public void TestNewPseudoAtom_String_Point3d()
{
IChemObjectBuilder builder = RootObject.Builder;
IPseudoAtom atom = builder.NewPseudoAtom("Foo", new Vector3(1, 2, 3));
Assert.IsNotNull(atom);
}
public bool AreRootAtomsDefined()
{
foreach (var rgpNum in RGroupDefinitions.Keys)
{
bool represented = false;
foreach (var rootAtom in this.RootStructure.Atoms)
{
if (rootAtom is IPseudoAtom && rootAtom.Symbol.StartsWithChar('R'))
{
IPseudoAtom pseudo = (IPseudoAtom)rootAtom;
if (pseudo.Label.Length > 1)
{
int rootAtomRgrpNumber = int.Parse(pseudo.Label.Substring(1), NumberFormatInfo.InvariantInfo);
if (rootAtomRgrpNumber == rgpNum)
{
represented = true;
goto Break_RootLoop;
}
}
}
}
Break_RootLoop:
;
if (!represented)
{
return(false);
}
}
return(true);
}
public void TestRGPLine()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = builder.NewAtomContainer();
IPseudoAtom atom1 = builder.NewPseudoAtom();
atom1.Symbol = "R";
atom1.Label = "R12";
IAtom atom2 = builder.NewAtom("C");
IBond bond = builder.NewBond(atom1, atom2);
IPseudoAtom atom3 = builder.NewPseudoAtom();
atom3.Symbol = "A";
atom3.Label = "A";
IBond bond2 = builder.NewBond(atom3, atom2);
molecule.Atoms.Add(atom1);
molecule.Atoms.Add(atom2);
molecule.Atoms.Add(atom3);
molecule.Bonds.Add(bond);
molecule.Bonds.Add(bond2);
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
Assert.IsTrue(-1 != output.IndexOf("R#"), "Test for R#");
Assert.IsTrue(-1 != output.IndexOf("M RGP 1 1 12"), "Test for RGP line");
}
public void TestNewPseudoAtom_String()
{
IChemObjectBuilder builder = RootObject.Builder;
IPseudoAtom atom = builder.NewPseudoAtom("Foo");
Assert.IsNotNull(atom);
}
public void TestNewPseudoAtom_IAtom()
{
IChemObjectBuilder builder = RootObject.Builder;
IPseudoAtom atom = builder.NewPseudoAtom(builder.NewAtom());
Assert.IsNotNull(atom);
}
public void TestNewPseudoAtom_IElement()
{
IChemObjectBuilder builder = RootObject.Builder;
IPseudoAtom atom = builder.NewPseudoAtom(ChemicalElement.R);
Assert.IsNotNull(atom);
}
private void SerializePseudoAtomFields(INode rdfAtom, IPseudoAtom atom)
{
SerializeAtomFields(rdfAtom, atom);
if (atom.Label != null)
{
g.Assert(new Triple(rdfAtom, P_HASLABEL, g.CreateLiteralNode(atom.Label)));
}
}
/// <summary>
/// Safely access the label of a pseudo atom. If the label is null or empty, the default label is
/// returned.
/// </summary>
/// <param name="atom">the pseudo</param>
/// <returns>pseudo label</returns>
public static string AccessPseudoLabel(IPseudoAtom atom, string defaultLabel)
{
var label = atom.Label;
if (!string.IsNullOrEmpty(label))
{
return(label);
}
return(defaultLabel);
}
public void TestPseudoAtomLabels()
{
using (var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.pseudoatomsv3000.mol"))
using (MDLV3000Reader reader = new MDLV3000Reader(ins))
{
IAtomContainer molecule = builder.NewAtomContainer();
molecule = reader.Read(molecule);
reader.Close();
Assert.IsTrue(molecule.Atoms[9] is IPseudoAtom);
Assert.AreEqual("R", molecule.Atoms[9].Symbol);
IPseudoAtom pa = (IPseudoAtom)molecule.Atoms[9];
Assert.AreEqual("Leu", pa.Label);
}
}
public void TestWritePseudoAtoms_nullLabel()
{
IAtomContainer container = builder.NewAtomContainer();
IAtom c1 = builder.NewAtom("C");
IPseudoAtom nullAtom = builder.NewPseudoAtom("");
nullAtom.Label = null;
container.Atoms.Add(c1);
container.Atoms.Add(nullAtom);
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(container);
writer.Close();
string output = sw.ToString();
Assert.IsTrue(output.Contains("R"));
}
public override void TestSetExactMass_Double()
{
IPseudoAtom atom = (IPseudoAtom)NewChemObject();
atom.ExactMass = 12.001;
}
/// <summary> Read a Molecule from a file in MDL sd format
///
/// </summary>
/// <returns> The Molecule that was read from the MDL file.
/// </returns>
private IMolecule readMolecule(IMolecule molecule)
{
//logger.debug("Reading new molecule");
int linecount = 0;
int atoms = 0;
int bonds = 0;
int atom1 = 0;
int atom2 = 0;
int order = 0;
int stereo = 0;
int RGroupCounter = 1;
int Rnumber = 0;
System.String[] rGroup = null;
double x = 0.0;
double y = 0.0;
double z = 0.0;
double totalZ = 0.0;
//int[][] conMat = new int[0][0];
//String help;
IBond bond;
IAtom atom;
System.String line = "";
try
{
//logger.info("Reading header");
line = input.ReadLine(); linecount++;
if (line == null)
{
return(null);
}
//logger.debug("Line " + linecount + ": " + line);
if (line.StartsWith("$$$$"))
{
//logger.debug("File is empty, returning empty molecule");
return(molecule);
}
if (line.Length > 0)
{
molecule.setProperty(CDKConstants.TITLE, line);
}
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
if (line.Length > 0)
{
molecule.setProperty(CDKConstants.REMARK, line);
}
//logger.info("Reading rest of file");
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
atoms = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
//logger.debug("Atomcount: " + atoms);
bonds = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
//logger.debug("Bondcount: " + bonds);
// read ATOM block
//logger.info("Reading atom block");
for (int f = 0; f < atoms; f++)
{
line = input.ReadLine(); linecount++;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
x = System.Double.Parse(line.Substring(0, (10) - (0)).Trim());
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
y = System.Double.Parse(line.Substring(10, (20) - (10)).Trim());
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
z = System.Double.Parse(line.Substring(20, (30) - (20)).Trim());
totalZ += System.Math.Abs(z); // *all* values should be zero, not just the sum
//logger.debug("Coordinates: " + x + "; " + y + "; " + z);
System.String element = line.Substring(31, (34) - (31)).Trim();
//logger.debug("Atom type: ", element);
if (IsotopeFactory.getInstance(molecule.Builder).isElement(element))
{
atom = IsotopeFactory.getInstance(molecule.Builder).configure(molecule.Builder.newAtom(element));
}
else
{
//logger.debug("Atom ", element, " is not an regular element. Creating a PseudoAtom.");
//check if the element is R
rGroup = element.Split(new char[] { '^', 'R' }); // ????
if (rGroup.Length > 1)
{
try
{
Rnumber = System.Int32.Parse(rGroup[(rGroup.Length - 1)]);
RGroupCounter = Rnumber;
}
catch (System.Exception ex)
{
Rnumber = RGroupCounter;
RGroupCounter++;
}
element = "R" + Rnumber;
}
atom = molecule.Builder.newPseudoAtom(element);
}
// store as 3D for now, convert to 2D (if totalZ == 0.0) later
atom.setPoint3d(new Point3d(x, y, z));
// parse further fields
System.String massDiffString = line.Substring(34, (36) - (34)).Trim();
//logger.debug("Mass difference: ", massDiffString);
if (!(atom is IPseudoAtom))
{
try
{
int massDiff = System.Int32.Parse(massDiffString);
if (massDiff != 0)
{
IIsotope major = IsotopeFactory.getInstance(molecule.Builder).getMajorIsotope(element);
atom.AtomicNumber = major.AtomicNumber + massDiff;
}
}
catch (System.Exception exception)
{
//logger.error("Could not parse mass difference field");
}
}
else
{
//logger.error("Cannot set mass difference for a non-element!");
}
System.String chargeCodeString = line.Substring(36, (39) - (36)).Trim();
//logger.debug("Atom charge code: ", chargeCodeString);
int chargeCode = System.Int32.Parse(chargeCodeString);
if (chargeCode == 0)
{
// uncharged species
}
else if (chargeCode == 1)
{
atom.setFormalCharge(+3);
}
else if (chargeCode == 2)
{
atom.setFormalCharge(+2);
}
else if (chargeCode == 3)
{
atom.setFormalCharge(+1);
}
else if (chargeCode == 4)
{
}
else if (chargeCode == 5)
{
atom.setFormalCharge(-1);
}
else if (chargeCode == 6)
{
atom.setFormalCharge(-2);
}
else if (chargeCode == 7)
{
atom.setFormalCharge(-3);
}
try
{
// read the mmm field as position 61-63
System.String reactionAtomIDString = line.Substring(60, (63) - (60)).Trim();
//logger.debug("Parsing mapping id: ", reactionAtomIDString);
try
{
int reactionAtomID = System.Int32.Parse(reactionAtomIDString);
if (reactionAtomID != 0)
{
atom.ID = reactionAtomIDString;
}
}
catch (System.Exception exception)
{
//logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");
//logger.debug(exception);
}
}
catch (System.Exception exception)
{
// older mol files don't have all these fields...
//logger.warn("A few fields are missing. Older MDL MOL file?");
}
molecule.addAtom(atom);
}
// convert to 2D, if totalZ == 0
if (totalZ == 0.0 && !forceReadAs3DCoords.Set)
{
//logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");
IAtom[] atomsToUpdate = molecule.Atoms;
for (int f = 0; f < atomsToUpdate.Length; f++)
{
IAtom atomToUpdate = atomsToUpdate[f];
Point3d p3d = atomToUpdate.getPoint3d();
atomToUpdate.setPoint2d(new Point2d(p3d.x, p3d.y));
atomToUpdate.setPoint3d(null);
}
}
// read BOND block
//logger.info("Reading bond block");
for (int f = 0; f < bonds; f++)
{
line = input.ReadLine(); linecount++;
atom1 = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
atom2 = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
order = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
if (line.Length > 12)
{
stereo = System.Int32.Parse(line.Substring(9, (12) - (9)).Trim());
}
else
{
//logger.warn("Missing expected stereo field at line: " + line);
}
//if (//logger.DebugEnabled)
//{
// //logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order);
//}
if (stereo == 1)
{
// MDL up bond
stereo = CDKConstants.STEREO_BOND_UP;
}
else if (stereo == 6)
{
// MDL down bond
stereo = CDKConstants.STEREO_BOND_DOWN;
}
else if (stereo == 4)
{
//MDL bond undefined
stereo = CDKConstants.STEREO_BOND_UNDEFINED;
}
// interpret CTfile's special bond orders
IAtom a1 = molecule.getAtomAt(atom1 - 1);
IAtom a2 = molecule.getAtomAt(atom2 - 1);
if (order == 4)
{
// aromatic bond
bond = molecule.Builder.newBond(a1, a2, CDKConstants.BONDORDER_AROMATIC, stereo);
// mark both atoms and the bond as aromatic
bond.setFlag(CDKConstants.ISAROMATIC, true);
a1.setFlag(CDKConstants.ISAROMATIC, true);
a2.setFlag(CDKConstants.ISAROMATIC, true);
molecule.addBond(bond);
}
else
{
bond = molecule.Builder.newBond(a1, a2, (double)order, stereo);
molecule.addBond(bond);
}
}
// read PROPERTY block
//logger.info("Reading property block");
while (true)
{
line = input.ReadLine(); linecount++;
if (line == null)
{
throw new CDKException("The expected property block is missing!");
}
if (line.StartsWith("M END"))
{
break;
}
bool lineRead = false;
if (line.StartsWith("M CHG"))
{
// FIXME: if this is encountered for the first time, all
// atom charges should be set to zero first!
int infoCount = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
System.String token = st.NextToken();
int atomNumber = System.Int32.Parse(token.Trim());
token = st.NextToken();
int charge = System.Int32.Parse(token.Trim());
molecule.getAtomAt(atomNumber - 1).setFormalCharge(charge);
}
}
else if (line.StartsWith("M ISO"))
{
try
{
System.String countString = line.Substring(6, (9) - (6)).Trim();
int infoCount = System.Int32.Parse(countString);
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
int atomNumber = System.Int32.Parse(st.NextToken().Trim());
int absMass = System.Int32.Parse(st.NextToken().Trim());
if (absMass != 0)
{
IAtom isotope = molecule.getAtomAt(atomNumber - 1);
isotope.MassNumber = absMass;
}
}
}
catch (System.FormatException 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'"
System.String error = "Error (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in isotope information on line: " + line, exception);
}
}
else if (line.StartsWith("M RAD"))
{
try
{
System.String countString = line.Substring(6, (9) - (6)).Trim();
int infoCount = System.Int32.Parse(countString);
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
int atomNumber = System.Int32.Parse(st.NextToken().Trim());
int spinMultiplicity = System.Int32.Parse(st.NextToken().Trim());
if (spinMultiplicity > 1)
{
IAtom radical = molecule.getAtomAt(atomNumber - 1);
for (int j = 2; j <= spinMultiplicity; j++)
{
// 2 means doublet -> one unpaired electron
// 3 means triplet -> two unpaired electron
molecule.addElectronContainer(molecule.Builder.newSingleElectron(radical));
}
}
}
}
catch (System.FormatException 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'"
System.String error = "Error (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in radical information on line: " + line, exception);
}
}
else if (line.StartsWith("G "))
{
try
{
System.String atomNumberString = line.Substring(3, (6) - (3)).Trim();
int atomNumber = System.Int32.Parse(atomNumberString);
//String whatIsThisString = line.substring(6,9).trim();
System.String atomName = input.ReadLine();
// convert Atom into a PseudoAtom
IAtom prevAtom = molecule.getAtomAt(atomNumber - 1);
IPseudoAtom pseudoAtom = molecule.Builder.newPseudoAtom(atomName);
if (prevAtom.getPoint2d() != null)
{
pseudoAtom.setPoint2d(prevAtom.getPoint2d());
}
if (prevAtom.getPoint3d() != null)
{
pseudoAtom.setPoint3d(prevAtom.getPoint3d());
}
AtomContainerManipulator.replaceAtomByAtom(molecule, prevAtom, pseudoAtom);
}
catch (System.FormatException exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error (" + exception.ToString() + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in group information on line: " + line, exception);
}
}
if (!lineRead)
{
//logger.warn("Skipping line in property block: ", line);
}
}
}
catch (CDKException 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'"
System.String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw exception;
}
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'"
System.String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
return(molecule);
}
// Creates a CxSmilesState from a molecule with atom labels, repeat units, multi-center bonds etc
private static CxSmilesState GetCxSmilesState(SmiFlavors flavour, IAtomContainer mol)
{
CxSmilesState state = new CxSmilesState
{
atomCoords = new List <double[]>(),
coordFlag = false
};
// set the atom labels, values, and coordinates,
// and build the atom->idx map required by other parts
var atomidx = new Dictionary <IAtom, int>();
for (int idx = 0; idx < mol.Atoms.Count; idx++)
{
IAtom atom = mol.Atoms[idx];
if (atom is IPseudoAtom)
{
if (state.atomLabels == null)
{
state.atomLabels = new SortedDictionary <int, string>();
}
IPseudoAtom pseudo = (IPseudoAtom)atom;
if (pseudo.AttachPointNum > 0)
{
state.atomLabels[idx] = "_AP" + pseudo.AttachPointNum;
}
else
{
if (!"*".Equals(pseudo.Label, StringComparison.Ordinal))
{
state.atomLabels[idx] = pseudo.Label;
}
}
}
object comment = atom.GetProperty <object>(CDKPropertyName.Comment);
if (comment != null)
{
if (state.atomValues == null)
{
state.atomValues = new SortedDictionary <int, string>();
}
state.atomValues[idx] = comment.ToString();
}
atomidx[atom] = idx;
var p2 = atom.Point2D;
var p3 = atom.Point3D;
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.Cx2dCoordinates) && p2 != null)
{
state.atomCoords.Add(new double[] { p2.Value.X, p2.Value.Y, 0 });
state.coordFlag = true;
}
else if (SmiFlavorTool.IsSet(flavour, SmiFlavors.Cx3dCoordinates) && p3 != null)
{
state.atomCoords.Add(new double[] { p3.Value.X, p3.Value.Y, p3.Value.Z });
state.coordFlag = true;
}
else if (SmiFlavorTool.IsSet(flavour, SmiFlavors.CxCoordinates))
{
state.atomCoords.Add(new double[3]);
}
}
if (!state.coordFlag)
{
state.atomCoords = null;
}
// radicals
if (mol.SingleElectrons.Count > 0)
{
state.atomRads = new SortedDictionary <int, CxSmilesState.Radical>();
foreach (ISingleElectron radical in mol.SingleElectrons)
{
// 0->1, 1->2, 2->3
if (!state.atomRads.TryGetValue(EnsureNotNull(atomidx[radical.Atom]), out CxSmilesState.Radical val))
{
val = CxSmilesState.Radical.Monovalent;
}
else if (val == CxSmilesState.Radical.Monovalent)
{
val = CxSmilesState.Radical.Divalent;
}
else if (val == CxSmilesState.Radical.Divalent)
{
val = CxSmilesState.Radical.Trivalent;
}
else if (val == CxSmilesState.Radical.Trivalent)
{
throw new ArgumentException("Invalid radical state, can not be more than trivalent");
}
state.atomRads[atomidx[radical.Atom]] = val;
}
}
var sgroups = mol.GetCtabSgroups();
if (sgroups != null)
{
state.sgroups = new List <CxSmilesState.PolymerSgroup>();
state.positionVar = new SortedDictionary <int, IList <int> >();
foreach (Sgroup sgroup in sgroups)
{
switch (sgroup.Type)
{
// polymer SRU
case SgroupType.CtabStructureRepeatUnit:
case SgroupType.CtabMonomer:
case SgroupType.CtabMer:
case SgroupType.CtabCopolymer:
case SgroupType.CtabCrossLink:
case SgroupType.CtabModified:
case SgroupType.CtabMixture:
case SgroupType.CtabFormulation:
case SgroupType.CtabAnyPolymer:
case SgroupType.CtabGeneric:
case SgroupType.CtabComponent:
case SgroupType.CtabGraft:
string supscript = (string)sgroup.GetValue(SgroupKey.CtabConnectivity);
state.sgroups.Add(new CxSmilesState.PolymerSgroup(GetSgroupPolymerKey(sgroup),
ToAtomIdxs(sgroup.Atoms, atomidx),
sgroup.Subscript,
supscript));
break;
case SgroupType.ExtMulticenter:
IAtom beg = null;
List <IAtom> ends = new List <IAtom>();
ISet <IBond> bonds = sgroup.Bonds;
if (bonds.Count != 1)
{
throw new ArgumentException("Multicenter Sgroup in inconsistent state!");
}
IBond bond = bonds.First();
foreach (IAtom atom in sgroup.Atoms)
{
if (bond.Contains(atom))
{
if (beg != null)
{
throw new ArgumentException("Multicenter Sgroup in inconsistent state!");
}
beg = atom;
}
else
{
ends.Add(atom);
}
}
state.positionVar[EnsureNotNull(atomidx[beg])] =
ToAtomIdxs(ends, atomidx);
break;
case SgroupType.CtabAbbreviation:
case SgroupType.CtabMultipleGroup:
// display shortcuts are not output
break;
case SgroupType.CtabData:
// can be generated but currently ignored
break;
default:
throw new NotSupportedException("Unsupported Sgroup Polymer");
}
}
}
return(state);
}