stereo = bond_stereo;
}
if (bond_order == CDKConstants.BONDORDER_AROMATIC)
{
b.setFlag(CDKConstants.ISAROMATIC, true);
}
currentMolecule.addBond(b);
}
}
else if (objectType.Equals("a-axis"))
{
// set these variables
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.A = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("b-axis"))
{
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.B = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("c-axis"))
{
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.C = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("SetOfReactions"))
{
currentChemModel.SetOfReactions = currentSetOfReactions;
currentChemSequence.addChemModel(currentChemModel);
/* FIXME: this should be when document is closed! */
}
else if (objectType.Equals("Reaction"))
{
//logger.debug("Adding reaction to SOR");
currentSetOfReactions.addReaction(currentReaction);
}
else if (objectType.Equals("Reactant"))
{
currentReaction.addReactant((IMolecule)currentMolecule);
}
else if (objectType.Equals("Product"))
{
currentReaction.addProduct((IMolecule)currentMolecule);
}
else if (objectType.Equals("Crystal"))
{
//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("Crystal: " + currentMolecule);
}
}
/// <summary> Recursivly perfoms a depth first search in a molecular graphs contained in
/// the AtomContainer molecule, starting at the root atom and returning when it
/// hits the target atom.
/// CAUTION: This recursive method sets the VISITED flag of each atom
/// does not reset it after finishing the search. If you want to do the
/// operation on the same collection of atoms more than once, you have
/// to set all the VISITED flags to false before each operation
/// by looping of the atoms and doing a
/// "atom.setFlag((CDKConstants.VISITED, false));"
///
/// </summary>
/// <param name="molecule">The
/// AtomContainer to be searched
/// </param>
/// <param name="root"> The root atom
/// to start the search at
/// </param>
/// <param name="target"> The target
/// </param>
/// <param name="path"> An
/// AtomContainer to be filled with the path
/// </param>
/// <returns> true if the
/// target atom was found during this function call
/// </returns>
public static bool depthFirstTargetSearch(IAtomContainer molecule, IAtom root, IAtom target, IAtomContainer path)
{
IBond[] bonds = molecule.getConnectedBonds(root);
IAtom nextAtom;
root.setFlag(CDKConstants.VISITED, true);
for (int f = 0; f < bonds.Length; f++)
{
nextAtom = bonds[f].getConnectedAtom(root);
if (!nextAtom.getFlag(CDKConstants.VISITED))
{
path.addAtom(nextAtom);
path.addBond(bonds[f]);
if (nextAtom == target)
{
return true;
}
else
{
if (!depthFirstTargetSearch(molecule, nextAtom, target, path))
{
// we did not find the target
path.removeAtom(nextAtom);
path.removeElectronContainer(bonds[f]);
}
else
{
return true;
}
}
}
}
return false;
}
//////////////////////////////////////
// Manipulation tools
/// <summary> Projects a list of RMap on a molecule
///
/// </summary>
/// <param name="rMapList"> the list to project
/// </param>
/// <param name="g"> the molecule on which project
/// </param>
/// <param name="id"> the id in the RMap of the molecule g
/// </param>
/// <returns> an AtomContainer
/// </returns>
public static IAtomContainer project(System.Collections.IList rMapList, IAtomContainer g, int id)
{
IAtomContainer ac = g.Builder.newAtomContainer();
IBond[] bondList = g.Bonds;
System.Collections.Hashtable table = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
IAtom a1;
IAtom a2;
IAtom a;
IBond bond;
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator i = rMapList.GetEnumerator(); i.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'"
RMap rMap = (RMap)i.Current;
if (id == UniversalIsomorphismTester.ID1)
{
bond = bondList[rMap.Id1];
}
else
{
bond = bondList[rMap.Id2];
}
a = bond.getAtomAt(0);
a1 = (IAtom)table[a];
if (a1 == null)
{
try
{
a1 = (IAtom)a.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
SupportClass.WriteStackTrace(e, Console.Error);
}
ac.addAtom(a1);
table[a] = a1;
}
a = bond.getAtomAt(1);
a2 = (IAtom)table[a];
if (a2 == null)
{
try
{
a2 = (IAtom)a.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
SupportClass.WriteStackTrace(e, Console.Error);
}
ac.addAtom(a2);
table[a] = a2;
}
IBond newBond = g.Builder.newBond(a1, a2, bond.Order);
newBond.setFlag(CDKConstants.ISAROMATIC, bond.getFlag(CDKConstants.ISAROMATIC));
ac.addBond(newBond);
}
return(ac);
}
/// <summary> Reads the atoms, coordinates and charges.
///
/// <p>IMPORTANT: it does not support the atom list and its negation!
/// </summary>
public virtual void readAtomBlock(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END ATOM".Equals(command))
{
// FIXME: should check wether 3D is really 2D
foundEND = true;
}
else
{
//logger.debug("Parsing atom from: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
IAtom atom = readData.Builder.newAtom("C");
// parse the index
try
{
System.String indexString = tokenizer.NextToken();
atom.ID = indexString;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the element
System.String element = tokenizer.NextToken();
bool isElement = false;
try
{
isElement = IsotopeFactory.getInstance(atom.Builder).isElement(element);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine if element exists!", exception);
}
if (isPseudoAtom(element))
{
atom = readData.Builder.newPseudoAtom(atom);
}
else if (isElement)
{
atom.Symbol = element;
}
else
{
System.String error = "Cannot parse element of type: " + element;
//logger.error(error);
throw new CDKException("(Possible CDK bug) " + error);
}
// parse atom coordinates (in Angstrom)
try
{
System.String xString = tokenizer.NextToken();
System.String yString = tokenizer.NextToken();
System.String zString = tokenizer.NextToken();
double x = System.Double.Parse(xString);
double y = System.Double.Parse(yString);
double z = System.Double.Parse(zString);
atom.setPoint3d(new Point3d(x, y, z));
atom.setPoint2d(new Point2d(x, y)); // FIXME: dirty!
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom coordinates";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// atom-atom mapping
System.String mapping = tokenizer.NextToken();
if (!mapping.Equals("0"))
{
//logger.warn("Skipping atom-atom mapping: " + mapping);
} // else: default 0 is no mapping defined
// the rest are key value things
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (keys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CHG"))
{
int charge = System.Int32.Parse(value_Renamed);
if (charge != 0)
{
// zero is no charge specified
atom.setFormalCharge(charge);
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// store atom
readData.addAtom(atom);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Added atom: " + atom);
}
}
}
/// <summary> Method that saturates an atom in a molecule by adding explicit hydrogens.
///
/// </summary>
/// <param name="atom"> Atom to saturate
/// </param>
/// <param name="container">AtomContainer containing the atom
/// </param>
/// <param name="count"> Number of hydrogens to add
/// </param>
/// <param name="totalContainer">In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
///
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, int count, IAtomContainer totalContainer)
{
//boolean create2DCoordinates = GeometryTools.has2DCoordinates(container);
IIsotope isotope = IsotopeFactory.getInstance(container.Builder).getMajorIsotope("H");
atom.setHydrogenCount(0);
IAtomContainer changedAtomsAndBonds = container.Builder.newAtomContainer();
for (int i = 1; i <= count; i++)
{
IAtom hydrogen = container.Builder.newAtom("H");
IsotopeFactory.getInstance(container.Builder).configure(hydrogen, isotope);
totalContainer.addAtom(hydrogen);
IBond newBond = container.Builder.newBond((IAtom) atom, hydrogen, 1.0);
totalContainer.addBond(newBond);
changedAtomsAndBonds.addAtom(hydrogen);
changedAtomsAndBonds.addBond(newBond);
}
return changedAtomsAndBonds;
}
/// <summary> Reads the atoms, coordinates and charges.
///
/// <p>IMPORTANT: it does not support the atom list and its negation!
/// </summary>
public virtual void readAtomBlock(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END ATOM".Equals(command))
{
// FIXME: should check wether 3D is really 2D
foundEND = true;
}
else
{
//logger.debug("Parsing atom from: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
IAtom atom = readData.Builder.newAtom("C");
// parse the index
try
{
System.String indexString = tokenizer.NextToken();
atom.ID = indexString;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the element
System.String element = tokenizer.NextToken();
bool isElement = false;
try
{
isElement = IsotopeFactory.getInstance(atom.Builder).isElement(element);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine if element exists!", exception);
}
if (isPseudoAtom(element))
{
atom = readData.Builder.newPseudoAtom(atom);
}
else if (isElement)
{
atom.Symbol = element;
}
else
{
System.String error = "Cannot parse element of type: " + element;
//logger.error(error);
throw new CDKException("(Possible CDK bug) " + error);
}
// parse atom coordinates (in Angstrom)
try
{
System.String xString = tokenizer.NextToken();
System.String yString = tokenizer.NextToken();
System.String zString = tokenizer.NextToken();
double x = System.Double.Parse(xString);
double y = System.Double.Parse(yString);
double z = System.Double.Parse(zString);
atom.setPoint3d(new Point3d(x, y, z));
atom.setPoint2d(new Point2d(x, y)); // FIXME: dirty!
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom coordinates";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// atom-atom mapping
System.String mapping = tokenizer.NextToken();
if (!mapping.Equals("0"))
{
//logger.warn("Skipping atom-atom mapping: " + mapping);
} // else: default 0 is no mapping defined
// the rest are key value things
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (keys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CHG"))
{
int charge = System.Int32.Parse(value_Renamed);
if (charge != 0)
{
// zero is no charge specified
atom.setFormalCharge(charge);
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// store atom
readData.addAtom(atom);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Added atom: " + atom);
}
}
}
/// <summary> Reads a set of coordinates into ChemModel.
///
/// </summary>
/// <param name="model">the destination ChemModel
/// </param>
/// <throws> IOException if an I/O error occurs </throws>
private void readCoordinates(IChemModel model)
{
IAtomContainer container = model.Builder.newAtomContainer();
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 = 0;
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 System.IO.IOException("Error reading coordinates");
}
token.NextToken();
// ignore third token
double x = 0.0;
double y = 0.0;
double z = 0.0;
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
x = token.nval;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
y = token.nval;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
z = token.nval;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
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));
container.addAtom(atom);
}
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addMolecule(model.Builder.newMolecule(container));
model.SetOfMolecules = moleculeSet;
}