public void TestReactionCustomization()
{
var writer = new StringWriter();
var reaction = builder.NewReaction();
reaction.Id = "reaction1";
IAtomContainer reactant = reaction.Builder.NewAtomContainer();
reactant.Id = "react";
IAtomContainer product = reaction.Builder.NewAtomContainer();
product.Id = "product";
IAtomContainer agent = reaction.Builder.NewAtomContainer();
agent.Id = "agent";
reaction.Reactants.Add(reactant);
reaction.Products.Add(product);
reaction.Agents.Add(agent);
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(reaction);
cmlWriter.Close();
string cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"reaction1") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"react") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"product") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"agent") != -1);
}
public void TestNewReaction()
{
IChemObjectBuilder builder = RootObject.Builder;
IReaction reaction = builder.NewReaction();
Assert.IsNotNull(reaction);
}
public void SetUp()
{
molecule1 = builder.NewAtomContainer();
atomInMol1 = builder.NewAtom("Cl");
molecule1.Atoms.Add(atomInMol1);
molecule1.Atoms.Add(builder.NewAtom("Cl"));
bondInMol1 = builder.NewBond(atomInMol1, molecule1.Atoms[1]);
molecule1.Bonds.Add(bondInMol1);
molecule2 = builder.NewAtomContainer();
atomInMol2 = builder.NewAtom("O");
atomInMol2.ImplicitHydrogenCount = 2;
molecule2.Atoms.Add(atomInMol2);
moleculeSet = builder.NewChemObjectSet <IAtomContainer>();
moleculeSet.Add(molecule1);
moleculeSet.Add(molecule2);
reaction = builder.NewReaction();
reaction.Reactants.Add(molecule1);
reaction.Products.Add(molecule2);
reactionSet = builder.NewReactionSet();
reactionSet.Add(reaction);
chemModel = builder.NewChemModel();
chemModel.MoleculeSet = moleculeSet;
chemModel.ReactionSet = reactionSet;
chemSequence1 = builder.NewChemSequence();
chemSequence1.Add(chemModel);
chemSequence2 = builder.NewChemSequence();
chemFile = builder.NewChemFile();
chemFile.Add(chemSequence1);
chemFile.Add(chemSequence2);
}
public void TestGetBondLengthAverageIReaction()
{
var atom1 = builder.NewAtom("C");
atom1.Point2D = Vector2.Zero;
var atom2 = builder.NewAtom("C");
atom2.Point2D = new Vector2(1, 0);
var acont = builder.NewAtomContainer();
var reaction = builder.NewReaction();
reaction.Reactants.Add(acont);
acont.Atoms.Add(atom1);
acont.Atoms.Add(atom2);
acont.AddBond(acont.Atoms[0], acont.Atoms[1], BondOrder.Single);
Assert.AreEqual(1.0, GeometryUtil.GetBondLengthAverage(reaction), 0.0);
}
public void TestReadReactions1()
{
string filename1 = "NCDK.Data.MDL.reaction-1.rxn";
Trace.TraceInformation("Testing: " + filename1);
var ins1 = ResourceLoader.GetAsStream(filename1);
MDLRXNReader reader1 = new MDLRXNReader(ins1);
IReaction reaction1 = builder.NewReaction();
reaction1 = (IReaction)reader1.Read(reaction1);
reader1.Close();
Assert.IsNotNull(reaction1);
Assert.AreEqual(2, reaction1.Reactants.Count);
Assert.AreEqual(1, reaction1.Products.Count);
var educts = reaction1.Reactants;
// Check Atom symbols of first educt
string[] atomSymbolsOfEduct1 = { "C", "C", "O", "Cl" };
for (int i = 0; i < educts[0].Atoms.Count; i++)
{
Assert.AreEqual(atomSymbolsOfEduct1[i], educts[0].Atoms[i].Symbol);
}
// Check Atom symbols of second educt
for (int i = 0; i < educts[1].Atoms.Count; i++)
{
Assert.AreEqual("C", educts[1].Atoms[i].Symbol);
}
// Check Atom symbols of first product
var products = reaction1.Products;
string[] atomSymbolsOfProduct1 = { "C", "C", "C", "C", "C", "C", "C", "O", "C" };
for (int i = 0; i < products[0].Atoms.Count; i++)
{
Assert.AreEqual(atomSymbolsOfProduct1[i], products[0].Atoms[i].Symbol);
}
}
public void TestAddReaction_IReaction_int()
{
ReactionChain chain = new ReactionChain();
IReaction reaction1 = builder.NewReaction();
reaction1.Id = "reaction1";
IReaction reaction2 = builder.NewReaction();
reaction1.Id = "reaction2";
IReaction reaction3 = builder.NewReaction();
reaction1.Id = "reaction3";
chain.Add(reaction1, 0);
chain.Add(reaction2, 1);
chain.Add(reaction3, 2);
Assert.IsNotNull(chain);
}
public void TestIsEmpty_ReactionSet()
{
var model = (IChemModel)NewChemObject();
IChemObjectBuilder builder = model.Builder;
IAtomContainer molecule = builder.NewAtomContainer();
IReaction reaction = builder.NewReaction();
reaction.Reactants.Add(molecule);
IReactionSet set = builder.NewReactionSet();
model.ReactionSet = set;
Assert.IsTrue(model.IsEmpty(), "model has an empty reaction set and should be empty");
set.Add(reaction);
Assert.IsFalse(model.IsEmpty(), "model has a reaction set and should not be empty");
model.ReactionSet = null;
Assert.IsTrue(model.IsEmpty(), "model has no reaction set");
}
public void TestBug1851202()
{
string filename1 = "NCDK.Data.MDL.0002.stg01.rxn";
Trace.TraceInformation("Testing: " + filename1);
var ins1 = ResourceLoader.GetAsStream(filename1);
MDLRXNV2000Reader reader = new MDLRXNV2000Reader(ins1, ChemObjectReaderMode.Strict);
IReaction reaction = (IReaction)reader.Read(builder.NewReaction());
Assert.IsNotNull(reaction);
IAtomContainer reactant = reaction.Reactants[0];
IAtomContainer product = reaction.Products[0];
Fingerprinter fingerprinter = new Fingerprinter(64 * 26, 8);
Assert.IsNotNull(fingerprinter.GetBitFingerprint(reactant));
Assert.IsNotNull(fingerprinter.GetBitFingerprint(product));
}
public void TestRoundtrip()
{
IReaction reaction = builder.NewReaction();
IAtomContainer hydroxide = builder.NewAtomContainer();
hydroxide.Atoms.Add(builder.NewAtom("O"));
reaction.Reactants.Add(hydroxide);
IAtomContainer proton = builder.NewAtomContainer();
proton.Atoms.Add(builder.NewAtom("H"));
reaction.Reactants.Add(proton);
IAtomContainer water = builder.NewAtomContainer();
water.Atoms.Add(builder.NewAtom("O"));
reaction.Products.Add(water);
reaction.Mappings.Add(new Mapping(hydroxide.Atoms[0], water.Atoms[0]));
// now serialize to MDL RXN
StringWriter writer = new StringWriter();
string file = "";
MDLRXNWriter mdlWriter = new MDLRXNWriter(writer);
mdlWriter.Write(reaction);
mdlWriter.Close();
file = writer.ToString();
Assert.IsTrue(file.Length > 0);
// now deserialize the MDL RXN output
IReaction reaction2 = builder.NewReaction();
MDLRXNReader reader = new MDLRXNReader(new StringReader(file));
reaction2 = (IReaction)reader.Read(reaction2);
reader.Close();
Assert.AreEqual(2, reaction2.Reactants.Count);
Assert.AreEqual(1, reaction2.Products.Count);
Assert.AreEqual(1, reaction2.Mappings.Count);
}
/// <summary>
/// Parse a reaction SMILES.
/// </summary>
/// <param name="smiles">The SMILES string to parse</param>
/// <returns>An instance of <see cref="IReaction"/></returns>
/// <exception cref="InvalidSmilesException">if the string cannot be parsed</exception>
/// <seealso cref="ParseSmiles(string)"/>
public IReaction ParseReactionSmiles(string smiles)
{
if (!smiles.Contains(">"))
{
throw new InvalidSmilesException("Not a reaction SMILES: " + smiles);
}
var first = smiles.IndexOf('>');
var second = smiles.IndexOf('>', first + 1);
if (second < 0)
{
throw new InvalidSmilesException("Invalid reaction SMILES:" + smiles);
}
var reactants = smiles.Substring(0, first);
var agents = smiles.Substring(first + 1, second - (first + 1));
var products = smiles.Substring(second + 1, smiles.Length - (second + 1));
var reaction = builder.NewReaction();
// add reactants
if (!(reactants.Count() == 0))
{
var reactantContainer = ParseSmiles(reactants, true);
var reactantSet = ConnectivityChecker.PartitionIntoMolecules(reactantContainer);
foreach (var reactant in reactantSet)
{
reaction.Reactants.Add(reactant);
}
}
// add agents
if (!(agents.Count() == 0))
{
var agentContainer = ParseSmiles(agents, true);
var agentSet = ConnectivityChecker.PartitionIntoMolecules(agentContainer);
foreach (var agent in agentSet)
{
reaction.Agents.Add(agent);
}
}
string title = null;
// add products
if (!(products.Count() == 0))
{
var productContainer = ParseSmiles(products, true);
var productSet = ConnectivityChecker.PartitionIntoMolecules(productContainer);
foreach (var product in productSet)
{
reaction.Products.Add(product);
}
reaction.SetProperty(CDKPropertyName.Title, title = productContainer.Title);
}
try
{
//CXSMILES layer
ParseRxnCXSMILES(title, reaction);
}
catch (Exception e)
{
//e.StackTrace
throw new InvalidSmilesException("Error parsing CXSMILES:" + e.Message);
}
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 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);
}
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>
/// 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);
}
public void TestGetAllMolecules_IReactionSet()
{
IReactionSet reactionSet = builder.NewReactionSet();
reactionSet.Add(builder.NewReaction()); // 1
reactionSet.Add(builder.NewReaction()); // 2
Assert.AreEqual(0, ReactionSetManipulator.GetAllMolecules(reactionSet).Count);
}
protected static IChemObject[] AcceptableChemObjects()
{
return(new IChemObject[] { builder.NewChemFile(), builder.NewChemModel(), builder.NewAtomContainer(), builder.NewReaction(), new RGroupQuery() });
}
public void TestGetAllMolecules_IReactionScheme()
{
IReactionScheme reactionScheme = builder.NewReactionScheme();
IReaction reaction1 = builder.NewReaction();
reaction1.Products.Add(builder.NewAtomContainer());
IReaction reaction2 = builder.NewReaction();
reaction2.Products.Add(builder.NewAtomContainer());
reactionScheme.Add(reaction1); // 1
reactionScheme.Add(reaction2); // 2
Assert.AreEqual(2, ReactionSchemeManipulator.GetAllAtomContainers(reactionScheme).Count);
}