/// <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];
}