Пример #1
0
        /// <summary>
        /// Remove the following features from a molecule
        ///  - Atom non-standard mass
        ///  - Stereo chemistry
        ///  - explicit hydrogens
        /// </summary>
        /// <param name="src"></param>
        /// <returns>Modified mol</returns>

        public static IAtomContainer RemoveIsotopesStereoExplicitHydrogens(
            IAtomContainer src)
        {
            IAtom[] atoms = new IAtom[src.getAtomCount()];
            IBond[] bonds = new IBond[src.getBondCount()];

            IChemObjectBuilder builder = src.getBuilder();

            for (int i = 0; i < atoms.Length; i++)
            {
                IAtom atom  = src.getAtom(i);
                IAtom atom2 = (IAtom)builder.newInstance(typeof(IAtom), atom.getSymbol());
                SetImplicitHydrogenCount(atom2, GetImplicitHydrogenCount(atom));
                atom2.setPoint2d(atom.getPoint2d());
                atoms[i] = atom2;
            }

            for (int i = 0; i < bonds.Length; i++)
            {
                IBond bond = src.getBond(i);

                int   u     = src.getAtomNumber(bond.getAtom(0));
                int   v     = src.getAtomNumber(bond.getAtom(1));
                IBond bond2 = (IBond)builder.newInstance(typeof(IBond), atoms[u], atoms[v]);

                bond2.setIsAromatic(bond.isAromatic());
                bond2.setIsInRing(bond.isInRing());
                bond2.setOrder(bond.getOrder());

                bond2.setFlag(CDKConstants.ISAROMATIC, bond.getFlag(CDKConstants.ISAROMATIC));
                bond2.setFlag(CDKConstants.SINGLE_OR_DOUBLE, bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE));

                bonds[i] = bond2;
            }

            IAtomContainer dest = (IAtomContainer)builder.newInstance(typeof(IAtomContainer));

            dest.setAtoms(atoms);
            dest.setBonds(bonds);

            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(dest);
            dest = AtomContainerManipulator.suppressHydrogens(dest);
            GetHydrogenAdder().addImplicitHydrogens(dest);

            return(dest);
        }
Пример #2
0
        /// <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);
                }
            }
        }
Пример #3
0
        /// <summary>  Read a Molecule from a file in MDL sd format
        ///
        /// </summary>
        /// <returns>    The Molecule that was read from the MDL file.
        /// </returns>
        private IMolecule readMolecule(IMolecule molecule)
        {
            //logger.debug("Reading new molecule");
            int linecount     = 0;
            int atoms         = 0;
            int bonds         = 0;
            int atom1         = 0;
            int atom2         = 0;
            int order         = 0;
            int stereo        = 0;
            int RGroupCounter = 1;
            int Rnumber       = 0;

            System.String[] rGroup = null;
            double          x      = 0.0;
            double          y      = 0.0;
            double          z      = 0.0;
            double          totalZ = 0.0;
            //int[][] conMat = new int[0][0];
            //String help;
            IBond bond;
            IAtom atom;

            System.String line = "";

            try
            {
                //logger.info("Reading header");
                line = input.ReadLine(); linecount++;
                if (line == null)
                {
                    return(null);
                }
                //logger.debug("Line " + linecount + ": " + line);

                if (line.StartsWith("$$$$"))
                {
                    //logger.debug("File is empty, returning empty molecule");
                    return(molecule);
                }
                if (line.Length > 0)
                {
                    molecule.setProperty(CDKConstants.TITLE, line);
                }
                line = input.ReadLine(); linecount++;
                //logger.debug("Line " + linecount + ": " + line);
                line = input.ReadLine(); linecount++;
                //logger.debug("Line " + linecount + ": " + line);
                if (line.Length > 0)
                {
                    molecule.setProperty(CDKConstants.REMARK, line);
                }

                //logger.info("Reading rest of file");
                line = input.ReadLine(); linecount++;
                //logger.debug("Line " + linecount + ": " + line);
                atoms = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
                //logger.debug("Atomcount: " + atoms);
                bonds = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
                //logger.debug("Bondcount: " + bonds);

                // read ATOM block
                //logger.info("Reading atom block");
                for (int f = 0; f < atoms; f++)
                {
                    line = input.ReadLine(); linecount++;
                    //UPGRADE_TODO: The differences in the format  of parameters for constructor 'java.lang.Double.Double'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
                    x = System.Double.Parse(line.Substring(0, (10) - (0)).Trim());
                    //UPGRADE_TODO: The differences in the format  of parameters for constructor 'java.lang.Double.Double'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
                    y = System.Double.Parse(line.Substring(10, (20) - (10)).Trim());
                    //UPGRADE_TODO: The differences in the format  of parameters for constructor 'java.lang.Double.Double'  may cause compilation errors.  "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
                    z       = System.Double.Parse(line.Substring(20, (30) - (20)).Trim());
                    totalZ += System.Math.Abs(z); // *all* values should be zero, not just the sum
                    //logger.debug("Coordinates: " + x + "; " + y + "; " + z);
                    System.String element = line.Substring(31, (34) - (31)).Trim();

                    //logger.debug("Atom type: ", element);
                    if (IsotopeFactory.getInstance(molecule.Builder).isElement(element))
                    {
                        atom = IsotopeFactory.getInstance(molecule.Builder).configure(molecule.Builder.newAtom(element));
                    }
                    else
                    {
                        //logger.debug("Atom ", element, " is not an regular element. Creating a PseudoAtom.");
                        //check if the element is R
                        rGroup = element.Split(new char[] { '^', 'R' }); // ????
                        if (rGroup.Length > 1)
                        {
                            try
                            {
                                Rnumber       = System.Int32.Parse(rGroup[(rGroup.Length - 1)]);
                                RGroupCounter = Rnumber;
                            }
                            catch (System.Exception ex)
                            {
                                Rnumber = RGroupCounter;
                                RGroupCounter++;
                            }
                            element = "R" + Rnumber;
                        }
                        atom = molecule.Builder.newPseudoAtom(element);
                    }

                    // store as 3D for now, convert to 2D (if totalZ == 0.0) later
                    atom.setPoint3d(new Point3d(x, y, z));

                    // parse further fields
                    System.String massDiffString = line.Substring(34, (36) - (34)).Trim();
                    //logger.debug("Mass difference: ", massDiffString);
                    if (!(atom is IPseudoAtom))
                    {
                        try
                        {
                            int massDiff = System.Int32.Parse(massDiffString);
                            if (massDiff != 0)
                            {
                                IIsotope major = IsotopeFactory.getInstance(molecule.Builder).getMajorIsotope(element);
                                atom.AtomicNumber = major.AtomicNumber + massDiff;
                            }
                        }
                        catch (System.Exception exception)
                        {
                            //logger.error("Could not parse mass difference field");
                        }
                    }
                    else
                    {
                        //logger.error("Cannot set mass difference for a non-element!");
                    }


                    System.String chargeCodeString = line.Substring(36, (39) - (36)).Trim();
                    //logger.debug("Atom charge code: ", chargeCodeString);
                    int chargeCode = System.Int32.Parse(chargeCodeString);
                    if (chargeCode == 0)
                    {
                        // uncharged species
                    }
                    else if (chargeCode == 1)
                    {
                        atom.setFormalCharge(+3);
                    }
                    else if (chargeCode == 2)
                    {
                        atom.setFormalCharge(+2);
                    }
                    else if (chargeCode == 3)
                    {
                        atom.setFormalCharge(+1);
                    }
                    else if (chargeCode == 4)
                    {
                    }
                    else if (chargeCode == 5)
                    {
                        atom.setFormalCharge(-1);
                    }
                    else if (chargeCode == 6)
                    {
                        atom.setFormalCharge(-2);
                    }
                    else if (chargeCode == 7)
                    {
                        atom.setFormalCharge(-3);
                    }

                    try
                    {
                        // read the mmm field as position 61-63
                        System.String reactionAtomIDString = line.Substring(60, (63) - (60)).Trim();
                        //logger.debug("Parsing mapping id: ", reactionAtomIDString);
                        try
                        {
                            int reactionAtomID = System.Int32.Parse(reactionAtomIDString);
                            if (reactionAtomID != 0)
                            {
                                atom.ID = reactionAtomIDString;
                            }
                        }
                        catch (System.Exception exception)
                        {
                            //logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");
                            //logger.debug(exception);
                        }
                    }
                    catch (System.Exception exception)
                    {
                        // older mol files don't have all these fields...
                        //logger.warn("A few fields are missing. Older MDL MOL file?");
                    }

                    molecule.addAtom(atom);
                }

                // convert to 2D, if totalZ == 0
                if (totalZ == 0.0 && !forceReadAs3DCoords.Set)
                {
                    //logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");
                    IAtom[] atomsToUpdate = molecule.Atoms;
                    for (int f = 0; f < atomsToUpdate.Length; f++)
                    {
                        IAtom   atomToUpdate = atomsToUpdate[f];
                        Point3d p3d          = atomToUpdate.getPoint3d();
                        atomToUpdate.setPoint2d(new Point2d(p3d.x, p3d.y));
                        atomToUpdate.setPoint3d(null);
                    }
                }

                // read BOND block
                //logger.info("Reading bond block");
                for (int f = 0; f < bonds; f++)
                {
                    line  = input.ReadLine(); linecount++;
                    atom1 = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
                    atom2 = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
                    order = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
                    if (line.Length > 12)
                    {
                        stereo = System.Int32.Parse(line.Substring(9, (12) - (9)).Trim());
                    }
                    else
                    {
                        //logger.warn("Missing expected stereo field at line: " + line);
                    }
                    //if (//logger.DebugEnabled)
                    //{
                    //    //logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order);
                    //}
                    if (stereo == 1)
                    {
                        // MDL up bond
                        stereo = CDKConstants.STEREO_BOND_UP;
                    }
                    else if (stereo == 6)
                    {
                        // MDL down bond
                        stereo = CDKConstants.STEREO_BOND_DOWN;
                    }
                    else if (stereo == 4)
                    {
                        //MDL bond undefined
                        stereo = CDKConstants.STEREO_BOND_UNDEFINED;
                    }
                    // interpret CTfile's special bond orders
                    IAtom a1 = molecule.getAtomAt(atom1 - 1);
                    IAtom a2 = molecule.getAtomAt(atom2 - 1);
                    if (order == 4)
                    {
                        // aromatic bond
                        bond = molecule.Builder.newBond(a1, a2, CDKConstants.BONDORDER_AROMATIC, stereo);
                        // mark both atoms and the bond as aromatic
                        bond.setFlag(CDKConstants.ISAROMATIC, true);
                        a1.setFlag(CDKConstants.ISAROMATIC, true);
                        a2.setFlag(CDKConstants.ISAROMATIC, true);
                        molecule.addBond(bond);
                    }
                    else
                    {
                        bond = molecule.Builder.newBond(a1, a2, (double)order, stereo);
                        molecule.addBond(bond);
                    }
                }

                // read PROPERTY block
                //logger.info("Reading property block");
                while (true)
                {
                    line = input.ReadLine(); linecount++;
                    if (line == null)
                    {
                        throw new CDKException("The expected property block is missing!");
                    }
                    if (line.StartsWith("M  END"))
                    {
                        break;
                    }

                    bool lineRead = false;
                    if (line.StartsWith("M  CHG"))
                    {
                        // FIXME: if this is encountered for the first time, all
                        // atom charges should be set to zero first!
                        int infoCount             = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
                        SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
                        for (int i = 1; i <= infoCount; i++)
                        {
                            System.String token      = st.NextToken();
                            int           atomNumber = System.Int32.Parse(token.Trim());
                            token = st.NextToken();
                            int charge = System.Int32.Parse(token.Trim());
                            molecule.getAtomAt(atomNumber - 1).setFormalCharge(charge);
                        }
                    }
                    else if (line.StartsWith("M  ISO"))
                    {
                        try
                        {
                            System.String          countString = line.Substring(6, (9) - (6)).Trim();
                            int                    infoCount   = System.Int32.Parse(countString);
                            SupportClass.Tokenizer st          = new SupportClass.Tokenizer(line.Substring(9));
                            for (int i = 1; i <= infoCount; i++)
                            {
                                int atomNumber = System.Int32.Parse(st.NextToken().Trim());
                                int absMass    = System.Int32.Parse(st.NextToken().Trim());
                                if (absMass != 0)
                                {
                                    IAtom isotope = molecule.getAtomAt(atomNumber - 1);
                                    isotope.MassNumber = absMass;
                                }
                            }
                        }
                        catch (System.FormatException exception)
                        {
                            //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                            System.String error = "Error (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
                            //logger.error(error);
                            throw new CDKException("NumberFormatException in isotope information on line: " + line, exception);
                        }
                    }
                    else if (line.StartsWith("M  RAD"))
                    {
                        try
                        {
                            System.String          countString = line.Substring(6, (9) - (6)).Trim();
                            int                    infoCount   = System.Int32.Parse(countString);
                            SupportClass.Tokenizer st          = new SupportClass.Tokenizer(line.Substring(9));
                            for (int i = 1; i <= infoCount; i++)
                            {
                                int atomNumber       = System.Int32.Parse(st.NextToken().Trim());
                                int spinMultiplicity = System.Int32.Parse(st.NextToken().Trim());
                                if (spinMultiplicity > 1)
                                {
                                    IAtom radical = molecule.getAtomAt(atomNumber - 1);
                                    for (int j = 2; j <= spinMultiplicity; j++)
                                    {
                                        // 2 means doublet -> one unpaired electron
                                        // 3 means triplet -> two unpaired electron
                                        molecule.addElectronContainer(molecule.Builder.newSingleElectron(radical));
                                    }
                                }
                            }
                        }
                        catch (System.FormatException exception)
                        {
                            //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                            System.String error = "Error (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
                            //logger.error(error);
                            throw new CDKException("NumberFormatException in radical information on line: " + line, exception);
                        }
                    }
                    else if (line.StartsWith("G  "))
                    {
                        try
                        {
                            System.String atomNumberString = line.Substring(3, (6) - (3)).Trim();
                            int           atomNumber       = System.Int32.Parse(atomNumberString);
                            //String whatIsThisString = line.substring(6,9).trim();

                            System.String atomName = input.ReadLine();

                            // convert Atom into a PseudoAtom
                            IAtom       prevAtom   = molecule.getAtomAt(atomNumber - 1);
                            IPseudoAtom pseudoAtom = molecule.Builder.newPseudoAtom(atomName);
                            if (prevAtom.getPoint2d() != null)
                            {
                                pseudoAtom.setPoint2d(prevAtom.getPoint2d());
                            }
                            if (prevAtom.getPoint3d() != null)
                            {
                                pseudoAtom.setPoint3d(prevAtom.getPoint3d());
                            }
                            AtomContainerManipulator.replaceAtomByAtom(molecule, prevAtom, pseudoAtom);
                        }
                        catch (System.FormatException exception)
                        {
                            //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                            System.String error = "Error (" + exception.ToString() + ") while parsing line " + linecount + ": " + line + " in property block.";
                            //logger.error(error);
                            throw new CDKException("NumberFormatException in group information on line: " + line, exception);
                        }
                    }
                    if (!lineRead)
                    {
                        //logger.warn("Skipping line in property block: ", line);
                    }
                }
            }
            catch (CDKException exception)
            {
                //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                System.String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.Message;
                //logger.error(error);
                //logger.debug(exception);
                throw exception;
            }
            catch (System.Exception exception)
            {
                //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
                System.String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.Message;
                //logger.error(error);
                //logger.debug(exception);
                throw new CDKException(error, exception);
            }
            return(molecule);
        }