/// <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; }