/// <summary> Creates amino acid AminoAcid objects. /// /// </summary> /// <returns> aminoAcids, a HashMap containing the amino acids as AminoAcids. /// </returns> public static AminoAcid[] createAAs() { if (aminoAcids != null) { return(aminoAcids); } // Create set of AtomContainers aminoAcids = new AminoAcid[20]; IChemFile list = new ChemFile(); //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'" CMLReader reader = new CMLReader(Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + "list_aminoacids.cml"));//typeof(AminoAcids).getClassLoader().getResourceAsStream("data/templates/list_aminoacids.cml")); try { list = (IChemFile)reader.read(list); IAtomContainer[] containers = ChemFileManipulator.getAllAtomContainers(list); for (int i = 0; i < containers.Length; i++) { //logger.debug("Adding AA: ", containers[i]); // convert into an AminoAcid AminoAcid aminoAcid = new AminoAcid(); IAtom[] atoms = containers[i].Atoms; System.Collections.IEnumerator props = containers[i].Properties.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 (props.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.Object next = props.Current; //UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Class.getName' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'" //logger.debug("Prop class: " + next.GetType().FullName); //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("Prop: " + next.ToString()); if (next is DictRef) { DictRef dictRef = (DictRef)next; // System.out.println("DictRef type: " + dictRef.getType()); if (dictRef.Type.Equals("pdb:residueName")) { //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'" aminoAcid.setProperty(RESIDUE_NAME, containers[i].getProperty(dictRef).ToString().ToUpper()); } else if (dictRef.Type.Equals("pdb:oneLetterCode")) { aminoAcid.setProperty(RESIDUE_NAME_SHORT, containers[i].getProperty(dictRef)); } else if (dictRef.Type.Equals("pdb:id")) { aminoAcid.setProperty(ID, containers[i].getProperty(dictRef)); //logger.debug("Set AA ID to: ", containers[i].getProperty(dictRef)); } else { //logger.error("Cannot deal with dictRef!"); } } } for (int atomCount = 0; atomCount < atoms.Length; atomCount++) { IAtom atom = atoms[atomCount]; System.String dictRef = (System.String)atom.getProperty("org.openscience.cdk.dict"); if (dictRef != null && dictRef.Equals("pdb:nTerminus")) { aminoAcid.addNTerminus(atom); } else if (dictRef != null && dictRef.Equals("pdb:cTerminus")) { aminoAcid.addCTerminus(atom); } else { aminoAcid.addAtom(atom); } } IBond[] bonds = containers[i].Bonds; for (int bondCount = 0; bondCount < bonds.Length; bondCount++) { aminoAcid.addBond(bonds[bondCount]); } AminoAcidManipulator.removeAcidicOxygen(aminoAcid); aminoAcid.setProperty(NO_ATOMS, "" + aminoAcid.AtomCount); aminoAcid.setProperty(NO_BONDS, "" + aminoAcid.getBondCount()); if (i < aminoAcids.Length) { aminoAcids[i] = aminoAcid; } else { //logger.error("Could not store AminoAcid! Array too short!"); } } } 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'" //logger.error("Failed reading file: ", exception.Message); //logger.debug(exception); } return(aminoAcids); }