/// <summary> Reads the atom types from the CDK based atom type list.
///
/// </summary>
/// <param name="builder">IChemObjectBuilder used to construct the IAtomType's.
/// </param>
/// <throws> IOException when a problem occured with reading from the InputStream </throws>
/// <returns> A Vector with read IAtomType's.
/// </returns>
public virtual System.Collections.ArrayList readAtomTypes(IChemObjectBuilder builder)
{
System.Collections.ArrayList atomTypes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(0));
if (ins == null)
{
try
{
ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + configFile);
}
catch (System.Exception exc)
{
//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(exc.Message);
//logger.debug(exc);
throw new System.IO.IOException("There was a problem getting a stream for " + configFile + " with getClass.getClassLoader.getResourceAsStream");
}
if (ins == null)
{
try
{
//UPGRADE_ISSUE: Method 'java.lang.Class.getResourceAsStream' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassgetResourceAsStream_javalangString'"
ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + configFile);
}
catch (System.Exception exc)
{
//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(exc.Message);
//logger.debug(exc);
throw new System.IO.IOException("There was a problem getting a stream for " + configFile + " with getClass.getResourceAsStream");
}
}
}
if (ins == null)
throw new System.IO.IOException("There was a problem getting an input stream");
AtomTypeReader reader = new AtomTypeReader(new System.IO.StreamReader(ins, System.Text.Encoding.Default));
atomTypes = reader.readAtomTypes(builder);
for (int f = 0; f < atomTypes.Count; f++)
{
System.Object object_Renamed = atomTypes[f];
if (object_Renamed == null)
{
System.Console.Out.WriteLine("Expecting an object but found null!");
if (!(object_Renamed is IAtomType))
{
//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'"
System.Console.Out.WriteLine("Expecting cdk.AtomType class, but got: " + object_Renamed.GetType().FullName);
}
}
}
return atomTypes;
}
/// <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> Constructs an IsotopeHandler used by the IsotopeReader.
///
/// </summary>
/// <param name="builder">The IChemObjectBuilder used to create new IIsotope's.
/// </param>
public IsotopeHandler(IChemObjectBuilder builder)
{
//logger = new LoggingTool(this);
this.builder = builder;
}
//private IChemObjectBuilder builder;
/// <summary> Default constructor</summary>
public SmilesGenerator(IChemObjectBuilder builder)
{
//this.builder = builder;
try
{
isotopeFactory = IsotopeFactory.getInstance(builder);
}
catch (System.IO.IOException e)
{
SupportClass.WriteStackTrace(e, Console.Error);
}
//UPGRADE_NOTE: Exception 'java.lang.ClassNotFoundException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
//UPGRADE_ISSUE: Method 'java.lang.ClassNotFoundException.printStackTrace' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassNotFoundExceptionprintStackTrace'"
//e.printStackTrace();
}
}
/// <summary> Returns an IsotopeFactory instance.
///
/// </summary>
/// <param name="builder"> ChemObjectBuilder used to construct the Isotope's
/// </param>
/// <returns> The instance value
/// </returns>
/// <exception cref="IOException"> Description of the Exception
/// </exception>
/// <exception cref="OptionalDataException"> Description of the Exception
/// </exception>
/// <exception cref="ClassNotFoundException"> Description of the Exception
/// </exception>
public static IsotopeFactory getInstance(IChemObjectBuilder builder)
{
if (ifac == null)
{
ifac = new IsotopeFactory(builder);
}
return ifac;
}
/// <summary> Reads the atom types from the data file.
///
/// </summary>
/// <param name="builder">The IChemObjectBuilder used to create new IAtomType's.
/// </param>
/// <returns> a Vector with atom types. Is empty if some reading error occured.
/// </returns>
public virtual System.Collections.ArrayList readAtomTypes(IChemObjectBuilder builder)
{
System.Collections.ArrayList isotopes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
try
{
parser.setFeature("http://xml.org/sax/features/validation", false);
//logger.info("Deactivated validation");
}
//UPGRADE_TODO: Class 'org.xml.sax.SAXException' was converted to 'System.Xml.XmlException' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
catch (System.Xml.XmlException exception)
{
//logger.warn("Cannot deactivate validation: ", exception.Message);
//logger.debug(exception);
}
AtomTypeHandler handler = new AtomTypeHandler(builder);
parser.setContentHandler(handler);
try
{
parser.parse(new XmlSourceSupport(input));
isotopes = handler.AtomTypes;
}
catch (System.IO.IOException 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("IOException: ", exception.Message);
//logger.debug(exception);
}
//UPGRADE_TODO: Class 'org.xml.sax.SAXException' was converted to 'System.Xml.XmlException' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
catch (System.Xml.XmlException saxe)
{
//logger.error("SAXException: ", saxe.Message);
//logger.debug(saxe);
}
return isotopes;
}
public virtual IAtomContainer readConnectionTable(IChemObjectBuilder builder)
{
IAtomContainer readData = builder.newAtomContainer();
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END CTAB".Equals(command))
{
foundEND = true;
}
else if ("BEGIN CTAB".Equals(command))
{
// that's fine
}
else if ("COUNTS".Equals(command))
{
// don't think I need to parse this
}
else if ("BEGIN ATOM".Equals(command))
{
readAtomBlock(readData);
}
else if ("BEGIN BOND".Equals(command))
{
readBondBlock(readData);
}
else if ("BEGIN SGROUP".Equals(command))
{
readSGroup(readData);
}
else
{
//logger.warn("Unrecognized command: " + command);
}
}
return readData;
}
public void SetUp()
{
builder = ChemObjectBuilder.Instance;
}
/// <summary> Method to create a default AtomTypeFactory, using the given InputStream.
/// An AtomType of this kind is not cached.
///
/// </summary>
/// <seealso cref="getInstance(String, IChemObjectBuilder)">
/// </seealso>
/// <param name="ins"> InputStream containing the data
/// </param>
/// <param name="format"> String representing the possible formats ('xml' and 'txt')
/// </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.IO.Stream ins, System.String format, IChemObjectBuilder builder)
{
return new AtomTypeFactory(ins, format, builder);
}
private void readConfiguration(System.IO.Stream ins, System.String format, IChemObjectBuilder builder)
{
IAtomTypeConfigurator atc = constructConfigurator(format);
if (atc != null)
{
atc.InputStream = ins;
try
{
atomTypes = atc.readAtomTypes(builder);
}
catch (System.Exception exc)
{
//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("Could not read AtomType's from file due to: ", exc.Message);
//logger.debug(exc);
}
}
else
{
//logger.debug("AtomTypeConfigurator was null!");
atomTypes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
}
}
/// <summary>
/// Creates a new instance.
/// </summary>
/// <param name="symbol">the atom symbol</param>
/// <param name="builder"></param>
public AliphaticSymbolAtom(string symbol, IChemObjectBuilder builder)
: base(builder)
{
IsAromatic = true;
Symbol = symbol;
}
/// <summary> Read the config from a text file.
///
/// </summary>
/// <param name="configFile"> name of the config file
/// </param>
/// <param name="builder"> IChemObjectBuilder used to make IChemObject instances
/// </param>
private void readConfiguration(System.String fileName, IChemObjectBuilder builder)
{
//logger.info("Reading config file from ", fileName);
System.IO.Stream ins = null;
{
//try to see if this is a resource
//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'"
ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + fileName);
if (ins == null)
{
// try to see if this configFile is an actual file
System.IO.FileInfo file = new System.IO.FileInfo(fileName);
bool tmpBool;
if (System.IO.File.Exists(file.FullName))
tmpBool = true;
else
tmpBool = System.IO.Directory.Exists(file.FullName);
if (tmpBool)
{
//logger.debug("configFile is a File");
// what's next?
try
{
//UPGRADE_TODO: Constructor 'java.io.FileInputStream.FileInputStream' was converted to 'System.IO.FileStream.FileStream' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javaioFileInputStreamFileInputStream_javaioFile'"
ins = new System.IO.FileStream(file.FullName, System.IO.FileMode.Open, System.IO.FileAccess.Read);
}
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(exception.Message);
//logger.debug(exception);
}
}
else
{
//logger.error("no stream and no file");
}
}
}
System.String format = XML_EXTENSION;
if (fileName.EndsWith(TXT_EXTENSION))
{
format = TXT_EXTENSION;
}
else if (fileName.EndsWith(XML_EXTENSION))
{
format = XML_EXTENSION;
}
readConfiguration(ins, format, builder);
}
/// <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];
}
/// <summary> Method to create a default AtomTypeFactory, using the structgen atom type list.
///
/// </summary>
/// <seealso cref="getInstance(String, IChemObjectBuilder)">
/// </seealso>
/// <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(IChemObjectBuilder builder)
{
return getInstance("structgen_atomtypes.xml", builder);
}
/// <summary>
/// Creates a new instance
/// </summary>
public AromaticAtom(IChemObjectBuilder builder)
: base(builder)
{
IsAromatic = true;
}
/// <summary>
/// Initiate the MolecularFormulaGenerator.
/// </summary>
/// <param name="minMass">Lower boundary of the target mass range</param>
/// <param name="maxMass">Upper boundary of the target mass range</param>
/// <param name="mfRange">A range of elemental compositions defining the search space</param>
/// <exception cref="ArgumentOutOfRangeException">In case some of the isotopes in mfRange has undefined exact mass or in case illegal parameters are provided (e.g., negative mass values or empty MolecularFormulaRange)</exception>
/// <seealso cref="MolecularFormulaRange"/>
public FullEnumerationFormulaGenerator(IChemObjectBuilder builder,
double minMass, double maxMass,
MolecularFormulaRange mfRange)
{
Trace.TraceInformation("Initiate MolecularFormulaGenerator, mass range " + minMass + "-" + maxMass);
// Check parameter values
if (minMass < 0.0)
{
throw (new ArgumentOutOfRangeException(nameof(minMass), "The minimum and maximum mass values must be >=0"));
}
if (maxMass < 0.0)
{
throw (new ArgumentOutOfRangeException(nameof(maxMass), "The minimum and maximum mass values must be >=0"));
}
if ((minMass > maxMass))
{
throw (new ArgumentException("Minimum mass must be <= maximum mass"));
}
if ((mfRange == null) || (mfRange.GetIsotopes().Count() == 0))
{
throw (new ArgumentException("The MolecularFormulaRange parameter must be non-null and must contain at least one isotope"));
}
// Save the parameters
this.builder = builder;
this.minMass = minMass;
this.maxMass = maxMass;
// Sort the elements by mass in ascending order. That speeds up
// the search.
var isotopesSet = new SortedSet <IIsotope>(
new IIsotopeSorterByMass());
foreach (IIsotope isotope in mfRange.GetIsotopes())
{
// Check if exact mass of each isotope is set
if (isotope.ExactMass == null)
{
throw new ArgumentException($"The exact mass value of isotope {isotope} is not set");
}
isotopesSet.Add(isotope);
}
isotopes = isotopesSet.ToArray();
// Save the element counts from the provided MolecularFormulaRange
minCounts = new int[isotopes.Length];
maxCounts = new int[isotopes.Length];
for (int i = 0; i < isotopes.Length; i++)
{
minCounts[i] = mfRange.GetIsotopeCountMin(isotopes[i]);
maxCounts[i] = mfRange.GetIsotopeCountMax(isotopes[i]);
// Update the maximum count according to the mass limit
int maxCountAccordingToMass = (int)Math.Floor(maxMass
/ isotopes[i].ExactMass.Value);
if (maxCounts[i] > maxCountAccordingToMass)
{
maxCounts[i] = maxCountAccordingToMass;
}
}
// Set the current counters to minimal values, initially
currentCounts = Arrays.CopyOf(minCounts, minCounts.Length);
}
private IReaction ReadReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.NewReaction();
ReadLine(); // first line should be $RXN
ReadLine(); // second line
ReadLine(); // third line
ReadLine(); // fourth line
int reactantCount = 0;
int productCount = 0;
bool foundCOUNTS = false;
while (!foundCOUNTS)
{
string command = ReadCommand();
if (command.StartsWith("COUNTS", StringComparison.Ordinal))
{
var tokenizer = Strings.Tokenize(command);
try
{
reactantCount = int.Parse(tokenizer[1], NumberFormatInfo.InvariantInfo);
Trace.TraceInformation($"Expecting {reactantCount} reactants in file");
productCount = int.Parse(tokenizer[2], NumberFormatInfo.InvariantInfo);
Trace.TraceInformation($"Expecting {productCount } products in file");
}
catch (Exception exception)
{
Debug.WriteLine(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
foundCOUNTS = true;
}
else
{
Trace.TraceWarning("Waiting for COUNTS line, but found: " + command);
}
}
// now read the reactants
for (int i = 1; i <= reactantCount; i++)
{
var molFile = new StringBuilder();
string announceMDLFileLine = ReadCommand();
if (!string.Equals(announceMDLFileLine, "BEGIN REACTANT", StringComparison.Ordinal))
{
string error = "Excepted start of reactant, but found: " + announceMDLFileLine;
Trace.TraceError(error);
throw new CDKException(error);
}
string molFileLine = "";
while (!molFileLine.EndsWith("END REACTANT", StringComparison.Ordinal))
{
molFileLine = ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
}
;
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(molFile.ToString()), base.ReaderMode);
IAtomContainer reactant = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add reactant
reaction.Reactants.Add(reactant);
}
catch (Exception exception)
{
if (!(exception is ArgumentException ||
exception is CDKException ||
exception is IOException))
{
throw;
}
string error = "Error while reading reactant: " + exception.Message;
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
}
// now read the products
for (int i = 1; i <= productCount; i++)
{
var molFile = new StringBuilder();
string announceMDLFileLine = ReadCommand();
if (!string.Equals(announceMDLFileLine, "BEGIN PRODUCT", StringComparison.Ordinal))
{
string error = "Excepted start of product, but found: " + announceMDLFileLine;
Trace.TraceError(error);
throw new CDKException(error);
}
string molFileLine = "";
while (!molFileLine.EndsWith("END PRODUCT", StringComparison.Ordinal))
{
molFileLine = ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
}
;
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(molFile.ToString()));
IAtomContainer product = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add product
reaction.Products.Add(product);
}
catch (Exception exception)
{
if (!(exception is ArgumentException ||
exception is CDKException ||
exception is IOException))
{
throw;
}
string error = "Error while reading product: " + exception.Message;
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
}
return(reaction);
}
/// <summary> Private constructor for the AtomTypeFactory singleton.
///
/// </summary>
/// <exception cref="IOException"> Thrown if something goes wrong with reading the config
/// </exception>
/// <exception cref="ClassNotFoundException"> Thrown if a class was not found :-)
/// </exception>
private AtomTypeFactory(System.IO.Stream ins, System.String format, IChemObjectBuilder builder)
{
//if (//logger == null)
//{
// //logger = new LoggingTool(this);
//}
atomTypes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(100));
readConfiguration(ins, format, builder);
}
/// <summary>
/// Creates a new instance.
/// </summary>
/// <param name="atomicNumber"></param>
public AtomicNumberAtom(int atomicNumber, IChemObjectBuilder builder)
: base(builder)
{
this.AtomicNumber = atomicNumber;
}
/// <summary>
/// Constructs a new EnumerablePCCompoundXLReader that can read Molecule from a given Stream and IChemObjectBuilder.
/// </summary>
/// <param name="ins">The input stream</param>
/// <param name="builder">The builder</param>
/// <exception cref="Exception">if there is a problem creating a <see cref="StreamReader"/></exception>
public EnumerablePCCompoundXMLReader(Stream ins, IChemObjectBuilder builder)
: this(new StreamReader(ins), builder)
{
}
/// <summary> Read a Reaction from a file in MDL RXN format
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IReaction readReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.newReaction();
try
{
input.ReadLine(); // first line should be $RXN
input.ReadLine(); // second line
input.ReadLine(); // third line
input.ReadLine(); // fourth line
}
catch (System.IO.IOException exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try
{
System.String countsLine = input.ReadLine();
/* this line contains the number of reactants
and products */
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(countsLine);
reactantCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + reactantCount + " reactants in file");
productCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + productCount + " products in file");
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try
{
for (int i = 1; i <= reactantCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
input.ReadLine(); // announceMDLFileLine
System.String molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}
while (!molFileLine.Equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
}
catch (CDKException exception)
{
// rethrow exception from MDLReader
throw exception;
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try
{
for (int i = 1; i <= productCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
input.ReadLine(); // String announceMDLFileLine =
System.String molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}
while (!molFileLine.Equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
IMolecule product = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
}
catch (CDKException exception)
{
// rethrow exception from MDLReader
throw exception;
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
//logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
IMolecule[] molecules = reaction.Reactants.Molecules;
for (int i = 0; i < molecules.Length; i++)
{
reactingSide.add(molecules[i]);
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.Products.Molecules;
for (int i = 0; i < molecules.Length; i++)
{
producedSide.add(molecules[i]);
}
// map the atoms
int mappingCount = 0;
IAtom[] reactantAtoms = reactingSide.Atoms;
IAtom[] producedAtoms = producedSide.Atoms;
for (int i = 0; i < reactantAtoms.Length; i++)
{
for (int j = 0; j < producedAtoms.Length; j++)
{
if (reactantAtoms[i].ID != null && reactantAtoms[i].ID.Equals(producedAtoms[j].ID))
{
reaction.addMapping(builder.newMapping(reactantAtoms[i], producedAtoms[j]));
mappingCount++;
break;
}
}
}
//logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
/// <summary>
/// Build fingerprint
/// </summary>
/// <param name="mol"></param>
public static BitSetFingerprint BuildBitSetFingerprint(
IAtomContainer mol,
FingerprintType fpType,
int fpSubtype = -1,
int fpLen = -1)
{
// Data for Tanimoto similarity using various fingerprint types for CorpId 123456 query.
// Cart - Standard MDL Oracle Cartridge scores
//
// Similarity Score
// ------------------------------------------------
// Size -> 192 896 1024 1024 128 1024 320
// CorpId Cart MACCS PbChm ECFP4 EXT EState Basic Sbstr
// ------ ---- ---- ---- ---- ---- ---- ---- ----
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.95 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.94 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.91 1.00 0.81 1.00 1.00 1.00 1.00
// 123456 0.98 0.95 1.00 0.74 0.92 1.00 0.93 0.94
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 0.83 0.76 0.77 0.90 0.76 0.94
// LSH Bin Count - The number of LSH bins (of 25) that match the query bin values
//--------------
// CorpId MAC PbC ECFP EX
// ------ --- --- --- ---
// 123456 25 25 25 25
// 123456 25 20 7 16
// 123456 25 20 9 19
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 20 25 9 25
// 123456 21 25 11 17
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 25 9 6 11
// Data for Tanimoto similarity using various Circular fingerprint types.
// Using 2 molecules where the 2nd just has an added methyl group.
//
// Measure Score
// -------- -----
// ECFP0 1.00
// ECFP2 .88
// ECFP4 .75
// ECFP6 .64
// FCFP0 1.00
// FCFP2 .92
// FCFP4 .84
// FCFP6 .74
IFingerprinter ifptr = null;
IBitFingerprint ibfp = null;
BitSetFingerprint bfp = null;
BitSet bs;
IAtomContainer mol2;
string s = "";
DateTime t0 = DateTime.Now;
double getFptrTime = 0, buildFpTime = 0;
if (fpType == FingerprintType.Basic) // size = 1024
{
ifptr = new Fingerprinter();
}
else if (fpType == FingerprintType.Circular) // size variable
{
int cfpClass = fpSubtype;
if (cfpClass < CircularFingerprinter.CLASS_ECFP0 || cfpClass > CircularFingerprinter.CLASS_ECFP6)
{
cfpClass = CircularFingerprintType.DefaultCircularClass; // default class
}
if (fpLen < 0)
{
fpLen = CircularFingerprintType.DefaultCircularLength; // default length
}
ifptr = new CircularFingerprinter(cfpClass, fpLen);
//CircularFingerprinter cfp = (CircularFingerprinter)ifptr;
//ICountFingerprint cntFp = cfp.getCountFingerprint(mol); // debug
//s = CircularFpToString(cfp); // debug
}
else if (fpType == FingerprintType.Extended) // size = 1024
{
ifptr = new ExtendedFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.EState) // size = 128
{
ifptr = new EStateFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.MACCS) // size = 192
{
if (MACCSFp == null)
{
MACCSFp = new MACCSFingerprinter();
}
ifptr = MACCSFp;
}
else if (fpType == FingerprintType.PubChem) // size = 896
{
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
ifptr = new PubchemFingerprinter(builder);
}
else if (fpType == FingerprintType.ShortestPath) // size =
{
ifptr = new ShortestPathFingerprinter(); // fails with atom type issue for many structures (e.g. 123456)
}
else if (fpType == FingerprintType.Signature) // size =
{
ifptr = new SignatureFingerprinter(); // can't convert array fingerprint to bitsetfingerprint
}
else if (fpType == FingerprintType.Substructure) // size = 320
{
ifptr = new SubstructureFingerprinter();
}
else
{
throw new Exception("Invalid CdkFingerprintType: " + fpType);
}
getFptrTime = TimeOfDay.Delta(ref t0);
ibfp = ifptr.getBitFingerprint(mol);
bfp = (BitSetFingerprint)ibfp;
buildFpTime = TimeOfDay.Delta(ref t0);
//long size = bfp.size();
//int card = bfp.cardinality();
return(bfp);
}
public virtual IMolecule readMolecule(IChemObjectBuilder builder)
{
return builder.newMolecule(readConnectionTable(builder));
}
public TotalHCountAtom(int totalHCount, IChemObjectBuilder builder)
: base(builder)
{
this.totalHCount = totalHCount;
}
/// <summary> Reads a text based configuration file.
///
/// </summary>
/// <param name="builder">IChemObjectBuilder used to construct the IAtomType's.
/// </param>
/// <throws> IOException when a problem occured with reading from the InputStream </throws>
/// <returns> A Vector with read IAtomType's.
/// </returns>
public virtual System.Collections.ArrayList readAtomTypes(IChemObjectBuilder builder)
{
System.Collections.ArrayList atomTypes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
if (ins == null)
{
// trying the default
//System.out.println("readAtomTypes getResourceAsStream:"
// + configFile);
//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'"
ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + configFile);
}
if (ins == null)
throw new System.IO.IOException("There was a problem getting the default stream: " + configFile);
// read the contents from file
//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'"
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
System.IO.StreamReader reader = new System.IO.StreamReader(new System.IO.StreamReader(ins, System.Text.Encoding.Default).BaseStream, new System.IO.StreamReader(ins, System.Text.Encoding.Default).CurrentEncoding, false, 1024);
SupportClass.Tokenizer tokenizer;
System.String string_Renamed;
while (true)
{
string_Renamed = reader.ReadLine();
if (string_Renamed == null)
{
break;
}
if (!string_Renamed.StartsWith("#"))
{
System.String name = "";
System.String rootType = "";
int atomicNumber = 0, colorR = 0, colorG = 0, colorB = 0;
double mass = 0.0, vdwaals = 0.0, covalent = 0.0;
tokenizer = new SupportClass.Tokenizer(string_Renamed, "\t ,;");
int tokenCount = tokenizer.Count;
if (tokenCount == 9)
{
name = tokenizer.NextToken();
rootType = tokenizer.NextToken();
System.String san = tokenizer.NextToken();
System.String sam = tokenizer.NextToken();
System.String svdwaals = tokenizer.NextToken();
System.String scovalent = tokenizer.NextToken();
System.String sColorR = tokenizer.NextToken();
System.String sColorG = tokenizer.NextToken();
System.String sColorB = tokenizer.NextToken();
try
{
//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'"
mass = System.Double.Parse(sam);
//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'"
vdwaals = System.Double.Parse(svdwaals);
//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'"
covalent = System.Double.Parse(scovalent);
atomicNumber = System.Int32.Parse(san);
colorR = System.Int32.Parse(sColorR);
colorG = System.Int32.Parse(sColorG);
colorB = System.Int32.Parse(sColorB);
}
catch (System.FormatException nfe)
{
throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Malformed Number");
}
IAtomType atomType = builder.newAtomType(name, rootType);
atomType.AtomicNumber = atomicNumber;
atomType.setExactMass(mass);
atomType.VanderwaalsRadius = vdwaals;
atomType.CovalentRadius = covalent;
System.Drawing.Color color = System.Drawing.Color.FromArgb(colorR, colorG, colorB);
atomType.setProperty("org.openscience.cdk.renderer.color", color);
atomTypes.Add(atomType);
}
else
{
throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Wrong Number of fields");
}
}
} // end while
ins.Close();
return atomTypes;
}
/// <summary>
/// Constructs an empty query bond.
/// </summary>
public QueryBond(IChemObjectBuilder builder)
{
this.builder = builder;
}
/// <summary>
/// Constructs a query bond with a single query bond order..
/// </summary>
/// <param name="atom1">the first Atom in the query bond</param>
/// <param name="atom2">the second Atom in the query bond</param>
/// <param name="order"></param>
/// <param name="builder"></param>
public QueryBond(IAtom atom1, IAtom atom2, BondOrder order, IChemObjectBuilder builder)
: base(atom1, atom2, order)
{
this.builder = builder;
}
/// <summary>
/// Constructs a multi-center query bond, with undefined order and no stereo information.
/// </summary>
/// <param name="atoms">An array of IAtom containing the atoms constituting the query bond</param>
public QueryBond(IAtom[] atoms, IChemObjectBuilder builder)
{
this.builder = builder;
SetAtoms(atoms);
}
//private LoggingTool //logger;
/// <summary> Private constructor for the IsotopeFactory object.
///
/// </summary>
/// <exception cref="IOException"> A problem with reading the isotopes.xml
/// file
/// </exception>
/// <exception cref="OptionalDataException"> Unexpected data appeared in the isotope
/// ObjectInputStream
/// </exception>
/// <exception cref="ClassNotFoundException"> A problem instantiating the isotopes
/// </exception>
private IsotopeFactory(IChemObjectBuilder builder)
{
//logger = new LoggingTool(this);
//logger.info("Creating new IsotopeFactory");
System.IO.Stream ins = null;
// ObjIn in = null;
System.String errorMessage = "There was a problem getting org.openscience.cdk." + "config.isotopes.xml as a stream";
try
{
System.String configFile = "isotopes.xml";
//if (debug)
//logger.debug("Getting stream for ", configFile);
//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'"
ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + configFile);
//this.GetType().getClassLoader().getResourceAsStream(configFile);
}
catch (System.Exception exception)
{
//logger.error(errorMessage);
//logger.debug(exception);
throw new System.IO.IOException(errorMessage);
}
if (ins == null)
{
//logger.error(errorMessage);
throw new System.IO.IOException(errorMessage);
}
IsotopeReader reader = new IsotopeReader(ins, builder);
//in = new ObjIn(ins, new Config().aliasID(false));
//isotopes = (Vector) in.readObject();
isotopes = reader.readIsotopes();
//if (debug)
//logger.debug("Found #isotopes in file: ", isotopes.Count);
/* for (int f = 0; f < isotopes.size(); f++) {
Isotope isotope = (Isotope)isotopes.elementAt(f);
} What's this loop for?? */
majorIsotopes = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
/// <summary>
/// Constructs a multi-center query bond, with a specified order and no stereo information.
/// </summary>
/// <param name="atoms">An array of IAtom containing the atoms constituting the query bond</param>
/// <param name="order">The order of the query bond</param>
public QueryBond(IAtom[] atoms, BondOrder order, IChemObjectBuilder builder)
{
this.builder = builder;
SetAtoms(atoms);
this.order = order;
}
public Convertor(IChemObjectBuilder builder)
{
this.builder = builder;
}
/// <summary>
/// Constructs a query bond with a given order and stereo orientation from an array of atoms.
/// </summary>
/// <param name="atom1">the first Atom in the query bond</param>
/// <param name="atom2">the second Atom in the query bond</param>
/// <param name="order">the query bond order</param>
/// <param name="stereo">a descriptor the stereochemical orientation of this query bond</param>
public QueryBond(IAtom atom1, IAtom atom2, BondOrder order, BondStereo stereo, IChemObjectBuilder builder)
{
this.builder = builder;
SetAtoms(new[] { atom1, atom2 });
this.order = order;
this.stereo = stereo;
}
/// <summary> Constructs a new AtomTypeHandler and will create IAtomType
/// implementations using the given IChemObjectBuilder.
///
/// </summary>
/// <param name="build">The IChemObjectBuilder used to create the IAtomType's.
/// </param>
public AtomTypeHandler(IChemObjectBuilder build)
{
//logger = new LoggingTool(this);
builder = build;
}
private IReaction readReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.newReaction();
readLine(); // first line should be $RXN
readLine(); // second line
readLine(); // third line
readLine(); // fourth line
int reactantCount = 0;
int productCount = 0;
bool foundCOUNTS = false;
while (Ready && !foundCOUNTS)
{
System.String command = readCommand();
if (command.StartsWith("COUNTS"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
try
{
tokenizer.NextToken();
reactantCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + reactantCount + " reactants in file");
productCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + productCount + " products in file");
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
foundCOUNTS = true;
}
else
{
//logger.warn("Waiting for COUNTS line, but found: " + command);
}
}
// now read the reactants
for (int i = 1; i <= reactantCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
System.String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.Equals("BEGIN REACTANT"))
{
System.String error = "Excepted start of reactant, but found: " + announceMDLFileLine;
//logger.error(error);
throw new CDKException(error);
}
System.String molFileLine = "";
while (!molFileLine.EndsWith("END REACTANT"))
{
molFileLine = readLine();
molFile.Append(molFileLine);
molFile.Append("\n");
};
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
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 reading reactant: " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
// now read the products
for (int i = 1; i <= productCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
System.String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.Equals("BEGIN PRODUCT"))
{
System.String error = "Excepted start of product, but found: " + announceMDLFileLine;
//logger.error(error);
throw new CDKException(error);
}
System.String molFileLine = "";
while (!molFileLine.EndsWith("END PRODUCT"))
{
molFileLine = readLine();
molFile.Append(molFileLine);
molFile.Append("\n");
};
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
IMolecule product = (IMolecule)reader.read(builder.newMolecule());
// add product
reaction.addProduct(product);
}
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 reading product: " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
return reaction;
}