public void TestNewMapping_IChemObject_IChemObject()
{
IChemObjectBuilder builder = RootObject.Builder;
IMapping mapping = builder.NewMapping(builder.NewChemObject(),
builder.NewChemObject());
Assert.IsNotNull(mapping);
}
/// <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 (IOException exception)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
int agentCount = 0;
try
{
string countsLine = input.ReadLine();
// this line contains the number of reactants and products
var tokenizer = Strings.Tokenize(countsLine).GetEnumerator();
tokenizer.MoveNext();
reactantCount = int.Parse(tokenizer.Current, NumberFormatInfo.InvariantInfo);
Trace.TraceInformation("Expecting " + reactantCount + " reactants in file");
tokenizer.MoveNext();
productCount = int.Parse(tokenizer.Current, NumberFormatInfo.InvariantInfo);
if (tokenizer.MoveNext())
{
agentCount = int.Parse(tokenizer.Current, NumberFormatInfo.InvariantInfo);
// ChemAxon extension, technically BIOVIA now support this but
// not documented yet
if (ReaderMode == ChemObjectReaderMode.Strict && agentCount > 0)
{
throw new CDKException("RXN files uses agent count extension");
}
}
Trace.TraceInformation("Expecting " + productCount + " products in file");
}
catch (Exception exception)
{
if (exception is IOException | exception is FormatException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
throw;
}
// now read the reactants
try
{
for (int i = 1; i <= reactantCount; i++)
{
var molFile = new StringBuilder();
input.ReadLine(); // announceMDLFileLine
string molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
} while (!string.Equals(molFileLine, "M END", StringComparison.Ordinal));
// read MDL molfile content
// Changed this to mdlv2000 reader
MDLV2000Reader reader = new MDLV2000Reader(new StringReader(molFile.ToString()), base.ReaderMode);
IAtomContainer reactant = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add reactant
reaction.Reactants.Add(reactant);
}
}
catch (CDKException)
{
// rethrow exception from MDLReader
throw;
}
catch (Exception exception)
{
if (exception is IOException | exception is ArgumentException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading products", exception);
}
throw;
}
// now read the products
try
{
for (int i = 1; i <= agentCount; i++)
{
var molFile = new StringBuilder();
input.ReadLine(); // String announceMDLFileLine =
string molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
} while (!string.Equals(molFileLine, "M END", StringComparison.Ordinal));
// read MDL molfile content
MDLV2000Reader reader = new MDLV2000Reader(new StringReader(molFile.ToString()));
IAtomContainer product = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add reactant
reaction.Agents.Add(product);
}
}
catch (CDKException)
{
// rethrow exception from MDLReader
throw;
}
catch (Exception exception)
{
if (exception is IOException | exception is ArgumentException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading reactant", exception);
}
throw;
}
// now read the products
try
{
for (int i = 1; i <= productCount; i++)
{
var molFile = new StringBuilder();
input.ReadLine(); // string announceMDLFileLine =
string molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
} while (!string.Equals(molFileLine, "M END", StringComparison.Ordinal));
// read MDL molfile content
MDLV2000Reader reader = new MDLV2000Reader(new StringReader(molFile.ToString()));
IAtomContainer product = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add reactant
reaction.Products.Add(product);
}
}
catch (CDKException)
{
// rethrow exception from MDLReader
throw;
}
catch (Exception exception)
{
if (exception is IOException | exception is ArgumentException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading products", exception);
}
throw;
}
// now try to map things, if wanted
Trace.TraceInformation("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.NewAtomContainer();
foreach (var molecule in reaction.Reactants)
{
reactingSide.Add(molecule);
}
IAtomContainer producedSide = builder.NewAtomContainer();
foreach (var molecule in reaction.Products)
{
producedSide.Add(molecule);
}
// map the atoms
int mappingCount = 0;
// IAtom[] reactantAtoms = reactingSide.GetAtoms();
// IAtom[] producedAtoms = producedSide.GetAtoms();
for (int i = 0; i < reactingSide.Atoms.Count; i++)
{
for (int j = 0; j < producedSide.Atoms.Count; j++)
{
IAtom eductAtom = reactingSide.Atoms[i];
IAtom productAtom = producedSide.Atoms[j];
if (eductAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping) != null &&
eductAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping).Equals(
productAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping)))
{
reaction.Mappings.Add(builder.NewMapping(eductAtom, productAtom));
mappingCount++;
break;
}
}
}
Trace.TraceInformation("Mapped atom pairs: " + mappingCount);
return(reaction);
}
/// <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 $RXN
input.ReadLine(); // second line
input.ReadLine(); // third line
input.ReadLine(); // fourth line
}
catch (IOException exception)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int numReactans = 0;
int numProducts = 0;
int agentCount = 0;
try
{
var countsLine = input.ReadLine();
// this line contains the number of reactants and products
var tokenizer = Strings.Tokenize(countsLine).GetEnumerator();
tokenizer.MoveNext();
numReactans = int.Parse(tokenizer.Current, NumberFormatInfo.InvariantInfo);
Trace.TraceInformation($"Expecting {numReactans} reactants in file");
tokenizer.MoveNext();
numProducts = int.Parse(tokenizer.Current, NumberFormatInfo.InvariantInfo);
if (tokenizer.MoveNext())
{
agentCount = int.Parse(tokenizer.Current, NumberFormatInfo.InvariantInfo);
// ChemAxon extension, technically BIOVIA now support this but
// not documented yet
if (ReaderMode == ChemObjectReaderMode.Strict && agentCount > 0)
{
throw new CDKException("RXN files uses agent count extension");
}
}
Trace.TraceInformation($"Expecting {numProducts} products in file");
}
catch (Exception exception)
{
if (exception is IOException | exception is FormatException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
throw;
}
// now read the molecules
try
{
var line = input.ReadLine();
if (line == null || !line.StartsWith("$MOL", StringComparison.Ordinal))
{
throw new CDKException("Expected $MOL to start, was" + line);
}
var components = new List <IAtomContainer>();
var sb = new StringBuilder();
while ((line = input.ReadLine()) != null)
{
if (line.StartsWith("$MOL", StringComparison.Ordinal))
{
ProcessMol(builder.NewAtomContainer(), components, sb);
sb.Clear();
}
else
{
sb.Append(line).Append('\n');
}
}
// last record
if (sb.Length > 0)
{
ProcessMol(builder.NewAtomContainer(), components, sb);
}
foreach (var component in components.GetRange(0, numReactans))
{
reaction.Reactants.Add(component);
}
foreach (var component in components.GetRange(numReactans, numProducts))
{
reaction.Products.Add(component);
}
foreach (var component in components.GetRange(numReactans + numProducts, components.Count - (numReactans + numProducts)))
{
reaction.Agents.Add(component);
}
}
catch (CDKException)
{
// rethrow exception from MDLReader
throw;
}
catch (Exception exception)
{
if (exception is IOException | exception is ArgumentException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading reactant", exception);
}
throw;
}
// now try to map things, if wanted
Trace.TraceInformation("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
var reactingSide = builder.NewAtomContainer();
foreach (var molecule in reaction.Reactants)
{
reactingSide.Add(molecule);
}
var producedSide = builder.NewAtomContainer();
foreach (var molecule in reaction.Products)
{
producedSide.Add(molecule);
}
// map the atoms
int mappingCount = 0;
for (int i = 0; i < reactingSide.Atoms.Count; i++)
{
for (int j = 0; j < producedSide.Atoms.Count; j++)
{
var eductAtom = reactingSide.Atoms[i];
var productAtom = producedSide.Atoms[j];
if (eductAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping) != null &&
eductAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping).Equals(
productAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping)))
{
reaction.Mappings.Add(builder.NewMapping(eductAtom, productAtom));
mappingCount++;
break;
}
}
}
Trace.TraceInformation("Mapped atom pairs: " + mappingCount);
return(reaction);
}