public override ICDKObject Clone(CDKObjectMap map)
{
var clone = (SingleElectron)base.Clone(map);
clone.atom = (IAtom)atom?.Clone(map);
return(clone);
}
private static IAtomContainer PermuteA(int[] p, IAtomContainer atomContainer)
{
IAtomContainer permutedContainer = null;
permutedContainer = atomContainer.Builder.NewAtomContainer();
foreach (var pp in p)
{
IAtom atom = atomContainer.Atoms[pp];
permutedContainer.Atoms.Add((IAtom)atom.Clone());
}
foreach (var bond in atomContainer.Bonds)
{
IBond clonedBond = (IBond)bond.Clone();
clonedBond.SetAtoms(new IAtom[clonedBond.Atoms.Count]);
int i = 0;
foreach (var atom in bond.Atoms)
{
int index = atomContainer.Atoms.IndexOf(atom);
IAtom permutedAtom = permutedContainer.Atoms[p[index]];
clonedBond.Atoms[i++] = permutedAtom;
}
permutedContainer.Bonds.Add(clonedBond);
}
return(permutedContainer);
}
public override ICDKObject Clone(CDKObjectMap map)
{
var clone = (LonePair)base.Clone(map);
clone.atom = (IAtom)atom?.Clone(map);
return(clone);
}
public virtual void TestCloneFractionalPoint3d()
{
IAtom atom = (IAtom)NewChemObject();
atom.FractionalPoint3D = new Vector3(2, 3, 4);
IAtom clone = (IAtom)atom.Clone();
Assert.AreEqual(clone.FractionalPoint3D.Value.X, 2.0, 0.001);
}
public virtual void TestClonePoint2d()
{
IAtom atom = (IAtom)NewChemObject();
atom.Point2D = new Vector2(2, 3);
IAtom clone = (IAtom)atom.Clone();
Assert.AreEqual(clone.Point2D.Value.X, 2.0, 0.001);
}
public virtual void TestCloneCharge()
{
IAtom atom = (IAtom)NewChemObject();
atom.Charge = 1.0;
IAtom clone = (IAtom)atom.Clone();
// test cloning
atom.Charge = 5.0;
Assert.AreEqual(1.0, clone.Charge.Value, 0.001);
}
public virtual void TestCloneStereoParity()
{
IAtom atom = (IAtom)NewChemObject();
atom.StereoParity = 3;
IAtom clone = (IAtom)atom.Clone();
// test cloning
atom.StereoParity = 4;
Assert.AreEqual(3, clone.StereoParity);
}
public virtual void TestCloneHydrogenCount()
{
IAtom atom = (IAtom)NewChemObject();
atom.ImplicitHydrogenCount = 3;
IAtom clone = (IAtom)atom.Clone();
// test cloning
atom.ImplicitHydrogenCount = 4;
Assert.AreEqual(3, clone.ImplicitHydrogenCount.Value);
}
public override void TestClone()
{
IAtom atom = (IAtom)NewChemObject();
object clone = atom.Clone();
Assert.IsTrue(clone is IAtom);
// test that everything has been cloned properly
string diff = AtomDiff.Diff(atom, (IAtom)clone);
Assert.IsNotNull(diff);
Assert.AreEqual(0, diff.Length);
}
/// <summary> Clones this AtomParity object.
///
/// </summary>
/// <returns> The cloned object
/// </returns>
public override System.Object Clone()
{
AtomParity clone = (AtomParity)base.Clone();
// clone Atom's
clone.centralAtom = (IAtom)centralAtom.Clone();
clone.neighbors = new IAtom[4];
clone.neighbors[0] = (IAtom)(neighbors[0].Clone());
clone.neighbors[1] = (IAtom)(neighbors[1].Clone());
clone.neighbors[2] = (IAtom)(neighbors[2].Clone());
clone.neighbors[3] = (IAtom)(neighbors[3].Clone());
return(clone);
}
public void TestMap_Map_Map()
{
IChemObjectBuilder builder = ChemObjectBuilder.Instance;
IAtom c1 = builder.NewAtom("C");
IAtom o2 = builder.NewAtom("O");
IAtom n3 = builder.NewAtom("N");
IAtom c4 = builder.NewAtom("C");
IAtom h5 = builder.NewAtom("H");
// new stereo element
ITetrahedralChirality original = new TetrahedralChirality(c1, new IAtom[] { o2, n3, c4, h5 }, TetrahedralStereo.Clockwise);
// clone the atoms and place in a map
var mapping = new CDKObjectMap();
IAtom c1clone = (IAtom)c1.Clone();
mapping.Set(c1, c1clone);
IAtom o2clone = (IAtom)o2.Clone();
mapping.Set(o2, o2clone);
IAtom n3clone = (IAtom)n3.Clone();
mapping.Set(n3, n3clone);
IAtom c4clone = (IAtom)c4.Clone();
mapping.Set(c4, c4clone);
IAtom h5clone = (IAtom)h5.Clone();
mapping.Set(h5, h5clone);
// map the existing element a new element
ITetrahedralChirality mapped = (ITetrahedralChirality)original.Clone(mapping);
Assert.AreNotSame(original.ChiralAtom, mapped.ChiralAtom, "mapped chiral atom was the same as the original");
Assert.AreSame(c1clone, mapped.ChiralAtom, "mapped chiral atom was not the clone");
var originalLigands = original.Ligands;
var mappedLigands = mapped.Ligands;
Assert.AreNotSame(originalLigands[0], mappedLigands[0], "first ligand was the same as the original");
Assert.AreSame(o2clone, mappedLigands[0], "first mapped ligand was not the clone");
Assert.AreNotSame(originalLigands[1], mappedLigands[1], "second ligand was the same as the original");
Assert.AreSame(n3clone, mappedLigands[1], "second mapped ligand was not the clone");
Assert.AreNotSame(originalLigands[2], mappedLigands[2], "third ligand was the same as the original");
Assert.AreSame(c4clone, mappedLigands[2], "third mapped ligand was not the clone");
Assert.AreNotSame(originalLigands[3], mappedLigands[3], "forth ligand was te same as the original");
Assert.AreSame(h5clone, mappedLigands[3], "forth mapped ligand was not the clone");
Assert.AreEqual(original.Stereo, mapped.Stereo, "stereo was not mapped");
}
/// <inheritdoc/>
public override ICDKObject Clone(CDKObjectMap map)
{
return(atom.Clone(map));
}
/// <summary> Produces an AtomContainer without explicit Hs but with H count from one with Hs.
/// The new molecule is a deep copy.
///
/// </summary>
/// <param name="atomContainer">The AtomContainer from which to remove the hydrogens
/// </param>
/// <returns> The molecule without Hs.
/// </returns>
/// <cdk.keyword> hydrogen, removal </cdk.keyword>
public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
{
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
System.Collections.IDictionary map = new System.Collections.Hashtable(); // maps original atoms to clones.
System.Collections.IList remove = new System.Collections.ArrayList(); // lists removed Hs.
// Clone atoms except those to be removed.
IMolecule mol = atomContainer.Builder.newMolecule();
int count = atomContainer.AtomCount;
for (int i = 0; i < count; i++)
{
// Clone/remove this atom?
IAtom atom = atomContainer.getAtomAt(i);
if (!atom.Symbol.Equals("H"))
{
IAtom clonedAtom = null;
try
{
clonedAtom = (IAtom)atom.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' 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)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clonedAtom.setHydrogenCount(0);
mol.addAtom(clonedAtom);
map[atom] = clonedAtom;
}
else
{
remove.Add(atom); // maintain list of removed H.
}
}
// Clone bonds except those involving removed atoms.
count = atomContainer.getBondCount();
for (int i = 0; i < count; i++)
{
// Check bond.
//UPGRADE_NOTE: Final was removed from the declaration of 'bond '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
IBond bond = atomContainer.getBondAt(i);
IAtom[] atoms = bond.getAtoms();
bool removedBond = false;
//UPGRADE_NOTE: Final was removed from the declaration of 'length '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
int length = atoms.Length;
for (int k = 0; k < length; k++)
{
if (remove.Contains(atoms[k]))
{
removedBond = true;
break;
}
}
// Clone/remove this bond?
if (!removedBond)
// if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
{
IBond clone = null;
try
{
clone = (IBond)atomContainer.getBondAt(i).Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' 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)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clone.setAtoms(new IAtom[] { (IAtom)map[atoms[0]], (IAtom)map[atoms[1]] });
mol.addBond(clone);
}
}
// Recompute hydrogen counts of neighbours of removed Hydrogens.
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator i = remove.GetEnumerator(); i.MoveNext();)
{
// Process neighbours.
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator n = atomContainer.getConnectedAtomsVector((IAtom)i.Current).GetEnumerator(); n.MoveNext();)
{
//UPGRADE_NOTE: Final was removed from the declaration of 'neighb '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
IAtom neighb = (IAtom)map[n.Current];
neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
}
}
mol.Properties = atomContainer.Properties;
mol.Flags = atomContainer.Flags;
return(mol);
}