/// <summary>
/// Get integer FormalCharge for an atom
/// </summary>
/// <param name="atom"></param>
/// <returns></returns>
public static int GetFormalCharge(IAtom atom)
{
if (atom.getFormalCharge() == null)
{
return(0);
}
else
{
return(atom.getFormalCharge().intValue());
}
}
/// <summary> Determines if the atom can be of type AtomType. That is, it sees if this
/// AtomType only differs in bond orders, or implicit hydrogen count.
/// </summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
//logger.debug("couldMatchAtomType: formal charge matches...");
if (atom.Hybridization == type.Hybridization)
{
//logger.debug("couldMatchAtomType: hybridization is OK...");
if (bondOrderSum + hcount <= type.BondOrderSum)
{
//logger.debug("couldMatchAtomType: bond order sum is OK...");
if (maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("couldMatchAtomType: max bond order is OK... We have a match!");
return(true);
}
}
else
{
//logger.debug("couldMatchAtomType: no match", "" + (bondOrderSum + hcount), " > ", "" + type.BondOrderSum);
}
}
}
else
{
//logger.debug("couldMatchAtomType: formal charge does NOT match...");
}
//logger.debug("couldMatchAtomType: No Match");
return(false);
}
/// <summary> Checks if the current atom has exceeded its bond order sum value.
///
/// </summary>
/// <param name="atom">The Atom to check
/// </param>
/// <param name="ac"> The atomcontainer context
/// </param>
/// <returns> oversaturated or not
/// </returns>
public virtual bool isOverSaturated(IAtom atom, IAtomContainer ac)
{
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
{
return(false);
}
double bondOrderSum = ac.getBondOrderSum(atom);
double maxBondOrder = ac.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
try
{
//logger.debug("*** Checking saturation of atom " + ac.getAtomNumber(atom) + " ***");
//logger.debug("bondOrderSum: " + bondOrderSum);
//logger.debug("maxBondOrder: " + maxBondOrder);
//logger.debug("hcount: " + hcount);
}
catch (System.Exception exc)
{
}
for (int f = 0; f < atomTypes.Length; f++)
{
if (bondOrderSum - charge + hcount > atomTypes[f].BondOrderSum)
{
//logger.debug("*** Good ! ***");
return(true);
}
}
//logger.debug("*** Bad ! ***");
return(false);
}
/// <summary> Calculate the number of missing hydrogens by substracting the number of
/// bonds for the atom from the expected number of bonds. Charges are included
/// in the calculation. The number of expected bonds is defined by the AtomType
/// generated with the AtomTypeFactory.
///
/// </summary>
/// <param name="atom"> Description of the Parameter
/// </param>
/// <param name="throwExceptionForUnknowAtom"> Should an exception be thrown if an unknown atomtype is found or 0 returned ?
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <seealso cref="AtomTypeFactory">
/// </seealso>
public virtual int calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, IBond[] connectedBonds, bool throwExceptionForUnknowAtom)
{
int missingHydrogen = 0;
if (atom is IPseudoAtom)
{
// don't figure it out... it simply does not lack H's
}
else if (atom.AtomicNumber == 1 || atom.Symbol.Equals("H"))
{
//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'"
missingHydrogen = (int)(1 - bondOrderSum - atom.getFormalCharge());
}
else
{
//logger.info("Calculating number of missing hydrogen atoms");
// get default atom
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0 && throwExceptionForUnknowAtom)
{
return(0);
}
//logger.debug("Found atomtypes: " + atomTypes.Length);
if (atomTypes.Length > 0)
{
IAtomType defaultAtom = atomTypes[0];
//logger.debug("DefAtom: ", defaultAtom);
//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'"
missingHydrogen = (int)(defaultAtom.BondOrderSum - bondOrderSum + atom.getFormalCharge());
if (atom.getFlag(CDKConstants.ISAROMATIC))
{
bool subtractOne = true;
for (int i = 0; i < connectedBonds.Length; i++)
{
if (connectedBonds[i].Order == 2 || connectedBonds[i].Order == CDKConstants.BONDORDER_AROMATIC)
{
subtractOne = false;
}
}
if (subtractOne)
{
missingHydrogen--;
}
}
//logger.debug("Atom: ", atom.Symbol);
//logger.debug(" max bond order: " + defaultAtom.BondOrderSum);
//logger.debug(" bond order sum: " + bondOrderSum);
//logger.debug(" charge : " + atom.getFormalCharge());
}
else
{
//logger.warn("Could not find atom type for ", atom.Symbol);
}
}
return(missingHydrogen);
}
/// <summary> Checks wether an Atom is saturated by comparing it with known AtomTypes.
/// It returns true if the atom is an PseudoAtom and when the element is not in the list.
/// </summary>
public virtual bool isSaturated(IAtom atom, IAtomContainer container)
{
if (atom is IPseudoAtom)
{
//logger.debug("don't figure it out... it simply does not lack H's");
return(true);
}
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
{
//logger.warn("Missing entry in atom type list for ", atom.Symbol);
return(true);
}
double bondOrderSum = container.getBondOrderSum(atom);
double maxBondOrder = container.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
//logger.debug("Checking saturation of atom ", atom.Symbol);
//logger.debug("bondOrderSum: ", bondOrderSum);
//logger.debug("maxBondOrder: ", maxBondOrder);
//logger.debug("hcount: ", hcount);
//logger.debug("charge: ", charge);
bool elementPlusChargeMatches = false;
for (int f = 0; f < atomTypes.Length; f++)
{
IAtomType type = atomTypes[f];
if (couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type))
{
if (bondOrderSum + hcount == type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("We have a match: ", type);
//logger.debug("Atom is saturated: ", atom.Symbol);
return(true);
}
else
{
// ok, the element and charge matche, but unfulfilled
elementPlusChargeMatches = true;
}
} // else: formal charges don't match
}
if (elementPlusChargeMatches)
{
//logger.debug("No, atom is not saturated.");
return(false);
}
// ok, the found atom was not in the list
throw new CDKException("The atom with element " + atom.Symbol + " and charge " + charge + " is not found.");
}
/// <summary> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
if (bondOrderSum + hcount <= type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug(" We have a match!");
return(true);
}
}
//logger.debug(" No Match");
return(false);
}
/// <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> Checks wether an Atom is saturated by comparing it with known AtomTypes.
/// It returns true if the atom is an PseudoAtom and when the element is not in the list.
/// </summary>
public virtual bool isSaturated(IAtom atom, IAtomContainer container)
{
if (atom is IPseudoAtom)
{
//logger.debug("don't figure it out... it simply does not lack H's");
return true;
}
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
{
//logger.warn("Missing entry in atom type list for ", atom.Symbol);
return true;
}
double bondOrderSum = container.getBondOrderSum(atom);
double maxBondOrder = container.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
//logger.debug("Checking saturation of atom ", atom.Symbol);
//logger.debug("bondOrderSum: ", bondOrderSum);
//logger.debug("maxBondOrder: ", maxBondOrder);
//logger.debug("hcount: ", hcount);
//logger.debug("charge: ", charge);
bool elementPlusChargeMatches = false;
for (int f = 0; f < atomTypes.Length; f++)
{
IAtomType type = atomTypes[f];
if (couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type))
{
if (bondOrderSum + hcount == type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("We have a match: ", type);
//logger.debug("Atom is saturated: ", atom.Symbol);
return true;
}
else
{
// ok, the element and charge matche, but unfulfilled
elementPlusChargeMatches = true;
}
} // else: formal charges don't match
}
if (elementPlusChargeMatches)
{
//logger.debug("No, atom is not saturated.");
return false;
}
// ok, the found atom was not in the list
throw new CDKException("The atom with element " + atom.Symbol + " and charge " + charge + " is not found.");
}
/// <summary> Determines if the atom can be of type AtomType. That is, it sees if this
/// AtomType only differs in bond orders, or implicit hydrogen count.
/// </summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
//logger.debug("couldMatchAtomType: formal charge matches...");
if (atom.Hybridization == type.Hybridization)
{
//logger.debug("couldMatchAtomType: hybridization is OK...");
if (bondOrderSum + hcount <= type.BondOrderSum)
{
//logger.debug("couldMatchAtomType: bond order sum is OK...");
if (maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("couldMatchAtomType: max bond order is OK... We have a match!");
return true;
}
}
else
{
//logger.debug("couldMatchAtomType: no match", "" + (bondOrderSum + hcount), " > ", "" + type.BondOrderSum);
}
}
}
else
{
//logger.debug("couldMatchAtomType: formal charge does NOT match...");
}
//logger.debug("couldMatchAtomType: No Match");
return false;
}
/// <summary> Creates a string for the charge of atom <code>a</code>. If the charge is 1
/// + is returned if it is -1 - is returned. The positive values all have + in
/// front of them.
///
/// </summary>
/// <param name="a"> Description of Parameter
/// </param>
/// <returns> string representing the charge on <code>a</code>
/// </returns>
private System.String generateChargeString(IAtom a)
{
int charge = a.getFormalCharge();
System.Text.StringBuilder buffer = new System.Text.StringBuilder(3);
if (charge > 0)
{
//Positive
buffer.Append('+');
if (charge > 1)
{
buffer.Append(charge);
}
}
else if (charge < 0)
{
//Negative
if (charge == -1)
{
buffer.Append('-');
}
else
{
buffer.Append(charge);
}
}
return buffer.ToString();
}
/// <summary> Tests the <code>ring</code> in the <code>molecule</code> for aromaticity. Uses the
/// Hückle rule (4n + 2) pie electrons. sp<sup>2</sup> hybridized C contibute 1 electron non
/// sp<sup>2</sup> hybridized heteroatoms contribute 2 electrons (N and O should never be sp in
/// or anything else in a ring and d electron elements get to complicated)
/// sp<sup>2</sup> hybridized heteroatoms contribute 1 electron hybridization is worked out by
/// counting the number of bonds with order 2. Therefore sp<sup>2</sup> hybridization is assumed
/// if there is one bond of order 2. Otherwise sp<sup>3</sup> hybridization is assumed.
///
/// </summary>
/// <param name="ring"> the ring to test
/// </param>
/// <param name="atomContainer"> the AtomContainer the ring is in
/// </param>
/// <returns> true if the ring is aromatic false otherwise.
/// </returns>
protected internal static bool isAromatic(IRing ring, IAtomContainer atomContainer)
{
IAtom[] ringAtoms = ring.Atoms;
int eCount = 0;
IBond[] conectedBonds;
int numDoubleBond = 0;
bool allConnectedBondsSingle;
for (int i = 0; i < ringAtoms.Length; i++)
{
IAtom atom = ringAtoms[i];
numDoubleBond = 0;
allConnectedBondsSingle = true;
conectedBonds = atomContainer.getConnectedBonds(atom);
for (int j = 0; j < conectedBonds.Length; j++)
{
IBond bond = conectedBonds[j];
if (bond.Order == 2 && ring.contains(bond))
{
numDoubleBond++;
}
// Count the Electron if bond order = 1.5
else if (bond.Order == 1.5 && ring.contains(bond))
{
numDoubleBond = 1;
}
if (bond.Order != 1)
{
allConnectedBondsSingle = false;
}
}
if (numDoubleBond == 1)
{
//C or heteroatoms both contibute 1 electron in sp2 hybridized form
eCount++;
}
else if (!atom.Symbol.Equals("C"))
{
//Heteroatom probably in sp3 hybrid therefore 2 electrons contributed.
eCount = eCount + 2;
}
else if (atom.getFlag(CDKConstants.ISAROMATIC))
{
eCount++;
}
else if (allConnectedBondsSingle && atom.Symbol.Equals("C") && atom.getFormalCharge() == 1.0)
{
// This is for tropylium and kinds.
// Dependence on hybridisation would be better:
// empty p-orbital is needed
continue;
}
else
{
return(false);
}
}
if (eCount - 2 != 0 && (eCount - 2) % 4 == 0)
{
return(true);
}
return(false);
}
/// <summary> Calculate the number of missing hydrogens by substracting the number of
/// bonds for the atom from the expected number of bonds. Charges are included
/// in the calculation. The number of expected bonds is defined by the AtomType
/// generated with the AtomTypeFactory.
///
/// </summary>
/// <param name="atom"> Description of the Parameter
/// </param>
/// <param name="throwExceptionForUnknowAtom"> Should an exception be thrown if an unknown atomtype is found or 0 returned ?
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <seealso cref="AtomTypeFactory">
/// </seealso>
public virtual int calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, IBond[] connectedBonds, bool throwExceptionForUnknowAtom)
{
int missingHydrogen = 0;
if (atom is IPseudoAtom)
{
// don't figure it out... it simply does not lack H's
}
else if (atom.AtomicNumber == 1 || atom.Symbol.Equals("H"))
{
//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'"
missingHydrogen = (int) (1 - bondOrderSum - atom.getFormalCharge());
}
else
{
//logger.info("Calculating number of missing hydrogen atoms");
// get default atom
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0 && throwExceptionForUnknowAtom)
return 0;
//logger.debug("Found atomtypes: " + atomTypes.Length);
if (atomTypes.Length > 0)
{
IAtomType defaultAtom = atomTypes[0];
//logger.debug("DefAtom: ", defaultAtom);
//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'"
missingHydrogen = (int) (defaultAtom.BondOrderSum - bondOrderSum + atom.getFormalCharge());
if (atom.getFlag(CDKConstants.ISAROMATIC))
{
bool subtractOne = true;
for (int i = 0; i < connectedBonds.Length; i++)
{
if (connectedBonds[i].Order == 2 || connectedBonds[i].Order == CDKConstants.BONDORDER_AROMATIC)
subtractOne = false;
}
if (subtractOne)
missingHydrogen--;
}
//logger.debug("Atom: ", atom.Symbol);
//logger.debug(" max bond order: " + defaultAtom.BondOrderSum);
//logger.debug(" bond order sum: " + bondOrderSum);
//logger.debug(" charge : " + atom.getFormalCharge());
}
else
{
//logger.warn("Could not find atom type for ", atom.Symbol);
}
}
return missingHydrogen;
}
/// <summary> Checks if the current atom has exceeded its bond order sum value.
///
/// </summary>
/// <param name="atom">The Atom to check
/// </param>
/// <param name="ac"> The atomcontainer context
/// </param>
/// <returns> oversaturated or not
/// </returns>
public virtual bool isOverSaturated(IAtom atom, IAtomContainer ac)
{
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
return false;
double bondOrderSum = ac.getBondOrderSum(atom);
double maxBondOrder = ac.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
try
{
//logger.debug("*** Checking saturation of atom " + ac.getAtomNumber(atom) + " ***");
//logger.debug("bondOrderSum: " + bondOrderSum);
//logger.debug("maxBondOrder: " + maxBondOrder);
//logger.debug("hcount: " + hcount);
}
catch (System.Exception exc)
{
}
for (int f = 0; f < atomTypes.Length; f++)
{
if (bondOrderSum - charge + hcount > atomTypes[f].BondOrderSum)
{
//logger.debug("*** Good ! ***");
return true;
}
}
//logger.debug("*** Bad ! ***");
return false;
}
/// <summary> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
if (bondOrderSum + hcount <= type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug(" We have a match!");
return true;
}
}
//logger.debug(" No Match");
return false;
}
