public void Save()
{
InsertMethParamsVisibility = false;
NewTabVisibility = true;
if (MainWindowViewModel.Instance.typeOfChallenge == "Chemical")
{
ChemModel chemModel = new ChemModel(MainWindowViewModel.dataServiceInstance,
MainWindowViewModel.methParamsInstance,
MainWindowViewModel.Instance.iconRepository.GetIcons());
chemModel.MakeExIcons();
chemModel.MakeCohorts();
chemModel.MakeCIPs();
Dictionary <int, DailyReport> report;
report = chemModel.MakeReport();
MainWindowViewModel.Instance.ShowReport(report);
}
else if (MainWindowViewModel.Instance.typeOfChallenge == "Nuclear")
{
NuclearAgent.CalculateNucChallenge(MainWindowViewModel.Instance.iconRepository.GetIcons());
/*
*
* Convert NuclearAgent.OutputTable(DataTable) to Dictionary
*
* */
//MainWindowViewModel.Instance.ShowReport(GetDict(NuclearAgent.OutputTable));
}
}
public override void StartDocument()
{
ChemFile = new ChemFile();
chemSequence = new ChemSequence();
chemModel = new ChemModel();
setOfMolecules = new ChemObjectSet <IAtomContainer>();
}
public void TestCreateNewMolecule_IChemModel()
{
var model = new ChemModel();
IAtomContainer ac = ChemModelManipulator.CreateNewMolecule(model);
Assert.AreEqual(1, model.MoleculeSet.Count);
Assert.AreEqual(ac, model.MoleculeSet[0]);
}
public void TestGetAllAtomContainers_IChemModel()
{
var filename = "NCDK.Data.MDL.a-pinene.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
ChemModel chemFile = (ChemModel)reader.Read((ChemObject) new ChemModel());
Assert.IsNotNull(chemFile);
var containersList = ChemModelManipulator.GetAllAtomContainers(chemFile);
Assert.AreEqual(1, containersList.Count());
}
public void TestGetAllAtomContainers_IChemModel_WithReactions()
{
var filename = "NCDK.Data.MDL.0024.stg02.rxn";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
MDLRXNV2000Reader reader = new MDLRXNV2000Reader(ins, ChemObjectReaderMode.Strict);
ChemModel chemFile = (ChemModel)reader.Read((ChemObject) new ChemModel());
Assert.IsNotNull(chemFile);
var containersList = ChemModelManipulator.GetAllAtomContainers(chemFile);
Assert.AreEqual(2, containersList.Count());
}
public void TestRemoveAtomAndConnectedElectronContainers_IChemModel_IAtom()
{
IAtomContainer mol1 = new AtomContainer();
IAtom atom1 = new Atom("Cl");
mol1.Atoms.Add(atom1);
mol1.Atoms.Add(new Atom("Cl"));
IBond bond1 = new Bond(mol1.Atoms[0], mol1.Atoms[1]);
mol1.Bonds.Add(bond1);
IAtomContainer mol2 = new AtomContainer();
IAtom atom2 = new Atom("I");
mol2.Atoms.Add(atom2);
mol2.Atoms.Add(new Atom("I"));
IBond bond2 = new Bond(mol2.Atoms[0], mol2.Atoms[1]);
mol2.Bonds.Add(bond2);
var molSet = ChemObjectBuilder.Instance.NewAtomContainerSet();
molSet.Add(mol1);
IReaction r = new Reaction();
r.Products.Add(mol2);
IReactionSet rSet = new ReactionSet
{
r
};
var model = new ChemModel
{
MoleculeSet = molSet,
ReactionSet = rSet
};
IAtom otherAtom = new Atom("Cl");
Assert.AreEqual(2, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(4, ChemModelManipulator.GetAtomCount(model));
ChemModelManipulator.RemoveAtomAndConnectedElectronContainers(model, otherAtom);
Assert.AreEqual(2, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(4, ChemModelManipulator.GetAtomCount(model));
ChemModelManipulator.RemoveAtomAndConnectedElectronContainers(model, atom1);
Assert.AreEqual(1, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(3, ChemModelManipulator.GetAtomCount(model));
ChemModelManipulator.RemoveAtomAndConnectedElectronContainers(model, atom2);
Assert.AreEqual(0, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(2, ChemModelManipulator.GetAtomCount(model));
}
public void TestMoleculeSet()
{
var list = new ChemObjectSet <IAtomContainer>
{
new AtomContainer(),
new AtomContainer()
};
var model = new ChemModel {
MoleculeSet = list
};
IChemModel roundTripped = CMLRoundTripTool.RoundTripChemModel(convertor, model);
var newList = roundTripped.MoleculeSet;
Assert.IsNotNull(newList);
Assert.AreEqual(2, newList.Count());
Assert.IsNotNull(newList[0]);
Assert.IsNotNull(newList[1]);
}
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);
}
public IEnumerable <KeyValuePair <int, DailyReport> > GetChemical([FromBody] Input input)
{
ChemModel model = new ChemModel(new DataService(), input.MethParams, input.Icons);
return(model.MakeReport());
}
private void createNiceMACiETitle(ChemModel chemModel)
{
//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'"
chemModel.setProperty(CDKConstants.TITLE, "MACIE " + currentEntry.getProperty(EnzymeName) + "= " + "PDB: " + currentEntry.getProperty(PDBCode) + ", " + "EC: " + currentEntry.getProperty(ECNumber));
}
/// <summary> Read a Reaction from a file in MACiE RDF format.
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IChemObject readReactions(bool selectEntry)
{
ChemSequence entries = new ChemSequence();
currentEntry = null;
int entryCounter = 0;
currentReactionStepSet = null;
while (input.Peek() != -1)
{
//UPGRADE_WARNING: Method 'java.io.LineNumberReader.readLine' was converted to 'System.IO.StreamReader.ReadLine' which may throw an exception. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1101'"
System.String line = input.ReadLine();
if (line.StartsWith("$RDFILE"))
{
entries = new ChemSequence();
}
else if (line.StartsWith("$DATM"))
{
entries.setProperty(CreationDate, line.Substring(7));
}
else if (line.StartsWith("$RIREG"))
{
// new entry, store previous entry if any
if (currentEntry != null)
{
// store previous entry
currentEntry.SetOfReactions = currentReactionStepSet;
createNiceMACiETitle(currentEntry);
entries.addChemModel(currentEntry);
fireFrameRead();
if (selectEntry && (entryCounter == selectedEntry.SettingValue))
{
//logger.info("Starting reading wanted frame: ", selectedEntry);
return(currentEntry);
}
else
{
//logger.debug("Not reading unwanted frame: " + entryCounter);
}
}
currentEntry = new ChemModel();
entryCounter++;
if (!selectEntry || entryCounter == selectedEntry.SettingValue)
{
readThisEntry = true;
}
else
{
readThisEntry = false;
}
currentReactionStepSet = new SetOfReactions();
}
else if (line.StartsWith("$DTYPE"))
{
System.String[] tuple = readDtypeDatumTuple(line);
System.String dataType = tuple[0];
System.String datum = tuple[1];
// now some regular expression wizardry
Match subLevelMatcher = subLevelDatum.Match(dataType);
if (subLevelMatcher.Success)
{
// sub level field found
System.String field = subLevelMatcher.Groups[2].Value;
System.String fieldNumber = subLevelMatcher.Groups[3].Value;
System.String subfield = subLevelMatcher.Groups[4].Value;
processSubLevelField(field, fieldNumber, subfield, datum);
}
else
{
Match topLevelMatcher = topLevelDatum.Match(dataType);
if (topLevelMatcher.Success)
{
// top level field found
System.String field = topLevelMatcher.Groups[2].Value;
processTopLevelField(field, datum);
}
else
{
//UPGRADE_ISSUE: Method 'java.io.LineNumberReader.getLineNumber' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioLineNumberReadergetLineNumber'"
//logger.error("Could not parse datum tuple of type ", dataType, " around line " + input.getLineNumber());
}
}
}
else
{
//UPGRADE_ISSUE: Method 'java.io.LineNumberReader.getLineNumber' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioLineNumberReadergetLineNumber'"
//logger.warn("Unrecognized command on line " + input.getLineNumber(), ": ", line);
}
}
if (currentEntry != null)
{
createNiceMACiETitle(currentEntry);
// store last entry
currentEntry.SetOfReactions = currentReactionStepSet;
entries.addChemModel(currentEntry);
fireFrameRead();
}
if (selectEntry)
{
// apparently selected last one, other already returned
return(currentEntry);
}
return(entries);
}
private void createNiceMACiETitle(ChemModel chemModel)
{
//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'"
chemModel.setProperty(CDKConstants.TITLE, "MACIE " + currentEntry.getProperty(EnzymeName) + "= " + "PDB: " + currentEntry.getProperty(PDBCode) + ", " + "EC: " + currentEntry.getProperty(ECNumber));
}
/// <summary> Read a Reaction from a file in MACiE RDF format.
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IChemObject readReactions(bool selectEntry)
{
ChemSequence entries = new ChemSequence();
currentEntry = null;
int entryCounter = 0;
currentReactionStepSet = null;
while (input.Peek() != -1)
{
//UPGRADE_WARNING: Method 'java.io.LineNumberReader.readLine' was converted to 'System.IO.StreamReader.ReadLine' which may throw an exception. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1101'"
System.String line = input.ReadLine();
if (line.StartsWith("$RDFILE"))
{
entries = new ChemSequence();
}
else if (line.StartsWith("$DATM"))
{
entries.setProperty(CreationDate, line.Substring(7));
}
else if (line.StartsWith("$RIREG"))
{
// new entry, store previous entry if any
if (currentEntry != null)
{
// store previous entry
currentEntry.SetOfReactions = currentReactionStepSet;
createNiceMACiETitle(currentEntry);
entries.addChemModel(currentEntry);
fireFrameRead();
if (selectEntry && (entryCounter == selectedEntry.SettingValue))
{
//logger.info("Starting reading wanted frame: ", selectedEntry);
return currentEntry;
}
else
{
//logger.debug("Not reading unwanted frame: " + entryCounter);
}
}
currentEntry = new ChemModel();
entryCounter++;
if (!selectEntry || entryCounter == selectedEntry.SettingValue)
{
readThisEntry = true;
}
else
{
readThisEntry = false;
}
currentReactionStepSet = new SetOfReactions();
}
else if (line.StartsWith("$DTYPE"))
{
System.String[] tuple = readDtypeDatumTuple(line);
System.String dataType = tuple[0];
System.String datum = tuple[1];
// now some regular expression wizardry
Match subLevelMatcher = subLevelDatum.Match(dataType);
if (subLevelMatcher.Success)
{
// sub level field found
System.String field = subLevelMatcher.Groups[2].Value;
System.String fieldNumber = subLevelMatcher.Groups[3].Value;
System.String subfield = subLevelMatcher.Groups[4].Value;
processSubLevelField(field, fieldNumber, subfield, datum);
}
else
{
Match topLevelMatcher = topLevelDatum.Match(dataType);
if (topLevelMatcher.Success)
{
// top level field found
System.String field = topLevelMatcher.Groups[2].Value;
processTopLevelField(field, datum);
}
else
{
//UPGRADE_ISSUE: Method 'java.io.LineNumberReader.getLineNumber' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioLineNumberReadergetLineNumber'"
//logger.error("Could not parse datum tuple of type ", dataType, " around line " + input.getLineNumber());
}
}
}
else
{
//UPGRADE_ISSUE: Method 'java.io.LineNumberReader.getLineNumber' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioLineNumberReadergetLineNumber'"
//logger.warn("Unrecognized command on line " + input.getLineNumber(), ": ", line);
}
}
if (currentEntry != null)
{
createNiceMACiETitle(currentEntry);
// store last entry
currentEntry.SetOfReactions = currentReactionStepSet;
entries.addChemModel(currentEntry);
fireFrameRead();
}
if (selectEntry)
{
// apparently selected last one, other already returned
return currentEntry;
}
return entries;
}