private void markEnzymeResidueLocatorAtoms(Reaction currentReaction)
{
IAtom[] atoms = ReactionManipulator.getAllInOneContainer(currentReaction).Atoms;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] is EnzymeResidueLocator)
{
// skip atom
}
else if (atoms[i] is PseudoAtom)
{
PseudoAtom pseudo = (PseudoAtom)atoms[i];
//logger.debug("pseudo atom label: ", pseudo.Label);
//logger.debug("pseudo class: ", pseudo.GetType().FullName);
Match residueLocatorMatcher = residueLocator.Match(pseudo.Label);
if (residueLocatorMatcher.Success)
{
//logger.debug("Found residueLocator: ", pseudo.Label);
// replace atom with enzymeResidueLocator
IAtomContainer container = ReactionManipulator.getRelevantAtomContainer(currentReaction, pseudo);
//logger.debug("Replacing the pseudo atom with a ezymeResidueLocator atom");
AtomContainerManipulator.replaceAtomByAtom(container, pseudo, new EnzymeResidueLocator(pseudo));
}
}
}
}
public void UnknownSymbol_Pseudo()
{
var a = new PseudoAtom("R1")
{
ImplicitHydrogenCount = 0
};
Assert.AreEqual(Beam.Element.Unknown, new CDKToBeam().ToBeamAtom(a).Element);
}
public void TestGetDefaultAtomColor()
{
CDKAtomColors colors = new CDKAtomColors();
Assert.IsNotNull(colors);
IAtom imaginary = new PseudoAtom("Ix");
Assert.AreEqual(WPF::Media.Colors.Orange, colors.GetAtomColor(imaginary, WPF::Media.Colors.Orange));
}
public void TestGetDefaultAtomColor()
{
CDK2DAtomColors colors = new CDK2DAtomColors();
Assert.IsNotNull(colors);
IAtom imaginary = new PseudoAtom("Ix");
Assert.AreEqual(Color.FromRgb(0, 0, 0), colors.GetAtomColor(imaginary, WPF::Media.Colors.Black));
}
public void TestPseudoAtom()
{
var mol = new AtomContainer();
PseudoAtom atom = new PseudoAtom("N")
{
Label = "Glu55"
};
mol.Atoms.Add(atom);
IAtomContainer roundTrippedMol = CMLRoundTripTool.RoundTripMolecule(convertor, mol);
Assert.AreEqual(1, roundTrippedMol.Atoms.Count);
IAtom roundTrippedAtom = roundTrippedMol.Atoms[0];
Assert.IsNotNull(roundTrippedAtom);
Assert.IsTrue(roundTrippedAtom is IPseudoAtom);
Assert.AreEqual("Glu55", ((IPseudoAtom)roundTrippedAtom).Label);
}
public void TestChemModel()
{
ChemModel model = new ChemModel();
var moleculeSet = new ChemObjectSet <IAtomContainer>();
var mol = new AtomContainer();
PseudoAtom atom = new PseudoAtom("N");
mol.Atoms.Add(atom);
moleculeSet.Add(mol);
model.MoleculeSet = moleculeSet;
IChemModel roundTrippedModel = CMLRoundTripTool.RoundTripChemModel(convertor, model);
var roundTrippedMolSet = roundTrippedModel.MoleculeSet;
Assert.IsNotNull(roundTrippedMolSet);
Assert.AreEqual(1, roundTrippedMolSet.Count);
IAtomContainer roundTrippedMolecule = roundTrippedMolSet[0];
Assert.IsNotNull(roundTrippedMolecule);
Assert.AreEqual(1, roundTrippedMolecule.Atoms.Count);
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="s"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <exception cref="InvalidSmilesException"> Description of the Exception
/// </exception>
private Atom assembleAtom(System.String s)
{
//logger.debug("assembleAtom(): Assembling atom from: ", s);
Atom atom = null;
int position = 0;
System.String currentSymbol = null;
System.Text.StringBuilder isotopicNumber = new System.Text.StringBuilder();
char mychar;
//logger.debug("Parse everythings before and including element symbol");
do
{
try
{
mychar = s[position];
//logger.debug("Parsing char: " + mychar);
if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z'))
{
currentSymbol = getElementSymbol(s, position);
if (currentSymbol == null)
{
throw new InvalidSmilesException("Expected element symbol, found null!");
}
else
{
//logger.debug("Found element symbol: ", currentSymbol);
position = position + currentSymbol.Length;
if (currentSymbol.Length == 1)
{
if (!(currentSymbol.ToUpper()).Equals(currentSymbol))
{
currentSymbol = currentSymbol.ToUpper();
atom = new Atom(currentSymbol);
atom.Hybridization = CDKConstants.HYBRIDIZATION_SP2;
if (atom.getHydrogenCount() > 0)
{
atom.setHydrogenCount(atom.getHydrogenCount() - 1);
}
}
else
{
atom = new Atom(currentSymbol);
}
}
else
{
atom = new Atom(currentSymbol);
}
//logger.debug("Made atom: ", atom);
}
break;
}
else if (mychar >= '0' && mychar <= '9')
{
isotopicNumber.Append(mychar);
position++;
}
else if (mychar == '*')
{
currentSymbol = "*";
atom = new PseudoAtom(currentSymbol);
//logger.debug("Made atom: ", atom);
position++;
break;
}
else
{
throw new InvalidSmilesException("Found unexpected char: " + mychar);
}
}
catch (InvalidSmilesException exc)
{
//logger.error("InvalidSmilesException while parsing atom string: " + s);
//logger.debug(exc);
throw exc;
}
catch (System.Exception exception)
{
//logger.error("Could not parse atom string: ", s);
//logger.debug(exception);
throw new InvalidSmilesException("Could not parse atom string: " + s);
}
}while (position < s.Length);
if (isotopicNumber.ToString().Length > 0)
{
try
{
atom.MassNumber = System.Int32.Parse(isotopicNumber.ToString());
}
catch (System.Exception exception)
{
//logger.error("Could not set atom's atom number.");
//logger.debug(exception);
}
}
//logger.debug("Parsing part after element symbol (like charge): ", s.Substring(position));
int charge = 0;
int implicitHydrogens = 0;
while (position < s.Length)
{
try
{
mychar = s[position];
//logger.debug("Parsing char: " + mychar);
if (mychar == 'H')
{
// count implicit hydrogens
implicitHydrogens = getImplicitHydrogenCount(s, position);
position++;
if (implicitHydrogens > 1)
{
position++;
}
atom.setHydrogenCount(implicitHydrogens);
}
else if (mychar == '+' || mychar == '-')
{
charge = getCharge(s, position);
position++;
if (charge < -1 || charge > 1)
{
position++;
}
atom.setFormalCharge(charge);
}
else if (mychar == '@')
{
if (position < s.Length - 1 && s[position + 1] == '@')
{
position++;
}
//logger.warn("Ignoring stereo information for atom");
position++;
}
else
{
throw new InvalidSmilesException("Found unexpected char: " + mychar);
}
}
catch (InvalidSmilesException exc)
{
//logger.error("InvalidSmilesException while parsing atom string: ", s);
//logger.debug(exc);
throw exc;
}
catch (System.Exception exception)
{
//logger.error("Could not parse atom string: ", s);
//logger.debug(exception);
throw new InvalidSmilesException("Could not parse atom string: " + s);
}
}
return(atom);
}
/// <summary> Parses a SMILES string and returns a Molecule object.
///
/// </summary>
/// <param name="smiles"> A SMILES string
/// </param>
/// <returns> A Molecule representing the constitution
/// given in the SMILES string
/// </returns>
/// <exception cref="InvalidSmilesException"> Exception thrown when the SMILES string
/// is invalid
/// </exception>
public virtual Molecule parseSmiles(System.String smiles)
{
//logger.debug("parseSmiles()...");
Bond bond = null;
nodeCounter = 0;
bondStatus = 0;
bondIsAromatic = false;
bool bondExists = true;
thisRing = -1;
currentSymbol = null;
molecule = new Molecule();
position = 0;
// we don't want more than 1024 rings
rings = new Atom[1024];
ringbonds = new double[1024];
for (int f = 0; f < 1024; f++)
{
rings[f] = null;
ringbonds[f] = -1;
}
char mychar = 'X';
char[] chars = new char[1];
Atom lastNode = null;
System.Collections.ArrayList atomStack = new System.Collections.ArrayList();
System.Collections.ArrayList bondStack = new System.Collections.ArrayList();
Atom atom = null;
do
{
try
{
mychar = smiles[position];
//logger.debug("");
//logger.debug("Processing: " + mychar);
if (lastNode != null)
{
//logger.debug("Lastnode: ", lastNode.GetHashCode());
}
if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z') || (mychar == '*'))
{
status = 1;
//logger.debug("Found a must-be 'organic subset' element");
// only 'organic subset' elements allowed
atom = null;
if (mychar == '*')
{
currentSymbol = "*";
atom = new PseudoAtom("*");
}
else
{
currentSymbol = getSymbolForOrganicSubsetElement(smiles, position);
if (currentSymbol != null)
{
if (currentSymbol.Length == 1)
{
if (!(currentSymbol.ToUpper()).Equals(currentSymbol))
{
currentSymbol = currentSymbol.ToUpper();
atom = new Atom(currentSymbol);
atom.Hybridization = CDKConstants.HYBRIDIZATION_SP2;
}
else
{
atom = new Atom(currentSymbol);
}
}
else
{
atom = new Atom(currentSymbol);
}
//logger.debug("Made atom: ", atom);
}
else
{
throw new InvalidSmilesException("Found element which is not a 'organic subset' element. You must " + "use [" + mychar + "].");
}
}
molecule.addAtom(atom);
//logger.debug("Adding atom ", atom.GetHashCode());
if ((lastNode != null) && bondExists)
{
//logger.debug("Creating bond between ", atom.Symbol, " and ", lastNode.Symbol);
bond = new Bond(atom, lastNode, bondStatus);
if (bondIsAromatic)
{
bond.setFlag(CDKConstants.ISAROMATIC, true);
}
molecule.addBond(bond);
}
bondStatus = CDKConstants.BONDORDER_SINGLE;
lastNode = atom;
nodeCounter++;
position = position + currentSymbol.Length;
bondExists = true;
bondIsAromatic = false;
}
else if (mychar == '=')
{
position++;
if (status == 2 || smiles.Length == position + 1 || !(smiles[position] >= '0' && smiles[position] <= '9'))
{
bondStatus = CDKConstants.BONDORDER_DOUBLE;
}
else
{
bondStatusForRingClosure = CDKConstants.BONDORDER_DOUBLE;
}
}
else if (mychar == '#')
{
position++;
if (status == 2 || smiles.Length == position + 1 || !(smiles[position] >= '0' && smiles[position] <= '9'))
{
bondStatus = CDKConstants.BONDORDER_TRIPLE;
}
else
{
bondStatusForRingClosure = CDKConstants.BONDORDER_TRIPLE;
}
}
else if (mychar == '(')
{
atomStack.Add(lastNode);
//logger.debug("Stack:");
System.Collections.IEnumerator ses = atomStack.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' 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_javautilEnumerationhasMoreElements'"
while (ses.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' 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_javautilEnumerationnextElement'"
Atom a = (Atom)ses.Current;
//logger.debug("", a.GetHashCode());
}
//logger.debug("------");
bondStack.Add((double)bondStatus);
position++;
}
else if (mychar == ')')
{
lastNode = (Atom)SupportClass.StackSupport.Pop(atomStack);
//logger.debug("Stack:");
System.Collections.IEnumerator ses = atomStack.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' 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_javautilEnumerationhasMoreElements'"
while (ses.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' 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_javautilEnumerationnextElement'"
Atom a = (Atom)ses.Current;
//logger.debug("", a.GetHashCode());
}
//logger.debug("------");
bondStatus = ((System.Double)SupportClass.StackSupport.Pop(bondStack));
position++;
}
else if (mychar >= '0' && mychar <= '9')
{
status = 2;
chars[0] = mychar;
currentSymbol = new System.String(chars);
thisRing = (System.Int32.Parse(currentSymbol));
handleRing(lastNode);
position++;
}
else if (mychar == '%')
{
currentSymbol = getRingNumber(smiles, position);
thisRing = (System.Int32.Parse(currentSymbol));
handleRing(lastNode);
position += currentSymbol.Length + 1;
}
else if (mychar == '[')
{
currentSymbol = getAtomString(smiles, position);
atom = assembleAtom(currentSymbol);
molecule.addAtom(atom);
//logger.debug("Added atom: ", atom);
if (lastNode != null && bondExists)
{
bond = new Bond(atom, lastNode, bondStatus);
if (bondIsAromatic)
{
bond.setFlag(CDKConstants.ISAROMATIC, true);
}
molecule.addBond(bond);
//logger.debug("Added bond: ", bond);
}
bondStatus = CDKConstants.BONDORDER_SINGLE;
bondIsAromatic = false;
lastNode = atom;
nodeCounter++;
position = position + currentSymbol.Length + 2;
// plus two for [ and ]
bondExists = true;
}
else if (mychar == '.')
{
bondExists = false;
position++;
}
else if (mychar == '-')
{
bondExists = true;
// a simple single bond
position++;
}
else if (mychar == ':')
{
bondExists = true;
bondIsAromatic = true;
position++;
}
else if (mychar == '/' || mychar == '\\')
{
//logger.warn("Ignoring stereo information for double bond");
position++;
}
else if (mychar == '@')
{
if (position < smiles.Length - 1 && smiles[position + 1] == '@')
{
position++;
}
//logger.warn("Ignoring stereo information for atom");
position++;
}
else
{
throw new InvalidSmilesException("Unexpected character found: " + mychar);
}
}
catch (InvalidSmilesException exc)
{
//logger.error("InvalidSmilesException while parsing char (in parseSmiles()): " + mychar);
//logger.debug(exc);
throw exc;
}
catch (System.Exception exception)
{
//logger.error("Error while parsing char: " + mychar);
//logger.debug(exception);
throw new InvalidSmilesException("Error while parsing char: " + mychar);
}
//logger.debug("Parsing next char");
}while (position < smiles.Length);
// add implicit hydrogens
try
{
//logger.debug("before H-adding: ", molecule);
hAdder.addImplicitHydrogensToSatisfyValency(molecule);
//logger.debug("after H-adding: ", molecule);
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Error while calculation Hcount for SMILES atom: ", exception.Message);
}
// setup missing bond orders
try
{
valencyChecker.saturate(molecule);
//logger.debug("after adding missing bond orders: ", molecule);
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Error while calculation Hcount for SMILES atom: ", exception.Message);
}
// conceive aromatic perception
IMolecule[] moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule).Molecules;
//logger.debug("#mols ", moleculeSet.Length);
for (int i = 0; i < moleculeSet.Length; i++)
{
//logger.debug("mol: ", moleculeSet[i]);
try
{
valencyChecker.saturate(moleculeSet[i]);
//logger.debug(" after saturation: ", moleculeSet[i]);
if (HueckelAromaticityDetector.detectAromaticity(moleculeSet[i]))
{
//logger.debug("Structure is aromatic...");
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Could not perceive aromaticity: ", exception.Message);
//logger.debug(exception);
}
}
return(molecule);
}
private void processAnnotation(System.String field, System.String value_Renamed, Reaction reaction)
{
//logger.debug("Annote: ", field, "=", value_Renamed);
if (field.Equals("RxnAtts") || field.Equals("RxnType"))
{
// reaction attributes
System.String dictionary = "macie";
if (value_Renamed.Equals("Acid") || value_Renamed.Equals("Base"))
{
dictionary = "chemical";
}
addDictRefedAnnotation(reaction, "Attributes", value_Renamed);
}
else if (field.Equals("ResiduesPresent") || field.Equals("GroupTransferred") || field.Equals("BondFormed") || field.Equals("ReactiveCentres") || field.Equals("BondCleaved") || field.Equals("BondFormed") || field.Equals("Products") || field.Equals("ResiduesPresent"))
{
reaction.setProperty(new DictRef("macie:" + field, value_Renamed), value_Renamed);
}
else if (field.Equals("Reversible"))
{
if (value_Renamed.ToUpper().Equals("yes".ToUpper()))
{
reaction.Direction = IReaction_Fields.BIDIRECTIONAL;
addDictRefedAnnotation(reaction, "ReactionType", "ReversibleReaction");
}
}
else if (field.Equals("OverallReactionType"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed, ",");
int i = 0;
while (tokenizer.HasMoreTokens())
{
System.String token = tokenizer.NextToken();
i++;
reaction.setProperty(DictionaryDatabase.DICTREFPROPERTYNAME + ":field:overallReactionType:" + i, "macie:" + token.ToLower());
}
}
else
{
Match residueLocatorMatcher = residueLocator.Match(field);
if (residueLocatorMatcher.Success)
{
//logger.debug("Found residueLocator: ", field);
IAtom[] atoms = ReactionManipulator.getAllInOneContainer(reaction).Atoms;
bool found = false;
//logger.debug("Searching for given residueLocator through #atom: ", atoms.Length);
//logger.debug("Taken from reaction ", reaction.ID);
for (int i = 0; (i < atoms.Length && !found); i++)
{
if (atoms[i] is PseudoAtom)
{
// that is what we are looking for
PseudoAtom atom = (PseudoAtom)atoms[i];
if (atom.Label.Equals(field))
{
// we have a hit, now mark Atom with dict refs
addDictRefedAnnotation(atom, "ResidueRole", value_Renamed);
found = true;
}
}
}
if (!found)
{
//logger.error("MACiE annotation mentions a residue that does not exist: " + field);
}
}
else
{
//logger.error("Did not parse annotation: ", field);
}
}
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="s"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <exception cref="InvalidSmilesException"> Description of the Exception
/// </exception>
private Atom assembleAtom(System.String s)
{
//logger.debug("assembleAtom(): Assembling atom from: ", s);
Atom atom = null;
int position = 0;
System.String currentSymbol = null;
System.Text.StringBuilder isotopicNumber = new System.Text.StringBuilder();
char mychar;
//logger.debug("Parse everythings before and including element symbol");
do
{
try
{
mychar = s[position];
//logger.debug("Parsing char: " + mychar);
if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z'))
{
currentSymbol = getElementSymbol(s, position);
if (currentSymbol == null)
{
throw new InvalidSmilesException("Expected element symbol, found null!");
}
else
{
//logger.debug("Found element symbol: ", currentSymbol);
position = position + currentSymbol.Length;
if (currentSymbol.Length == 1)
{
if (!(currentSymbol.ToUpper()).Equals(currentSymbol))
{
currentSymbol = currentSymbol.ToUpper();
atom = new Atom(currentSymbol);
atom.Hybridization = CDKConstants.HYBRIDIZATION_SP2;
if (atom.getHydrogenCount() > 0)
{
atom.setHydrogenCount(atom.getHydrogenCount() - 1);
}
}
else
{
atom = new Atom(currentSymbol);
}
}
else
{
atom = new Atom(currentSymbol);
}
//logger.debug("Made atom: ", atom);
}
break;
}
else if (mychar >= '0' && mychar <= '9')
{
isotopicNumber.Append(mychar);
position++;
}
else if (mychar == '*')
{
currentSymbol = "*";
atom = new PseudoAtom(currentSymbol);
//logger.debug("Made atom: ", atom);
position++;
break;
}
else
{
throw new InvalidSmilesException("Found unexpected char: " + mychar);
}
}
catch (InvalidSmilesException exc)
{
//logger.error("InvalidSmilesException while parsing atom string: " + s);
//logger.debug(exc);
throw exc;
}
catch (System.Exception exception)
{
//logger.error("Could not parse atom string: ", s);
//logger.debug(exception);
throw new InvalidSmilesException("Could not parse atom string: " + s);
}
}
while (position < s.Length);
if (isotopicNumber.ToString().Length > 0)
{
try
{
atom.MassNumber = System.Int32.Parse(isotopicNumber.ToString());
}
catch (System.Exception exception)
{
//logger.error("Could not set atom's atom number.");
//logger.debug(exception);
}
}
//logger.debug("Parsing part after element symbol (like charge): ", s.Substring(position));
int charge = 0;
int implicitHydrogens = 0;
while (position < s.Length)
{
try
{
mychar = s[position];
//logger.debug("Parsing char: " + mychar);
if (mychar == 'H')
{
// count implicit hydrogens
implicitHydrogens = getImplicitHydrogenCount(s, position);
position++;
if (implicitHydrogens > 1)
{
position++;
}
atom.setHydrogenCount(implicitHydrogens);
}
else if (mychar == '+' || mychar == '-')
{
charge = getCharge(s, position);
position++;
if (charge < - 1 || charge > 1)
{
position++;
}
atom.setFormalCharge(charge);
}
else if (mychar == '@')
{
if (position < s.Length - 1 && s[position + 1] == '@')
{
position++;
}
//logger.warn("Ignoring stereo information for atom");
position++;
}
else
{
throw new InvalidSmilesException("Found unexpected char: " + mychar);
}
}
catch (InvalidSmilesException exc)
{
//logger.error("InvalidSmilesException while parsing atom string: ", s);
//logger.debug(exc);
throw exc;
}
catch (System.Exception exception)
{
//logger.error("Could not parse atom string: ", s);
//logger.debug(exception);
throw new InvalidSmilesException("Could not parse atom string: " + s);
}
}
return atom;
}
/// <summary> Parses a SMILES string and returns a Molecule object.
///
/// </summary>
/// <param name="smiles"> A SMILES string
/// </param>
/// <returns> A Molecule representing the constitution
/// given in the SMILES string
/// </returns>
/// <exception cref="InvalidSmilesException"> Exception thrown when the SMILES string
/// is invalid
/// </exception>
public virtual Molecule parseSmiles(System.String smiles)
{
//logger.debug("parseSmiles()...");
Bond bond = null;
nodeCounter = 0;
bondStatus = 0;
bondIsAromatic = false;
bool bondExists = true;
thisRing = - 1;
currentSymbol = null;
molecule = new Molecule();
position = 0;
// we don't want more than 1024 rings
rings = new Atom[1024];
ringbonds = new double[1024];
for (int f = 0; f < 1024; f++)
{
rings[f] = null;
ringbonds[f] = - 1;
}
char mychar = 'X';
char[] chars = new char[1];
Atom lastNode = null;
System.Collections.ArrayList atomStack = new System.Collections.ArrayList();
System.Collections.ArrayList bondStack = new System.Collections.ArrayList();
Atom atom = null;
do
{
try
{
mychar = smiles[position];
//logger.debug("");
//logger.debug("Processing: " + mychar);
if (lastNode != null)
{
//logger.debug("Lastnode: ", lastNode.GetHashCode());
}
if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z') || (mychar == '*'))
{
status = 1;
//logger.debug("Found a must-be 'organic subset' element");
// only 'organic subset' elements allowed
atom = null;
if (mychar == '*')
{
currentSymbol = "*";
atom = new PseudoAtom("*");
}
else
{
currentSymbol = getSymbolForOrganicSubsetElement(smiles, position);
if (currentSymbol != null)
{
if (currentSymbol.Length == 1)
{
if (!(currentSymbol.ToUpper()).Equals(currentSymbol))
{
currentSymbol = currentSymbol.ToUpper();
atom = new Atom(currentSymbol);
atom.Hybridization = CDKConstants.HYBRIDIZATION_SP2;
}
else
{
atom = new Atom(currentSymbol);
}
}
else
{
atom = new Atom(currentSymbol);
}
//logger.debug("Made atom: ", atom);
}
else
{
throw new InvalidSmilesException("Found element which is not a 'organic subset' element. You must " + "use [" + mychar + "].");
}
}
molecule.addAtom(atom);
//logger.debug("Adding atom ", atom.GetHashCode());
if ((lastNode != null) && bondExists)
{
//logger.debug("Creating bond between ", atom.Symbol, " and ", lastNode.Symbol);
bond = new Bond(atom, lastNode, bondStatus);
if (bondIsAromatic)
{
bond.setFlag(CDKConstants.ISAROMATIC, true);
}
molecule.addBond(bond);
}
bondStatus = CDKConstants.BONDORDER_SINGLE;
lastNode = atom;
nodeCounter++;
position = position + currentSymbol.Length;
bondExists = true;
bondIsAromatic = false;
}
else if (mychar == '=')
{
position++;
if (status == 2 || smiles.Length == position + 1 || !(smiles[position] >= '0' && smiles[position] <= '9'))
{
bondStatus = CDKConstants.BONDORDER_DOUBLE;
}
else
{
bondStatusForRingClosure = CDKConstants.BONDORDER_DOUBLE;
}
}
else if (mychar == '#')
{
position++;
if (status == 2 || smiles.Length == position + 1 || !(smiles[position] >= '0' && smiles[position] <= '9'))
{
bondStatus = CDKConstants.BONDORDER_TRIPLE;
}
else
{
bondStatusForRingClosure = CDKConstants.BONDORDER_TRIPLE;
}
}
else if (mychar == '(')
{
atomStack.Add(lastNode);
//logger.debug("Stack:");
System.Collections.IEnumerator ses = atomStack.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' 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_javautilEnumerationhasMoreElements'"
while (ses.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' 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_javautilEnumerationnextElement'"
Atom a = (Atom) ses.Current;
//logger.debug("", a.GetHashCode());
}
//logger.debug("------");
bondStack.Add((double) bondStatus);
position++;
}
else if (mychar == ')')
{
lastNode = (Atom) SupportClass.StackSupport.Pop(atomStack);
//logger.debug("Stack:");
System.Collections.IEnumerator ses = atomStack.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' 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_javautilEnumerationhasMoreElements'"
while (ses.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' 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_javautilEnumerationnextElement'"
Atom a = (Atom) ses.Current;
//logger.debug("", a.GetHashCode());
}
//logger.debug("------");
bondStatus = ((System.Double) SupportClass.StackSupport.Pop(bondStack));
position++;
}
else if (mychar >= '0' && mychar <= '9')
{
status = 2;
chars[0] = mychar;
currentSymbol = new System.String(chars);
thisRing = (System.Int32.Parse(currentSymbol));
handleRing(lastNode);
position++;
}
else if (mychar == '%')
{
currentSymbol = getRingNumber(smiles, position);
thisRing = (System.Int32.Parse(currentSymbol));
handleRing(lastNode);
position += currentSymbol.Length + 1;
}
else if (mychar == '[')
{
currentSymbol = getAtomString(smiles, position);
atom = assembleAtom(currentSymbol);
molecule.addAtom(atom);
//logger.debug("Added atom: ", atom);
if (lastNode != null && bondExists)
{
bond = new Bond(atom, lastNode, bondStatus);
if (bondIsAromatic)
{
bond.setFlag(CDKConstants.ISAROMATIC, true);
}
molecule.addBond(bond);
//logger.debug("Added bond: ", bond);
}
bondStatus = CDKConstants.BONDORDER_SINGLE;
bondIsAromatic = false;
lastNode = atom;
nodeCounter++;
position = position + currentSymbol.Length + 2;
// plus two for [ and ]
bondExists = true;
}
else if (mychar == '.')
{
bondExists = false;
position++;
}
else if (mychar == '-')
{
bondExists = true;
// a simple single bond
position++;
}
else if (mychar == ':')
{
bondExists = true;
bondIsAromatic = true;
position++;
}
else if (mychar == '/' || mychar == '\\')
{
//logger.warn("Ignoring stereo information for double bond");
position++;
}
else if (mychar == '@')
{
if (position < smiles.Length - 1 && smiles[position + 1] == '@')
{
position++;
}
//logger.warn("Ignoring stereo information for atom");
position++;
}
else
{
throw new InvalidSmilesException("Unexpected character found: " + mychar);
}
}
catch (InvalidSmilesException exc)
{
//logger.error("InvalidSmilesException while parsing char (in parseSmiles()): " + mychar);
//logger.debug(exc);
throw exc;
}
catch (System.Exception exception)
{
//logger.error("Error while parsing char: " + mychar);
//logger.debug(exception);
throw new InvalidSmilesException("Error while parsing char: " + mychar);
}
//logger.debug("Parsing next char");
}
while (position < smiles.Length);
// add implicit hydrogens
try
{
//logger.debug("before H-adding: ", molecule);
hAdder.addImplicitHydrogensToSatisfyValency(molecule);
//logger.debug("after H-adding: ", molecule);
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Error while calculation Hcount for SMILES atom: ", exception.Message);
}
// setup missing bond orders
try
{
valencyChecker.saturate(molecule);
//logger.debug("after adding missing bond orders: ", molecule);
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Error while calculation Hcount for SMILES atom: ", exception.Message);
}
// conceive aromatic perception
IMolecule[] moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule).Molecules;
//logger.debug("#mols ", moleculeSet.Length);
for (int i = 0; i < moleculeSet.Length; i++)
{
//logger.debug("mol: ", moleculeSet[i]);
try
{
valencyChecker.saturate(moleculeSet[i]);
//logger.debug(" after saturation: ", moleculeSet[i]);
if (HueckelAromaticityDetector.detectAromaticity(moleculeSet[i]))
{
//logger.debug("Structure is aromatic...");
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Could not perceive aromaticity: ", exception.Message);
//logger.debug(exception);
}
}
return molecule;
}
