/// <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;
}
private int addArrayElementsTo(System.Collections.ArrayList toAddto, System.String array)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(array);
int i = 0;
while (tokenizer.HasMoreTokens())
{
toAddto.Add(tokenizer.NextToken());
i++;
}
return i;
}
public virtual void endElement(CMLStack xpath, System.String uri, System.String name, System.String raw)
{
////logger.debug("EndElement: ", name);
System.String cData = currentChars;
if ("bond".Equals(name))
{
if (!stereoGiven)
bondStereo.Add("");
if (bondStereo.Count > bondDictRefs.Count)
bondDictRefs.Add(null);
}
else if ("atom".Equals(name))
{
if (atomCounter > eltitles.Count)
{
eltitles.Add(null);
}
if (atomCounter > hCounts.Count)
{
/* while strictly undefined, assume zero
implicit hydrogens when no number is given */
hCounts.Add("0");
}
if (atomCounter > atomDictRefs.Count)
{
atomDictRefs.Add(null);
}
if (atomCounter > isotope.Count)
{
isotope.Add(null);
}
if (atomCounter > spinMultiplicities.Count)
{
spinMultiplicities.Add(null);
}
if (atomCounter > formalCharges.Count)
{
/* while strictly undefined, assume zero
implicit hydrogens when no number is given */
formalCharges.Add("0");
}
/* It may happen that not all atoms have
associated 2D or 3D coordinates. accept that */
if (atomCounter > x2.Count && x2.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
x2.Add(null);
y2.Add(null);
}
if (atomCounter > x3.Count && x3.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
x3.Add(null);
y3.Add(null);
z3.Add(null);
}
if (atomCounter > xfract.Count && xfract.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
xfract.Add(null);
yfract.Add(null);
zfract.Add(null);
}
}
else if ("molecule".Equals(name))
{
storeData();
cdo.endObject("Molecule");
}
else if ("crystal".Equals(name))
{
if (crystalScalar > 0)
{
// convert unit cell parameters to cartesians
Vector3d[] axes = CrystalGeometryTools.notionalToCartesian(unitcellparams[0], unitcellparams[1], unitcellparams[2], unitcellparams[3], unitcellparams[4], unitcellparams[5]);
aAxis = axes[0];
bAxis = axes[1];
cAxis = axes[2];
cartesianAxesSet = true;
cdo.startObject("a-axis");
cdo.setObjectProperty("a-axis", "x", aAxis.x.ToString());
cdo.setObjectProperty("a-axis", "y", aAxis.y.ToString());
cdo.setObjectProperty("a-axis", "z", aAxis.z.ToString());
cdo.endObject("a-axis");
cdo.startObject("b-axis");
cdo.setObjectProperty("b-axis", "x", bAxis.x.ToString());
cdo.setObjectProperty("b-axis", "y", bAxis.y.ToString());
cdo.setObjectProperty("b-axis", "z", bAxis.z.ToString());
cdo.endObject("b-axis");
cdo.startObject("c-axis");
cdo.setObjectProperty("c-axis", "x", cAxis.x.ToString());
cdo.setObjectProperty("c-axis", "y", cAxis.y.ToString());
cdo.setObjectProperty("c-axis", "z", cAxis.z.ToString());
cdo.endObject("c-axis");
}
else
{
////logger.error("Could not find crystal unit cell parameters");
}
cdo.endObject("Crystal");
}
else if ("list".Equals(name))
{
cdo.endObject("SetOfMolecules");
}
else if ("coordinate3".Equals(name))
{
if (BUILTIN.Equals("xyz3"))
{
////logger.debug("New coord3 xyz3 found: ", currentChars);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(currentChars);
x3.Add(st.NextToken());
y3.Add(st.NextToken());
z3.Add(st.NextToken());
////logger.debug("coord3 x3.length: ", x3.Count);
////logger.debug("coord3 y3.length: ", y3.Count);
////logger.debug("coord3 z3.length: ", z3.Count);
}
catch (System.Exception exception)
{
////logger.error("CMLParsing error while setting coordinate3!");
////logger.debug(exception);
}
}
else
{
////logger.warn("Unknown coordinate3 BUILTIN: " + BUILTIN);
}
}
else if ("string".Equals(name))
{
if (BUILTIN.Equals("elementType"))
{
////logger.debug("Element: ", cData.Trim());
elsym.Add(cData);
}
else if (BUILTIN.Equals("atomRef"))
{
curRef++;
////logger.debug("Bond: ref #", curRef);
if (curRef == 1)
{
bondARef1.Add(cData.Trim());
}
else if (curRef == 2)
{
bondARef2.Add(cData.Trim());
}
}
else if (BUILTIN.Equals("order"))
{
////logger.debug("Bond: order ", cData.Trim());
order.Add(cData.Trim());
}
else if (BUILTIN.Equals("formalCharge"))
{
// NOTE: this combination is in violation of the CML DTD!!!
////logger.warn("formalCharge BUILTIN accepted but violating CML DTD");
////logger.debug("Charge: ", cData.Trim());
System.String charge = cData.Trim();
if (charge.StartsWith("+") && charge.Length > 1)
{
charge = charge.Substring(1);
}
formalCharges.Add(charge);
}
}
else if ("float".Equals(name))
{
if (BUILTIN.Equals("x3"))
{
x3.Add(cData.Trim());
}
else if (BUILTIN.Equals("y3"))
{
y3.Add(cData.Trim());
}
else if (BUILTIN.Equals("z3"))
{
z3.Add(cData.Trim());
}
else if (BUILTIN.Equals("x2"))
{
x2.Add(cData.Trim());
}
else if (BUILTIN.Equals("y2"))
{
y2.Add(cData.Trim());
}
else if (BUILTIN.Equals("order"))
{
// NOTE: this combination is in violation of the CML DTD!!!
order.Add(cData.Trim());
}
else if (BUILTIN.Equals("charge") || BUILTIN.Equals("partialCharge"))
{
partialCharges.Add(cData.Trim());
}
}
else if ("integer".Equals(name))
{
if (BUILTIN.Equals("formalCharge"))
{
formalCharges.Add(cData.Trim());
}
}
else if ("coordinate2".Equals(name))
{
if (BUILTIN.Equals("xy2"))
{
////logger.debug("New coord2 xy2 found.", cData);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
x2.Add(st.NextToken());
y2.Add(st.NextToken());
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 175, 1);
}
}
}
else if ("stringArray".Equals(name))
{
if (BUILTIN.Equals("id") || BUILTIN.Equals("atomId") || BUILTIN.Equals("atomID"))
{
// invalid according to CML1 DTD but found in OpenBabel 1.x output
try
{
bool countAtoms = (atomCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countAtoms)
{
atomCounter++;
}
System.String token = st.NextToken();
////logger.debug("StringArray (Token): ", token);
elid.Add(token);
}
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 186, 1);
}
}
else if (BUILTIN.Equals("elementType"))
{
try
{
bool countAtoms = (atomCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countAtoms)
{
atomCounter++;
}
elsym.Add(st.NextToken());
}
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("atomRefs"))
{
curRef++;
////logger.debug("New atomRefs found: ", curRef);
try
{
bool countBonds = (bondCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countBonds)
{
bondCounter++;
}
System.String token = st.NextToken();
////logger.debug("Token: ", token);
if (curRef == 1)
{
bondARef1.Add(token);
}
else if (curRef == 2)
{
bondARef2.Add(token);
}
}
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("atomRef"))
{
curRef++;
////logger.debug("New atomRef found: ", curRef); // this is CML1 stuff, we get things like:
/*
<bondArray>
<stringArray builtin="atomRef">a2 a2 a2 a2 a3 a3 a4 a4 a5 a6 a7 a9</stringArray>
<stringArray builtin="atomRef">a9 a11 a12 a13 a5 a4 a6 a9 a7 a8 a8 a10</stringArray>
<stringArray builtin="order">1 1 1 1 2 1 2 1 1 1 2 2</stringArray>
</bondArray>
*/
try
{
bool countBonds = (bondCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countBonds)
{
bondCounter++;
}
System.String token = st.NextToken();
////logger.debug("Token: ", token);
if (curRef == 1)
{
bondARef1.Add(token);
}
else if (curRef == 2)
{
bondARef2.Add(token);
}
}
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("order"))
{
////logger.debug("New bond order found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
System.String token = st.NextToken();
////logger.debug("Token: ", token);
order.Add(token);
}
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
}
else if ("integerArray".Equals(name))
{
////logger.debug("IntegerArray: builtin = ", BUILTIN);
if (BUILTIN.Equals("formalCharge"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
System.String token = st.NextToken();
////logger.debug("Charge added: ", token);
formalCharges.Add(token);
}
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
}
else if ("scalar".Equals(name))
{
if (xpath.ToString().EndsWith("crystal/scalar/"))
{
////logger.debug("Going to set a crystal parameter: " + crystalScalar, " to ", cData);
try
{
unitcellparams[crystalScalar - 1] = System.Double.Parse(cData.Trim());
}
catch (System.FormatException exception)
{
////logger.error("Content must a float: " + cData);
}
}
else
{
if (xpath.ToString().EndsWith("bond/scalar/"))
{
if (DICTREF.Equals("mdl:stereo"))
{
bondStereo.Add(cData.Trim());
stereoGiven = true;
}
}
else
{
if (xpath.ToString().EndsWith("atom/scalar/"))
{
if (DICTREF.Equals("cdk:partialCharge"))
{
partialCharges.Add(cData.Trim());
}
}
else
{
if (xpath.ToString().EndsWith("molecule/scalar/"))
{
if (DICTREF.Equals("pdb:id"))
{
cdo.setObjectProperty("Molecule", DICTREF, cData);
}
}
else
{
////logger.warn("Ignoring scalar: " + xpath);
}
}
}
}
}
else if ("floatArray".Equals(name))
{
if (BUILTIN.Equals("x3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
x3.Add(st.NextToken());
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
else if (BUILTIN.Equals("y3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
y3.Add(st.NextToken());
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 213, 1);
}
}
else if (BUILTIN.Equals("z3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
z3.Add(st.NextToken());
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 221, 1);
}
}
else if (BUILTIN.Equals("x2"))
{
////logger.debug("New floatArray found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
x2.Add(st.NextToken());
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
else if (BUILTIN.Equals("y2"))
{
////logger.debug("New floatArray found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
y2.Add(st.NextToken());
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 454, 1);
}
}
else if (BUILTIN.Equals("partialCharge"))
{
////logger.debug("New floatArray with partial charges found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
partialCharges.Add(st.NextToken());
}
catch (System.Exception e)
{
//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'"
notify("CMLParsing error: " + e, SYSTEMID, 462, 1);
}
}
}
else if ("basic".Equals(name))
{
// assuming this is the child element of <identifier>
this.inchi = cData;
}
else if ("name".Equals(name))
{
if (xpath.ToString().EndsWith("molecule/name/"))
{
cdo.setObjectProperty("Molecule", DICTREF, cData);
}
}
else
{
////logger.warn("Skipping element: " + name);
}
currentChars = "";
BUILTIN = "";
elementTitle = "";
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
System.String s = new System.String(ch, start, length).Trim();
if (isELSYM)
{
elsym.Add(s);
}
else if (isBond)
{
//logger.debug("CD (bond): " + s);
if (connect_root.Length > 0)
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(s);
while (st.HasMoreTokens())
{
System.String atom = (System.String)st.NextToken();
if (!atom.Equals("0"))
{
//logger.debug("new bond: " + connect_root + "-" + atom);
cdo.startObject("Bond");
int atom1 = System.Int32.Parse(connect_root) - 1;
int atom2 = System.Int32.Parse(atom) - 1;
cdo.setObjectProperty("Bond", "atom1", ((System.Int32)atom1).ToString());
cdo.setObjectProperty("Bond", "atom2", ((System.Int32)atom2).ToString());
cdo.setObjectProperty("Bond", "order", "1");
cdo.endObject("Bond");
}
}
}
}
else
{
base.characterData(xpath, ch, start, length);
}
}
/// <summary> Read a Reaction from a file in MDL RXN format
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IMolecule readMolecule(IMolecule molecule)
{
AtomTypeFactory atFactory = null;
try
{
atFactory = AtomTypeFactory.getInstance("mol2_atomtypes.xml", molecule.Builder);
}
catch (System.Exception exception)
{
System.String error = "Could not instantiate an AtomTypeFactory";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
try
{
System.String line = input.ReadLine();
int atomCount = 0;
int bondCount = 0;
while (line != null)
{
if (line.StartsWith("@<TRIPOS>MOLECULE"))
{
//logger.info("Reading molecule block");
// second line has atom/bond counts?
input.ReadLine(); // disregard the name line
System.String counts = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(counts);
try
{
atomCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom count from MOLECULE block";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
if (tokenizer.HasMoreTokens())
{
try
{
bondCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom and bond counts";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
else
{
bondCount = 0;
}
//logger.info("Reading #atoms: ", atomCount);
//logger.info("Reading #bonds: ", bondCount);
//logger.warn("Not reading molecule qualifiers");
}
else if (line.StartsWith("@<TRIPOS>ATOM"))
{
//logger.info("Reading atom block");
for (int i = 0; i < atomCount; i++)
{
line = input.ReadLine().Trim();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String nameStr = tokenizer.NextToken();
System.String xStr = tokenizer.NextToken();
System.String yStr = tokenizer.NextToken();
System.String zStr = tokenizer.NextToken();
System.String atomTypeStr = tokenizer.NextToken();
IAtomType atomType = atFactory.getAtomType(atomTypeStr);
if (atomType == null)
{
atomType = atFactory.getAtomType("X");
//logger.error("Could not find specified atom type: ", atomTypeStr);
}
IAtom atom = molecule.Builder.newAtom("X");
atom.ID = nameStr;
atom.AtomTypeName = atomTypeStr;
atFactory.configure(atom);
try
{
double x = System.Double.Parse(xStr);
double y = System.Double.Parse(yStr);
double z = System.Double.Parse(zStr);
atom.setPoint3d(new Point3d(x, y, z));
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom coordinates";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
molecule.addAtom(atom);
}
}
else if (line.StartsWith("@<TRIPOS>BOND"))
{
//logger.info("Reading bond block");
for (int i = 0; i < bondCount; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String atom1Str = tokenizer.NextToken();
System.String atom2Str = tokenizer.NextToken();
System.String orderStr = tokenizer.NextToken();
try
{
int atom1 = System.Int32.Parse(atom1Str);
int atom2 = System.Int32.Parse(atom2Str);
double order = 0;
if ("1".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("2".Equals(orderStr))
{
order = CDKConstants.BONDORDER_DOUBLE;
}
else if ("3".Equals(orderStr))
{
order = CDKConstants.BONDORDER_TRIPLE;
}
else if ("am".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("ar".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("du".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("un".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("nc".Equals(orderStr))
{
// not connected
order = 0;
}
if (order != 0)
{
molecule.addBond(atom1 - 1, atom2 - 1, order);
}
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading bond information";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
}
line = input.ReadLine();
}
}
catch (System.IO.IOException exception)
{
System.String error = "Error while reading general structure";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
return molecule;
}
private void addDictRefedAnnotation(IChemObject object_Renamed, System.String type, System.String values)
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(values, ",");
while (tokenizer.HasMoreTokens())
{
System.String token = tokenizer.NextToken();
object_Renamed.setProperty(new DictRef("macie:" + type, token), token);
//logger.debug("Added dict ref ", token, " to ", object_Renamed.GetType().FullName);
}
}
private void processAnnotation(System.String field, System.String value_Renamed, Reaction reaction)
{
//logger.debug("Annote: ", field, "=", value_Renamed);
if (field.Equals("RxnAtts") || field.Equals("RxnType"))
{
// reaction attributes
System.String dictionary = "macie";
if (value_Renamed.Equals("Acid") || value_Renamed.Equals("Base"))
{
dictionary = "chemical";
}
addDictRefedAnnotation(reaction, "Attributes", value_Renamed);
}
else if (field.Equals("ResiduesPresent") || field.Equals("GroupTransferred") || field.Equals("BondFormed") || field.Equals("ReactiveCentres") || field.Equals("BondCleaved") || field.Equals("BondFormed") || field.Equals("Products") || field.Equals("ResiduesPresent"))
{
reaction.setProperty(new DictRef("macie:" + field, value_Renamed), value_Renamed);
}
else if (field.Equals("Reversible"))
{
if (value_Renamed.ToUpper().Equals("yes".ToUpper()))
{
reaction.Direction = IReaction_Fields.BIDIRECTIONAL;
addDictRefedAnnotation(reaction, "ReactionType", "ReversibleReaction");
}
}
else if (field.Equals("OverallReactionType"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed, ",");
int i = 0;
while (tokenizer.HasMoreTokens())
{
System.String token = tokenizer.NextToken();
i++;
reaction.setProperty(DictionaryDatabase.DICTREFPROPERTYNAME + ":field:overallReactionType:" + i, "macie:" + token.ToLower());
}
}
else
{
Match residueLocatorMatcher = residueLocator.Match(field);
if (residueLocatorMatcher.Success)
{
//logger.debug("Found residueLocator: ", field);
IAtom[] atoms = ReactionManipulator.getAllInOneContainer(reaction).Atoms;
bool found = false;
//logger.debug("Searching for given residueLocator through #atom: ", atoms.Length);
//logger.debug("Taken from reaction ", reaction.ID);
for (int i = 0; (i < atoms.Length && !found); i++)
{
if (atoms[i] is PseudoAtom)
{
// that is what we are looking for
PseudoAtom atom = (PseudoAtom)atoms[i];
if (atom.Label.Equals(field))
{
// we have a hit, now mark Atom with dict refs
addDictRefedAnnotation(atom, "ResidueRole", value_Renamed);
found = true;
}
}
}
if (!found)
{
//logger.error("MACiE annotation mentions a residue that does not exist: " + field);
}
}
else
{
//logger.error("Did not parse annotation: ", field);
}
}
}
/// <summary> Reads a set of vibrations into ChemFrame.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <exception cref="IOException"> if an I/O error occurs
/// </exception>
// private void readFrequencies(IChemModel model) throws IOException
// {
/*
* FIXME: this is yet to be ported
* String line;
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* while ((line != null) && line.startsWith(" Frequencies --")) {
* Vector currentVibs = new Vector();
* StringReader vibValRead = new StringReader(line.substring(15));
* StreamTokenizer token = new StreamTokenizer(vibValRead);
* while (token.nextToken() != StreamTokenizer.TT_EOF) {
* Vibration vib = new Vibration(Double.toString(token.nval));
* currentVibs.addElement(vib);
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* for (int i = 0; i < frame.getAtomCount(); ++i) {
* line = input.readLine();
* StringReader vectorRead = new StringReader(line);
* token = new StreamTokenizer(vectorRead);
* token.nextToken();
* / ignore first token
* token.nextToken();
* / ignore second token
* for (int j = 0; j < currentVibs.size(); ++j) {
* double[] v = new double[3];
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[0] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[1] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[2] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* ((Vibration) currentVibs.elementAt(j)).addAtomVector(v);
* }
* }
* for (int i = 0; i < currentVibs.size(); ++i) {
* frame.addVibration((Vibration) currentVibs.elementAt(i));
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* }
*/
// }
/// <summary> Reads NMR nuclear shieldings.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <param name="labelLine">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
private void readNMRData(IChemModel model, System.String labelLine)
{
IAtomContainer ac = ChemModelManipulator.getAllInOneContainer(model);
// Determine label for properties
System.String label;
if (labelLine.IndexOf("Diamagnetic") >= 0)
{
label = "Diamagnetic Magnetic shielding (Isotropic)";
}
else if (labelLine.IndexOf("Paramagnetic") >= 0)
{
label = "Paramagnetic Magnetic shielding (Isotropic)";
}
else
{
label = "Magnetic shielding (Isotropic)";
}
int atomIndex = 0;
for (int i = 0; i < atomCount; ++i)
{
try
{
System.String line = input.ReadLine().Trim();
while (line.IndexOf("Isotropic") < 0)
{
if (line == null)
{
return;
}
line = input.ReadLine().Trim();
}
SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(line);
// Find Isotropic label
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("Isotropic"))
{
break;
}
}
// Find Isotropic value
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("="))
break;
}
double shielding = System.Double.Parse(st1.NextToken());
//logger.info("Type of shielding: " + label);
ac.getAtomAt(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, (System.Object)shielding);
++atomIndex;
}
catch (System.Exception exc)
{
//logger.debug("failed to read line from gaussian98 file where I expected one.");
}
}
}