/// <summary> Method that assign properties to an atom given a particular atomType. /// /// </summary> /// <param name="atom"> Atom to configure /// </param> /// <param name="atomType"> AtomType /// </param> public static void configure(IAtom atom, IAtomType atomType) { atom.AtomTypeName = atomType.AtomTypeName; atom.MaxBondOrder = atomType.MaxBondOrder; atom.BondOrderSum = atomType.BondOrderSum; atom.VanderwaalsRadius = atomType.VanderwaalsRadius; atom.CovalentRadius = atomType.CovalentRadius; atom.Valency = atomType.Valency; atom.setFormalCharge(atomType.getFormalCharge()); atom.Hybridization = atomType.Hybridization; atom.FormalNeighbourCount = atomType.FormalNeighbourCount; atom.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR)); atom.setFlag(CDKConstants.IS_HYDROGENBOND_DONOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_DONOR)); System.Object constant = atomType.getProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT); if (constant != null) { atom.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, constant); } atom.setFlag(CDKConstants.ISAROMATIC, atomType.getFlag(CDKConstants.ISAROMATIC)); System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color"); if (color != null) { atom.setProperty("org.openscience.cdk.renderer.color", color); } if (atomType.AtomicNumber != 0) { atom.AtomicNumber = atomType.AtomicNumber; } if (atomType.getExactMass() > 0.0) { atom.setExactMass(atomType.getExactMass()); } }
/// <summary> Method that assign properties to an atom given a particular atomType. /// /// </summary> /// <param name="atom"> Atom to configure /// </param> /// <param name="atomType"> AtomType /// </param> public static void configure(IAtom atom, IAtomType atomType) { atom.AtomTypeName = atomType.AtomTypeName; atom.MaxBondOrder = atomType.MaxBondOrder; atom.BondOrderSum = atomType.BondOrderSum; atom.VanderwaalsRadius = atomType.VanderwaalsRadius; atom.CovalentRadius = atomType.CovalentRadius; atom.Valency = atomType.Valency; atom.setFormalCharge(atomType.getFormalCharge()); atom.Hybridization = atomType.Hybridization; atom.FormalNeighbourCount = atomType.FormalNeighbourCount; atom.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR)); atom.setFlag(CDKConstants.IS_HYDROGENBOND_DONOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_DONOR)); System.Object constant = atomType.getProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT); if (constant != null) { atom.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, constant); } atom.setFlag(CDKConstants.ISAROMATIC, atomType.getFlag(CDKConstants.ISAROMATIC)); System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color"); if (color != null) { atom.setProperty("org.openscience.cdk.renderer.color", color); } if (atomType.AtomicNumber != 0) { atom.AtomicNumber = atomType.AtomicNumber; } if (atomType.getExactMass() > 0.0) { atom.setExactMass(atomType.getExactMass()); } }
/// <summary> /// Set integer FormalCharge for an atom /// </summary> /// <param name="atom"></param> /// <param name="charge"></param> public static void SetFormalCharge( IAtom atom, int charge) { atom.setFormalCharge(new java.lang.Integer(charge)); return; }
/// <summary> Procedure required by the CDOInterface. This function is only /// supposed to be called by the JCFL library /// </summary> public virtual void setObjectProperty(System.String objectType, System.String propertyType, System.String propertyValue) { //logger.debug("objectType: " + objectType); //logger.debug("propType: " + propertyType); //logger.debug("property: " + propertyValue); if (objectType == null) { //logger.error("Cannot add property for null object"); return; } if (propertyType == null) { //logger.error("Cannot add property for null property type"); return; } if (propertyValue == null) { //logger.warn("Will not add null property"); return; } if (objectType.Equals("Molecule")) { if (propertyType.Equals("id")) { currentMolecule.ID = propertyValue; } else if (propertyType.Equals("inchi")) { currentMolecule.setProperty("iupac.nist.chemical.identifier", propertyValue); } else if (propertyType.Equals("pdb:residueName")) { currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue); } else if (propertyType.Equals("pdb:oneLetterCode")) { currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue); } else if (propertyType.Equals("pdb:id")) { currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue); } else { //logger.warn("Not adding molecule property!"); } } else if (objectType.Equals("PseudoAtom")) { if (propertyType.Equals("label")) { if (!(currentAtom is IPseudoAtom)) { currentAtom = currentChemFile.Builder.newPseudoAtom(currentAtom); } ((IPseudoAtom)currentAtom).Label = propertyValue; } } else if (objectType.Equals("Atom")) { if (propertyType.Equals("type")) { if (propertyValue.Equals("R") && !(currentAtom is IPseudoAtom)) { currentAtom = currentChemFile.Builder.newPseudoAtom(currentAtom); } currentAtom.Symbol = propertyValue; } else if (propertyType.Equals("x2")) { //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'" currentAtom.X2d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("y2")) { //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'" currentAtom.Y2d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("x3")) { //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'" currentAtom.X3d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("y3")) { //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'" currentAtom.Y3d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("z3")) { //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'" currentAtom.Z3d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("xFract")) { //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'" currentAtom.FractX3d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("yFract")) { //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'" currentAtom.FractY3d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("zFract")) { //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'" currentAtom.FractZ3d = System.Double.Parse(propertyValue); } else if (propertyType.Equals("formalCharge")) { currentAtom.setFormalCharge(System.Int32.Parse(propertyValue)); } else if (propertyType.Equals("charge") || propertyType.Equals("partialCharge")) { //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'" currentAtom.setCharge(System.Double.Parse(propertyValue)); } else if (propertyType.Equals("hydrogenCount")) { currentAtom.setHydrogenCount(System.Int32.Parse(propertyValue)); } else if (propertyType.Equals("dictRef")) { currentAtom.setProperty("org.openscience.cdk.dict", propertyValue); } else if (propertyType.Equals("atomicNumber")) { currentAtom.AtomicNumber = System.Int32.Parse(propertyValue); } else if (propertyType.Equals("massNumber")) { //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'" currentAtom.MassNumber = (int)(System.Double.Parse(propertyValue)); } else if (propertyType.Equals("spinMultiplicity")) { int unpairedElectrons = System.Int32.Parse(propertyValue) - 1; for (int i = 0; i < unpairedElectrons; i++) { currentMolecule.addElectronContainer(currentChemFile.Builder.newSingleElectron(currentAtom)); } } else if (propertyType.Equals("id")) { //logger.debug("id: ", propertyValue); currentAtom.ID = propertyValue; atomEnumeration[propertyValue] = (System.Int32)numberOfAtoms; } } else if (objectType.Equals("Bond")) { if (propertyType.Equals("atom1")) { bond_a1 = System.Int32.Parse(propertyValue); } else if (propertyType.Equals("atom2")) { bond_a2 = System.Int32.Parse(propertyValue); } else if (propertyType.Equals("id")) { //logger.debug("id: " + propertyValue); bond_id = propertyValue; } else if (propertyType.Equals("order")) { try { bond_order = System.Double.Parse(propertyValue); } catch (System.Exception e) { //logger.error("Cannot convert to double: " + propertyValue); bond_order = 1.0; } } else if (propertyType.Equals("stereo")) { if (propertyValue.Equals("H")) { bond_stereo = CDKConstants.STEREO_BOND_DOWN; } else if (propertyValue.Equals("W")) { bond_stereo = CDKConstants.STEREO_BOND_UP; } } } else if (objectType.Equals("Reaction")) { if (propertyType.Equals("id")) { currentReaction.ID = propertyValue; } } else if (objectType.Equals("SetOfReactions")) { if (propertyType.Equals("id")) { currentSetOfReactions.ID = propertyValue; } } else if (objectType.Equals("Reactant")) { if (propertyType.Equals("id")) { currentMolecule.ID = propertyValue; } } else if (objectType.Equals("Product")) { if (propertyType.Equals("id")) { currentMolecule.ID = propertyValue; } } else if (objectType.Equals("Crystal")) { // set these variables if (currentMolecule is ICrystal) { ICrystal current = (ICrystal)currentMolecule; if (propertyType.Equals("spacegroup")) { //logger.debug("Setting crystal spacegroup to: " + propertyValue); current.SpaceGroup = propertyValue; } else if (propertyType.Equals("z")) { try { //logger.debug("Setting z to: " + propertyValue); current.Z = System.Int32.Parse(propertyValue); } catch (System.FormatException exception) { //logger.error("Error in format of Z value"); } } } else { //logger.warn("Cannot add crystal cell parameters to a non " + "Crystal class!"); } } else if (objectType.Equals("a-axis") || objectType.Equals("b-axis") || objectType.Equals("c-axis")) { // set these variables if (currentMolecule is ICrystal) { //logger.debug("Setting axis (" + objectType + "): " + propertyValue); if (propertyType.Equals("x")) { crystal_axis_x = System.Double.Parse(propertyValue); } else if (propertyType.Equals("y")) { crystal_axis_y = System.Double.Parse(propertyValue); } else if (propertyType.Equals("z")) { crystal_axis_z = System.Double.Parse(propertyValue); } } else { //logger.warn("Cannot add crystal cell parameters to a non " + "Crystal class!"); } } //logger.debug("Object property set..."); }
/// <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); } } }