/// <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> 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> Read a Molecule from a file in MDL sd format /// /// </summary> /// <returns> The Molecule that was read from the MDL file. /// </returns> private IMolecule readMolecule(IMolecule molecule) { //logger.debug("Reading new molecule"); int linecount = 0; int atoms = 0; int bonds = 0; int atom1 = 0; int atom2 = 0; int order = 0; int stereo = 0; int RGroupCounter = 1; int Rnumber = 0; System.String[] rGroup = null; double x = 0.0; double y = 0.0; double z = 0.0; double totalZ = 0.0; //int[][] conMat = new int[0][0]; //String help; IBond bond; IAtom atom; System.String line = ""; try { //logger.info("Reading header"); line = input.ReadLine(); linecount++; if (line == null) { return(null); } //logger.debug("Line " + linecount + ": " + line); if (line.StartsWith("$$$$")) { //logger.debug("File is empty, returning empty molecule"); return(molecule); } if (line.Length > 0) { molecule.setProperty(CDKConstants.TITLE, line); } line = input.ReadLine(); linecount++; //logger.debug("Line " + linecount + ": " + line); line = input.ReadLine(); linecount++; //logger.debug("Line " + linecount + ": " + line); if (line.Length > 0) { molecule.setProperty(CDKConstants.REMARK, line); } //logger.info("Reading rest of file"); line = input.ReadLine(); linecount++; //logger.debug("Line " + linecount + ": " + line); atoms = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim()); //logger.debug("Atomcount: " + atoms); bonds = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim()); //logger.debug("Bondcount: " + bonds); // read ATOM block //logger.info("Reading atom block"); for (int f = 0; f < atoms; f++) { line = input.ReadLine(); linecount++; //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(line.Substring(0, (10) - (0)).Trim()); //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(line.Substring(10, (20) - (10)).Trim()); //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(line.Substring(20, (30) - (20)).Trim()); totalZ += System.Math.Abs(z); // *all* values should be zero, not just the sum //logger.debug("Coordinates: " + x + "; " + y + "; " + z); System.String element = line.Substring(31, (34) - (31)).Trim(); //logger.debug("Atom type: ", element); if (IsotopeFactory.getInstance(molecule.Builder).isElement(element)) { atom = IsotopeFactory.getInstance(molecule.Builder).configure(molecule.Builder.newAtom(element)); } else { //logger.debug("Atom ", element, " is not an regular element. Creating a PseudoAtom."); //check if the element is R rGroup = element.Split(new char[] { '^', 'R' }); // ???? if (rGroup.Length > 1) { try { Rnumber = System.Int32.Parse(rGroup[(rGroup.Length - 1)]); RGroupCounter = Rnumber; } catch (System.Exception ex) { Rnumber = RGroupCounter; RGroupCounter++; } element = "R" + Rnumber; } atom = molecule.Builder.newPseudoAtom(element); } // store as 3D for now, convert to 2D (if totalZ == 0.0) later atom.setPoint3d(new Point3d(x, y, z)); // parse further fields System.String massDiffString = line.Substring(34, (36) - (34)).Trim(); //logger.debug("Mass difference: ", massDiffString); if (!(atom is IPseudoAtom)) { try { int massDiff = System.Int32.Parse(massDiffString); if (massDiff != 0) { IIsotope major = IsotopeFactory.getInstance(molecule.Builder).getMajorIsotope(element); atom.AtomicNumber = major.AtomicNumber + massDiff; } } catch (System.Exception exception) { //logger.error("Could not parse mass difference field"); } } else { //logger.error("Cannot set mass difference for a non-element!"); } System.String chargeCodeString = line.Substring(36, (39) - (36)).Trim(); //logger.debug("Atom charge code: ", chargeCodeString); int chargeCode = System.Int32.Parse(chargeCodeString); if (chargeCode == 0) { // uncharged species } else if (chargeCode == 1) { atom.setFormalCharge(+3); } else if (chargeCode == 2) { atom.setFormalCharge(+2); } else if (chargeCode == 3) { atom.setFormalCharge(+1); } else if (chargeCode == 4) { } else if (chargeCode == 5) { atom.setFormalCharge(-1); } else if (chargeCode == 6) { atom.setFormalCharge(-2); } else if (chargeCode == 7) { atom.setFormalCharge(-3); } try { // read the mmm field as position 61-63 System.String reactionAtomIDString = line.Substring(60, (63) - (60)).Trim(); //logger.debug("Parsing mapping id: ", reactionAtomIDString); try { int reactionAtomID = System.Int32.Parse(reactionAtomIDString); if (reactionAtomID != 0) { atom.ID = reactionAtomIDString; } } catch (System.Exception exception) { //logger.error("Mapping number ", reactionAtomIDString, " is not an integer."); //logger.debug(exception); } } catch (System.Exception exception) { // older mol files don't have all these fields... //logger.warn("A few fields are missing. Older MDL MOL file?"); } molecule.addAtom(atom); } // convert to 2D, if totalZ == 0 if (totalZ == 0.0 && !forceReadAs3DCoords.Set) { //logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure"); IAtom[] atomsToUpdate = molecule.Atoms; for (int f = 0; f < atomsToUpdate.Length; f++) { IAtom atomToUpdate = atomsToUpdate[f]; Point3d p3d = atomToUpdate.getPoint3d(); atomToUpdate.setPoint2d(new Point2d(p3d.x, p3d.y)); atomToUpdate.setPoint3d(null); } } // read BOND block //logger.info("Reading bond block"); for (int f = 0; f < bonds; f++) { line = input.ReadLine(); linecount++; atom1 = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim()); atom2 = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim()); order = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim()); if (line.Length > 12) { stereo = System.Int32.Parse(line.Substring(9, (12) - (9)).Trim()); } else { //logger.warn("Missing expected stereo field at line: " + line); } //if (//logger.DebugEnabled) //{ // //logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order); //} if (stereo == 1) { // MDL up bond stereo = CDKConstants.STEREO_BOND_UP; } else if (stereo == 6) { // MDL down bond stereo = CDKConstants.STEREO_BOND_DOWN; } else if (stereo == 4) { //MDL bond undefined stereo = CDKConstants.STEREO_BOND_UNDEFINED; } // interpret CTfile's special bond orders IAtom a1 = molecule.getAtomAt(atom1 - 1); IAtom a2 = molecule.getAtomAt(atom2 - 1); if (order == 4) { // aromatic bond bond = molecule.Builder.newBond(a1, a2, CDKConstants.BONDORDER_AROMATIC, stereo); // mark both atoms and the bond as aromatic bond.setFlag(CDKConstants.ISAROMATIC, true); a1.setFlag(CDKConstants.ISAROMATIC, true); a2.setFlag(CDKConstants.ISAROMATIC, true); molecule.addBond(bond); } else { bond = molecule.Builder.newBond(a1, a2, (double)order, stereo); molecule.addBond(bond); } } // read PROPERTY block //logger.info("Reading property block"); while (true) { line = input.ReadLine(); linecount++; if (line == null) { throw new CDKException("The expected property block is missing!"); } if (line.StartsWith("M END")) { break; } bool lineRead = false; if (line.StartsWith("M CHG")) { // FIXME: if this is encountered for the first time, all // atom charges should be set to zero first! int infoCount = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim()); SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9)); for (int i = 1; i <= infoCount; i++) { System.String token = st.NextToken(); int atomNumber = System.Int32.Parse(token.Trim()); token = st.NextToken(); int charge = System.Int32.Parse(token.Trim()); molecule.getAtomAt(atomNumber - 1).setFormalCharge(charge); } } else if (line.StartsWith("M ISO")) { try { System.String countString = line.Substring(6, (9) - (6)).Trim(); int infoCount = System.Int32.Parse(countString); SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9)); for (int i = 1; i <= infoCount; i++) { int atomNumber = System.Int32.Parse(st.NextToken().Trim()); int absMass = System.Int32.Parse(st.NextToken().Trim()); if (absMass != 0) { IAtom isotope = molecule.getAtomAt(atomNumber - 1); isotope.MassNumber = absMass; } } } catch (System.FormatException 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 (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block."; //logger.error(error); throw new CDKException("NumberFormatException in isotope information on line: " + line, exception); } } else if (line.StartsWith("M RAD")) { try { System.String countString = line.Substring(6, (9) - (6)).Trim(); int infoCount = System.Int32.Parse(countString); SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9)); for (int i = 1; i <= infoCount; i++) { int atomNumber = System.Int32.Parse(st.NextToken().Trim()); int spinMultiplicity = System.Int32.Parse(st.NextToken().Trim()); if (spinMultiplicity > 1) { IAtom radical = molecule.getAtomAt(atomNumber - 1); for (int j = 2; j <= spinMultiplicity; j++) { // 2 means doublet -> one unpaired electron // 3 means triplet -> two unpaired electron molecule.addElectronContainer(molecule.Builder.newSingleElectron(radical)); } } } } catch (System.FormatException 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 (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block."; //logger.error(error); throw new CDKException("NumberFormatException in radical information on line: " + line, exception); } } else if (line.StartsWith("G ")) { try { System.String atomNumberString = line.Substring(3, (6) - (3)).Trim(); int atomNumber = System.Int32.Parse(atomNumberString); //String whatIsThisString = line.substring(6,9).trim(); System.String atomName = input.ReadLine(); // convert Atom into a PseudoAtom IAtom prevAtom = molecule.getAtomAt(atomNumber - 1); IPseudoAtom pseudoAtom = molecule.Builder.newPseudoAtom(atomName); if (prevAtom.getPoint2d() != null) { pseudoAtom.setPoint2d(prevAtom.getPoint2d()); } if (prevAtom.getPoint3d() != null) { pseudoAtom.setPoint3d(prevAtom.getPoint3d()); } AtomContainerManipulator.replaceAtomByAtom(molecule, prevAtom, pseudoAtom); } catch (System.FormatException exception) { //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'" System.String error = "Error (" + exception.ToString() + ") while parsing line " + linecount + ": " + line + " in property block."; //logger.error(error); throw new CDKException("NumberFormatException in group information on line: " + line, exception); } } if (!lineRead) { //logger.warn("Skipping line in property block: ", line); } } } catch (CDKException 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 line " + linecount + ": " + line + " -> " + exception.Message; //logger.error(error); //logger.debug(exception); throw exception; } 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 line " + linecount + ": " + line + " -> " + exception.Message; //logger.error(error); //logger.debug(exception); throw new CDKException(error, exception); } return(molecule); }
/// <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, 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> Produces an AtomContainer without explicit Hs but with H count from one with Hs. /// The new molecule is a deep copy. /// /// </summary> /// <param name="atomContainer">The AtomContainer from which to remove the hydrogens /// </param> /// <returns> The molecule without Hs. /// </returns> /// <cdk.keyword> hydrogen, removal </cdk.keyword> public static IAtomContainer removeHydrogens(IAtomContainer atomContainer) { //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.IDictionary map = new System.Collections.Hashtable(); // maps original atoms to clones. System.Collections.IList remove = new System.Collections.ArrayList(); // lists removed Hs. // Clone atoms except those to be removed. IMolecule mol = atomContainer.Builder.newMolecule(); int count = atomContainer.AtomCount; for (int i = 0; i < count; i++) { // Clone/remove this atom? IAtom atom = atomContainer.getAtomAt(i); if (!atom.Symbol.Equals("H")) { IAtom clonedAtom = null; try { clonedAtom = (IAtom)atom.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) { // TODO Auto-generated catch block SupportClass.WriteStackTrace(e, Console.Error); } clonedAtom.setHydrogenCount(0); mol.addAtom(clonedAtom); map[atom] = clonedAtom; } else { remove.Add(atom); // maintain list of removed H. } } // Clone bonds except those involving removed atoms. count = atomContainer.getBondCount(); for (int i = 0; i < count; i++) { // Check bond. //UPGRADE_NOTE: Final was removed from the declaration of 'bond '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'" IBond bond = atomContainer.getBondAt(i); IAtom[] atoms = bond.getAtoms(); bool removedBond = false; //UPGRADE_NOTE: Final was removed from the declaration of 'length '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'" int length = atoms.Length; for (int k = 0; k < length; k++) { if (remove.Contains(atoms[k])) { removedBond = true; break; } } // Clone/remove this bond? if (!removedBond) // if (!remove.contains(atoms[0]) && !remove.contains(atoms[1])) { IBond clone = null; try { clone = (IBond)atomContainer.getBondAt(i).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) { // TODO Auto-generated catch block SupportClass.WriteStackTrace(e, Console.Error); } clone.setAtoms(new IAtom[] { (IAtom)map[atoms[0]], (IAtom)map[atoms[1]] }); mol.addBond(clone); } } // Recompute hydrogen counts of neighbours of removed Hydrogens. //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 = remove.GetEnumerator(); i.MoveNext();) { // Process neighbours. //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'" //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 n = atomContainer.getConnectedAtomsVector((IAtom)i.Current).GetEnumerator(); n.MoveNext();) { //UPGRADE_NOTE: Final was removed from the declaration of 'neighb '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'" //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'" IAtom neighb = (IAtom)map[n.Current]; neighb.setHydrogenCount(neighb.getHydrogenCount() + 1); } } mol.Properties = atomContainer.Properties; mol.Flags = atomContainer.Flags; return(mol); }
/// <summary> Private method that actually parses the input to read a ChemFile /// object. In its current state it is able to read all the molecules /// (if more than one is present) in the specified HIN file. These are /// placed in a SetOfMolecules object which in turn is placed in a ChemModel /// which in turn is placed in a ChemSequence object and which is finally /// placed in a ChemFile object and returned to the user. /// /// </summary> /// <returns> A ChemFile containing the data parsed from input. /// </returns> private IChemFile readChemFile(IChemFile file) { IChemSequence chemSequence = file.Builder.newChemSequence(); IChemModel chemModel = file.Builder.newChemModel(); ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules(); System.String info; SupportClass.Tokenizer tokenizer; try { System.String line; // read in header info while (true) { line = input.ReadLine(); if (line.IndexOf("mol ") == 0) { info = getMolName(line); break; } } // start the actual molecule data - may be multiple molecule line = input.ReadLine(); while (true) { if (line == null) { break; // end of file } if (line.IndexOf(';') == 0) { continue; // comment line } if (line.IndexOf("mol ") == 0) { info = getMolName(line); line = input.ReadLine(); } IMolecule m = file.Builder.newMolecule(); m.setProperty(CDKConstants.TITLE, info); // Each elemnt of cons is an ArrayList of length 3 which stores // the start and end indices and bond order of each bond // found in the HIN file. Before adding bonds we need to reduce // the number of bonds so as not to count the same bond twice System.Collections.ArrayList cons = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10)); // read data for current molecule int atomSerial = 0; while (true) { if (line.IndexOf("endmol ") >= 0) { break; } if (line.IndexOf(';') == 0) { continue; // comment line } tokenizer = new SupportClass.Tokenizer(line, " "); int ntoken = tokenizer.Count; System.String[] toks = new System.String[ntoken]; for (int i = 0; i < ntoken; i++) { toks[i] = tokenizer.NextToken(); } System.String sym = new System.Text.StringBuilder(toks[3]).ToString(); double charge = System.Double.Parse(toks[6]); double x = System.Double.Parse(toks[7]); double y = System.Double.Parse(toks[8]); double z = System.Double.Parse(toks[9]); int nbond = System.Int32.Parse(toks[10]); IAtom atom = file.Builder.newAtom(sym, new Point3d(x, y, z)); atom.setCharge(charge); for (int j = 11; j < (11 + nbond * 2); j += 2) { double bo = 1; int s = System.Int32.Parse(toks[j]) - 1; // since atoms start from 1 in the file char bt = toks[j + 1][0]; switch (bt) { case 's': bo = 1; break; case 'd': bo = 2; break; case 't': bo = 3; break; case 'a': bo = 1.5; break; } System.Collections.ArrayList ar = new System.Collections.ArrayList(3); ar.Add((System.Int32)atomSerial); ar.Add((System.Int32)s); ar.Add((double)bo); cons.Add(ar); } m.addAtom(atom); atomSerial++; line = input.ReadLine(); } // before storing the molecule lets include the connections // First we reduce the number of bonds stored, since we have // stored both, say, C1-H1 and H1-C1. System.Collections.ArrayList blist = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10)); for (int i = 0; i < cons.Count; i++) { System.Collections.ArrayList ar = (System.Collections.ArrayList)cons[i]; // make a reversed list System.Collections.ArrayList arev = new System.Collections.ArrayList(3); arev.Add(ar[1]); arev.Add(ar[0]); arev.Add(ar[2]); // Now see if ar or arev are already in blist if (blist.Contains(ar) || blist.Contains(arev)) { continue; } else { blist.Add(ar); } } // now just store all the bonds we have for (int i = 0; i < blist.Count; i++) { System.Collections.ArrayList ar = (System.Collections.ArrayList)blist[i]; int s = ((System.Int32)ar[0]); int e = ((System.Int32)ar[1]); double bo = ((System.Double)ar[2]); m.addBond(s, e, bo); } setOfMolecules.addMolecule(m); line = input.ReadLine(); // read in the 'mol N' } // got all the molecule in the HIN file (hopefully!) chemModel.SetOfMolecules = setOfMolecules; chemSequence.addChemModel(chemModel); file.addChemSequence(chemSequence); } catch (System.IO.IOException e) { // should make some noise now file = null; } return(file); }