private void writeChemFile(IChemFile file)
{
IAtomContainer[] molecules = ChemFileManipulator.getAllAtomContainers(file);
for (int i = 0; i < molecules.Length; i++)
{
try
{
bool[] isVisible = new bool[molecules[i].AtomCount];
for (int k = 0; k < isVisible.Length; k++)
{
isVisible[k] = true;
}
writeMolecule(file.Builder.newMolecule(molecules[i]), isVisible);
}
catch (System.Exception exc)
{
}
}
}
/// <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);
}