/// <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); }
/// <summary> Reads the atoms, coordinates and charges. /// /// <p>IMPORTANT: it does not support the atom list and its negation! /// </summary> public virtual void readAtomBlock(IAtomContainer readData) { bool foundEND = false; while (Ready && !foundEND) { System.String command = readCommand(); if ("END ATOM".Equals(command)) { // FIXME: should check wether 3D is really 2D foundEND = true; } else { //logger.debug("Parsing atom from: " + command); SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command); IAtom atom = readData.Builder.newAtom("C"); // parse the index try { System.String indexString = tokenizer.NextToken(); atom.ID = indexString; } catch (System.Exception exception) { System.String error = "Error while parsing atom index"; //logger.error(error); //logger.debug(exception); throw new CDKException(error, exception); } // parse the element System.String element = tokenizer.NextToken(); bool isElement = false; try { isElement = IsotopeFactory.getInstance(atom.Builder).isElement(element); } catch (System.Exception exception) { throw new CDKException("Could not determine if element exists!", exception); } if (isPseudoAtom(element)) { atom = readData.Builder.newPseudoAtom(atom); } else if (isElement) { atom.Symbol = element; } else { System.String error = "Cannot parse element of type: " + element; //logger.error(error); throw new CDKException("(Possible CDK bug) " + error); } // parse atom coordinates (in Angstrom) try { System.String xString = tokenizer.NextToken(); System.String yString = tokenizer.NextToken(); System.String zString = tokenizer.NextToken(); double x = System.Double.Parse(xString); double y = System.Double.Parse(yString); double z = System.Double.Parse(zString); atom.setPoint3d(new Point3d(x, y, z)); atom.setPoint2d(new Point2d(x, y)); // FIXME: dirty! } catch (System.Exception exception) { System.String error = "Error while parsing atom coordinates"; //logger.error(error); //logger.debug(exception); throw new CDKException(error, exception); } // atom-atom mapping System.String mapping = tokenizer.NextToken(); if (!mapping.Equals("0")) { //logger.warn("Skipping atom-atom mapping: " + mapping); } // else: default 0 is no mapping defined // the rest are key value things if (command.IndexOf("=") != -1) { System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer)); System.Collections.IEnumerator keys = options.Keys.GetEnumerator(); //UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'" while (keys.MoveNext()) { //UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'" System.String key = (System.String)keys.Current; System.String value_Renamed = (System.String)options[key]; try { if (key.Equals("CHG")) { int charge = System.Int32.Parse(value_Renamed); if (charge != 0) { // zero is no charge specified atom.setFormalCharge(charge); } } else { //logger.warn("Not parsing key: " + key); } } catch (System.Exception exception) { //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'" System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message; //logger.error(error); //logger.debug(exception); throw new CDKException(error, exception); } } } // store atom readData.addAtom(atom); //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'" //logger.debug("Added atom: " + atom); } } }
/// <summary> 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); }