/// <summary> Method to create a specialized AtomTypeFactory. Available lists in CDK are: /// <ul> /// <li>org/openscience/cdk/config/data/jmol_atomtypes.txt /// <li>org/openscience/cdk/config/data/mol2_atomtypes.xml /// <li>org/openscience/cdk/config/data/structgen_atomtypes.xml /// <li>org/openscience/cdk/config/data/valency_atomtypes.xml /// <li>org/openscience/cdk/config/data/mm2_atomtypes.xml /// <li>org/openscience/cdk/config/data/mmff94_atomtypes.xml /// </ul> /// /// </summary> /// <param name="configFile"> String the name of the data file /// </param> /// <param name="builder"> IChemObjectBuilder used to make IChemObject instances /// </param> /// <returns> The AtomTypeFactory for the given data file /// </returns> /// <throws> IOException when the file cannot be read </throws> /// <throws> ClassNotFoundException when the AtomTypeFactory cannot be found </throws> public static AtomTypeFactory getInstance(System.String configFile, IChemObjectBuilder builder) { if (tables == null) { tables = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable()); } if (!(tables.ContainsKey(configFile))) { tables[configFile] = new AtomTypeFactory(configFile, builder); } return((AtomTypeFactory)tables[configFile]); }
/// <param name="builder">the ChemObjectBuilder implementation used to construct the AtomType's. /// </param> protected internal virtual AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder) { if (structgenATF == null) { try { structgenATF = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/structgen_atomtypes.xml", builder); } catch (System.Exception exception) { //logger.debug(exception); throw new CDKException("Could not instantiate AtomTypeFactory!", exception); } } return structgenATF; }
/// <param name="builder">the ChemObjectBuilder implementation used to construct the AtomType's. /// </param> protected internal virtual AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder) { if (structgenATF == null) { try { structgenATF = AtomTypeFactory.getInstance(atomTypeList, builder); } catch (System.Exception exception) { //logger.debug(exception); throw new CDKException("Could not instantiate AtomTypeFactory!", exception); } } return structgenATF; }
/// <summary> /// Takes an object which subclasses IChemObject, e.g. Molecule, and will /// read this (from file, database, internet etc). If the specific /// implementation does not support a specific IChemObject it will throw /// an Exception. /// /// </summary> /// <param name="oObj"> The object that subclasses IChemObject /// </param> /// <returns> The IChemObject read /// </returns> /// <exception cref="CDKException"> /// /// </exception> public override IChemObject read(IChemObject oObj) { if (oObj is IChemFile) { if (pdbFactory == null) { try { pdbFactory = AtomTypeFactory.getInstance("pdb_atomtypes.xml", ((IChemFile)oObj).Builder); } catch (System.Exception exception) { //logger.debug(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'" throw new CDKException("Could not setup list of PDB atom types! " + exception.Message); } } return readChemFile((IChemFile)oObj); } else { throw new CDKException("Only supported is reading of ChemFile objects."); } }
/// <summary> /// Contructs a new PDBReader that can read Molecules from a given /// Reader. /// /// </summary> /// <param name="oIn"> The Reader to read from /// /// </param> //UPGRADE_ISSUE: Class hierarchy differences between 'java.io.Reader' and 'System.IO.StreamReader' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'" public PDBReader(System.IO.StreamReader oIn) { //logger = new LoggingTool(this.GetType()); //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'" _oInput = oIn; initIOSettings(); pdbFactory = null; }
/// <summary> Method to create a specialized AtomTypeFactory. Available lists in CDK are: /// <ul> /// <li>org/openscience/cdk/config/data/jmol_atomtypes.txt /// <li>org/openscience/cdk/config/data/mol2_atomtypes.xml /// <li>org/openscience/cdk/config/data/structgen_atomtypes.xml /// <li>org/openscience/cdk/config/data/valency_atomtypes.xml /// <li>org/openscience/cdk/config/data/mm2_atomtypes.xml /// <li>org/openscience/cdk/config/data/mmff94_atomtypes.xml /// </ul> /// /// </summary> /// <param name="configFile"> String the name of the data file /// </param> /// <param name="builder"> IChemObjectBuilder used to make IChemObject instances /// </param> /// <returns> The AtomTypeFactory for the given data file /// </returns> /// <throws> IOException when the file cannot be read </throws> /// <throws> ClassNotFoundException when the AtomTypeFactory cannot be found </throws> public static AtomTypeFactory getInstance(System.String configFile, IChemObjectBuilder builder) { if (tables == null) { tables = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable()); } if (!(tables.ContainsKey(configFile))) { tables[configFile] = new AtomTypeFactory(configFile, builder); } return (AtomTypeFactory)tables[configFile]; }