public static void removeElectronContainer(IChemModel chemModel, IElectronContainer electrons)
{
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
if (crystal.contains(electrons))
{
crystal.removeElectronContainer(electrons);
}
return;
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
SetOfMoleculesManipulator.removeElectronContainer(moleculeSet, electrons);
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
SetOfReactionsManipulator.removeElectronContainer(reactionSet, electrons);
}
}
public static void RemoveElectronContainer(IReaction reaction, IElectronContainer electrons)
{
var reactants = reaction.Reactants;
for (int i = 0; i < reactants.Count; i++)
{
IAtomContainer mol = reactants[i];
if (mol.Contains(electrons))
{
mol.Remove(electrons);
}
}
var agents = reaction.Reactants;
for (int i = 0; i < agents.Count; i++)
{
var mol = agents[i];
if (mol.Contains(electrons))
{
mol.Remove(electrons);
}
}
var products = reaction.Products;
for (int i = 0; i < products.Count; i++)
{
var mol = products[i];
if (mol.Contains(electrons))
{
mol.Remove(electrons);
}
}
}
/// <summary> Partitions the atoms in an AtomContainer into covalently connected components.
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be partitioned into connected components, i.e. molecules
/// </param>
/// <returns> A SetOfMolecules.
///
/// </returns>
/// <cdk.dictref> blue-obelisk:graphPartitioning </cdk.dictref>
public static ISetOfMolecules partitionIntoMolecules(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IElectronContainer eContainer = null;
IMolecule molecule = null;
ISetOfMolecules molecules = atomContainer.Builder.newSetOfMolecules();
System.Collections.ArrayList sphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
atom.setFlag(CDKConstants.VISITED, false);
ac.addAtom(atom);
}
IElectronContainer[] eContainers = atomContainer.ElectronContainers;
for (int f = 0; f < eContainers.Length; f++)
{
eContainer = eContainers[f];
eContainer.setFlag(CDKConstants.VISITED, false);
ac.addElectronContainer(eContainer);
}
while (ac.AtomCount > 0)
{
atom = ac.getAtomAt(0);
molecule = atomContainer.Builder.newMolecule();
sphere.Clear();
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
molecules.addMolecule(molecule);
ac.remove(molecule);
}
return(molecules);
}
public void TestMatchAgainstItself()
{
var m_atom1 = new Mock <IElectronContainer>(); IElectronContainer atom1 = m_atom1.Object;
string result = ElectronContainerDiff.Diff(atom1, atom1);
AssertZeroLength(result);
}
/// <summary> Returns the adjacency matrix for the given AtomContainer.
///
/// </summary>
/// <param name="container">The AtomContainer for which the matrix is calculated
/// </param>
/// <returns> A adjacency matrix representating this AtomContainer
/// </returns>
public static int[][] getMatrix(IAtomContainer container)
{
IElectronContainer electronContainer = null;
int indexAtom1;
int indexAtom2;
int[][] conMat = new int[container.AtomCount][];
for (int i = 0; i < container.AtomCount; i++)
{
conMat[i] = new int[container.AtomCount];
}
for (int f = 0; f < container.ElectronContainerCount; f++)
{
electronContainer = container.getElectronContainerAt(f);
if (electronContainer is IBond)
{
IBond bond = (IBond)electronContainer;
indexAtom1 = container.getAtomNumber(bond.getAtomAt(0));
indexAtom2 = container.getAtomNumber(bond.getAtomAt(1));
conMat[indexAtom1][indexAtom2] = 1;
conMat[indexAtom2][indexAtom1] = 1;
}
}
return(conMat);
}
public virtual void TestSetElectronCount_Integer()
{
IElectronContainer ec = (IElectronContainer)NewChemObject();
ec.ElectronCount = 3;
Assert.AreEqual(3, ec.ElectronCount.Value);
}
/// <summary>
/// Remove an ElectronContainer from all AtomContainers
/// inside an IChemModel.
/// </summary>
/// <param name="chemModel">The IChemModel object.</param>
/// <param name="electrons">The ElectronContainer to remove.</param>
public static void RemoveElectronContainer(IChemModel chemModel, IElectronContainer electrons)
{
var crystal = chemModel.Crystal;
if (crystal != null)
{
if (crystal.Contains(electrons))
{
crystal.Remove(electrons);
}
return;
}
var moleculeSet = chemModel.MoleculeSet;
if (moleculeSet != null)
{
MoleculeSetManipulator.RemoveElectronContainer(moleculeSet, electrons);
}
var reactionSet = chemModel.ReactionSet;
if (reactionSet != null)
{
ReactionSetManipulator.RemoveElectronContainer(reactionSet, electrons);
}
}
public void TestNewElectronContainer()
{
IChemObjectBuilder builder = RootObject.Builder;
IElectronContainer container = builder.NewElectronContainer();
Assert.IsNotNull(container);
}
public static void RemoveElectronContainer(IReactionSet set, IElectronContainer electrons)
{
foreach (var reaction in set)
{
ReactionManipulator.RemoveElectronContainer(reaction, electrons);
}
}
/// <summary> Uses precomputed set of ALL rings and performs an aromaticity detection
/// based on Hueckels 4n + 2 rule.
///
/// </summary>
/// <param name="ringSet"> set of ALL rings
/// </param>
/// <param name="removeAromaticityFlags"> Leaves ChemObjects that are already marked as
/// aromatic as they are
/// </param>
/// <param name="atomContainer"> AtomContainer to be searched for rings
/// </param>
/// <returns> True, if molecules contains an
/// aromatic feature
/// </returns>
public static bool detectAromaticity(IAtomContainer atomContainer, IRingSet ringSet, bool removeAromaticityFlags)
{
bool foundSomething = false;
if (removeAromaticityFlags)
{
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atomContainer.getAtomAt(f).setFlag(CDKConstants.ISAROMATIC, false);
}
for (int f = 0; f < atomContainer.ElectronContainerCount; f++)
{
IElectronContainer electronContainer = atomContainer.getElectronContainerAt(f);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
((IRing)ringSet.getAtomContainer(f)).setFlag(CDKConstants.ISAROMATIC, false);
}
}
IRing ring = null;
RingSetManipulator.sort(ringSet);
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
ring = (IRing)ringSet.getAtomContainer(f);
//logger.debug("Testing for aromaticity in ring no ", f);
if (AromaticityCalculator.isAromatic(ring, atomContainer))
{
ring.setFlag(CDKConstants.ISAROMATIC, true);
for (int g = 0; g < ring.AtomCount; g++)
{
ring.getAtomAt(g).setFlag(CDKConstants.ISAROMATIC, true);
}
for (int g = 0; g < ring.ElectronContainerCount; g++)
{
IElectronContainer electronContainer = ring.getElectronContainerAt(g);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, true);
}
}
foundSomething = true;
//logger.debug("This ring is aromatic: ", f);
}
else
{
//logger.debug("This ring is *not* aromatic: ", f);
}
}
return(foundSomething);
}
private void SerializeElectronContainerFields(INode rdfBond, IElectronContainer bond)
{
SerializeChemObjectFields(rdfBond, bond);
if (bond.ElectronCount != null)
{
g.Assert(new Triple(rdfBond, P_HASELECTRONCOUNT, g.CreateLiteralNode(bond.ElectronCount.ToString())));
}
}
public static void removeElectronContainer(ISetOfReactions set_Renamed, IElectronContainer electrons)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.removeElectronContainer(reaction, electrons);
}
}
public static void removeElectronContainer(ISetOfReactions set_Renamed, IElectronContainer electrons)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.removeElectronContainer(reaction, electrons);
}
}
public override void TestSetElectronCount_Integer()
{
IElectronContainer ec = (IElectronContainer)NewChemObject();
ec.ElectronCount = 3;
Assert.AreEqual(2, ec.ElectronCount.Value);
ec.ElectronCount = null;
Assert.AreEqual(2, ec.ElectronCount.Value);
}
private void DeserializeElectronContainerFields(INode rdfObject, IElectronContainer bond)
{
DeserializeChemObjectFields(rdfObject, bond);
var count = g.GetTriplesWithSubjectPredicate(rdfObject, P_HASELECTRONCOUNT).Select(n => n.Object).FirstOrDefault();
if (count != null)
{
bond.ElectronCount = int.Parse(count.ToString(), NumberFormatInfo.InvariantInfo);
}
}
public override void TestClone()
{
IElectronContainer ec = (IElectronContainer)NewChemObject();
ec.ElectronCount = 2;
object clone = ec.Clone();
Assert.IsNotNull(clone);
Assert.IsTrue(clone is IElectronContainer);
}
public virtual void TestToString()
{
IElectronContainer at = (IElectronContainer)NewChemObject();
string description = at.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue(description[i] != '\n');
Assert.IsTrue(description[i] != '\r');
}
}
public void TestDifference()
{
var m_ec1 = new Mock <IElectronContainer>(); IElectronContainer ec1 = m_ec1.Object;
var m_ec2 = new Mock <IElectronContainer>(); IElectronContainer ec2 = m_ec2.Object;
m_ec1.SetupGet(n => n.ElectronCount).Returns(2);
m_ec2.SetupGet(n => n.ElectronCount).Returns(3);
IDifference difference = ElectronContainerDiff.Difference(ec1, ec2);
Assert.IsNotNull(difference);
}
public ValidationReport ValidateElectronContainer(IElectronContainer subject)
{
Trace.TraceInformation($"Validating {nameof(IElectronContainer)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateElectronContainer(subject));
}
// traverse into super class
report.Add(ValidateChemObject(subject));
// traverse into hierarchy
return(report);
}
public void TestDiff()
{
var m_ec1 = new Mock <IElectronContainer>(); IElectronContainer ec1 = m_ec1.Object;
var m_ec2 = new Mock <IElectronContainer>(); IElectronContainer ec2 = m_ec2.Object;
m_ec1.SetupGet(n => n.ElectronCount).Returns(2);
m_ec2.SetupGet(n => n.ElectronCount).Returns(3);
string result = ElectronContainerDiff.Diff(ec1, ec2);
Assert.IsNotNull(result);
Assert.AreNotSame(0, result.Length);
AssertContains(result, "ElectronContainerDiff");
AssertContains(result, "eCount");
AssertContains(result, "2/3");
}
/// <summary> Returns the next bond in order, relative to a given bond and atom.
/// Example: Let the ring be composed of 0-1, 1-2, 2-3 and 3-0. A request getNextBond(1-2, 2)
/// will return Bond 2-3.
///
/// </summary>
/// <param name="bond"> A bond for which an atom from a consecutive bond is sought
/// </param>
/// <param name="atom"> A atom from the bond above to assign a search direction
/// </param>
/// <returns> The next bond in the order given by the above assignment
/// </returns>
public virtual IBond getNextBond(IBond bond, IAtom atom)
{
Bond tempBond;
for (int f = 0; f < ElectronContainerCount; f++)
{
IElectronContainer electronContainer = getElectronContainerAt(f);
if (electronContainer is IBond)
{
tempBond = (Bond)electronContainer;
if (tempBond.contains(atom) && bond != tempBond)
{
return(tempBond);
}
}
}
return(null);
}
public static void removeElectronContainer(IReaction reaction, IElectronContainer electrons)
{
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
IMolecule mol = reactants[i];
if (mol.contains(electrons))
{
mol.removeElectronContainer(electrons);
}
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
IMolecule mol = products[i];
if (mol.contains(electrons))
{
mol.removeElectronContainer(electrons);
}
}
}
public static void removeElectronContainer(ISetOfAtomContainers set_Renamed, IElectronContainer electrons)
{
IAtomContainer[] acs = set_Renamed.AtomContainers;
for (int i = 0; i < acs.Length; i++)
{
IAtomContainer container = acs[i];
if (container.contains(electrons))
{
container.removeElectronContainer(electrons);
IMolecule[] molecules = ConnectivityChecker.partitionIntoMolecules(container).Molecules;
if (molecules.Length > 1)
{
set_Renamed.removeAtomContainer(container);
for (int k = 0; k < molecules.Length; k++)
{
set_Renamed.addAtomContainer(molecules[k]);
}
}
return;
}
}
}
/// <summary>
/// Compare two <see cref="IChemObject"/> classes and return the difference as an <see cref="IDifference"/>.
///
/// <param name="first">the first of the two classes to compare</param>
/// <param name="second">the second of the two classes to compare</param>
/// <returns>an <see cref="IDifference"/> representation of the difference between the first and second <see cref="IChemObject"/>.</returns>
/// </summary>
public static IDifference Difference(IChemObject first, IChemObject second)
{
if (!(first is IElectronContainer && second is IElectronContainer))
{
return(null);
}
IElectronContainer firstEC = (IElectronContainer)first;
IElectronContainer secondEC = (IElectronContainer)second;
IDifferenceList totalDiff = new ChemObjectDifference("ElectronContainerDiff");
totalDiff.AddChild(IntegerDifference.Construct("eCount", firstEC.ElectronCount,
secondEC.ElectronCount));
totalDiff.AddChild(ChemObjectDiff.Difference(first, second));
if (totalDiff.ChildCount() > 0)
{
return(totalDiff);
}
else
{
return(null);
}
}
public static void removeElectronContainer(ISetOfAtomContainers set_Renamed, IElectronContainer electrons)
{
IAtomContainer[] acs = set_Renamed.AtomContainers;
for (int i = 0; i < acs.Length; i++)
{
IAtomContainer container = acs[i];
if (container.contains(electrons))
{
container.removeElectronContainer(electrons);
IMolecule[] molecules = ConnectivityChecker.partitionIntoMolecules(container).Molecules;
if (molecules.Length > 1)
{
set_Renamed.removeAtomContainer(container);
for (int k = 0; k < molecules.Length; k++)
{
set_Renamed.addAtomContainer(molecules[k]);
}
}
return;
}
}
}
public void Remove(IElectronContainer electronContainer)
{
}
public bool Contains(IElectronContainer electronContainer) => false;
public void Add(IElectronContainer electronContainer)
{
throw new InvalidOperationException("not supported");
}
public static void RemoveElectronContainer(IChemObjectSet <IAtomContainer> set, IElectronContainer electrons)
{
foreach (var atomContainer in set)
{
if (atomContainer.Contains(electrons))
{
atomContainer.Remove(electrons);
var molecules = ConnectivityChecker.PartitionIntoMolecules(atomContainer);
if (molecules.Count > 1)
{
set.Remove(atomContainer);
for (int k = 0; k < molecules.Count; k++)
{
set.Add(molecules[k]);
}
}
return;
}
}
}
public static void removeElectronContainer(IReaction reaction, IElectronContainer electrons)
{
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
IMolecule mol = reactants[i];
if (mol.contains(electrons))
{
mol.removeElectronContainer(electrons);
}
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
IMolecule mol = products[i];
if (mol.contains(electrons))
{
mol.removeElectronContainer(electrons);
}
}
}
public static void RemoveElectronContainer(IChemObjectSet <IAtomContainer> set, IElectronContainer electrons)
{
AtomContainerSetManipulator.RemoveElectronContainer(set, electrons);
}
public virtual ValidationReport ValidateElectronContainer(IElectronContainer subject)
{
var report = new ValidationReport();
return(report);
}
public static void removeElectronContainer(ISetOfMolecules set_Renamed, IElectronContainer electrons)
{
SetOfAtomContainersManipulator.removeElectronContainer(set_Renamed, electrons);
}