/// <summary> Generates the SMILES string for the atom
///
/// </summary>
/// <param name="a"> the atom to generate the SMILES for.
/// </param>
/// <param name="buffer"> the string buffer that the atom is to be
/// apended to.
/// </param>
/// <param name="container"> the AtomContainer to analyze.
/// </param>
/// <param name="chiral"> is a chiral smiles wished?
/// </param>
/// <param name="parent"> the atom we came from.
/// </param>
/// <param name="atomsInOrderOfSmiles"> a vector containing the atoms in the order
/// they are in the smiles.
/// </param>
/// <param name="currentChain"> The chain we currently deal with.
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
private void parseAtom(IAtom a, System.Text.StringBuilder buffer, IAtomContainer container, bool chiral, bool[] doubleBondConfiguration, IAtom parent, System.Collections.ArrayList atomsInOrderOfSmiles, System.Collections.ArrayList currentChain)
{
System.String symbol = a.Symbol;
bool stereo = BondTools.isStereo(container, a);
bool brackets = symbol.Equals("B") || symbol.Equals("C") || symbol.Equals("N") || symbol.Equals("O") || symbol.Equals("P") || symbol.Equals("S") || symbol.Equals("F") || symbol.Equals("Br") || symbol.Equals("I") || symbol.Equals("Cl");
brackets = !brackets;
//System.out.println("in parseAtom()");
//Deal with the start of a double bond configuration
if (isStartOfDoubleBond(container, a, parent, doubleBondConfiguration))
{
buffer.Append('/');
}
if (a is IPseudoAtom)
{
buffer.Append("[*]");
}
else
{
System.String mass = generateMassString(a);
brackets = brackets | !mass.Equals("");
System.String charge = generateChargeString(a);
brackets = brackets | !charge.Equals("");
if (chiral && stereo)
{
brackets = true;
}
if (brackets)
{
buffer.Append('[');
}
buffer.Append(mass);
if (a.getFlag(CDKConstants.ISAROMATIC))
{
// Strictly speaking, this is wrong. Lower case is only used for sp2 atoms!
buffer.Append(a.Symbol.ToLower());
}
else if (a.Hybridization == CDKConstants.HYBRIDIZATION_SP2)
{
buffer.Append(a.Symbol.ToLower());
}
else
{
buffer.Append(symbol);
}
if (a.getProperty(RING_CONFIG) != null && a.getProperty(RING_CONFIG).Equals(UP))
{
buffer.Append('/');
}
if (a.getProperty(RING_CONFIG) != null && a.getProperty(RING_CONFIG).Equals(DOWN))
{
buffer.Append('\\');
}
if (chiral && stereo && (BondTools.isTrigonalBipyramidalOrOctahedral(container, a) != 0 || BondTools.isSquarePlanar(container, a) || BondTools.isTetrahedral(container, a, false) != 0))
{
buffer.Append('@');
}
if (chiral && stereo && BondTools.isSquarePlanar(container, a))
{
buffer.Append("SP1");
}
//chiral
//hcount
buffer.Append(charge);
if (brackets)
{
buffer.Append(']');
}
}
//System.out.println("in parseAtom() after dealing with Pseudoatom or not");
//Deal with the end of a double bond configuration
if (isEndOfDoubleBond(container, a, parent, doubleBondConfiguration))
{
IAtom viewFrom = null;
for (int i = 0; i < currentChain.Count; i++)
{
if (currentChain[i] == parent)
{
int k = i - 1;
while (k > -1)
{
if (currentChain[k] is IAtom)
{
viewFrom = (IAtom)currentChain[k];
break;
}
k--;
}
}
}
if (viewFrom == null)
{
for (int i = 0; i < atomsInOrderOfSmiles.Count; i++)
{
if (atomsInOrderOfSmiles[i] == parent)
{
viewFrom = (IAtom)atomsInOrderOfSmiles[i - 1];
}
}
}
bool afterThisAtom = false;
IAtom viewTo = null;
for (int i = 0; i < currentChain.Count; i++)
{
if (afterThisAtom && currentChain[i] is IAtom)
{
viewTo = (IAtom)currentChain[i];
break;
}
if (afterThisAtom && currentChain[i] is System.Collections.ArrayList)
{
viewTo = (IAtom)((System.Collections.ArrayList)currentChain[i])[0];
break;
}
if (a == currentChain[i])
{
afterThisAtom = true;
}
}
try
{
if (BondTools.isCisTrans(viewFrom, a, parent, viewTo, container))
{
buffer.Append('\\');
}
else
{
buffer.Append('/');
}
}
catch (CDKException ex)
{
//If the user wants a double bond configuration, where there is none, we ignore this.
}
}
System.Collections.ArrayList v = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
System.Collections.IEnumerator it = getRingOpenings(a, v).GetEnumerator();
System.Collections.IEnumerator it2 = v.GetEnumerator();
//System.out.println("in parseAtom() after checking for Ring openings");
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (it.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
System.Int32 integer = (System.Int32)it.Current;
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
IBond b = container.getBond((IAtom)it2.Current, a);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int type = (int)b.Order;
if (type == 2 && !b.getFlag(CDKConstants.ISAROMATIC))
{
buffer.Append("=");
}
else if (type == 3 && !b.getFlag(CDKConstants.ISAROMATIC))
{
buffer.Append("#");
}
buffer.Append(integer);
}
atomsInOrderOfSmiles.Add(a);
//System.out.println("End of parseAtom()");
}
/// <summary> Creates amino acid AminoAcid objects.
///
/// </summary>
/// <returns> aminoAcids, a HashMap containing the amino acids as AminoAcids.
/// </returns>
public static AminoAcid[] createAAs()
{
if (aminoAcids != null)
{
return(aminoAcids);
}
// Create set of AtomContainers
aminoAcids = new AminoAcid[20];
IChemFile list = new ChemFile();
//UPGRADE_ISSUE: Method 'java.lang.ClassLoader.getResourceAsStream' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassLoader'"
//UPGRADE_ISSUE: Method 'java.lang.Class.getClassLoader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassgetClassLoader'"
CMLReader reader = new CMLReader(Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + "list_aminoacids.cml"));//typeof(AminoAcids).getClassLoader().getResourceAsStream("data/templates/list_aminoacids.cml"));
try
{
list = (IChemFile)reader.read(list);
IAtomContainer[] containers = ChemFileManipulator.getAllAtomContainers(list);
for (int i = 0; i < containers.Length; i++)
{
//logger.debug("Adding AA: ", containers[i]);
// convert into an AminoAcid
AminoAcid aminoAcid = new AminoAcid();
IAtom[] atoms = containers[i].Atoms;
System.Collections.IEnumerator props = containers[i].Properties.Keys.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 (props.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'"
System.Object next = props.Current;
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Class.getName' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Prop class: " + next.GetType().FullName);
//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.debug("Prop: " + next.ToString());
if (next is DictRef)
{
DictRef dictRef = (DictRef)next;
// System.out.println("DictRef type: " + dictRef.getType());
if (dictRef.Type.Equals("pdb:residueName"))
{
//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'"
aminoAcid.setProperty(RESIDUE_NAME, containers[i].getProperty(dictRef).ToString().ToUpper());
}
else if (dictRef.Type.Equals("pdb:oneLetterCode"))
{
aminoAcid.setProperty(RESIDUE_NAME_SHORT, containers[i].getProperty(dictRef));
}
else if (dictRef.Type.Equals("pdb:id"))
{
aminoAcid.setProperty(ID, containers[i].getProperty(dictRef));
//logger.debug("Set AA ID to: ", containers[i].getProperty(dictRef));
}
else
{
//logger.error("Cannot deal with dictRef!");
}
}
}
for (int atomCount = 0; atomCount < atoms.Length; atomCount++)
{
IAtom atom = atoms[atomCount];
System.String dictRef = (System.String)atom.getProperty("org.openscience.cdk.dict");
if (dictRef != null && dictRef.Equals("pdb:nTerminus"))
{
aminoAcid.addNTerminus(atom);
}
else if (dictRef != null && dictRef.Equals("pdb:cTerminus"))
{
aminoAcid.addCTerminus(atom);
}
else
{
aminoAcid.addAtom(atom);
}
}
IBond[] bonds = containers[i].Bonds;
for (int bondCount = 0; bondCount < bonds.Length; bondCount++)
{
aminoAcid.addBond(bonds[bondCount]);
}
AminoAcidManipulator.removeAcidicOxygen(aminoAcid);
aminoAcid.setProperty(NO_ATOMS, "" + aminoAcid.AtomCount);
aminoAcid.setProperty(NO_BONDS, "" + aminoAcid.getBondCount());
if (i < aminoAcids.Length)
{
aminoAcids[i] = aminoAcid;
}
else
{
//logger.error("Could not store AminoAcid! Array too short!");
}
}
}
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("Failed reading file: ", exception.Message);
//logger.debug(exception);
}
return(aminoAcids);
}
