private int addArrayElementsTo(System.Collections.ArrayList toAddto, System.String array)
 {
     SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(array);
     int i = 0;
     while (tokenizer.HasMoreTokens())
     {
         toAddto.Add(tokenizer.NextToken());
         i++;
     }
     return i;
 }
        /// <summary> Reads a text based configuration file.
        /// 
        /// </summary>
        /// <param name="builder">IChemObjectBuilder used to construct the IAtomType's.
        /// </param>
        /// <throws>         IOException when a problem occured with reading from the InputStream </throws>
        /// <returns>        A Vector with read IAtomType's.
        /// </returns>
        public virtual System.Collections.ArrayList readAtomTypes(IChemObjectBuilder builder)
        {
            System.Collections.ArrayList atomTypes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));

            if (ins == null)
            {
                // trying the default
                //System.out.println("readAtomTypes getResourceAsStream:"
                //                   + configFile);
                //UPGRADE_ISSUE: Method 'java.lang.ClassLoader.getResourceAsStream' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassLoader'"
                //UPGRADE_ISSUE: Method 'java.lang.Class.getClassLoader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassgetClassLoader'"
                ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + configFile);
            }
            if (ins == null)
                throw new System.IO.IOException("There was a problem getting the default stream: " + configFile);

            // read the contents from file
            //UPGRADE_TODO: The differences in the expected value  of parameters for constructor 'java.io.BufferedReader.BufferedReader'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
            //UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
            System.IO.StreamReader reader = new System.IO.StreamReader(new System.IO.StreamReader(ins, System.Text.Encoding.Default).BaseStream, new System.IO.StreamReader(ins, System.Text.Encoding.Default).CurrentEncoding, false, 1024);
            SupportClass.Tokenizer tokenizer;
            System.String string_Renamed;

            while (true)
            {
                string_Renamed = reader.ReadLine();
                if (string_Renamed == null)
                {
                    break;
                }
                if (!string_Renamed.StartsWith("#"))
                {
                    System.String name = "";
                    System.String rootType = "";
                    int atomicNumber = 0, colorR = 0, colorG = 0, colorB = 0;
                    double mass = 0.0, vdwaals = 0.0, covalent = 0.0;
                    tokenizer = new SupportClass.Tokenizer(string_Renamed, "\t ,;");
                    int tokenCount = tokenizer.Count;

                    if (tokenCount == 9)
                    {
                        name = tokenizer.NextToken();
                        rootType = tokenizer.NextToken();
                        System.String san = tokenizer.NextToken();
                        System.String sam = tokenizer.NextToken();
                        System.String svdwaals = tokenizer.NextToken();
                        System.String scovalent = tokenizer.NextToken();
                        System.String sColorR = tokenizer.NextToken();
                        System.String sColorG = tokenizer.NextToken();
                        System.String sColorB = tokenizer.NextToken();

                        try
                        {
                            //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'"
                            mass = System.Double.Parse(sam);
                            //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'"
                            vdwaals = System.Double.Parse(svdwaals);
                            //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'"
                            covalent = System.Double.Parse(scovalent);
                            atomicNumber = System.Int32.Parse(san);
                            colorR = System.Int32.Parse(sColorR);
                            colorG = System.Int32.Parse(sColorG);
                            colorB = System.Int32.Parse(sColorB);
                        }
                        catch (System.FormatException nfe)
                        {
                            throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Malformed Number");
                        }

                        IAtomType atomType = builder.newAtomType(name, rootType);
                        atomType.AtomicNumber = atomicNumber;
                        atomType.setExactMass(mass);
                        atomType.VanderwaalsRadius = vdwaals;
                        atomType.CovalentRadius = covalent;
                        System.Drawing.Color color = System.Drawing.Color.FromArgb(colorR, colorG, colorB);
                        atomType.setProperty("org.openscience.cdk.renderer.color", color);
                        atomTypes.Add(atomType);
                    }
                    else
                    {
                        throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Wrong Number of fields");
                    }
                }
            } // end while
            ins.Close();

            return atomTypes;
        }
        /// <summary> Creates a String of the Class name of the <code>IChemObject</code> reader
        /// for this file format. The input is read line-by-line
        /// until a line containing an identifying string is
        /// found.
        /// 
        /// <p>The ReaderFactory detects more formats than the CDK
        /// has Readers for.
        /// 
        /// <p>This method is not able to detect the format of gziped files.
        /// Use <code>guessFormat(InputStream)</code> instead for such files.
        /// 
        /// </summary>
        /// <throws>  IOException  if an I/O error occurs </throws>
        /// <throws>  IllegalArgumentException if the input is null </throws>
        /// <summary> 
        /// </summary>
        /// <seealso cref="guessFormat(InputStream)">
        /// </seealso>
        public virtual IChemFormat guessFormat(StreamReader input)
        {
            if (input == null)
            {
                throw new System.ArgumentException("input cannot be null");
            }

            // make a copy of the header
            char[] header = new char[this.headerLength];
            //UPGRADE_ISSUE: Method 'java.io.BufferedReader.markSupported' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000'"
            //if (!input.markSupported())
            //{
            //    //logger.error("Mark not supported");
            //    throw new System.ArgumentException("input must support mark");
            //}
            //int pos = this.headerLength;//input.mark(this.headerLength);
            input.Read(header, 0, this.headerLength);
            input.BaseStream.Seek(0, SeekOrigin.Begin);

            //UPGRADE_ISSUE: Constructor 'java.io.BufferedReader.BufferedReader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderBufferedReader_javaioReader'"
            System.IO.StringReader buffer = new StringReader(new System.String(header));

            /* Search file for a line containing an identifying keyword */
            System.String line = null;
            int lineNumber = 1;
            while ((line = buffer.ReadLine()) != null)
            {
                //logger.debug(lineNumber + ": ", line);
                for (int i = 0; i < formats.Count; i++)
                {
                    IChemFormatMatcher cfMatcher = (IChemFormatMatcher)formats[i];
                    if (cfMatcher.matches(lineNumber, line))
                    {
                        //logger.info("Detected format: ", cfMatcher.FormatName);
                        return cfMatcher;
                    }
                }
                lineNumber++;
            }

            //logger.warn("Now comes the tricky and more difficult ones....");
            //UPGRADE_ISSUE: Constructor 'java.io.BufferedReader.BufferedReader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderBufferedReader_javaioReader'"
            buffer = new StringReader(new System.String(header));

            line = buffer.ReadLine();
            // is it a XYZ file?
            SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line.Trim());
            try
            {
                int tokenCount = tokenizer.Count;
                if (tokenCount == 1)
                {
                    System.Int32.Parse(tokenizer.NextToken());
                    // if not failed, then it is a XYZ file
                    return null;// new org.openscience.cdk.io.formats.XYZFormat();
                }
                else if (tokenCount == 2)
                {
                    System.Int32.Parse(tokenizer.NextToken());
                    if ("Bohr".ToUpper().Equals(tokenizer.NextToken().ToUpper()))
                    {
                        return null;// new org.openscience.cdk.io.formats.XYZFormat();
                    }
                }
            }
            catch (System.FormatException exception)
            {
                //logger.info("No, it's not a XYZ file");
            }

            //logger.warn("File format undetermined");
            return null;
        }
Beispiel #4
0
        /// <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;
        }
        /// <summary>  Private method that actually parses the input to read a ChemFile
        /// object.
        /// 
        /// </summary>
        /// <returns> A ChemFile containing the data parsed from input.
        /// </returns>
        private IChemFile readChemFile(IChemFile file)
        {
            IChemSequence chemSequence = file.Builder.newChemSequence();

            int number_of_atoms = 0;
            SupportClass.Tokenizer tokenizer;

            try
            {
                System.String line = input.ReadLine();
                while (line.StartsWith("#"))
                    line = input.ReadLine();
                /*while (input.ready() && line != null) 
                {*/
                //        System.out.println("lauf");
                // parse frame by frame
                tokenizer = new SupportClass.Tokenizer(line, "\t ,;");

                System.String token = tokenizer.NextToken();
                number_of_atoms = System.Int32.Parse(token);
                System.String info = input.ReadLine();

                IChemModel chemModel = file.Builder.newChemModel();
                ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();

                IMolecule m = file.Builder.newMolecule();
                m.setProperty(CDKConstants.TITLE, info);

                System.String[] types = new System.String[number_of_atoms];
                double[] d = new double[number_of_atoms]; int[] d_atom = new int[number_of_atoms]; // Distances
                double[] a = new double[number_of_atoms]; int[] a_atom = new int[number_of_atoms]; // Angles
                double[] da = new double[number_of_atoms]; int[] da_atom = new int[number_of_atoms]; // Diederangles
                //Point3d[] pos = new Point3d[number_of_atoms]; // calculated positions

                int i = 0;
                while (i < number_of_atoms)
                {
                    line = input.ReadLine();
                    //          System.out.println("line:\""+line+"\"");
                    if (line == null)
                        break;
                    if (line.StartsWith("#"))
                    {
                        // skip comment in file
                    }
                    else
                    {
                        d[i] = 0d; d_atom[i] = -1;
                        a[i] = 0d; a_atom[i] = -1;
                        da[i] = 0d; da_atom[i] = -1;

                        tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
                        int fields = tokenizer.Count;

                        if (fields < System.Math.Min(i * 2 + 1, 7))
                        {
                            // this is an error but cannot throw exception
                        }
                        else if (i == 0)
                        {
                            types[i] = tokenizer.NextToken();
                            i++;
                        }
                        else if (i == 1)
                        {
                            types[i] = tokenizer.NextToken();
                            d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
                            //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'"
                            d[i] = (System.Double.Parse(tokenizer.NextToken()));
                            i++;
                        }
                        else if (i == 2)
                        {
                            types[i] = tokenizer.NextToken();
                            d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
                            //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'"
                            d[i] = (System.Double.Parse(tokenizer.NextToken()));
                            a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
                            //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'"
                            a[i] = (System.Double.Parse(tokenizer.NextToken()));
                            i++;
                        }
                        else
                        {
                            types[i] = tokenizer.NextToken();
                            d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
                            //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'"
                            d[i] = (System.Double.Parse(tokenizer.NextToken()));
                            a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
                            //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'"
                            a[i] = (System.Double.Parse(tokenizer.NextToken()));
                            da_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
                            //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'"
                            da[i] = (System.Double.Parse(tokenizer.NextToken()));
                            i++;
                        }
                    }
                }

                // calculate cartesian coordinates
                Point3d[] cartCoords = ZMatrixTools.zmatrixToCartesian(d, d_atom, a, a_atom, da, da_atom);

                for (i = 0; i < number_of_atoms; i++)
                {
                    m.addAtom(file.Builder.newAtom(types[i], cartCoords[i]));
                }

                //        System.out.println("molecule:\n"+m);

                setOfMolecules.addMolecule(m);
                chemModel.SetOfMolecules = setOfMolecules;
                chemSequence.addChemModel(chemModel);
                line = input.ReadLine();
                file.addChemSequence(chemSequence);
            }
            catch (System.IO.IOException e)
            {
                // should make some noise now
                file = null;
            }
            return file;
        }
		/// <summary>  Description of the Method
		/// 
		/// </summary>
		/// <param name="smiles">                     Description of the Parameter
		/// </param>
		/// <returns>                             Description of the Return Value
		/// </returns>
		/// <exception cref="InvalidSmilesException"> Description of the Exception
		/// </exception>
		public virtual Reaction parseReactionSmiles(System.String smiles)
		{
			SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(smiles, ">");
			System.String reactantSmiles = tokenizer.NextToken();
			System.String agentSmiles = "";
			System.String productSmiles = tokenizer.NextToken();
			if (tokenizer.HasMoreTokens())
			{
				agentSmiles = productSmiles;
				productSmiles = tokenizer.NextToken();
			}
			
			Reaction reaction = new Reaction();
			
			// add reactants
			IMolecule reactantContainer = parseSmiles(reactantSmiles);
			ISetOfMolecules reactantSet = ConnectivityChecker.partitionIntoMolecules(reactantContainer);
			IMolecule[] reactants = reactantSet.Molecules;
			for (int i = 0; i < reactants.Length; i++)
			{
				reaction.addReactant(reactants[i]);
			}
			
			// add reactants
			if (agentSmiles.Length > 0)
			{
				IMolecule agentContainer = parseSmiles(agentSmiles);
				ISetOfMolecules agentSet = ConnectivityChecker.partitionIntoMolecules(agentContainer);
				IMolecule[] agents = agentSet.Molecules;
				for (int i = 0; i < agents.Length; i++)
				{
					reaction.addAgent(agents[i]);
				}
			}
			
			// add products
			IMolecule productContainer = parseSmiles(productSmiles);
			ISetOfMolecules productSet = ConnectivityChecker.partitionIntoMolecules(productContainer);
			IMolecule[] products = productSet.Molecules;
			for (int i = 0; i < products.Length; i++)
			{
				reaction.addProduct(products[i]);
			}
			
			return reaction;
		}
        private IChemModel readChemModel(IChemModel 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> Read a Reaction from a file in MDL RXN format
        /// 
        /// </summary>
        /// <returns>  The Reaction that was read from the MDL file.
        /// </returns>
        private IReaction readReaction(IChemObjectBuilder builder)
        {
            IReaction reaction = builder.newReaction();
            try
            {
                input.ReadLine(); // first line should be $RXN
                input.ReadLine(); // second line
                input.ReadLine(); // third line
                input.ReadLine(); // fourth line
            }
            catch (System.IO.IOException exception)
            {
                //logger.debug(exception);
                throw new CDKException("Error while reading header of RXN file", exception);
            }

            int reactantCount = 0;
            int productCount = 0;
            try
            {
                System.String countsLine = input.ReadLine();
                /* this line contains the number of reactants
                and products */
                SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(countsLine);
                reactantCount = System.Int32.Parse(tokenizer.NextToken());
                //logger.info("Expecting " + reactantCount + " reactants in file");
                productCount = System.Int32.Parse(tokenizer.NextToken());
                //logger.info("Expecting " + productCount + " products in file");
            }
            catch (System.Exception exception)
            {
                //logger.debug(exception);
                throw new CDKException("Error while counts line of RXN file", exception);
            }

            // now read the reactants
            try
            {
                for (int i = 1; i <= reactantCount; i++)
                {
                    System.Text.StringBuilder molFile = new System.Text.StringBuilder();
                    input.ReadLine(); // announceMDLFileLine
                    System.String molFileLine = "";
                    do
                    {
                        molFileLine = input.ReadLine();
                        molFile.Append(molFileLine);
                        molFile.Append("\n");
                    }
                    while (!molFileLine.Equals("M  END"));

                    // read MDL molfile content
                    MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
                    IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());

                    // add reactant
                    reaction.addReactant(reactant);
                }
            }
            catch (CDKException exception)
            {
                // rethrow exception from MDLReader
                throw exception;
            }
            catch (System.Exception exception)
            {
                //logger.debug(exception);
                throw new CDKException("Error while reading reactant", exception);
            }

            // now read the products
            try
            {
                for (int i = 1; i <= productCount; i++)
                {
                    System.Text.StringBuilder molFile = new System.Text.StringBuilder();
                    input.ReadLine(); // String announceMDLFileLine = 
                    System.String molFileLine = "";
                    do
                    {
                        molFileLine = input.ReadLine();
                        molFile.Append(molFileLine);
                        molFile.Append("\n");
                    }
                    while (!molFileLine.Equals("M  END"));

                    // read MDL molfile content
                    MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
                    IMolecule product = (IMolecule)reader.read(builder.newMolecule());

                    // add reactant
                    reaction.addProduct(product);
                }
            }
            catch (CDKException exception)
            {
                // rethrow exception from MDLReader
                throw exception;
            }
            catch (System.Exception exception)
            {
                //logger.debug(exception);
                throw new CDKException("Error while reading products", exception);
            }

            // now try to map things, if wanted
            //logger.info("Reading atom-atom mapping from file");
            // distribute all atoms over two AtomContainer's
            IAtomContainer reactingSide = builder.newAtomContainer();
            IMolecule[] molecules = reaction.Reactants.Molecules;
            for (int i = 0; i < molecules.Length; i++)
            {
                reactingSide.add(molecules[i]);
            }
            IAtomContainer producedSide = builder.newAtomContainer();
            molecules = reaction.Products.Molecules;
            for (int i = 0; i < molecules.Length; i++)
            {
                producedSide.add(molecules[i]);
            }

            // map the atoms
            int mappingCount = 0;
            IAtom[] reactantAtoms = reactingSide.Atoms;
            IAtom[] producedAtoms = producedSide.Atoms;
            for (int i = 0; i < reactantAtoms.Length; i++)
            {
                for (int j = 0; j < producedAtoms.Length; j++)
                {
                    if (reactantAtoms[i].ID != null && reactantAtoms[i].ID.Equals(producedAtoms[j].ID))
                    {
                        reaction.addMapping(builder.newMapping(reactantAtoms[i], producedAtoms[j]));
                        mappingCount++;
                        break;
                    }
                }
            }
            //logger.info("Mapped atom pairs: " + mappingCount);

            return reaction;
        }
Beispiel #9
0
        /// <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;
        }
Beispiel #10
0
 private void processAnnotation(System.String field, System.String value_Renamed, Reaction reaction)
 {
     //logger.debug("Annote: ", field, "=", value_Renamed);
     if (field.Equals("RxnAtts") || field.Equals("RxnType"))
     {
         // reaction attributes
         System.String dictionary = "macie";
         if (value_Renamed.Equals("Acid") || value_Renamed.Equals("Base"))
         {
             dictionary = "chemical";
         }
         addDictRefedAnnotation(reaction, "Attributes", value_Renamed);
     }
     else if (field.Equals("ResiduesPresent") || field.Equals("GroupTransferred") || field.Equals("BondFormed") || field.Equals("ReactiveCentres") || field.Equals("BondCleaved") || field.Equals("BondFormed") || field.Equals("Products") || field.Equals("ResiduesPresent"))
     {
         reaction.setProperty(new DictRef("macie:" + field, value_Renamed), value_Renamed);
     }
     else if (field.Equals("Reversible"))
     {
         if (value_Renamed.ToUpper().Equals("yes".ToUpper()))
         {
             reaction.Direction = IReaction_Fields.BIDIRECTIONAL;
             addDictRefedAnnotation(reaction, "ReactionType", "ReversibleReaction");
         }
     }
     else if (field.Equals("OverallReactionType"))
     {
         SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed, ",");
         int i = 0;
         while (tokenizer.HasMoreTokens())
         {
             System.String token = tokenizer.NextToken();
             i++;
             reaction.setProperty(DictionaryDatabase.DICTREFPROPERTYNAME + ":field:overallReactionType:" + i, "macie:" + token.ToLower());
         }
     }
     else
     {
         Match residueLocatorMatcher = residueLocator.Match(field);
         if (residueLocatorMatcher.Success)
         {
             //logger.debug("Found residueLocator: ", field);
             IAtom[] atoms = ReactionManipulator.getAllInOneContainer(reaction).Atoms;
             bool found = false;
             //logger.debug("Searching for given residueLocator through #atom: ", atoms.Length);
             //logger.debug("Taken from reaction ", reaction.ID);
             for (int i = 0; (i < atoms.Length && !found); i++)
             {
                 if (atoms[i] is PseudoAtom)
                 {
                     // that is what we are looking for
                     PseudoAtom atom = (PseudoAtom)atoms[i];
                     if (atom.Label.Equals(field))
                     {
                         // we have a hit, now mark Atom with dict refs
                         addDictRefedAnnotation(atom, "ResidueRole", value_Renamed);
                         found = true;
                     }
                 }
             }
             if (!found)
             {
                 //logger.error("MACiE annotation mentions a residue that does not exist: " + field);
             }
         }
         else
         {
             //logger.error("Did not parse annotation: ", field);
         }
     }
 }
Beispiel #11
0
 private void addDictRefedAnnotation(IChemObject object_Renamed, System.String type, System.String values)
 {
     SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(values, ",");
     while (tokenizer.HasMoreTokens())
     {
         System.String token = tokenizer.NextToken();
         object_Renamed.setProperty(new DictRef("macie:" + type, token), token);
         //logger.debug("Added dict ref ", token, " to ", object_Renamed.GetType().FullName);
     }
 }
        /// <summary> Select the theory and basis set from the first archive line.
        /// 
        /// </summary>
        /// <param name="line">Description of the Parameter
        /// </param>
        /// <returns> Description of the Return Value
        /// </returns>
        private System.String parseLevelOfTheory(System.String line)
        {
            System.Text.StringBuilder summary = new System.Text.StringBuilder();
            summary.Append(line);
            try
            {

                do
                {
                    line = input.ReadLine().Trim();
                    summary.Append(line);
                }
                while (!(line.IndexOf("@") >= 0));
            }
            catch (System.Exception exc)
            {
                //logger.debug("syntax problem while parsing summary of g98 section: ");
                //logger.debug(exc);
            }
            //logger.debug("parseLoT(): " + summary.ToString());
            SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(summary.ToString(), "\\");

            // Must contain at least 6 tokens
            if (st1.Count < 6)
            {
                return null;
            }

            // Skip first four tokens
            for (int i = 0; i < 4; ++i)
            {
                st1.NextToken();
            }

            return st1.NextToken() + "/" + st1.NextToken();
        }
        /// <summary>  Reads a set of vibrations into ChemFrame.
        /// 
        /// </summary>
        /// <param name="model">           Description of the Parameter
        /// </param>
        /// <exception cref="IOException"> if an I/O error occurs
        /// </exception>
        //	private void readFrequencies(IChemModel model) throws IOException
        //	{
        /*
        *  FIXME: this is yet to be ported
        *  String line;
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  while ((line != null) && line.startsWith(" Frequencies --")) {
        *  Vector currentVibs = new Vector();
        *  StringReader vibValRead = new StringReader(line.substring(15));
        *  StreamTokenizer token = new StreamTokenizer(vibValRead);
        *  while (token.nextToken() != StreamTokenizer.TT_EOF) {
        *  Vibration vib = new Vibration(Double.toString(token.nval));
        *  currentVibs.addElement(vib);
        *  }
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  for (int i = 0; i < frame.getAtomCount(); ++i) {
        *  line = input.readLine();
        *  StringReader vectorRead = new StringReader(line);
        *  token = new StreamTokenizer(vectorRead);
        *  token.nextToken();
        *  / ignore first token
        *  token.nextToken();
        *  / ignore second token
        *  for (int j = 0; j < currentVibs.size(); ++j) {
        *  double[] v = new double[3];
        *  if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
        *  v[0] = token.nval;
        *  } else {
        *  throw new IOException("Error reading frequency");
        *  }
        *  if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
        *  v[1] = token.nval;
        *  } else {
        *  throw new IOException("Error reading frequency");
        *  }
        *  if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
        *  v[2] = token.nval;
        *  } else {
        *  throw new IOException("Error reading frequency");
        *  }
        *  ((Vibration) currentVibs.elementAt(j)).addAtomVector(v);
        *  }
        *  }
        *  for (int i = 0; i < currentVibs.size(); ++i) {
        *  frame.addVibration((Vibration) currentVibs.elementAt(i));
        *  }
        *  line = input.readLine();
        *  line = input.readLine();
        *  line = input.readLine();
        *  }
        */
        //	}


        /// <summary> Reads NMR nuclear shieldings.
        /// 
        /// </summary>
        /// <param name="model">    Description of the Parameter
        /// </param>
        /// <param name="labelLine">Description of the Parameter
        /// </param>
        /// <throws>  CDKException Description of the Exception </throws>
        private void readNMRData(IChemModel model, System.String labelLine)
        {
            IAtomContainer ac = ChemModelManipulator.getAllInOneContainer(model);
            // Determine label for properties
            System.String label;
            if (labelLine.IndexOf("Diamagnetic") >= 0)
            {
                label = "Diamagnetic Magnetic shielding (Isotropic)";
            }
            else if (labelLine.IndexOf("Paramagnetic") >= 0)
            {
                label = "Paramagnetic Magnetic shielding (Isotropic)";
            }
            else
            {
                label = "Magnetic shielding (Isotropic)";
            }
            int atomIndex = 0;
            for (int i = 0; i < atomCount; ++i)
            {
                try
                {
                    System.String line = input.ReadLine().Trim();
                    while (line.IndexOf("Isotropic") < 0)
                    {
                        if (line == null)
                        {
                            return;
                        }
                        line = input.ReadLine().Trim();
                    }
                    SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(line);

                    // Find Isotropic label
                    while (st1.HasMoreTokens())
                    {
                        if (st1.NextToken().Equals("Isotropic"))
                        {
                            break;
                        }
                    }

                    // Find Isotropic value
                    while (st1.HasMoreTokens())
                    {
                        if (st1.NextToken().Equals("="))
                            break;
                    }
                    double shielding = System.Double.Parse(st1.NextToken());
                    //logger.info("Type of shielding: " + label);
                    ac.getAtomAt(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, (System.Object)shielding);
                    ++atomIndex;
                }
                catch (System.Exception exc)
                {
                    //logger.debug("failed to read line from gaussian98 file where I expected one.");
                }
            }
        }
 public override void characterData(CMLStack xpath, char[] ch, int start, int length)
 {
     System.String s = new System.String(ch, start, length).Trim();
     //logger.debug("Start PMP chardata (" + CurrentElement + ") :" + s);
     //logger.debug(" ElTitle: " + elementTitle);
     if (xpath.ToString().EndsWith("string/") && BUILTIN.Equals("spacegroup"))
     {
         System.String sg = "P1";
         // standardize space group names (see Crystal.java)
         if ("P 21 21 21 (1)".Equals(s))
         {
             sg = "P 2_1 2_1 2_1";
         }
         cdo.setObjectProperty("Crystal", "spacegroup", sg);
     }
     else
     {
         if (xpath.ToString().EndsWith("floatArray/") && (elementTitle.Equals("a") || elementTitle.Equals("b") || elementTitle.Equals("c")))
         {
             System.String axis = elementTitle + "-axis";
             cdo.startObject(axis);
             try
             {
                 SupportClass.Tokenizer st = new SupportClass.Tokenizer(s);
                 //logger.debug("Tokens: " + st.Count);
                 if (st.Count > 2)
                 {
                     System.String token = st.NextToken();
                     //logger.debug("FloatArray (Token): " + token);
                     cdo.setObjectProperty(axis, "x", token);
                     token = st.NextToken();
                     //logger.debug("FloatArray (Token): " + token);
                     cdo.setObjectProperty(axis, "y", token);
                     token = st.NextToken();
                     //logger.debug("FloatArray (Token): " + token);
                     cdo.setObjectProperty(axis, "z", token);
                 }
                 else
                 {
                     //logger.debug("PMP Convention error: incorrect number of cell axis fractions!\n");
                 }
             }
             catch (System.Exception e)
             {
                 //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'"
                 //logger.debug("PMP Convention error: " + e.ToString());
             }
             cdo.endObject(axis);
         }
         else
         {
             base.characterData(xpath, ch, start, length);
         }
     }
     //logger.debug("End PMP chardata");
 }
        public virtual void startElement(CMLStack xpath, System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
        {

            System.String name = local;
            ////logger.debug("StartElement");
            currentChars = "";

            BUILTIN = "";
            DICTREF = "";

            for (int i = 0; i < atts.GetLength(); i++)
            {
                System.String qname = atts.GetFullName(i);
                if (qname.Equals("builtin"))
                {
                    BUILTIN = atts.GetValue(i);
                    ////logger.debug(name, "->BUILTIN found: ", atts.GetValue(i));
                }
                else if (qname.Equals("dictRef"))
                {
                    DICTREF = atts.GetValue(i);
                    ////logger.debug(name, "->DICTREF found: ", atts.GetValue(i));
                }
                else if (qname.Equals("title"))
                {
                    elementTitle = atts.GetValue(i);
                    ////logger.debug(name, "->TITLE found: ", atts.GetValue(i));
                }
                else
                {
                    ////logger.debug("Qname: ", qname);
                }
            }

            if ("atom".Equals(name))
            {
                atomCounter++;
                for (int i = 0; i < atts.GetLength(); i++)
                {

                    System.String att = atts.GetFullName(i);
                    System.String value_Renamed = atts.GetValue(i);

                    if (att.Equals("id"))
                    {
                        // this is supported in CML 1.x
                        elid.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("elementType"))
                    {
                        elsym.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("title"))
                    {
                        eltitles.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("x2"))
                    {
                        x2.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("xy2"))
                    {
                        SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
                        x2.Add(tokenizer.NextToken());
                        y2.Add(tokenizer.NextToken());
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("xyzFract"))
                    {
                        SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
                        xfract.Add(tokenizer.NextToken());
                        yfract.Add(tokenizer.NextToken());
                        zfract.Add(tokenizer.NextToken());
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("xyz3"))
                    {
                        SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
                        x3.Add(tokenizer.NextToken());
                        y3.Add(tokenizer.NextToken());
                        z3.Add(tokenizer.NextToken());
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("y2"))
                    {
                        y2.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("x3"))
                    {
                        x3.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("y3"))
                    {
                        y3.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("z3"))
                    {
                        z3.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("xFract"))
                    {
                        xfract.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("yFract"))
                    {
                        yfract.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("zFract"))
                    {
                        zfract.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("formalCharge"))
                    {
                        formalCharges.Add(value_Renamed);
                    }
                    // this is supported in CML 2.0 
                    else if (att.Equals("hydrogenCount"))
                    {
                        hCounts.Add(value_Renamed);
                    }
                    else if (att.Equals("isotope"))
                    {
                        isotope.Add(value_Renamed);
                    }
                    else if (att.Equals("dictRef"))
                    {
                        atomDictRefs.Add(value_Renamed);
                    }
                    else if (att.Equals("spinMultiplicity"))
                    {
                        spinMultiplicities.Add(value_Renamed);
                    }
                    else
                    {
                        ////logger.warn("Unparsed attribute: " + att);
                    }
                }
            }
            else if ("atomArray".Equals(name))
            {
                bool atomsCounted = false;
                for (int i = 0; i < atts.GetLength(); i++)
                {
                    System.String att = atts.GetFullName(i);
                    int count = 0;
                    if (att.Equals("atomID"))
                    {
                        count = addArrayElementsTo(elid, atts.GetValue(i));
                    }
                    else if (att.Equals("elementType"))
                    {
                        count = addArrayElementsTo(elsym, atts.GetValue(i));
                    }
                    else if (att.Equals("x2"))
                    {
                        count = addArrayElementsTo(x2, atts.GetValue(i));
                    }
                    else if (att.Equals("y2"))
                    {
                        count = addArrayElementsTo(y2, atts.GetValue(i));
                    }
                    else if (att.Equals("x3"))
                    {
                        count = addArrayElementsTo(x3, atts.GetValue(i));
                    }
                    else if (att.Equals("y3"))
                    {
                        count = addArrayElementsTo(y3, atts.GetValue(i));
                    }
                    else if (att.Equals("z3"))
                    {
                        count = addArrayElementsTo(z3, atts.GetValue(i));
                    }
                    else if (att.Equals("xFract"))
                    {
                        count = addArrayElementsTo(xfract, atts.GetValue(i));
                    }
                    else if (att.Equals("yFract"))
                    {
                        count = addArrayElementsTo(yfract, atts.GetValue(i));
                    }
                    else if (att.Equals("zFract"))
                    {
                        count = addArrayElementsTo(zfract, atts.GetValue(i));
                    }
                    else
                    {
                        ////logger.warn("Unparsed attribute: " + att);
                    }
                    if (!atomsCounted)
                    {
                        atomCounter += count;
                        atomsCounted = true;
                    }
                }
            }
            else if ("bond".Equals(name))
            {
                bondCounter++;
                for (int i = 0; i < atts.GetLength(); i++)
                {
                    System.String att = atts.GetFullName(i);
                    ////logger.debug("B2 ", att, "=", atts.GetValue(i));

                    if (att.Equals("id"))
                    {
                        bondid.Add(atts.GetValue(i));
                        ////logger.debug("B3 ", bondid);
                    }
                    else if (att.Equals("atomRefs") || att.Equals("atomRefs2"))
                    {
                        // this is CML 2.0 support

                        // expect exactly two references
                        try
                        {
                            SupportClass.Tokenizer st = new SupportClass.Tokenizer(atts.GetValue(i));
                            bondARef1.Add((System.String)st.NextToken());
                            bondARef2.Add((System.String)st.NextToken());
                        }
                        catch (System.Exception e)
                        {
                            //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                            ////logger.error("Error in CML file: ", e.Message);
                            ////logger.debug(e);
                        }
                    }
                    else if (att.Equals("order"))
                    {
                        // this is CML 2.0 support
                        order.Add(atts.GetValue(i).Trim());
                    }
                    else if (att.Equals("dictRef"))
                    {
                        bondDictRefs.Add(atts.GetValue(i).Trim());
                    }
                }

                stereoGiven = false;
                curRef = 0;
            }
            else if ("bondArray".Equals(name))
            {
                bool bondsCounted = false;
                for (int i = 0; i < atts.GetLength(); i++)
                {
                    System.String att = atts.GetFullName(i);
                    int count = 0;
                    if (att.Equals("bondID"))
                    {
                        count = addArrayElementsTo(bondid, atts.GetValue(i));
                    }
                    else if (att.Equals("atomRefs1"))
                    {
                        count = addArrayElementsTo(bondARef1, atts.GetValue(i));
                    }
                    else if (att.Equals("atomRefs2"))
                    {
                        count = addArrayElementsTo(bondARef2, atts.GetValue(i));
                    }
                    else if (att.Equals("atomRef1"))
                    {
                        count = addArrayElementsTo(bondARef1, atts.GetValue(i));
                    }
                    else if (att.Equals("atomRef2"))
                    {
                        count = addArrayElementsTo(bondARef2, atts.GetValue(i));
                    }
                    else if (att.Equals("order"))
                    {
                        count = addArrayElementsTo(order, atts.GetValue(i));
                    }
                    else
                    {
                        ////logger.warn("Unparsed attribute: " + att);
                    }
                    if (!bondsCounted)
                    {
                        bondCounter += count;
                        bondsCounted = true;
                    }
                }
                curRef = 0;
            }
            else if ("molecule".Equals(name))
            {
                newMolecule();
                BUILTIN = "";
                cdo.startObject("Molecule");
                for (int i = 0; i < atts.GetLength(); i++)
                {
                    if (atts.GetFullName(i).Equals("id"))
                    {
                        cdo.setObjectProperty("Molecule", "id", atts.GetValue(i));
                    }
                    else if (atts.GetFullName(i).Equals("dictRef"))
                    {
                        cdo.setObjectProperty("Molecule", "dictRef", atts.GetValue(i));
                    }
                }
            }
            else if ("crystal".Equals(name))
            {
                newCrystalData();
                cdo.startObject("Crystal");
                for (int i = 0; i < atts.GetLength(); i++)
                {
                    System.String att = atts.GetFullName(i);
                    if (att.Equals("z"))
                    {
                        cdo.setObjectProperty("Crystal", "z", atts.GetValue(i));
                    }
                }
            }
            else if ("symmetry".Equals(name))
            {
                for (int i = 0; i < atts.GetLength(); i++)
                {
                    System.String att = atts.GetFullName(i);
                    if (att.Equals("spaceGroup"))
                    {
                        cdo.setObjectProperty("Crystal", "spacegroup", atts.GetValue(i));
                    }
                }
            }
            else if ("scalar".Equals(name))
            {
                if (xpath.ToString().EndsWith("crystal/scalar/"))
                    crystalScalar++;
            }
            else if ("list".Equals(name))
            {
                cdo.startObject("SetOfMolecules");
            }
        }
        public override void characterData(CMLStack xpath, char[] ch, int start, int length)
        {

            System.String s = new System.String(ch, start, length).Trim();

            if (isELSYM)
            {
                elsym.Add(s);
            }
            else if (isBond)
            {
                //logger.debug("CD (bond): " + s);

                if (connect_root.Length > 0)
                {

                    SupportClass.Tokenizer st = new SupportClass.Tokenizer(s);

                    while (st.HasMoreTokens())
                    {

                        System.String atom = (System.String)st.NextToken();

                        if (!atom.Equals("0"))
                        {
                            //logger.debug("new bond: " + connect_root + "-" + atom);
                            cdo.startObject("Bond");

                            int atom1 = System.Int32.Parse(connect_root) - 1;
                            int atom2 = System.Int32.Parse(atom) - 1;
                            cdo.setObjectProperty("Bond", "atom1", ((System.Int32)atom1).ToString());
                            cdo.setObjectProperty("Bond", "atom2", ((System.Int32)atom2).ToString());
                            cdo.setObjectProperty("Bond", "order", "1");
                            cdo.endObject("Bond");
                        }
                    }
                }
            }
            else
            {
                base.characterData(xpath, ch, start, length);
            }
        }
        public virtual void endElement(CMLStack xpath, System.String uri, System.String name, System.String raw)
        {
            ////logger.debug("EndElement: ", name);

            System.String cData = currentChars;

            if ("bond".Equals(name))
            {
                if (!stereoGiven)
                    bondStereo.Add("");
                if (bondStereo.Count > bondDictRefs.Count)
                    bondDictRefs.Add(null);
            }
            else if ("atom".Equals(name))
            {
                if (atomCounter > eltitles.Count)
                {
                    eltitles.Add(null);
                }
                if (atomCounter > hCounts.Count)
                {
                    /* while strictly undefined, assume zero 
                    implicit hydrogens when no number is given */
                    hCounts.Add("0");
                }
                if (atomCounter > atomDictRefs.Count)
                {
                    atomDictRefs.Add(null);
                }
                if (atomCounter > isotope.Count)
                {
                    isotope.Add(null);
                }
                if (atomCounter > spinMultiplicities.Count)
                {
                    spinMultiplicities.Add(null);
                }
                if (atomCounter > formalCharges.Count)
                {
                    /* while strictly undefined, assume zero 
                    implicit hydrogens when no number is given */
                    formalCharges.Add("0");
                }
                /* It may happen that not all atoms have
                associated 2D or 3D coordinates. accept that */
                if (atomCounter > x2.Count && x2.Count != 0)
                {
                    /* apparently, the previous atoms had atomic
                    coordinates, add 'null' for this atom */
                    x2.Add(null);
                    y2.Add(null);
                }
                if (atomCounter > x3.Count && x3.Count != 0)
                {
                    /* apparently, the previous atoms had atomic
                    coordinates, add 'null' for this atom */
                    x3.Add(null);
                    y3.Add(null);
                    z3.Add(null);
                }

                if (atomCounter > xfract.Count && xfract.Count != 0)
                {
                    /* apparently, the previous atoms had atomic
                    coordinates, add 'null' for this atom */
                    xfract.Add(null);
                    yfract.Add(null);
                    zfract.Add(null);
                }
            }
            else if ("molecule".Equals(name))
            {
                storeData();
                cdo.endObject("Molecule");
            }
            else if ("crystal".Equals(name))
            {
                if (crystalScalar > 0)
                {
                    // convert unit cell parameters to cartesians
                    Vector3d[] axes = CrystalGeometryTools.notionalToCartesian(unitcellparams[0], unitcellparams[1], unitcellparams[2], unitcellparams[3], unitcellparams[4], unitcellparams[5]);
                    aAxis = axes[0];
                    bAxis = axes[1];
                    cAxis = axes[2];
                    cartesianAxesSet = true;
                    cdo.startObject("a-axis");
                    cdo.setObjectProperty("a-axis", "x", aAxis.x.ToString());
                    cdo.setObjectProperty("a-axis", "y", aAxis.y.ToString());
                    cdo.setObjectProperty("a-axis", "z", aAxis.z.ToString());
                    cdo.endObject("a-axis");
                    cdo.startObject("b-axis");
                    cdo.setObjectProperty("b-axis", "x", bAxis.x.ToString());
                    cdo.setObjectProperty("b-axis", "y", bAxis.y.ToString());
                    cdo.setObjectProperty("b-axis", "z", bAxis.z.ToString());
                    cdo.endObject("b-axis");
                    cdo.startObject("c-axis");
                    cdo.setObjectProperty("c-axis", "x", cAxis.x.ToString());
                    cdo.setObjectProperty("c-axis", "y", cAxis.y.ToString());
                    cdo.setObjectProperty("c-axis", "z", cAxis.z.ToString());
                    cdo.endObject("c-axis");
                }
                else
                {
                    ////logger.error("Could not find crystal unit cell parameters");
                }
                cdo.endObject("Crystal");
            }
            else if ("list".Equals(name))
            {
                cdo.endObject("SetOfMolecules");
            }
            else if ("coordinate3".Equals(name))
            {
                if (BUILTIN.Equals("xyz3"))
                {
                    ////logger.debug("New coord3 xyz3 found: ", currentChars);

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(currentChars);
                        x3.Add(st.NextToken());
                        y3.Add(st.NextToken());
                        z3.Add(st.NextToken());
                        ////logger.debug("coord3 x3.length: ", x3.Count);
                        ////logger.debug("coord3 y3.length: ", y3.Count);
                        ////logger.debug("coord3 z3.length: ", z3.Count);
                    }
                    catch (System.Exception exception)
                    {
                        ////logger.error("CMLParsing error while setting coordinate3!");
                        ////logger.debug(exception);
                    }
                }
                else
                {
                    ////logger.warn("Unknown coordinate3 BUILTIN: " + BUILTIN);
                }
            }
            else if ("string".Equals(name))
            {
                if (BUILTIN.Equals("elementType"))
                {
                    ////logger.debug("Element: ", cData.Trim());
                    elsym.Add(cData);
                }
                else if (BUILTIN.Equals("atomRef"))
                {
                    curRef++;
                    ////logger.debug("Bond: ref #", curRef);

                    if (curRef == 1)
                    {
                        bondARef1.Add(cData.Trim());
                    }
                    else if (curRef == 2)
                    {
                        bondARef2.Add(cData.Trim());
                    }
                }
                else if (BUILTIN.Equals("order"))
                {
                    ////logger.debug("Bond: order ", cData.Trim());
                    order.Add(cData.Trim());
                }
                else if (BUILTIN.Equals("formalCharge"))
                {
                    // NOTE: this combination is in violation of the CML DTD!!!
                    ////logger.warn("formalCharge BUILTIN accepted but violating CML DTD");
                    ////logger.debug("Charge: ", cData.Trim());
                    System.String charge = cData.Trim();
                    if (charge.StartsWith("+") && charge.Length > 1)
                    {
                        charge = charge.Substring(1);
                    }
                    formalCharges.Add(charge);
                }
            }
            else if ("float".Equals(name))
            {
                if (BUILTIN.Equals("x3"))
                {
                    x3.Add(cData.Trim());
                }
                else if (BUILTIN.Equals("y3"))
                {
                    y3.Add(cData.Trim());
                }
                else if (BUILTIN.Equals("z3"))
                {
                    z3.Add(cData.Trim());
                }
                else if (BUILTIN.Equals("x2"))
                {
                    x2.Add(cData.Trim());
                }
                else if (BUILTIN.Equals("y2"))
                {
                    y2.Add(cData.Trim());
                }
                else if (BUILTIN.Equals("order"))
                {
                    // NOTE: this combination is in violation of the CML DTD!!!
                    order.Add(cData.Trim());
                }
                else if (BUILTIN.Equals("charge") || BUILTIN.Equals("partialCharge"))
                {
                    partialCharges.Add(cData.Trim());
                }
            }
            else if ("integer".Equals(name))
            {
                if (BUILTIN.Equals("formalCharge"))
                {
                    formalCharges.Add(cData.Trim());
                }
            }
            else if ("coordinate2".Equals(name))
            {
                if (BUILTIN.Equals("xy2"))
                {
                    ////logger.debug("New coord2 xy2 found.", cData);

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
                        x2.Add(st.NextToken());
                        y2.Add(st.NextToken());
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 175, 1);
                    }
                }
            }
            else if ("stringArray".Equals(name))
            {
                if (BUILTIN.Equals("id") || BUILTIN.Equals("atomId") || BUILTIN.Equals("atomID"))
                {
                    // invalid according to CML1 DTD but found in OpenBabel 1.x output

                    try
                    {
                        bool countAtoms = (atomCounter == 0) ? true : false;
                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                        {
                            if (countAtoms)
                            {
                                atomCounter++;
                            }
                            System.String token = st.NextToken();
                            ////logger.debug("StringArray (Token): ", token);
                            elid.Add(token);
                        }
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 186, 1);
                    }
                }
                else if (BUILTIN.Equals("elementType"))
                {

                    try
                    {
                        bool countAtoms = (atomCounter == 0) ? true : false;
                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                        {
                            if (countAtoms)
                            {
                                atomCounter++;
                            }
                            elsym.Add(st.NextToken());
                        }
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
                    }
                }
                else if (BUILTIN.Equals("atomRefs"))
                {
                    curRef++;
                    ////logger.debug("New atomRefs found: ", curRef);

                    try
                    {
                        bool countBonds = (bondCounter == 0) ? true : false;
                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                        {
                            if (countBonds)
                            {
                                bondCounter++;
                            }
                            System.String token = st.NextToken();
                            ////logger.debug("Token: ", token);

                            if (curRef == 1)
                            {
                                bondARef1.Add(token);
                            }
                            else if (curRef == 2)
                            {
                                bondARef2.Add(token);
                            }
                        }
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
                    }
                }
                else if (BUILTIN.Equals("atomRef"))
                {
                    curRef++;
                    ////logger.debug("New atomRef found: ", curRef); // this is CML1 stuff, we get things like:
                    /*
                    <bondArray>
                    <stringArray builtin="atomRef">a2 a2 a2 a2 a3 a3 a4 a4 a5 a6 a7 a9</stringArray>
                    <stringArray builtin="atomRef">a9 a11 a12 a13 a5 a4 a6 a9 a7 a8 a8 a10</stringArray>
                    <stringArray builtin="order">1 1 1 1 2 1 2 1 1 1 2 2</stringArray>
                    </bondArray>
                    */

                    try
                    {
                        bool countBonds = (bondCounter == 0) ? true : false;
                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                        {
                            if (countBonds)
                            {
                                bondCounter++;
                            }
                            System.String token = st.NextToken();
                            ////logger.debug("Token: ", token);

                            if (curRef == 1)
                            {
                                bondARef1.Add(token);
                            }
                            else if (curRef == 2)
                            {
                                bondARef2.Add(token);
                            }
                        }
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
                    }
                }
                else if (BUILTIN.Equals("order"))
                {
                    ////logger.debug("New bond order found.");

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                        {

                            System.String token = st.NextToken();
                            ////logger.debug("Token: ", token);
                            order.Add(token);
                        }
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
                    }
                }
            }
            else if ("integerArray".Equals(name))
            {
                ////logger.debug("IntegerArray: builtin = ", BUILTIN);

                if (BUILTIN.Equals("formalCharge"))
                {

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                        {

                            System.String token = st.NextToken();
                            ////logger.debug("Charge added: ", token);
                            formalCharges.Add(token);
                        }
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
                    }
                }
            }
            else if ("scalar".Equals(name))
            {
                if (xpath.ToString().EndsWith("crystal/scalar/"))
                {
                    ////logger.debug("Going to set a crystal parameter: " + crystalScalar, " to ", cData);
                    try
                    {
                        unitcellparams[crystalScalar - 1] = System.Double.Parse(cData.Trim());
                    }
                    catch (System.FormatException exception)
                    {
                        ////logger.error("Content must a float: " + cData);
                    }
                }
                else
                {
                    if (xpath.ToString().EndsWith("bond/scalar/"))
                    {
                        if (DICTREF.Equals("mdl:stereo"))
                        {
                            bondStereo.Add(cData.Trim());
                            stereoGiven = true;
                        }
                    }
                    else
                    {
                        if (xpath.ToString().EndsWith("atom/scalar/"))
                        {
                            if (DICTREF.Equals("cdk:partialCharge"))
                            {
                                partialCharges.Add(cData.Trim());
                            }
                        }
                        else
                        {
                            if (xpath.ToString().EndsWith("molecule/scalar/"))
                            {
                                if (DICTREF.Equals("pdb:id"))
                                {
                                    cdo.setObjectProperty("Molecule", DICTREF, cData);
                                }
                            }
                            else
                            {
                                ////logger.warn("Ignoring scalar: " + xpath);
                            }
                        }
                    }
                }
            }
            else if ("floatArray".Equals(name))
            {
                if (BUILTIN.Equals("x3"))
                {

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                            x3.Add(st.NextToken());
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
                    }
                }
                else if (BUILTIN.Equals("y3"))
                {

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                            y3.Add(st.NextToken());
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 213, 1);
                    }
                }
                else if (BUILTIN.Equals("z3"))
                {

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                            z3.Add(st.NextToken());
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 221, 1);
                    }
                }
                else if (BUILTIN.Equals("x2"))
                {
                    ////logger.debug("New floatArray found.");

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                            x2.Add(st.NextToken());
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
                    }
                }
                else if (BUILTIN.Equals("y2"))
                {
                    ////logger.debug("New floatArray found.");

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                            y2.Add(st.NextToken());
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 454, 1);
                    }
                }
                else if (BUILTIN.Equals("partialCharge"))
                {
                    ////logger.debug("New floatArray with partial charges found.");

                    try
                    {

                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);

                        while (st.HasMoreTokens())
                            partialCharges.Add(st.NextToken());
                    }
                    catch (System.Exception e)
                    {
                        //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'"
                        notify("CMLParsing error: " + e, SYSTEMID, 462, 1);
                    }
                }
            }
            else if ("basic".Equals(name))
            {
                // assuming this is the child element of <identifier>
                this.inchi = cData;
            }
            else if ("name".Equals(name))
            {
                if (xpath.ToString().EndsWith("molecule/name/"))
                {
                    cdo.setObjectProperty("Molecule", DICTREF, cData);
                }
            }
            else
            {
                ////logger.warn("Skipping element: " + name);
            }

            currentChars = "";
            BUILTIN = "";
            elementTitle = "";
        }
        /// <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);
                }
            }
        }
Beispiel #19
0
        private void processAtomLoopBlock(System.String firstLine)
        {
            int atomLabel = -1; // -1 means not found in this block
            int atomSymbol = -1;
            int atomFractX = -1;
            int atomFractY = -1;
            int atomFractZ = -1;
            int atomRealX = -1;
            int atomRealY = -1;
            int atomRealZ = -1;
            System.String line = firstLine.Trim();
            int headerCount = 0;
            bool hasParsableInformation = false;
            while (line != null && line[0] == '_')
            {
                headerCount++;
                if (line.Equals("_atom_site_label") || line.Equals("_atom_site_label_atom_id"))
                {
                    atomLabel = headerCount;
                    hasParsableInformation = true;
                    //logger.info("label found in col: " + atomLabel);
                }
                else if (line.StartsWith("_atom_site_fract_x"))
                {
                    atomFractX = headerCount;
                    hasParsableInformation = true;
                    //logger.info("frac x found in col: " + atomFractX);
                }
                else if (line.StartsWith("_atom_site_fract_y"))
                {
                    atomFractY = headerCount;
                    hasParsableInformation = true;
                    //logger.info("frac y found in col: " + atomFractY);
                }
                else if (line.StartsWith("_atom_site_fract_z"))
                {
                    atomFractZ = headerCount;
                    hasParsableInformation = true;
                    //logger.info("frac z found in col: " + atomFractZ);
                }
                else if (line.Equals("_atom_site.Cartn_x"))
                {
                    atomRealX = headerCount;
                    hasParsableInformation = true;
                    //logger.info("cart x found in col: " + atomRealX);
                }
                else if (line.Equals("_atom_site.Cartn_y"))
                {
                    atomRealY = headerCount;
                    hasParsableInformation = true;
                    //logger.info("cart y found in col: " + atomRealY);
                }
                else if (line.Equals("_atom_site.Cartn_z"))
                {
                    atomRealZ = headerCount;
                    hasParsableInformation = true;
                    //logger.info("cart z found in col: " + atomRealZ);
                }
                else if (line.Equals("_atom_site.type_symbol"))
                {
                    atomSymbol = headerCount;
                    hasParsableInformation = true;
                    //logger.info("type_symbol found in col: " + atomSymbol);
                }
                else
                {
                    //logger.warn("Ignoring atom loop block field: " + line);
                }
                line = input.ReadLine().Trim();
            }
            if (hasParsableInformation == false)
            {
                //logger.info("No parsable info found");
                skipUntilEmptyOrCommentLine(line);
            }
            else
            {
                // now that headers are parsed, read the data
                while (line != null && line.Length > 0 && line[0] != '#')
                {
                    //logger.debug("new row");
                    SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
                    if (tokenizer.Count < headerCount)
                    {
                        //logger.warn("Column count mismatch; assuming continued on next line");
                        //logger.debug("Found #expected, #found: " + headerCount + ", " + tokenizer.Count);
                        tokenizer = new SupportClass.Tokenizer(line + input.ReadLine());
                    }
                    int colIndex = 0;
                    // process one row
                    IAtom atom = crystal.Builder.newAtom("C");
                    Point3d frac = new Point3d();
                    Point3d real = new Point3d();
                    bool hasFractional = false;
                    bool hasCartesian = false;
                    while (tokenizer.HasMoreTokens())
                    {
                        colIndex++;
                        System.String field = tokenizer.NextToken();
                        //logger.debug("Parsing col,token: " + colIndex + "=" + field);
                        if (colIndex == atomLabel)
                        {
                            if (atomSymbol == -1)
                            {
                                // no atom symbol found, use label
                                System.String element = extractFirstLetters(field);
                                atom.Symbol = element;
                            }
                            atom.ID = field;
                        }
                        else if (colIndex == atomFractX)
                        {
                            hasFractional = true;
                            frac.x = parseIntoDouble(field);
                        }
                        else if (colIndex == atomFractY)
                        {
                            hasFractional = true;
                            frac.y = parseIntoDouble(field);
                        }
                        else if (colIndex == atomFractZ)
                        {
                            hasFractional = true;
                            frac.z = parseIntoDouble(field);
                        }
                        else if (colIndex == atomSymbol)
                        {
                            atom.Symbol = field;
                        }
                        else if (colIndex == atomRealX)
                        {
                            hasCartesian = true;
                            //logger.debug("Adding x3: " + parseIntoDouble(field));
                            real.x = parseIntoDouble(field);
                        }
                        else if (colIndex == atomRealY)
                        {
                            hasCartesian = true;
                            //logger.debug("Adding y3: " + parseIntoDouble(field));
                            real.y = parseIntoDouble(field);
                        }
                        else if (colIndex == atomRealZ)
                        {
                            hasCartesian = true;
                            //logger.debug("Adding x3: " + parseIntoDouble(field));
                            real.z = parseIntoDouble(field);
                        }
                    }
                    if (hasCartesian)
                    {
                        Vector3d a = crystal.A;
                        Vector3d b = crystal.B;
                        Vector3d c = crystal.C;
                        frac = CrystalGeometryTools.cartesianToFractional(a, b, c, real);
                        atom.setFractionalPoint3d(frac);
                    }
                    if (hasFractional)
                    {
                        atom.setFractionalPoint3d(frac);
                    }
                    //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("Adding atom: " + atom);
                    crystal.addAtom(atom);

                    // look up next row
                    line = input.ReadLine().Trim();
                }
            }
        }
        /// <summary> Reads the bond atoms, order and stereo configuration.</summary>
        public virtual void readBondBlock(IAtomContainer readData)
        {
            bool foundEND = false;
            while (Ready && !foundEND)
            {
                System.String command = readCommand();
                if ("END BOND".Equals(command))
                {
                    foundEND = true;
                }
                else
                {
                    //logger.debug("Parsing bond from: " + command);
                    SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
                    IBond bond = readData.Builder.newBond();
                    // parse the index
                    try
                    {
                        System.String indexString = tokenizer.NextToken();
                        bond.ID = indexString;
                    }
                    catch (System.Exception exception)
                    {
                        System.String error = "Error while parsing bond index";
                        //logger.error(error);
                        //logger.debug(exception);
                        throw new CDKException(error, exception);
                    }
                    // parse the order
                    try
                    {
                        System.String orderString = tokenizer.NextToken();
                        int order = System.Int32.Parse(orderString);
                        if (order >= 4)
                        {
                            //logger.warn("Query order types are not supported (yet). File a bug if you need it");
                        }
                        else
                        {
                            bond.Order = (double)order;
                        }
                    }
                    catch (System.Exception exception)
                    {
                        System.String error = "Error while parsing bond index";
                        //logger.error(error);
                        //logger.debug(exception);
                        throw new CDKException(error, exception);
                    }
                    // parse index atom 1
                    try
                    {
                        System.String indexAtom1String = tokenizer.NextToken();
                        int indexAtom1 = System.Int32.Parse(indexAtom1String);
                        IAtom atom1 = readData.getAtomAt(indexAtom1 - 1);
                        bond.setAtomAt(atom1, 0);
                    }
                    catch (System.Exception exception)
                    {
                        System.String error = "Error while parsing index atom 1 in bond";
                        //logger.error(error);
                        //logger.debug(exception);
                        throw new CDKException(error, exception);
                    }
                    // parse index atom 2
                    try
                    {
                        System.String indexAtom2String = tokenizer.NextToken();
                        int indexAtom2 = System.Int32.Parse(indexAtom2String);
                        IAtom atom2 = readData.getAtomAt(indexAtom2 - 1);
                        bond.setAtomAt(atom2, 1);
                    }
                    catch (System.Exception exception)
                    {
                        System.String error = "Error while parsing index atom 2 in bond";
                        //logger.error(error);
                        //logger.debug(exception);
                        throw new CDKException(error, exception);
                    }
                    // the rest are key=value fields
                    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("CFG"))
                                {
                                    int configuration = System.Int32.Parse(value_Renamed);
                                    if (configuration == 0)
                                    {
                                        bond.Stereo = CDKConstants.STEREO_BOND_NONE;
                                    }
                                    else if (configuration == 1)
                                    {
                                        bond.Stereo = CDKConstants.STEREO_BOND_UP;
                                    }
                                    else if (configuration == 2)
                                    {
                                        bond.Stereo = CDKConstants.STEREO_BOND_UNDEFINED;
                                    }
                                    else if (configuration == 3)
                                    {
                                        bond.Stereo = CDKConstants.STEREO_BOND_DOWN;
                                    }
                                }
                                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);
                            }
                        }
                    }

                    // storing bond
                    readData.addBond(bond);
                    //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 bond: " + bond);
                }
            }
        }
Beispiel #21
0
 private System.String getMolName(System.String line)
 {
     if (line == null)
         return ("");
     SupportClass.Tokenizer st = new SupportClass.Tokenizer(line, " ");
     int ntok = st.Count;
     System.String[] toks = new System.String[ntok];
     for (int j = 0; j < ntok; j++)
     {
         toks[j] = st.NextToken();
     }
     if (toks.Length == 3)
         return (toks[2]);
     else
         return ("");
 }
        /// <summary> Reads labels.</summary>
        public virtual void readSGroup(IAtomContainer readData)
        {
            bool foundEND = false;
            while (Ready && !foundEND)
            {
                System.String command = readCommand();
                if ("END SGROUP".Equals(command))
                {
                    foundEND = true;
                }
                else
                {
                    //logger.debug("Parsing Sgroup line: " + command);
                    SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
                    // parse the index
                    System.String indexString = tokenizer.NextToken();
                    //logger.warn("Skipping external index: " + indexString);
                    // parse command type
                    System.String type = tokenizer.NextToken();
                    // parse the external index
                    System.String externalIndexString = tokenizer.NextToken();
                    //logger.warn("Skipping external index: " + externalIndexString);

                    // the rest are key=value fields
                    System.Collections.Hashtable options = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
                    if (command.IndexOf("=") != -1)
                    {
                        options = parseOptions(exhaustStringTokenizer(tokenizer));
                    }

                    // now interpret line
                    if (type.StartsWith("SUP"))
                    {
                        System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
                        int atomID = -1;
                        System.String label = "";
                        //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("ATOMS"))
                                {
                                    SupportClass.Tokenizer atomsTokenizer = new SupportClass.Tokenizer(value_Renamed);
                                    System.Int32.Parse(atomsTokenizer.NextToken()); // should be 1, int atomCount = 
                                    atomID = System.Int32.Parse(atomsTokenizer.NextToken());
                                }
                                else if (key.Equals("LABEL"))
                                {
                                    label = value_Renamed;
                                }
                                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);
                            }
                            if (atomID != -1 && label.Length > 0)
                            {
                                IAtom atom = readData.getAtomAt(atomID - 1);
                                if (!(atom is IPseudoAtom))
                                {
                                    atom = readData.Builder.newPseudoAtom(atom);
                                }
                                ((IPseudoAtom)atom).Label = label;
                                readData.setAtomAt(atomID - 1, atom);
                            }
                        }
                    }
                    else
                    {
                        //logger.warn("Skipping unrecognized SGROUP type: " + type);
                    }
                }
            }
        }
Beispiel #23
0
        // private procedures

        /// <summary>  Private method that actually parses the input to read a ChemFile
        /// object.
        /// 
        /// </summary>
        /// <returns> A ChemFile containing the data parsed from input.
        /// </returns>
        private IChemFile readChemFile(IChemFile file)
        {
            IChemSequence chemSequence = file.Builder.newChemSequence();

            int number_of_atoms = 0;
            SupportClass.Tokenizer tokenizer;

            try
            {
                System.String line = input.ReadLine();
                while (input.Peek() != -1 && line != null)
                {
                    // parse frame by frame
                    tokenizer = new SupportClass.Tokenizer(line, "\t ,;");

                    System.String token = tokenizer.NextToken();
                    number_of_atoms = System.Int32.Parse(token);
                    System.String info = input.ReadLine();

                    IChemModel chemModel = file.Builder.newChemModel();
                    ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();

                    IMolecule m = file.Builder.newMolecule();
                    m.setProperty(CDKConstants.TITLE, info);

                    for (int i = 0; i < number_of_atoms; i++)
                    {
                        line = input.ReadLine();
                        if (line == null)
                            break;
                        if (line.StartsWith("#") && line.Length > 1)
                        {
                            System.Object comment = m.getProperty(CDKConstants.COMMENT);
                            if (comment == null)
                            {
                                comment = "";
                            }
                            //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                            comment = comment.ToString() + line.Substring(1).Trim();
                            m.setProperty(CDKConstants.COMMENT, comment);
                            //logger.debug("Found and set comment: ", comment);
                        }
                        else
                        {
                            double x = 0.0f, y = 0.0f, z = 0.0f;
                            double charge = 0.0f;
                            tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
                            int fields = tokenizer.Count;

                            if (fields < 4)
                            {
                                // this is an error but cannot throw exception
                            }
                            else
                            {
                                System.String atomtype = tokenizer.NextToken();
                                //UPGRADE_TODO: The differences in the format  of parameters for constructor 'java.lang.Double.Double'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
                                x = (System.Double.Parse(tokenizer.NextToken()));
                                //UPGRADE_TODO: The differences in the format  of parameters for constructor 'java.lang.Double.Double'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
                                y = (System.Double.Parse(tokenizer.NextToken()));
                                //UPGRADE_TODO: The differences in the format  of parameters for constructor 'java.lang.Double.Double'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
                                z = (System.Double.Parse(tokenizer.NextToken()));

                                if (fields == 8)
                                {
                                    //UPGRADE_TODO: The differences in the format  of parameters for constructor 'java.lang.Double.Double'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
                                    charge = (System.Double.Parse(tokenizer.NextToken()));
                                }

                                IAtom atom = file.Builder.newAtom(atomtype, new Point3d(x, y, z));
                                atom.setCharge(charge);
                                m.addAtom(atom);
                            }
                        }
                    }

                    setOfMolecules.addMolecule(m);
                    chemModel.SetOfMolecules = setOfMolecules;
                    chemSequence.addChemModel(chemModel);
                    line = input.ReadLine();
                }
                file.addChemSequence(chemSequence);
            }
            catch (System.IO.IOException e)
            {
                // should make some noise now
                file = null;
                //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                //logger.error("Error while reading file: ", e.Message);
                //logger.debug(e);
            }
            return file;
        }
        private IReaction readReaction(IChemObjectBuilder builder)
        {
            IReaction reaction = builder.newReaction();
            readLine(); // first line should be $RXN
            readLine(); // second line
            readLine(); // third line
            readLine(); // fourth line

            int reactantCount = 0;
            int productCount = 0;
            bool foundCOUNTS = false;
            while (Ready && !foundCOUNTS)
            {
                System.String command = readCommand();
                if (command.StartsWith("COUNTS"))
                {
                    SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
                    try
                    {
                        tokenizer.NextToken();
                        reactantCount = System.Int32.Parse(tokenizer.NextToken());
                        //logger.info("Expecting " + reactantCount + " reactants in file");
                        productCount = System.Int32.Parse(tokenizer.NextToken());
                        //logger.info("Expecting " + productCount + " products in file");
                    }
                    catch (System.Exception exception)
                    {
                        //logger.debug(exception);
                        throw new CDKException("Error while counts line of RXN file", exception);
                    }
                    foundCOUNTS = true;
                }
                else
                {
                    //logger.warn("Waiting for COUNTS line, but found: " + command);
                }
            }

            // now read the reactants
            for (int i = 1; i <= reactantCount; i++)
            {
                System.Text.StringBuilder molFile = new System.Text.StringBuilder();
                System.String announceMDLFileLine = readCommand();
                if (!announceMDLFileLine.Equals("BEGIN REACTANT"))
                {
                    System.String error = "Excepted start of reactant, but found: " + announceMDLFileLine;
                    //logger.error(error);
                    throw new CDKException(error);
                }
                System.String molFileLine = "";
                while (!molFileLine.EndsWith("END REACTANT"))
                {
                    molFileLine = readLine();
                    molFile.Append(molFileLine);
                    molFile.Append("\n");
                };

                try
                {
                    // read MDL molfile content
                    MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
                    IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());

                    // add reactant
                    reaction.addReactant(reactant);
                }
                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 reading reactant: " + exception.Message;
                    //logger.error(error);
                    //logger.debug(exception);
                    throw new CDKException(error, exception);
                }
            }

            // now read the products
            for (int i = 1; i <= productCount; i++)
            {
                System.Text.StringBuilder molFile = new System.Text.StringBuilder();
                System.String announceMDLFileLine = readCommand();
                if (!announceMDLFileLine.Equals("BEGIN PRODUCT"))
                {
                    System.String error = "Excepted start of product, but found: " + announceMDLFileLine;
                    //logger.error(error);
                    throw new CDKException(error);
                }
                System.String molFileLine = "";
                while (!molFileLine.EndsWith("END PRODUCT"))
                {
                    molFileLine = readLine();
                    molFile.Append(molFileLine);
                    molFile.Append("\n");
                };

                try
                {
                    // read MDL molfile content
                    MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
                    IMolecule product = (IMolecule)reader.read(builder.newMolecule());

                    // add product
                    reaction.addProduct(product);
                }
                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 reading product: " + exception.Message;
                    //logger.error(error);
                    //logger.debug(exception);
                    throw new CDKException(error, exception);
                }
            }

            return reaction;
        }