private static IRingSet toRingSet(IAtomContainer ac, System.Collections.ICollection cycles)
{
IRingSet ringSet = ac.Builder.newRingSet();
System.Collections.IEnumerator cycleIterator = cycles.GetEnumerator();
while (cycleIterator.MoveNext())
{
SimpleCycle cycle = (SimpleCycle)cycleIterator.Current;
IRing ring = ac.Builder.newRing();
System.Collections.IList vertices = cycle.vertexList();
IAtom[] atoms = new IAtom[vertices.Count];
atoms[0] = (IAtom)vertices[0];
for (int i = 1; i < vertices.Count; i++)
{
atoms[i] = (IAtom)vertices[i];
ring.addElectronContainer(ac.getBond(atoms[i - 1], atoms[i]));
}
ring.addElectronContainer(ac.getBond(atoms[vertices.Count - 1], atoms[0]));
ring.Atoms = atoms;
ringSet.addAtomContainer(ring);
}
return(ringSet);
}
/// <summary>
/// Count bonds connecting two heavy atoms
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static int GetHeavyBondCount(IAtomContainer mol)
{
int hbCnt = 0;
for (int bi = 0; bi < mol.getBondCount(); bi++)
{
IBond b = mol.getBond(bi);
if (b.getAtomCount() != 2)
{
continue;
}
IAtom a = b.getAtom(0); // first atom
if (a.getAtomicNumber().intValue() == 1 || // do not count hydrogens
a.getSymbol().Equals("H"))
{
a = b.getAtom(1); // second atom
}
if (a.getAtomicNumber().intValue() == 1 || // do not count hydrogens
a.getSymbol().Equals("H"))
{
continue;
}
hbCnt++;
}
return(hbCnt);
}
/// <summary> Says if an atom is the end of a double bond configuration
///
/// </summary>
/// <param name="atom"> The atom which is the end of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not end of configuration, true=is
/// </returns>
private static bool isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, bool[] doubleBondConfiguration)
{
if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.Length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
{
return(false);
}
int lengthAtom = container.getConnectedAtoms(atom).Length + atom.getHydrogenCount();
int lengthParent = container.getConnectedAtoms(parent).Length + parent.getHydrogenCount();
if (container.getBond(atom, parent) != null)
{
if (container.getBond(atom, parent).Order == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.Symbol.Equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.Symbol.Equals("N"))))
{
IAtom[] atoms = container.getConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && one == null)
{
one = atoms[i];
}
else if (atoms[i] != parent && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if ((one != null && two == null && atom.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(parent, atom, one, true)) > System.Math.PI / 10) || (!atom.Symbol.Equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)])))
{
return(true);
}
else
{
return(false);
}
}
}
return(false);
}
public static void makeUpDownBonds(IAtomContainer container)
{
for (int i = 0; i < container.AtomCount; i++)
{
IAtom a = container.getAtomAt(i);
if (container.getConnectedAtoms(a).Length == 4)
{
int up = 0;
int down = 0;
int hs = 0;
IAtom h = null;
for (int k = 0; k < 4; k++)
{
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_UP)
{
up++;
}
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
down++;
}
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_NONE && container.getConnectedAtoms(a)[k].Symbol.Equals("H"))
{
h = container.getConnectedAtoms(a)[k];
hs++;
}
}
if (up == 0 && down == 1 && h != null && hs == 1)
{
container.getBond(a, h).Stereo = CDKConstants.STEREO_BOND_UP;
}
if (up == 1 && down == 0 && h != null && hs == 1)
{
container.getBond(a, h).Stereo = CDKConstants.STEREO_BOND_DOWN;
}
}
}
}
/// <summary> Says if of four atoms connected two one atom the up and down bonds are
/// opposite or not, i. e.if it's tetrehedral or square planar. The method
/// doesnot check if there are four atoms and if two or up and two are down
///
/// </summary>
/// <param name="a"> The atom which is the center
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <returns> true=are opposite, false=are not
/// </returns>
public static bool stereosAreOpposite(IAtomContainer container, IAtom a)
{
System.Collections.IList atoms = container.getConnectedAtomsVector(a);
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 1; i < atoms.Count; i++)
{
hm[(double)giveAngle(a, (IAtom)atoms[0], ((IAtom)atoms[i]))] = (System.Int32)i;
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
int stereoOne = container.getBond(a, (IAtom)atoms[0]).Stereo;
int stereoOpposite = container.getBond(a, (IAtom)atoms[(((System.Int32)ohere[1]))]).Stereo;
if (stereoOpposite == stereoOne)
{
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Remove the following features from a molecule
/// - Atom non-standard mass
/// - Stereo chemistry
/// - explicit hydrogens
/// </summary>
/// <param name="src"></param>
/// <returns>Modified mol</returns>
public static IAtomContainer RemoveIsotopesStereoExplicitHydrogens(
IAtomContainer src)
{
IAtom[] atoms = new IAtom[src.getAtomCount()];
IBond[] bonds = new IBond[src.getBondCount()];
IChemObjectBuilder builder = src.getBuilder();
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = src.getAtom(i);
IAtom atom2 = (IAtom)builder.newInstance(typeof(IAtom), atom.getSymbol());
SetImplicitHydrogenCount(atom2, GetImplicitHydrogenCount(atom));
atom2.setPoint2d(atom.getPoint2d());
atoms[i] = atom2;
}
for (int i = 0; i < bonds.Length; i++)
{
IBond bond = src.getBond(i);
int u = src.getAtomNumber(bond.getAtom(0));
int v = src.getAtomNumber(bond.getAtom(1));
IBond bond2 = (IBond)builder.newInstance(typeof(IBond), atoms[u], atoms[v]);
bond2.setIsAromatic(bond.isAromatic());
bond2.setIsInRing(bond.isInRing());
bond2.setOrder(bond.getOrder());
bond2.setFlag(CDKConstants.ISAROMATIC, bond.getFlag(CDKConstants.ISAROMATIC));
bond2.setFlag(CDKConstants.SINGLE_OR_DOUBLE, bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE));
bonds[i] = bond2;
}
IAtomContainer dest = (IAtomContainer)builder.newInstance(typeof(IAtomContainer));
dest.setAtoms(atoms);
dest.setBonds(bonds);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(dest);
dest = AtomContainerManipulator.suppressHydrogens(dest);
GetHydrogenAdder().addImplicitHydrogens(dest);
return(dest);
}
/// <summary> Says if two atoms are in cis or trans position around a double bond.
/// The atoms have to be given to the method like this: firstOuterAtom - firstInnerAtom = secondInnterAtom - secondOuterAtom
///
/// </summary>
/// <param name="firstOuterAtom"> See above.
/// </param>
/// <param name="firstInnerAtom"> See above.
/// </param>
/// <param name="secondInnerAtom"> See above.
/// </param>
/// <param name="secondOuterAtom"> See above.
/// </param>
/// <param name="ac"> The atom container the atoms are in.
/// </param>
/// <returns> true=trans, false=cis.
/// </returns>
/// <exception cref="CDKException"> The atoms are not in a double bond configuration (no double bond in the middle, same atoms on one side)
/// </exception>
public static bool isCisTrans(IAtom firstOuterAtom, IAtom firstInnerAtom, IAtom secondInnerAtom, IAtom secondOuterAtom, IAtomContainer ac)
{
if (!isValidDoubleBondConfiguration(ac, ac.getBond(firstInnerAtom, secondInnerAtom)))
{
throw new CDKException("There is no valid double bond configuration between your inner atoms!");
}
bool firstDirection = isLeft(firstOuterAtom, firstInnerAtom, secondInnerAtom);
bool secondDirection = isLeft(secondOuterAtom, secondInnerAtom, firstInnerAtom);
if (firstDirection == secondDirection)
{
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Rebonds one atom by looking up nearby atom using the binary space partition tree.
/// </summary>
private void bondAtom(IAtomContainer container, IAtom atom)
{
double myCovalentRadius = atom.CovalentRadius;
double searchRadius = myCovalentRadius + maxCovalentRadius + bondTolerance;
Point tupleAtom = new Point(atom.X3d, atom.Y3d, atom.Z3d);
Bspt.EnumerateSphere e = bspt.enumHemiSphere(tupleAtom, searchRadius);
while (e.MoveNext())
{
IAtom atomNear = ((TupleAtom)e.Current).Atom;
if (atomNear != atom && container.getBond(atom, atomNear) == null)
{
bool isBonded_ = isBonded(myCovalentRadius, atomNear.CovalentRadius, e.foundDistance2());
if (isBonded_)
{
IBond bond = atom.Builder.newBond(atom, atomNear, 1.0);
container.addBond(bond);
}
}
}
}
/// <summary> Says if an atom is the start of a double bond configuration
///
/// </summary>
/// <param name="a"> The atom which is the start of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not start of configuration, true=is
/// </returns>
private static bool isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, bool[] doubleBondConfiguration)
{
int lengthAtom = container.getConnectedAtoms(a).Length + a.getHydrogenCount();
if (lengthAtom != 3 && (lengthAtom != 2 && (System.Object)a.Symbol != (System.Object)("N")))
{
return(false);
}
IAtom[] atoms = container.getConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && container.getBond(atoms[i], a).Order == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atoms[i], a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atoms[i];
}
if (atoms[i] != nextAtom && one == null)
{
one = atoms[i];
}
else if (atoms[i] != nextAtom && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if (one != null && ((!a.Symbol.Equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(nextAtom, a, parent, true)) > System.Math.PI / 10)))
{
return(true);
}
else
{
return(false);
}
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="ac"> Description of the Parameter
/// </param>
/// <param name="a"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
private IAtom hasWedges(IAtomContainer ac, IAtom a)
{
IAtom[] atoms = ac.getConnectedAtoms(a);
for (int i = 0; i < atoms.Length; i++)
{
if (ac.getBond(a, atoms[i]).Stereo != CDKConstants.STEREO_BOND_NONE && !atoms[i].Symbol.Equals("H"))
{
return (atoms[i]);
}
}
for (int i = 0; i < atoms.Length; i++)
{
if (ac.getBond(a, atoms[i]).Stereo != CDKConstants.STEREO_BOND_NONE)
{
return (atoms[i]);
}
}
return (null);
}
/// <summary> Generates the SMILES string for the atom
///
/// </summary>
/// <param name="a"> the atom to generate the SMILES for.
/// </param>
/// <param name="buffer"> the string buffer that the atom is to be
/// apended to.
/// </param>
/// <param name="container"> the AtomContainer to analyze.
/// </param>
/// <param name="chiral"> is a chiral smiles wished?
/// </param>
/// <param name="parent"> the atom we came from.
/// </param>
/// <param name="atomsInOrderOfSmiles"> a vector containing the atoms in the order
/// they are in the smiles.
/// </param>
/// <param name="currentChain"> The chain we currently deal with.
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
private void parseAtom(IAtom a, System.Text.StringBuilder buffer, IAtomContainer container, bool chiral, bool[] doubleBondConfiguration, IAtom parent, System.Collections.ArrayList atomsInOrderOfSmiles, System.Collections.ArrayList currentChain)
{
System.String symbol = a.Symbol;
bool stereo = BondTools.isStereo(container, a);
bool brackets = symbol.Equals("B") || symbol.Equals("C") || symbol.Equals("N") || symbol.Equals("O") || symbol.Equals("P") || symbol.Equals("S") || symbol.Equals("F") || symbol.Equals("Br") || symbol.Equals("I") || symbol.Equals("Cl");
brackets = !brackets;
//System.out.println("in parseAtom()");
//Deal with the start of a double bond configuration
if (isStartOfDoubleBond(container, a, parent, doubleBondConfiguration))
{
buffer.Append('/');
}
if (a is IPseudoAtom)
{
buffer.Append("[*]");
}
else
{
System.String mass = generateMassString(a);
brackets = brackets | !mass.Equals("");
System.String charge = generateChargeString(a);
brackets = brackets | !charge.Equals("");
if (chiral && stereo)
{
brackets = true;
}
if (brackets)
{
buffer.Append('[');
}
buffer.Append(mass);
if (a.getFlag(CDKConstants.ISAROMATIC))
{
// Strictly speaking, this is wrong. Lower case is only used for sp2 atoms!
buffer.Append(a.Symbol.ToLower());
}
else if (a.Hybridization == CDKConstants.HYBRIDIZATION_SP2)
{
buffer.Append(a.Symbol.ToLower());
}
else
{
buffer.Append(symbol);
}
if (a.getProperty(RING_CONFIG) != null && a.getProperty(RING_CONFIG).Equals(UP))
{
buffer.Append('/');
}
if (a.getProperty(RING_CONFIG) != null && a.getProperty(RING_CONFIG).Equals(DOWN))
{
buffer.Append('\\');
}
if (chiral && stereo && (BondTools.isTrigonalBipyramidalOrOctahedral(container, a) != 0 || BondTools.isSquarePlanar(container, a) || BondTools.isTetrahedral(container, a, false) != 0))
{
buffer.Append('@');
}
if (chiral && stereo && BondTools.isSquarePlanar(container, a))
{
buffer.Append("SP1");
}
//chiral
//hcount
buffer.Append(charge);
if (brackets)
{
buffer.Append(']');
}
}
//System.out.println("in parseAtom() after dealing with Pseudoatom or not");
//Deal with the end of a double bond configuration
if (isEndOfDoubleBond(container, a, parent, doubleBondConfiguration))
{
IAtom viewFrom = null;
for (int i = 0; i < currentChain.Count; i++)
{
if (currentChain[i] == parent)
{
int k = i - 1;
while (k > -1)
{
if (currentChain[k] is IAtom)
{
viewFrom = (IAtom)currentChain[k];
break;
}
k--;
}
}
}
if (viewFrom == null)
{
for (int i = 0; i < atomsInOrderOfSmiles.Count; i++)
{
if (atomsInOrderOfSmiles[i] == parent)
{
viewFrom = (IAtom)atomsInOrderOfSmiles[i - 1];
}
}
}
bool afterThisAtom = false;
IAtom viewTo = null;
for (int i = 0; i < currentChain.Count; i++)
{
if (afterThisAtom && currentChain[i] is IAtom)
{
viewTo = (IAtom)currentChain[i];
break;
}
if (afterThisAtom && currentChain[i] is System.Collections.ArrayList)
{
viewTo = (IAtom)((System.Collections.ArrayList)currentChain[i])[0];
break;
}
if (a == currentChain[i])
{
afterThisAtom = true;
}
}
try
{
if (BondTools.isCisTrans(viewFrom, a, parent, viewTo, container))
{
buffer.Append('\\');
}
else
{
buffer.Append('/');
}
}
catch (CDKException ex)
{
//If the user wants a double bond configuration, where there is none, we ignore this.
}
}
System.Collections.ArrayList v = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
System.Collections.IEnumerator it = getRingOpenings(a, v).GetEnumerator();
System.Collections.IEnumerator it2 = v.GetEnumerator();
//System.out.println("in parseAtom() after checking for Ring openings");
//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'"
while (it.MoveNext())
{
//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'"
System.Int32 integer = (System.Int32)it.Current;
//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'"
IBond b = container.getBond((IAtom)it2.Current, a);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int type = (int)b.Order;
if (type == 2 && !b.getFlag(CDKConstants.ISAROMATIC))
{
buffer.Append("=");
}
else if (type == 3 && !b.getFlag(CDKConstants.ISAROMATIC))
{
buffer.Append("#");
}
buffer.Append(integer);
}
atomsInOrderOfSmiles.Add(a);
//System.out.println("End of parseAtom()");
}
/// <summary> Append the symbol for the bond order between <code>a1</code> and <code>a2</code>
/// to the <code>line</code>.
///
/// </summary>
/// <param name="line"> the StringBuffer that the bond symbol is appended to.
/// </param>
/// <param name="a1"> Atom participating in the bond.
/// </param>
/// <param name="a2"> Atom participating in the bond.
/// </param>
/// <param name="atomContainer"> the AtomContainer that the SMILES string is generated
/// for.
/// </param>
private void parseBond(System.Text.StringBuilder line, IAtom a1, IAtom a2, IAtomContainer atomContainer)
{
//System.out.println("in parseBond()");
if (a1.getFlag(CDKConstants.ISAROMATIC) && a1.getFlag(CDKConstants.ISAROMATIC))
{
return;
}
if (atomContainer.getBond(a1, a2) == null)
{
return;
}
int type = 0;
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
type = (int)atomContainer.getBond(a1, a2).Order;
if (type == 1)
{
}
else if (type == 2)
{
line.Append("=");
}
else if (type == 3)
{
line.Append("#");
}
else
{
// //System.out.println("Unknown bond type");
}
}
/// <summary> Says if of four atoms connected two one atom the up and down bonds are
/// opposite or not, i. e.if it's tetrehedral or square planar. The method
/// doesnot check if there are four atoms and if two or up and two are down
///
/// </summary>
/// <param name="a"> The atom which is the center
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <returns> true=are opposite, false=are not
/// </returns>
public static bool stereosAreOpposite(IAtomContainer container, IAtom a)
{
System.Collections.IList atoms = container.getConnectedAtomsVector(a);
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 1; i < atoms.Count; i++)
{
hm[(double)giveAngle(a, (IAtom)atoms[0], ((IAtom)atoms[i]))] = (System.Int32)i;
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
int stereoOne = container.getBond(a, (IAtom)atoms[0]).Stereo;
int stereoOpposite = container.getBond(a, (IAtom)atoms[(((System.Int32)ohere[1]))]).Stereo;
if (stereoOpposite == stereoOne)
{
return true;
}
else
{
return false;
}
}
public static void makeUpDownBonds(IAtomContainer container)
{
for (int i = 0; i < container.AtomCount; i++)
{
IAtom a = container.getAtomAt(i);
if (container.getConnectedAtoms(a).Length == 4)
{
int up = 0;
int down = 0;
int hs = 0;
IAtom h = null;
for (int k = 0; k < 4; k++)
{
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_UP)
{
up++;
}
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
down++;
}
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_NONE && container.getConnectedAtoms(a)[k].Symbol.Equals("H"))
{
h = container.getConnectedAtoms(a)[k];
hs++;
}
}
if (up == 0 && down == 1 && h != null && hs == 1)
{
container.getBond(a, h).Stereo = CDKConstants.STEREO_BOND_UP;
}
if (up == 1 && down == 0 && h != null && hs == 1)
{
container.getBond(a, h).Stereo = CDKConstants.STEREO_BOND_DOWN;
}
}
}
}
/// <summary> The method is known to fail for certain compounds. For more information, see
/// cdk.test.limitations package.
///
/// </summary>
public virtual void saturate(IAtomContainer atomContainer)
{
/* newSaturate(atomContainer);
}
public void oldSaturate(AtomContainer atomContainer) throws CDKException { */
IAtom partner = null;
IAtom atom = null;
IAtom[] partners = null;
IAtomType[] atomTypes1 = null;
IAtomType[] atomTypes2 = null;
IBond bond = null;
for (int i = 1; i < 4; i++)
{
// handle atoms with degree 1 first and then proceed to higher order
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
//logger.debug("symbol: ", atom.Symbol);
atomTypes1 = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes1.Length > 0)
{
//logger.debug("first atom type: ", atomTypes1[0]);
if (atomContainer.getBondCount(atom) == i)
{
if (atom.getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
return ;
if (atomContainer.getBond(partner, atom).getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
if (atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
//logger.debug("Atom has " + atomContainer.getBondOrderSum(atom) + ", may have: " + atomTypes1[0].BondOrderSum);
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
return ;
if (atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
}
}
}
}
}
/// <summary>
/// (Converted from Java to C# for possible later modification)
/// Suppress any explicit hydrogens in the provided container. Only hydrogens
/// that can be represented as a hydrogen count value on the atom are
/// suppressed. The container is updated and no elements are copied, please
/// use either <seealso cref="#copyAndSuppressedHydrogens"/> if you would to preserve
/// the old instance.
/// </summary>
/// <param name="org"> the container from which to remove hydrogens </param>
/// <returns> the input for convenience </returns>
/// <seealso cref= #copyAndSuppressedHydrogens </seealso>
public IAtomContainer suppressHydrogens(IAtomContainer org)
{
bool anyHydrogenPresent = false;
for (int ai = 0; ai < org.getAtomCount(); ai++)
{
IAtom atom = org.getAtom(ai);
if ("H".Equals(atom.getSymbol()))
{
anyHydrogenPresent = true;
break;
}
}
if (!anyHydrogenPresent)
{
return(org);
}
// we need fast adjacency checks (to check for suppression and
// update hydrogen counts)
int[][] graph = GraphUtil.toAdjList(org);
int nOrgAtoms = org.getAtomCount();
int nOrgBonds = org.getBondCount();
int nCpyAtoms = 0;
int nCpyBonds = 0;
ISet <IAtom> hydrogens = new HashSet <IAtom>();
IAtom[] cpyAtoms = new IAtom[nOrgAtoms];
// filter the original container atoms for those that can/can't
// be suppressed
for (int v = 0; v < nOrgAtoms; v++)
{
IAtom atom = org.getAtom(v);
if (suppressibleHydrogen(org, graph, v))
{
hydrogens.Add(atom);
incrementImplHydrogenCount(org.getAtom(graph[v][0]));
}
else
{
cpyAtoms[nCpyAtoms++] = atom;
}
}
// none of the hydrogens could be suppressed - no changes need to be made
if (hydrogens.Count == 0)
{
return(org);
}
org.setAtoms(cpyAtoms);
// we now update the bonds - we have auxiliary variable remaining that
// bypasses the set membership checks if all suppressed bonds are found
IBond[] cpyBonds = new IBond[nOrgBonds - hydrogens.Count];
int remaining = hydrogens.Count;
for (int bi = 0; bi < org.getBondCount(); bi++)
{
IBond bond = org.getBond(bi);
if (remaining > 0 && (hydrogens.Contains(bond.getAtom(0)) || hydrogens.Contains(bond.getAtom(1))))
{
remaining--;
continue;
}
cpyBonds[nCpyBonds++] = bond;
}
// we know how many hydrogens we removed and we should have removed the
// same number of bonds otherwise the container is strange
if (nCpyBonds != cpyBonds.Length)
{
throw new System.ArgumentException("number of removed bonds was less than the number of removed hydrogens");
}
org.setBonds(cpyBonds);
return(org);
}
/// <summary>
/// Convert isotope labels to hilighting.
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public string ConvertIsotopeValuesToHilighting(
IAtomContainer mol)
{
bool hilight;
string molfile2 = "";
bool clearAttachmentPointLabels = true;
bool hilightAttachmentBond = true;
List <int> atomSet = new List <int>();
List <int> bondSet = new List <int>();
for (int bi = 0; bi < mol.getBondCount(); bi++)
{
IBond b = mol.getBond(bi);
if (b.getAtomCount() != 2)
{
continue;
}
IAtom a1 = b.getAtom(0);
IAtom a2 = b.getAtom(1);
if (hilightAttachmentBond)
{
hilight = (GetMassNumber(a1) != 0 && GetMassNumber(a2) != 0);
}
else
{
hilight = (GetMassNumber(a1) < 0 && GetMassNumber(a2) < 0);
}
if (hilight)
{
bondSet.Add(bi);
}
}
//String posMap = ""; // debug (note that hydrogens can get repositioned)
for (int ai = 0; ai < mol.getAtomCount(); ai++) // scan atoms for hilighting and reset isotope values
{
IAtom a = mol.getAtom(ai);
hilight = GetMassNumber(a) < 0;
if (hilight)
{
atomSet.Add(ai);
}
//posMap += ai.ToString() + ", " + a.getSymbol() + ", " + hilight + "\r\n"; // debug
int massNo = GetMassNumber(a);
if (massNo == hilightIsotopeValue)
{
a.setMassNumber(null); // set back to original value
}
else if (massNo < 0)
{
if (clearAttachmentPointLabels)
{
a.setMassNumber(null);
}
else
{
SetMassNumber(a, -massNo); // set back to positive
}
}
}
//mol = GenerateCoordinates(mol); // (should already be done)
try { molfile2 = AtomContainerToMolFileV3000(mol); }
catch (Exception ex) { ex = ex; }
if (Lex.IsUndefined(molfile2)) // couldn't convert to v3000, just return unhilighted v2000 file
{
molfile2 = AtomContainerToMolfile(mol);
return(molfile2);
}
string txt = "MDLV30/HILITE";
if (atomSet.Count > 0)
{
txt += " " + BuildV3000KeywordList("ATOMS", atomSet);
}
if (bondSet.Count > 0)
{
txt += " " + BuildV3000KeywordList("BONDS", bondSet);
}
txt = BuildV3000Lines(txt);
bool hasCollection = Lex.Contains(molfile2, "M V30 END COLLECTION");
if (hasCollection) // already have collection begin and end
{
txt = txt +
"M V30 END COLLECTION";
molfile2 = Lex.Replace(molfile2, "M V30 END COLLECTION", txt);
}
else // add collection begin & end
{
txt =
"M V30 BEGIN COLLECTION\n" +
txt +
"M V30 END COLLECTION\n" +
"M V30 END CTAB";
molfile2 = Lex.Replace(molfile2, "M V30 END CTAB", txt);
}
return(molfile2);
}
/// <summary> Says if two atoms are in cis or trans position around a double bond.
/// The atoms have to be given to the method like this: firstOuterAtom - firstInnerAtom = secondInnterAtom - secondOuterAtom
///
/// </summary>
/// <param name="firstOuterAtom"> See above.
/// </param>
/// <param name="firstInnerAtom"> See above.
/// </param>
/// <param name="secondInnerAtom"> See above.
/// </param>
/// <param name="secondOuterAtom"> See above.
/// </param>
/// <param name="ac"> The atom container the atoms are in.
/// </param>
/// <returns> true=trans, false=cis.
/// </returns>
/// <exception cref="CDKException"> The atoms are not in a double bond configuration (no double bond in the middle, same atoms on one side)
/// </exception>
public static bool isCisTrans(IAtom firstOuterAtom, IAtom firstInnerAtom, IAtom secondInnerAtom, IAtom secondOuterAtom, IAtomContainer ac)
{
if (!isValidDoubleBondConfiguration(ac, ac.getBond(firstInnerAtom, secondInnerAtom)))
{
throw new CDKException("There is no valid double bond configuration between your inner atoms!");
}
bool firstDirection = isLeft(firstOuterAtom, firstInnerAtom, secondInnerAtom);
bool secondDirection = isLeft(secondOuterAtom, secondInnerAtom, firstInnerAtom);
if (firstDirection == secondDirection)
{
return true;
}
else
{
return false;
}
}
/// <summary> Parse a branch
///
/// </summary>
/// <param name="v"> Description of Parameter
/// </param>
/// <param name="buffer"> Description of Parameter
/// </param>
/// <param name="container"> Description of Parameter
/// </param>
/// <param name="parent"> Description of Parameter
/// </param>
/// <param name="chiral"> Description of Parameter
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
/// <param name="atomsInOrderOfSmiles"> Description of Parameter
/// </param>
private void parseChain(System.Collections.ArrayList v, System.Text.StringBuilder buffer, IAtomContainer container, IAtom parent, bool chiral, bool[] doubleBondConfiguration, System.Collections.ArrayList atomsInOrderOfSmiles)
{
int positionInVector = 0;
IAtom atom;
//System.out.println("in parse chain. Size of tree: " + v.size());
for (int h = 0; h < v.Count; h++)
{
System.Object o = v[h];
if (o is IAtom)
{
atom = (IAtom)o;
if (parent != null)
{
parseBond(buffer, atom, parent, container);
}
else
{
if (chiral && BondTools.isStereo(container, atom))
{
parent = (IAtom)((System.Collections.ArrayList)v[1])[0];
}
}
parseAtom(atom, buffer, container, chiral, doubleBondConfiguration, parent, atomsInOrderOfSmiles, v);
//System.out.println("in parseChain after parseAtom()");
/*
* The principle of making chiral smiles is quite simple, although the code is
* pretty uggly. The Atoms connected to the chiral center are put in sorted[] in the
* order they have to appear in the smiles. Then the Vector v is rearranged according
* to sorted[]
*/
if (chiral && BondTools.isStereo(container, atom) && container.getBond(parent, atom) != null)
{
//System.out.println("in parseChain in isChiral");
IAtom[] sorted = null;
System.Collections.IList chiralNeighbours = container.getConnectedAtomsVector(atom);
if (BondTools.isTetrahedral(container, atom, false) > 0)
{
sorted = new IAtom[3];
}
if (BondTools.isTetrahedral(container, atom, false) == 1)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_NONE)
{
bool normalBindingIsLeft = false;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
if (BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom))
{
normalBindingIsLeft = true;
break;
}
}
}
}
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (normalBindingIsLeft)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
else
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
}
}
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 2)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
double angle1 = 0;
double angle2 = 0;
IAtom atom1 = null;
IAtom atom2 = null;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
if (angle1 == 0)
{
angle1 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom1 = (IAtom)chiralNeighbours[i];
}
else
{
angle2 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom2 = (IAtom)chiralNeighbours[i];
}
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
if (angle1 < angle2)
{
sorted[0] = atom2;
sorted[2] = atom1;
}
else
{
sorted[0] = atom1;
sorted[2] = atom2;
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 3)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = ohere.Length - 1; i > -1; i--)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == 0)
{
double angle1 = 0;
double angle2 = 0;
IAtom atom1 = null;
IAtom atom2 = null;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
if (angle1 == 0)
{
angle1 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom1 = (IAtom)chiralNeighbours[i];
}
else
{
angle2 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom2 = (IAtom)chiralNeighbours[i];
}
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
if (angle1 < angle2)
{
sorted[1] = atom2;
sorted[2] = atom1;
}
else
{
sorted[1] = atom1;
sorted[2] = atom2;
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 4)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = ohere.Length - 1; i > -1; i--)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == 0)
{
double angle1 = 0;
double angle2 = 0;
IAtom atom1 = null;
IAtom atom2 = null;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
if (angle1 == 0)
{
angle1 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom1 = (IAtom)chiralNeighbours[i];
}
else
{
angle2 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom2 = (IAtom)chiralNeighbours[i];
}
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
}
}
if (angle1 < angle2)
{
sorted[1] = atom2;
sorted[0] = atom1;
}
else
{
sorted[1] = atom1;
sorted[0] = atom2;
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 5)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_NONE)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 6)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_NONE)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
}
if (BondTools.isSquarePlanar(container, atom))
{
sorted = new IAtom[3];
//This produces a U=SP1 order in every case
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = 0; i < ohere.Length; i++)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom) != 0)
{
sorted = new IAtom[container.getConnectedAtoms(atom).Length - 1];
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == 0)
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[sorted.Length - 1] = (IAtom)chiralNeighbours[i];
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = 0; i < ohere.Length; i++)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == 0)
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[sorted.Length - 1] = (IAtom)chiralNeighbours[i];
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = 0; i < ohere.Length; i++)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == 0)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == 0)
{
hm[(double)(BondTools.giveAngleFromMiddle(atom, parent, ((IAtom)chiralNeighbours[i])))] = (System.Int32)i;
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[sorted.Length - 2] = (IAtom)chiralNeighbours[i];
}
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
sorted[sorted.Length - 1] = ((IAtom)chiralNeighbours[((System.Int32)ohere[ohere.Length - 1])]);
if (ohere.Length == 2)
{
sorted[sorted.Length - 3] = ((IAtom)chiralNeighbours[((System.Int32)ohere[0])]);
if (BondTools.giveAngleFromMiddle(atom, parent, ((IAtom)chiralNeighbours[((System.Int32)ohere[1])])) < 0)
{
IAtom dummy = sorted[sorted.Length - 2];
sorted[sorted.Length - 2] = sorted[0];
sorted[0] = dummy;
}
}
if (ohere.Length == 3)
{
sorted[sorted.Length - 3] = sorted[sorted.Length - 2];
sorted[sorted.Length - 2] = ((IAtom)chiralNeighbours[((System.Int32)ohere[ohere.Length - 2])]);
sorted[sorted.Length - 4] = ((IAtom)chiralNeighbours[((System.Int32)ohere[ohere.Length - 3])]);
}
}
}
//This builds an onew[] containing the objects after the center of the chirality in the order given by sorted[]
if (sorted != null)
{
int numberOfAtoms = 3;
if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom) != 0)
{
numberOfAtoms = container.getConnectedAtoms(atom).Length - 1;
}
System.Object[] omy = new System.Object[numberOfAtoms];
System.Object[] onew = new System.Object[numberOfAtoms];
for (int k = getRingOpenings(atom, null).Count; k < numberOfAtoms; k++)
{
if (positionInVector + 1 + k - getRingOpenings(atom, null).Count < v.Count)
{
omy[k] = v[positionInVector + 1 + k - getRingOpenings(atom, null).Count];
}
}
for (int k = 0; k < sorted.Length; k++)
{
if (sorted[k] != null)
{
for (int m = 0; m < omy.Length; m++)
{
if (omy[m] is IAtom)
{
if (omy[m] == sorted[k])
{
onew[k] = omy[m];
}
}
else
{
if (omy[m] == null)
{
onew[k] = null;
}
else
{
if (((System.Collections.ArrayList)omy[m])[0] == sorted[k])
{
onew[k] = omy[m];
}
}
}
}
}
else
{
onew[k] = null;
}
}
//This is a workaround for 3624.MOL.2 I don't have a better solution currently
bool doubleentry = false;
for (int m = 0; m < onew.Length; m++)
{
for (int k = 0; k < onew.Length; k++)
{
if (m != k && onew[k] == onew[m])
{
doubleentry = true;
}
}
}
if (!doubleentry)
{
//Make sure that the first atom in onew is the first one in the original smiles order. This is important to have a canonical smiles.
if (positionInVector + 1 < v.Count)
{
System.Object atomAfterCenterInOriginalSmiles = v[positionInVector + 1];
int l = 0;
while (onew[0] != atomAfterCenterInOriginalSmiles)
{
System.Object placeholder = onew[onew.Length - 1];
for (int k = onew.Length - 2; k > -1; k--)
{
onew[k + 1] = onew[k];
}
onew[0] = placeholder;
l++;
if (l > onew.Length)
{
break;
}
}
}
//This cares about ring openings. Here the ring closure (represendted by a figure) must be the first atom. In onew the closure is null.
if (getRingOpenings(atom, null).Count > 0)
{
int l = 0;
while (onew[0] != null)
{
System.Object placeholder = onew[0];
for (int k = 1; k < onew.Length; k++)
{
onew[k - 1] = onew[k];
}
onew[onew.Length - 1] = placeholder;
l++;
if (l > onew.Length)
{
break;
}
}
}
//The last in onew is a vector: This means we need to exchange the rest of the original smiles with the rest of this vector.
if (onew[numberOfAtoms - 1] is System.Collections.ArrayList)
{
for (int i = 0; i < numberOfAtoms; i++)
{
if (onew[i] is IAtom)
{
System.Collections.ArrayList vtemp = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
vtemp.Add(onew[i]);
for (int k = positionInVector + 1 + numberOfAtoms; k < v.Count; k++)
{
vtemp.Add(v[k]);
}
onew[i] = vtemp;
for (int k = v.Count - 1; k > positionInVector + 1 + numberOfAtoms - 1; k--)
{
v.RemoveAt(k);
}
for (int k = 1; k < ((System.Collections.ArrayList)onew[numberOfAtoms - 1]).Count; k++)
{
v.Add(((System.Collections.ArrayList)onew[numberOfAtoms - 1])[k]);
}
onew[numberOfAtoms - 1] = ((System.Collections.ArrayList)onew[numberOfAtoms - 1])[0];
break;
}
}
}
//Put the onew objects in the original Vector
int k2 = 0;
for (int m = 0; m < onew.Length; m++)
{
if (onew[m] != null)
{
v[positionInVector + 1 + k2] = onew[m];
k2++;
}
}
}
}
}
parent = atom;
}
else
{
//Have Vector
//System.out.println("in parseChain after else");
bool brackets = true;
System.Collections.ArrayList result = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
addAtoms((System.Collections.ArrayList)o, result);
if (isRingOpening(parent, result) && container.getBondCount(parent) < 4)
{
brackets = false;
}
if (brackets)
{
buffer.Append('(');
}
parseChain((System.Collections.ArrayList)o, buffer, container, parent, chiral, doubleBondConfiguration, atomsInOrderOfSmiles);
if (brackets)
{
buffer.Append(')');
}
}
positionInVector++;
//System.out.println("in parseChain after positionVector++");
}
}
/// <summary> Says if an atom is the end of a double bond configuration
///
/// </summary>
/// <param name="atom"> The atom which is the end of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not end of configuration, true=is
/// </returns>
private bool isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, bool[] doubleBondConfiguration)
{
if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.Length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
{
return false;
}
int lengthAtom = container.getConnectedAtoms(atom).Length + atom.getHydrogenCount();
int lengthParent = container.getConnectedAtoms(parent).Length + parent.getHydrogenCount();
if (container.getBond(atom, parent) != null)
{
if (container.getBond(atom, parent).Order == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.Symbol.Equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.Symbol.Equals("N"))))
{
IAtom[] atoms = container.getConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && one == null)
{
one = atoms[i];
}
else if (atoms[i] != parent && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if ((one != null && two == null && atom.Symbol.Equals("N") && System.Math.Abs(BondTools.giveAngleBothMethods(parent, atom, one, true)) > System.Math.PI / 10) || (!atom.Symbol.Equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)])))
{
return (true);
}
else
{
return (false);
}
}
}
return (false);
}
private static IRingSet toRingSet(IAtomContainer ac, System.Collections.ICollection cycles)
{
IRingSet ringSet = ac.Builder.newRingSet();
System.Collections.IEnumerator cycleIterator = cycles.GetEnumerator();
while (cycleIterator.MoveNext())
{
SimpleCycle cycle = (SimpleCycle)cycleIterator.Current;
IRing ring = ac.Builder.newRing();
System.Collections.IList vertices = cycle.vertexList();
IAtom[] atoms = new IAtom[vertices.Count];
atoms[0] = (IAtom)vertices[0];
for (int i = 1; i < vertices.Count; i++)
{
atoms[i] = (IAtom)vertices[i];
ring.addElectronContainer(ac.getBond(atoms[i - 1], atoms[i]));
}
ring.addElectronContainer(ac.getBond(atoms[vertices.Count - 1], atoms[0]));
ring.Atoms = atoms;
ringSet.addAtomContainer(ring);
}
return ringSet;
}
/// <summary> Says if an atom is the start of a double bond configuration
///
/// </summary>
/// <param name="a"> The atom which is the start of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not start of configuration, true=is
/// </returns>
private bool isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, bool[] doubleBondConfiguration)
{
int lengthAtom = container.getConnectedAtoms(a).Length + a.getHydrogenCount();
if (lengthAtom != 3 && (lengthAtom != 2 && (System.Object)a.Symbol != (System.Object)("N")))
{
return (false);
}
IAtom[] atoms = container.getConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && container.getBond(atoms[i], a).Order == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atoms[i], a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atoms[i];
}
if (atoms[i] != nextAtom && one == null)
{
one = atoms[i];
}
else if (atoms[i] != nextAtom && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if (one != null && ((!a.Symbol.Equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.Symbol.Equals("N") && System.Math.Abs(BondTools.giveAngleBothMethods(nextAtom, a, parent, true)) > System.Math.PI / 10)))
{
return (true);
}
else
{
return (false);
}
}
/// <summary>
/// Remove explicit and implicit hydrogens bonded to positive nitrogens
/// </summary>
/// <param name="org"></param>
/// <returns></returns>
public int RemoveHydrogensBondedToPositiveNitrogens(IAtomContainer org)
{
int chg, impHydCnt;
int implicitHydRemoved = 0;
HashSet <IAtom> atomsToRemove = new HashSet <IAtom>();
HashSet <IBond> bondsToRemove = new HashSet <IBond>();
int nOrgAtoms = org.getAtomCount();
int nOrgBonds = org.getBondCount();
// Get H atoms and their bonds to pos-charged Nitrogen, adjusting charge
for (int bi = 0; bi < org.getBondCount(); bi++)
{
IBond bond = org.getBond(bi);
if (bond.getAtomCount() != 2)
{
continue;
}
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
if (a1.getSymbol() == "H" && a2.getSymbol() == "N" && GetFormalCharge(a2) > 0)
{
chg = GetFormalCharge(a2) - 1;
SetFormalCharge(a2, chg);
atomsToRemove.Add(a1);
bondsToRemove.Add(bond);
}
else if (a2.getSymbol() == "H" && a1.getSymbol() == "N" && GetFormalCharge(a1) > 0)
{
chg = GetFormalCharge(a1) - 1;
SetFormalCharge(a1, chg);
atomsToRemove.Add(a2);
bondsToRemove.Add(bond);
}
}
// Check for implicit H attached to pos-charged N
for (int ai = 0; ai < nOrgAtoms; ai++)
{
IAtom a = org.getAtom(ai);
if (a.getSymbol() == "N" && GetFormalCharge(a) > 0 && GetImplicitHydrogenCount(a) > 0)
{
chg = GetFormalCharge(a) - 1;
SetFormalCharge(a, chg);
impHydCnt = GetImplicitHydrogenCount(a) - 1;
SetImplicitHydrogenCount(a, impHydCnt);
implicitHydRemoved++;
}
}
if (implicitHydRemoved > 0)
{
implicitHydRemoved = implicitHydRemoved; // debug
}
if (atomsToRemove.Count == 0)
{
return(implicitHydRemoved); // just return if no explicit H to remove
}
// Get list of atoms to keep
IAtom[] cpyAtoms = new IAtom[nOrgAtoms - atomsToRemove.Count];
int nCpyAtoms = 0;
for (int ai = 0; ai < nOrgAtoms; ai++)
{
IAtom atom = org.getAtom(ai);
if (!atomsToRemove.Contains(atom))
{
cpyAtoms[nCpyAtoms++] = atom;
}
}
org.setAtoms(cpyAtoms);
// Get list of bonds to keep
IBond[] cpyBonds = new IBond[nOrgBonds - bondsToRemove.Count];
int nCpyBonds = 0;
for (int bi = 0; bi < org.getBondCount(); bi++)
{
IBond bond = org.getBond(bi);
if (!bondsToRemove.Contains(bond))
{
cpyBonds[nCpyBonds++] = bond;
}
}
org.setBonds(cpyBonds);
return(atomsToRemove.Count + implicitHydRemoved);
}
/// <summary>
/// Rebonds one atom by looking up nearby atom using the binary space partition tree.
/// </summary>
private void bondAtom(IAtomContainer container, IAtom atom)
{
double myCovalentRadius = atom.CovalentRadius;
double searchRadius = myCovalentRadius + maxCovalentRadius + bondTolerance;
Point tupleAtom = new Point(atom.X3d, atom.Y3d, atom.Z3d);
Bspt.EnumerateSphere e = bspt.enumHemiSphere(tupleAtom, searchRadius);
while (e.MoveNext())
{
IAtom atomNear = ((TupleAtom)e.Current).Atom;
if (atomNear != atom && container.getBond(atom, atomNear) == null)
{
bool isBonded_ = isBonded(myCovalentRadius, atomNear.CovalentRadius, e.foundDistance2());
if (isBonded_)
{
IBond bond = atom.Builder.newBond(atom, atomNear, 1.0);
container.addBond(bond);
}
}
}
}
/// <summary> The method is known to fail for certain compounds. For more information, see
/// cdk.test.limitations package.
///
/// </summary>
public virtual void saturate(IAtomContainer atomContainer)
{
/* newSaturate(atomContainer);
* }
* public void oldSaturate(AtomContainer atomContainer) throws CDKException { */
IAtom partner = null;
IAtom atom = null;
IAtom[] partners = null;
IAtomType[] atomTypes1 = null;
IAtomType[] atomTypes2 = null;
IBond bond = null;
for (int i = 1; i < 4; i++)
{
// handle atoms with degree 1 first and then proceed to higher order
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
//logger.debug("symbol: ", atom.Symbol);
atomTypes1 = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes1.Length > 0)
{
//logger.debug("first atom type: ", atomTypes1[0]);
if (atomContainer.getBondCount(atom) == i)
{
if (atom.getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
{
return;
}
if (atomContainer.getBond(partner, atom).getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
if (atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
//logger.debug("Atom has " + atomContainer.getBondOrderSum(atom) + ", may have: " + atomTypes1[0].BondOrderSum);
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
{
return;
}
if (atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
}
}
}
}
}
