/// <summary> Tries to saturate a bond by increasing its bond orders by 1.0.
///
/// </summary>
/// <returns> true if the bond could be increased
/// </returns>
public virtual bool saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer, double increment)
{
IAtom[] atoms = bond.getAtoms();
IAtom atom = atoms[0];
IAtom partner = atoms[1];
//logger.debug(" saturating bond: ", atom.Symbol, "-", partner.Symbol);
IAtomType[] atomTypes1 = getAtomTypeFactory(bond.Builder).getAtomTypes(atom.Symbol);
IAtomType[] atomTypes2 = getAtomTypeFactory(bond.Builder).getAtomTypes(partner.Symbol);
for (int atCounter1 = 0; atCounter1 < atomTypes1.Length; atCounter1++)
{
IAtomType aType1 = atomTypes1[atCounter1];
//logger.debug(" condidering atom type: ", aType1);
if (couldMatchAtomType(atomContainer, atom, aType1))
{
//logger.debug(" trying atom type: ", aType1);
for (int atCounter2 = 0; atCounter2 < atomTypes2.Length; atCounter2++)
{
IAtomType aType2 = atomTypes2[atCounter2];
//logger.debug(" condidering partner type: ", aType1);
if (couldMatchAtomType(atomContainer, partner, atomTypes2[atCounter2]))
{
//logger.debug(" with atom type: ", aType2);
if (bond.Order < aType2.MaxBondOrder && bond.Order < aType1.MaxBondOrder)
{
bond.Order = bond.Order + increment;
//logger.debug("Bond order now ", bond.Order);
return(true);
}
}
}
}
}
return(false);
}
/// <summary>
/// Tells if a certain bond is center of a valid double bond configuration.
/// </summary>
/// <param name="container"> The atomcontainer.
/// </param>
/// <param name="bond"> The bond.
/// </param>
/// <returns> true=is a potential configuration, false=is not.
/// </returns>
public static bool isValidDoubleBondConfiguration(IAtomContainer container, IBond bond)
{
IAtom[] atoms = bond.getAtoms();
IAtom[] connectedAtoms = container.getConnectedAtoms(atoms[0]);
IAtom from = null;
for (int i = 0; i < connectedAtoms.Length; i++)
{
if (connectedAtoms[i] != atoms[1])
{
from = connectedAtoms[i];
}
}
bool[] array = new bool[container.Bonds.Length];
for (int i = 0; i < array.Length; i++)
{
array[i] = true;
}
if (isStartOfDoubleBond(container, atoms[0], from, array) && isEndOfDoubleBond(container, atoms[1], atoms[0], array) && !bond.getFlag(CDKConstants.ISAROMATIC))
{
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Tells if a certain bond is center of a valid double bond configuration.
/// </summary>
/// <param name="container"> The atomcontainer.
/// </param>
/// <param name="bond"> The bond.
/// </param>
/// <returns> true=is a potential configuration, false=is not.
/// </returns>
public static bool isValidDoubleBondConfiguration(IAtomContainer container, IBond bond)
{
IAtom[] atoms = bond.getAtoms();
IAtom[] connectedAtoms = container.getConnectedAtoms(atoms[0]);
IAtom from = null;
for (int i = 0; i < connectedAtoms.Length; i++)
{
if (connectedAtoms[i] != atoms[1])
{
from = connectedAtoms[i];
}
}
bool[] array = new bool[container.Bonds.Length];
for (int i = 0; i < array.Length; i++)
{
array[i] = true;
}
if (isStartOfDoubleBond(container, atoms[0], from, array) && isEndOfDoubleBond(container, atoms[1], atoms[0], array) && !bond.getFlag(CDKConstants.ISAROMATIC))
{
return (true);
}
else
{
return (false);
}
}
/// <summary> Returns wether a bond is saturated. A bond is saturated if
/// <b>both</b> Atoms in the bond are saturated.
/// </summary>
public virtual bool isSaturated(IBond bond, IAtomContainer atomContainer)
{
IAtom[] atoms = bond.getAtoms();
bool isSaturated = true;
for (int i = 0; i < atoms.Length; i++)
{
isSaturated = isSaturated && this.isSaturated(atoms[i], atomContainer);
}
return(isSaturated);
}
/// <summary> Returns wether a bond is unsaturated. A bond is unsaturated if
/// <b>all</b> Atoms in the bond are unsaturated.
/// </summary>
public virtual bool isUnsaturated(IBond bond, IAtomContainer atomContainer)
{
//logger.debug("isBondUnsaturated?: ", bond);
IAtom[] atoms = bond.getAtoms();
bool isUnsaturated = true;
for (int i = 0; i < atoms.Length && isUnsaturated; i++)
{
isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer);
}
//logger.debug("Bond is unsaturated?: ", isUnsaturated);
return(isUnsaturated);
}
/// <summary> Returns wether a bond is saturated. A bond is saturated if
/// <b>both</b> Atoms in the bond are saturated.
/// </summary>
public virtual bool isSaturated(IBond bond, IAtomContainer atomContainer)
{
//logger.debug("isBondSaturated?: ", bond);
IAtom[] atoms = bond.getAtoms();
bool isSaturated = true;
for (int i = 0; i < atoms.Length; i++)
{
//logger.debug("isSaturated(Bond, AC): atom I=", i);
isSaturated = isSaturated && this.isSaturated(atoms[i], atomContainer);
}
//logger.debug("isSaturated(Bond, AC): result=", isSaturated);
return(isSaturated);
}
/// <summary> Saturate atom by adjusting its bond orders.</summary>
public virtual bool saturate(IBond bond, IAtomContainer atomContainer)
{
IAtom[] atoms = bond.getAtoms();
IAtom atom = atoms[0];
IAtom partner = atoms[1];
//logger.debug(" saturating bond: ", atom.Symbol, "-", partner.Symbol);
bool bondOrderIncreased = true;
while (bondOrderIncreased && isUnsaturated(bond, atomContainer))
{
//logger.debug("Can increase bond order");
bondOrderIncreased = saturateByIncreasingBondOrder(bond, atomContainer, 1.0);
}
return(isSaturated(bond, atomContainer));
}
/// <summary>
/// Creates a molecule graph for use with jgrapht.
/// Bond orders are not respected.
/// </summary>
/// <param name="molecule">the specified molecule</param>
/// <returns>a graph representing the molecule</returns>
static public SimpleGraph getMoleculeGraph(IAtomContainer molecule)
{
SimpleGraph graph = new SimpleGraph();
for (int i = 0; i < molecule.AtomCount; i++)
{
IAtom atom = molecule.Atoms[i];
graph.addVertex(atom);
}
for (int i = 0; i < molecule.getBondCount(); i++)
{
IBond bond = molecule.Bonds[i];
/*
* int order = (int) bond.getOrder();
* for (int j=0; j<order; j++) {
* graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
* }
*/
graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
}
return(graph);
}
/// <summary> Saturate atom by adjusting its bond orders.</summary>
public virtual bool newSaturate(IBond bond, IAtomContainer atomContainer)
{
IAtom[] atoms = bond.getAtoms();
IAtom atom = atoms[0];
IAtom partner = atoms[1];
//logger.debug(" saturating bond: ", atom.Symbol, "-", partner.Symbol);
IAtomType[] atomTypes1 = getAtomTypeFactory(bond.Builder).getAtomTypes(atom.Symbol);
IAtomType[] atomTypes2 = getAtomTypeFactory(bond.Builder).getAtomTypes(partner.Symbol);
bool bondOrderIncreased = true;
while (bondOrderIncreased && !isSaturated(bond, atomContainer))
{
//logger.debug("Can increase bond order");
bondOrderIncreased = false;
for (int atCounter1 = 0; atCounter1 < atomTypes1.Length && !bondOrderIncreased; atCounter1++)
{
IAtomType aType1 = atomTypes1[atCounter1];
//logger.debug(" condidering atom type: ", aType1);
if (couldMatchAtomType(atomContainer, atom, aType1))
{
//logger.debug(" trying atom type: ", aType1);
for (int atCounter2 = 0; atCounter2 < atomTypes2.Length && !bondOrderIncreased; atCounter2++)
{
IAtomType aType2 = atomTypes2[atCounter2];
//logger.debug(" condidering partner type: ", aType1);
if (couldMatchAtomType(atomContainer, partner, atomTypes2[atCounter2]))
{
//logger.debug(" with atom type: ", aType2);
if (bond.Order >= aType2.MaxBondOrder || bond.Order >= aType1.MaxBondOrder)
{
//logger.debug("Bond order not increased: atoms has reached (or exceeded) maximum bond order for this atom type");
}
else if (bond.Order < aType2.MaxBondOrder && bond.Order < aType1.MaxBondOrder)
{
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
bondOrderIncreased = true;
}
}
}
}
}
}
return(isSaturated(bond, atomContainer));
}
/// <summary> Determines if this Bond contains 2D coordinates.
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="b"> Description of the Parameter
/// </param>
/// <returns> boolean indication that 2D coordinates are available
/// </returns>
public static bool has2DCoordinates(IBond b)
{
IAtom[] atoms = b.getAtoms();
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i].getPoint2d() == null)
{
return false;
}
}
return true;
}
public static void GenericBondSetup(IBond bond, bool sort, BondShadingDesc bShading,
out Vector3 direction, out Vector3 directionUV,
out IAtom[] atoms, out Vector3[] atomsPos,
out IMoleculeMaterial matA, out IMoleculeMaterial matB)
{
atoms = bond.getAtoms();
Vector3 v1 = new Vector3((float)atoms[0].X3d, (float)atoms[0].Y3d, (float)atoms[0].Z3d);
Vector3 v2 = new Vector3((float)atoms[1].X3d, (float)atoms[1].Y3d, (float)atoms[1].Z3d);
direction = v2 - v1;
atomsPos = new Vector3[2];
if (sort)
{
if (direction.Z < (v1 - v2).Z)
{
IAtom temp = atoms[0];
atoms[0] = atoms[1];
atoms[1] = temp;
atomsPos[0] = v2;
atomsPos[1] = v1;
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
direction = Vector3.Normalize(atomsPos[1] - atomsPos[0]);
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
directionUV = Vector3.Normalize(direction);
IMoleculeMaterialLookup lookup = bShading.MoleculeMaterials;
IMoleculeMaterialTemplate matTemp = lookup.ResolveBySymbol(atoms[0].Symbol);
if (matTemp != null)
{
matA = matTemp.BySymbol;
}
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[0].Properties["PeriodicTableElement"];
matA = lookup.GetBySeries(pe.ChemicalSerie);
}
matTemp = lookup.ResolveBySymbol(atoms[1].Symbol);
if (matTemp != null)
{
matB = matTemp.BySymbol;
}
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[1].Properties["PeriodicTableElement"];
matB = lookup.GetBySeries(pe.ChemicalSerie);
}
}
public static void GenericBondSetup(IBond bond, bool sort, BondShadingDesc bShading,
out Vector3 direction, out Vector3 directionUV,
out IAtom[] atoms, out Vector3[] atomsPos,
out IMoleculeMaterial matA, out IMoleculeMaterial matB)
{
atoms = bond.getAtoms();
Vector3 v1 = new Vector3((float)atoms[0].X3d, (float)atoms[0].Y3d, (float)atoms[0].Z3d);
Vector3 v2 = new Vector3((float)atoms[1].X3d, (float)atoms[1].Y3d, (float)atoms[1].Z3d);
direction = v2 - v1;
atomsPos = new Vector3[2];
if (sort)
{
if (direction.Z < (v1 - v2).Z)
{
IAtom temp = atoms[0];
atoms[0] = atoms[1];
atoms[1] = temp;
atomsPos[0] = v2;
atomsPos[1] = v1;
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
direction = Vector3.Normalize(atomsPos[1] - atomsPos[0]);
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
directionUV = Vector3.Normalize(direction);
IMoleculeMaterialLookup lookup = bShading.MoleculeMaterials;
IMoleculeMaterialTemplate matTemp = lookup.ResolveBySymbol(atoms[0].Symbol);
if (matTemp != null)
matA = matTemp.BySymbol;
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[0].Properties["PeriodicTableElement"];
matA = lookup.GetBySeries(pe.ChemicalSerie);
}
matTemp = lookup.ResolveBySymbol(atoms[1].Symbol);
if (matTemp != null)
matB = matTemp.BySymbol;
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[1].Properties["PeriodicTableElement"];
matB = lookup.GetBySeries(pe.ChemicalSerie);
}
}
/// <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);
}
/// <summary> Saturate atom by adjusting its bond orders.</summary>
public virtual bool saturate(IBond bond, IAtomContainer atomContainer)
{
IAtom[] atoms = bond.getAtoms();
IAtom atom = atoms[0];
IAtom partner = atoms[1];
//logger.debug(" saturating bond: ", atom.Symbol, "-", partner.Symbol);
bool bondOrderIncreased = true;
while (bondOrderIncreased && isUnsaturated(bond, atomContainer))
{
//logger.debug("Can increase bond order");
bondOrderIncreased = saturateByIncreasingBondOrder(bond, atomContainer, 1.0);
}
return isSaturated(bond, atomContainer);
}
/// <summary> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="container"> Molecule that is written to an OutputStream
/// </param>
/// <param name="isVisible">Should a certain atom be written to mdl?
/// </param>
public virtual void writeMolecule(IMolecule container, bool[] isVisible)
{
System.String line = "";
// taking care of the $$$$ signs:
// we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
if (moleculeNumber == 2)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
// write header block
// lines get shortened to 80 chars, that's in the spec
System.String title = (System.String)container.getProperty(CDKConstants.TITLE);
if (title == null)
{
title = "";
}
if (title.Length > 80)
{
title = title.Substring(0, (80) - (0));
}
writer.Write(title + "\n");
/* From CTX spec
* This line has the format:
* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
* (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
* User's first and last initials (l), program name (P),
* date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input, internal registry number (R)
* if input through MDL form.
* A blank line can be substituted for line 2.
*/
writer.Write(" CDK ");
//UPGRADE_ISSUE: Constructor 'java.text.SimpleDateFormat.SimpleDateFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextSimpleDateFormat'"
//UPGRADE_TODO: The equivalent in .NET for method 'java.util.Calendar.getTime' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.TimeZone generatedAux3 = System.TimeZone.CurrentTimeZone;
//writer.Write(SupportClass.FormatDateTime(new SimpleDateFormat("M/d/y,H:m", new System.Globalization.CultureInfo("en-US")), SupportClass.CalendarManager.manager.GetDateTime(new System.Globalization.GregorianCalendar())));
writer.Write('\n');
System.String comment = (System.String)container.getProperty(CDKConstants.REMARK);
if (comment == null)
{
comment = "";
}
if (comment.Length > 80)
{
comment = comment.Substring(0, (80) - (0));
}
writer.Write(comment + "\n");
// write Counts line
int upToWhichAtom = 0;
for (int i = 0; i < isVisible.Length; i++)
{
if (isVisible[i])
{
upToWhichAtom++;
}
}
line += formatMDLInt(upToWhichAtom, 3);
int numberOfBonds = 0;
if (upToWhichAtom < container.AtomCount)
{
for (int i = 0; i < container.getBondCount(); i++)
{
if (isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[1])])
{
numberOfBonds++;
}
}
}
else
{
numberOfBonds = container.getBondCount();
}
line += formatMDLInt(numberOfBonds, 3);
line += " 0 0 0 0 0 0 0 0999 V2000\n";
writer.Write(line);
// write Atom block
IAtom[] atoms = container.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
if (isVisible[f])
{
IAtom atom = atoms[f];
line = "";
if (atom.getPoint3d() != null)
{
//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'"
line += formatMDLFloat((float)atom.X3d);
//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'"
line += formatMDLFloat((float)atom.Y3d);
//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'"
line += (formatMDLFloat((float)atom.Z3d) + " ");
}
else if (atom.getPoint2d() != null)
{
//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'"
line += formatMDLFloat((float)atom.X2d);
//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'"
line += formatMDLFloat((float)atom.Y2d);
line += " 0.0000 ";
}
else
{
// if no coordinates available, then output a number
// of zeros
line += formatMDLFloat((float)0.0);
line += formatMDLFloat((float)0.0);
line += (formatMDLFloat((float)0.0) + " ");
}
if (container.getAtomAt(f) is IPseudoAtom)
{
line += formatMDLString(((IPseudoAtom)container.getAtomAt(f)).Label, 3);
}
else
{
line += formatMDLString(container.getAtomAt(f).Symbol, 3);
}
line += " 0 0 0 0 0 0 0 0 0 0 0 0";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write Bond block
IBond[] bonds = container.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
if (upToWhichAtom == container.AtomCount || (isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[1])]))
{
IBond bond = bonds[g];
if (bond.getAtoms().Length != 2)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.warn("Skipping bond with more/less than two atoms: " + bond);
}
else
{
if (bond.Stereo == CDKConstants.STEREO_BOND_UP_INV || bond.Stereo == CDKConstants.STEREO_BOND_DOWN_INV)
{
// turn around atom coding to correct for inv stereo
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
}
else
{
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
}
//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'"
line += formatMDLInt((int)bond.Order, 3);
line += " ";
switch (bond.Stereo)
{
case CDKConstants.STEREO_BOND_UP:
line += "1";
break;
case CDKConstants.STEREO_BOND_UP_INV:
line += "1";
break;
case CDKConstants.STEREO_BOND_DOWN:
line += "6";
break;
case CDKConstants.STEREO_BOND_DOWN_INV:
line += "6";
break;
default:
line += "0";
break;
}
line += " 0 0 0 ";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// write formal atomic charges
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
int charge = atom.getFormalCharge();
if (charge != 0)
{
writer.Write("M CHG 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(charge, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write formal isotope information
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
if (!(atom is IPseudoAtom))
{
int atomicMass = atom.MassNumber;
int majorMass = IsotopeFactory.getInstance(atom.Builder).getMajorIsotope(atom.Symbol).MassNumber;
if (atomicMass != 0 && atomicMass != majorMass)
{
writer.Write("M ISO 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(atomicMass, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// close molecule
writer.Write("M END");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//write sdfields, if any
if (sdFields != null)
{
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
CSGraphT.SupportClass.SetSupport set_Renamed = new CSGraphT.SupportClass.HashSetSupport(sdFields.Keys);
System.Collections.IEnumerator iterator = set_Renamed.GetEnumerator();
//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 (iterator.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.Object element = iterator.Current;
writer.Write("> <" + ((System.String)element) + ">");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
writer.Write(sdFields[element].ToString());
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// taking care of the $$$$ signs:
// we write such a sign at the end of all except the first molecule
if (moleculeNumber != 1)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
moleculeNumber++;
writer.Flush();
}
/// <summary> Returns wether a bond is saturated. A bond is saturated if
/// <b>both</b> Atoms in the bond are saturated.
/// </summary>
public virtual bool isSaturated(IBond bond, IAtomContainer atomContainer)
{
//logger.debug("isBondSaturated?: ", bond);
IAtom[] atoms = bond.getAtoms();
bool isSaturated = true;
for (int i = 0; i < atoms.Length; i++)
{
//logger.debug("isSaturated(Bond, AC): atom I=", i);
isSaturated = isSaturated && this.isSaturated(atoms[i], atomContainer);
}
//logger.debug("isSaturated(Bond, AC): result=", isSaturated);
return isSaturated;
}
/// <summary> Tries to saturate a bond by increasing its bond orders by 1.0.
///
/// </summary>
/// <returns> true if the bond could be increased
/// </returns>
public virtual bool saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer, double increment)
{
IAtom[] atoms = bond.getAtoms();
IAtom atom = atoms[0];
IAtom partner = atoms[1];
//logger.debug(" saturating bond: ", atom.Symbol, "-", partner.Symbol);
IAtomType[] atomTypes1 = getAtomTypeFactory(bond.Builder).getAtomTypes(atom.Symbol);
IAtomType[] atomTypes2 = getAtomTypeFactory(bond.Builder).getAtomTypes(partner.Symbol);
for (int atCounter1 = 0; atCounter1 < atomTypes1.Length; atCounter1++)
{
IAtomType aType1 = atomTypes1[atCounter1];
//logger.debug(" condidering atom type: ", aType1);
if (couldMatchAtomType(atomContainer, atom, aType1))
{
//logger.debug(" trying atom type: ", aType1);
for (int atCounter2 = 0; atCounter2 < atomTypes2.Length; atCounter2++)
{
IAtomType aType2 = atomTypes2[atCounter2];
//logger.debug(" condidering partner type: ", aType1);
if (couldMatchAtomType(atomContainer, partner, atomTypes2[atCounter2]))
{
//logger.debug(" with atom type: ", aType2);
if (bond.Order < aType2.MaxBondOrder && bond.Order < aType1.MaxBondOrder)
{
bond.Order = bond.Order + increment;
//logger.debug("Bond order now ", bond.Order);
return true;
}
}
}
}
}
return false;
}
/// <summary> Returns wether a bond is unsaturated. A bond is unsaturated if
/// <b>all</b> Atoms in the bond are unsaturated.
/// </summary>
public virtual bool isUnsaturated(IBond bond, IAtomContainer atomContainer)
{
//logger.debug("isBondUnsaturated?: ", bond);
IAtom[] atoms = bond.getAtoms();
bool isUnsaturated = true;
for (int i = 0; i < atoms.Length && isUnsaturated; i++)
{
isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer);
}
//logger.debug("Bond is unsaturated?: ", isUnsaturated);
return isUnsaturated;
}
/// <summary> This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
///
/// </summary>
/// <param name="l"> The list produced by the getMap method.
/// </param>
/// <param name="g1"> The first atom container.
/// </param>
/// <param name="g2"> The second one (first and second as in getMap)
/// </param>
/// <returns> The mapping found projected on g1. This is a List of RMap objects containing Ids of matching atoms.
/// </returns>
public static System.Collections.IList makeAtomsMapOfBondsMap(System.Collections.IList l, IAtomContainer g1, IAtomContainer g2)
{
if (l == null)
{
return(l);
}
IBond[] bonds1 = g1.Bonds;
IBond[] bonds2 = g2.Bonds;
System.Collections.IList result = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < l.Count; i++)
{
IBond bond1 = bonds1[((RMap)l[i]).Id1];
IBond bond2 = bonds2[((RMap)l[i]).Id2];
IAtom[] atom1 = bond1.getAtoms();
IAtom[] atom2 = bond2.getAtoms();
for (int j = 0; j < 2; j++)
{
IBond[] bondsConnectedToAtom1j = g1.getConnectedBonds(atom1[j]);
for (int k = 0; k < bondsConnectedToAtom1j.Length; k++)
{
if (bondsConnectedToAtom1j[k] != bond1)
{
IBond testBond = bondsConnectedToAtom1j[k];
for (int m = 0; m < l.Count; m++)
{
IBond testBond2;
if (((RMap)l[m]).Id1 == g1.getBondNumber(testBond))
{
testBond2 = bonds2[((RMap)l[m]).Id2];
for (int n = 0; n < 2; n++)
{
System.Collections.IList bondsToTest = g2.getConnectedBondsVector(atom2[n]);
if (bondsToTest.Contains(testBond2))
{
RMap map;
if (j == n)
{
map = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[0]));
}
else
{
map = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[0]));
}
if (!result.Contains(map))
{
result.Add(map);
}
RMap map2;
if (j == n)
{
map2 = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[1]));
}
else
{
map2 = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[1]));
}
if (!result.Contains(map2))
{
result.Add(map2);
}
}
}
}
}
}
}
}
}
return(result);
}
/// <summary> Saturate atom by adjusting its bond orders.</summary>
public virtual bool newSaturate(IBond bond, IAtomContainer atomContainer)
{
IAtom[] atoms = bond.getAtoms();
IAtom atom = atoms[0];
IAtom partner = atoms[1];
//logger.debug(" saturating bond: ", atom.Symbol, "-", partner.Symbol);
IAtomType[] atomTypes1 = getAtomTypeFactory(bond.Builder).getAtomTypes(atom.Symbol);
IAtomType[] atomTypes2 = getAtomTypeFactory(bond.Builder).getAtomTypes(partner.Symbol);
bool bondOrderIncreased = true;
while (bondOrderIncreased && !isSaturated(bond, atomContainer))
{
//logger.debug("Can increase bond order");
bondOrderIncreased = false;
for (int atCounter1 = 0; atCounter1 < atomTypes1.Length && !bondOrderIncreased; atCounter1++)
{
IAtomType aType1 = atomTypes1[atCounter1];
//logger.debug(" condidering atom type: ", aType1);
if (couldMatchAtomType(atomContainer, atom, aType1))
{
//logger.debug(" trying atom type: ", aType1);
for (int atCounter2 = 0; atCounter2 < atomTypes2.Length && !bondOrderIncreased; atCounter2++)
{
IAtomType aType2 = atomTypes2[atCounter2];
//logger.debug(" condidering partner type: ", aType1);
if (couldMatchAtomType(atomContainer, partner, atomTypes2[atCounter2]))
{
//logger.debug(" with atom type: ", aType2);
if (bond.Order >= aType2.MaxBondOrder || bond.Order >= aType1.MaxBondOrder)
{
//logger.debug("Bond order not increased: atoms has reached (or exceeded) maximum bond order for this atom type");
}
else if (bond.Order < aType2.MaxBondOrder && bond.Order < aType1.MaxBondOrder)
{
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
bondOrderIncreased = true;
}
}
}
}
}
}
return isSaturated(bond, atomContainer);
}
/// <summary> Returns wether a bond is saturated. A bond is saturated if
/// <b>both</b> Atoms in the bond are saturated.
/// </summary>
public virtual bool isSaturated(IBond bond, IAtomContainer atomContainer)
{
IAtom[] atoms = bond.getAtoms();
bool isSaturated = true;
for (int i = 0; i < atoms.Length; i++)
{
isSaturated = isSaturated && this.isSaturated(atoms[i], atomContainer);
}
return isSaturated;
}