public static IAtomContainer GetLargestMoleculeFragment(
IAtomContainer mol,
out int acc)
{
AtomContainerSet acs;
IAtomContainer mol2, molMain = null;
acs = null;
if (ConnectivityChecker.isConnected(mol))
{
acc = 1;
return(mol);
}
acs = (AtomContainerSet)ConnectivityChecker.partitionIntoMolecules(mol);
int largestAc = -1;
acc = acs.getAtomContainerCount();
for (int aci = 0; aci < acc; aci++)
{
mol2 = acs.getAtomContainer(aci);
int ac2 = mol2.getAtomCount();
if (ac2 > largestAc)
{
largestAc = mol2.getAtomCount();
molMain = mol2;
}
}
return(molMain);
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="smiles"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
/// <exception cref="InvalidSmilesException"> Description of the Exception
/// </exception>
public virtual Reaction parseReactionSmiles(System.String smiles)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(smiles, ">");
System.String reactantSmiles = tokenizer.NextToken();
System.String agentSmiles = "";
System.String productSmiles = tokenizer.NextToken();
if (tokenizer.HasMoreTokens())
{
agentSmiles = productSmiles;
productSmiles = tokenizer.NextToken();
}
Reaction reaction = new Reaction();
// add reactants
IMolecule reactantContainer = parseSmiles(reactantSmiles);
ISetOfMolecules reactantSet = ConnectivityChecker.partitionIntoMolecules(reactantContainer);
IMolecule[] reactants = reactantSet.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
reaction.addReactant(reactants[i]);
}
// add reactants
if (agentSmiles.Length > 0)
{
IMolecule agentContainer = parseSmiles(agentSmiles);
ISetOfMolecules agentSet = ConnectivityChecker.partitionIntoMolecules(agentContainer);
IMolecule[] agents = agentSet.Molecules;
for (int i = 0; i < agents.Length; i++)
{
reaction.addAgent(agents[i]);
}
}
// add products
IMolecule productContainer = parseSmiles(productSmiles);
ISetOfMolecules productSet = ConnectivityChecker.partitionIntoMolecules(productContainer);
IMolecule[] products = productSet.Molecules;
for (int i = 0; i < products.Length; i++)
{
reaction.addProduct(products[i]);
}
return(reaction);
}
/// <summary> Method that saturates a molecule by adding implicit hydrogens.
///
/// </summary>
/// <param name="container"> Molecule to saturate
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> implicit hydrogen </cdk.keyword>
//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'"
public virtual System.Collections.Hashtable addImplicitHydrogensToSatisfyValency(IAtomContainer container)
{
ISetOfMolecules moleculeSet = ConnectivityChecker.partitionIntoMolecules(container);
IMolecule[] molecules = moleculeSet.Molecules;
//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.Hashtable hydrogenAtomMap = new System.Collections.Hashtable();
for (int k = 0; k < molecules.Length; k++)
{
IMolecule molPart = molecules[k];
IAtom[] atoms = molPart.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
int[] hydrogens = addImplicitHydrogensToSatisfyValency(molPart, atoms[f]);
hydrogenAtomMap[atoms[f]] = hydrogens;
}
}
return(hydrogenAtomMap);
}
/// <summary>
/// Fragment a molecule
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static List <KeyValuePair <string, IAtomContainer> > FragmentMoleculeAndCanonicalizeSmiles(
IAtomContainer mol,
bool filterOutCommonCounterIons)
{
int aci, fi, i1;
KeyValuePair <string, IAtomContainer> kvp;
List <KeyValuePair <string, IAtomContainer> > frags = new List <KeyValuePair <string, IAtomContainer> >();
AtomContainerSet acs = (AtomContainerSet)ConnectivityChecker.partitionIntoMolecules(mol);
int acc = acs.getAtomContainerCount();
for (aci = 0; aci < acc; aci++)
{
IAtomContainer fragMol = acs.getAtomContainer(aci);
string fragSmiles = AtomContainerToSmiles(fragMol);
if (filterOutCommonCounterIons)
{
if (CommonSmallFragments.Contains(fragSmiles) ||
GetHeavyAtomCount(fragMol) <= 6)
{
continue;
}
}
kvp = new KeyValuePair <string, IAtomContainer>(fragSmiles, fragMol);
int ac = fragMol.getAtomCount();
for (fi = frags.Count - 1; fi >= 0; fi--) // insert into list so that fragments are ordered largest to smallest
{
if (frags[fi].Value.getAtomCount() >= ac)
{
break;
}
}
frags.Insert(fi + 1, kvp);
}
return(frags);
}
public static void removeElectronContainer(ISetOfAtomContainers set_Renamed, IElectronContainer electrons)
{
IAtomContainer[] acs = set_Renamed.AtomContainers;
for (int i = 0; i < acs.Length; i++)
{
IAtomContainer container = acs[i];
if (container.contains(electrons))
{
container.removeElectronContainer(electrons);
IMolecule[] molecules = ConnectivityChecker.partitionIntoMolecules(container).Molecules;
if (molecules.Length > 1)
{
set_Renamed.removeAtomContainer(container);
for (int k = 0; k < molecules.Length; k++)
{
set_Renamed.addAtomContainer(molecules[k]);
}
}
return;
}
}
}
/// <summary> Method that saturates a molecule by adding explicit hydrogens.
/// In order to get coordinates for these Hydrogens, you need to
/// remember the average bondlength of you molecule (coordinates for
/// all atoms should be available) by using
/// double bondLength = GeometryTools.getBondLengthAverage(atomContainer);
/// and then use this method here and then use
/// org.openscience.cdk.HydrogenPlacer(atomContainer, bondLength);
///
/// </summary>
/// <param name="molecule"> Molecule to saturate
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IMolecule molecule)
{
//logger.debug("Start of addExplicitHydrogensToSatisfyValency");
ISetOfMolecules moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule);
IMolecule[] molecules = moleculeSet.Molecules;
IAtomContainer changedAtomsAndBonds = molecule.Builder.newAtomContainer();
IAtomContainer intermediateContainer = null;
for (int k = 0; k < molecules.Length; k++)
{
IMolecule molPart = molecules[k];
IAtom[] atoms = molPart.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
intermediateContainer = addHydrogensToSatisfyValency(molPart, atoms[i], molecule);
changedAtomsAndBonds.add(intermediateContainer);
}
}
//logger.debug("End of addExplicitHydrogensToSatisfyValency");
return(changedAtomsAndBonds);
}
/// <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);
}
/// <summary>
/// BuildFingerprints
/// </summary>
public static void BuildFingerprints(
UniChemData icd)
{
IAtomContainer mol, mol2;
InChIGenerator ig = null;
int acc, aci, ci;
icd.Children.Clear();
string parentFIKHB = icd.GetFIKHB();
DateTime t0 = DateTime.Now;
mol = CdkMol.InChIToAtomContainer(icd.InChIString);
icd.CanonSmiles = CdkMol.AtomContainerToSmiles(mol);
InChIToAtomContainerTime += TimeOfDay.Delta(ref t0);
BitSetFingerprint fp = // generate a fingerprint
CdkFingerprint.BuildBitSetFingerprint(mol, FingerprintType.MACCS, -1, -1);
BuildFinterprintTime1 += TimeOfDay.Delta(ref t0);
icd.Fingerprint = fp;
if (ConnectivityChecker.isConnected(mol))
{
return; // single fragment
}
InChIGeneratorFactory igf = InChIGeneratorFactory.getInstance();
AtomContainerSet acs = (AtomContainerSet)ConnectivityChecker.partitionIntoMolecules(mol);
PartitionIntoMoleculesTime += TimeOfDay.Delta(ref t0);
acc = acs.getAtomContainerCount();
for (aci = 0; aci < acc; aci++)
{
mol2 = acs.getAtomContainer(aci);
GetAtomContainerTime += TimeOfDay.Delta(ref t0);
ig = igf.getInChIGenerator(mol2);
if (!IsAcceptableInchiStatus(ig))
{
continue;
}
string childKey = ig.getInchiKey();
string childFIKHB = UniChemUtil.GetFIKHB(childKey);
InChIGeneratorTime += TimeOfDay.Delta(ref t0);
fp = // generate a fingerprint for the fragment
CdkFingerprint.BuildBitSetFingerprint(mol2, FingerprintType.MACCS, -1, -1);
BuildFinterprintTime2 += TimeOfDay.Delta(ref t0);
for (ci = 0; ci < icd.Children.Count; ci++) // see if a dup child
{
if (icd.Children[ci].ChildFIKHB == childFIKHB)
{
break;
}
}
if (ci < icd.Children.Count)
{
continue; // skip if dup
}
UniChemFIKHBHierarchy fikhbHier = new UniChemFIKHBHierarchy();
fikhbHier.ParentFIKHB = parentFIKHB;
fikhbHier.ChildFIKHB = childFIKHB;
fikhbHier.CanonSmiles = CdkMol.AtomContainerToSmiles(mol2);
fikhbHier.Fingerprint = fp;
icd.Children.Add(fikhbHier);
}
return;
}
