public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
if ("entry".Equals(local) && !"bibtex:entry".Equals(raw) && !inEntry)
{
inEntry = true;
entry = new Entry();
for (int i = 0; i < atts.GetLength(); i++)
{
if (atts.GetFullName(i).Equals("id"))
{
entry.ID = atts.GetValue(i);
}
else if (atts.GetFullName(i).Equals("term"))
{
entry.Label = atts.GetValue(i);
}
}
}
if ("metadataList".Equals(local) && !inMetadataList)
{
inMetadataList = true;
}
// if we're in a metadataList then look at individual
// metadata nodes and check for any whose content refers
// to QSAR metadata and save that. Currently it does'nt
// differentiate between descriptorType or descriptorClass.
// Do we need to differentiate?
//
// RG: I think so and so I save a combination of the dictRef attribute
// and the content attribute
if ("metadata".Equals(local) && inMetadataList)
{
for (int i = 0; i < atts.GetLength() - 1; i += 2)
{
System.String dictRefValue = "";
if (atts.GetFullName(i).Equals("dictRef"))
{
dictRefValue = atts.GetValue(i);
}
if (atts.GetFullName(i + 1).Equals("content"))
{
System.String content = atts.GetValue(i + 1);
if (content.IndexOf("qsar-descriptors-metadata:") == 0)
{
entry.setDescriptorMetadata(dictRefValue + "/" + content);
}
}
}
}
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
//logger.debug("START Element: ", raw);
//logger.debug(" uri: ", uri);
//logger.debug(" local: ", local);
//logger.debug(" raw: ", raw);
if ("atomType".Equals(local))
{
atomType = builder.newAtomType("R");
for (int i = 0; i < atts.GetLength(); i++)
{
if ("id".Equals(atts.GetFullName(i)))
{
atomType.AtomTypeName = atts.GetValue(i);
}
}
}
else if ("atom".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("elementType".Equals(atts.GetFullName(i)))
{
atomType.Symbol = atts.GetValue(i);
}
else if ("formalCharge".Equals(atts.GetFullName(i)))
{
try
{
atomType.setFormalCharge(System.Int32.Parse(atts.GetValue(i)));
}
catch (System.FormatException exception)
{
//logger.error("Value of <atom> @", atts.GetFullName(i), " is not an integer: ", atts.GetValue(i));
//logger.debug(exception);
}
}
}
}
else if ("scalar".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("dictRef".Equals(atts.GetFullName(i)))
{
if ("cdk:maxBondOrder".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_MAXBONDORDER;
}
else if ("cdk:bondOrderSum".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_BONDORDERSUM;
}
else if ("cdk:hybridization".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_HYBRIDIZATION;
}
else if ("cdk:formalNeighbourCount".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_FORMALNEIGHBOURCOUNT;
}
else if ("cdk:valency".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_VALENCY;
}
else if ("cdk:formalCharge".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_FORMALCHARGE;
}
else if ("cdk:DA".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_DA;
}
else if ("cdk:sphericalMatcher".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_SPHERICALMATCHER;
}
else if ("cdk:ringSize".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_RINGSIZE;
}
else if ("cdk:ringConstant".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_CHEMICALGROUPCONSTANT;
}
else if ("cdk:aromaticAtom".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_ISAROMATIC;
}
else if ("emboss:vdwrad".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_VANDERWAALSRADIUS;
}
}
}
}
}
private System.String getElementSymbol(SaxAttributesSupport atts)
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("id".Equals(atts.GetFullName(i)))
{
return atts.GetValue(i);
}
}
return "";
}
private IIsotope createIsotopeOfElement(System.String currentElement, SaxAttributesSupport atts)
{
IIsotope isotope = builder.newIsotope(currentElement);
for (int i = 0; i < atts.GetLength(); i++)
{
try
{
if ("id".Equals(atts.GetFullName(i)))
{
isotope.ID = atts.GetValue(i);
}
else if ("isotopeNumber".Equals(atts.GetFullName(i)))
{
isotope.MassNumber = System.Int32.Parse(atts.GetValue(i));
}
else if ("elementType".Equals(atts.GetFullName(i)))
{
isotope.Symbol = atts.GetValue(i);
}
}
catch (System.FormatException exception)
{
//logger.error("Value of isotope@", atts.GetFullName(i), " is not as expected.");
//logger.debug(exception);
}
}
return isotope;
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
dictRef = "";
//logger.debug("startElement: ", raw);
//logger.debug("uri: ", uri);
//logger.debug("local: ", local);
//logger.debug("raw: ", raw);
if ("isotope".Equals(local))
{
workingIsotope = createIsotopeOfElement(currentElement, atts);
}
else if ("isotopeList".Equals(local))
{
currentElement = getElementSymbol(atts);
}
else if ("abundance".Equals(local))
{
//logger.warn("Disregarding dictRef for now...");
}
else if ("scalar".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("dictRef".Equals(atts.GetFullName(i)))
{
dictRef = atts.GetValue(i);
}
}
}
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
dictRef = "";
//logger.debug("startElement: ", raw);
//logger.debug("uri: ", uri);
//logger.debug("local: ", local);
//logger.debug("raw: ", raw);
if ("elementType".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("id".Equals(atts.GetFullName(i)))
{
elementType = new PeriodicTableElement(atts.GetValue(i));
}
}
}
else if ("scalar".Equals(local))
for (int i = 0; i < atts.GetLength(); i++)
{
if ("dictRef".Equals(atts.GetFullName(i)))
{
if ("cas:id".Equals(atts.GetValue(i)))
{
scalarType = LABEL_CAS;
}
else if ("cdk:name".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_NAME;
}
else if ("cdk:atomicNumber".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_ATOMICNUMBER;
}
else if ("cdk:name".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_NAME;
}
else if ("cdk:chemicalSerie".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_CHEMICALSERIE;
}
else if ("cdk:period".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_PERIOD;
}
else if ("cdk:group".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_GROUP;
}
else if ("cdk:phase".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_PHASE;
}
}
}
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
xpath.push(local);
//if (debug)
// logger.debug("<", raw, "> -> ", xpath);
// Detect CML modules, like CRML and CCML
if (local.StartsWith("reaction"))
{
// e.g. reactionList, reaction -> CRML module
//logger.info("Detected CRML module");
conv = new CMLReactionModule(conv);
conventionStack.push(conventionStack.current());
}
else
{
// assume CML Core
// Detect conventions
System.String convName = "";
for (int i = 0; i < atts.GetLength(); i++)
{
if (atts.GetFullName(i).Equals("convention"))
{
convName = atts.GetValue(i);
}
}
if (convName.Length > 0)
{
if (convName.Equals(conventionStack.current()))
{
//logger.debug("Same convention as parent");
}
else
{
//logger.info("New Convention: ", convName);
if (convName.Equals("CML"))
{
/* Don't reset the convention handler to CMLCore,
becuase all handlers should extend this handler,
and use it for any content other then specifically
put into the specific convention */
}
else if (convName.Equals("PDB"))
{
conv = new PDBConvention(conv);
}
else if (convName.Equals("PMP"))
{
conv = new PMPConvention(conv);
}
else if (convName.Equals("MDLMol"))
{
//if (debug)
// logger.debug("MDLMolConvention instantiated...");
conv = new MDLMolConvention(conv);
}
else if (convName.Equals("JMOL-ANIMATION"))
{
conv = new JMOLANIMATIONConvention(conv);
}
else if (userConventions.ContainsKey(convName))
{
//unknown convention. userConvention?
ICMLConvention newconv = (ICMLConvention)userConventions[convName];
newconv.inherit(conv);
conv = newconv;
}
else
{
//logger.warn("Detected unknown convention: ", convName);
}
}
conventionStack.push(convName);
}
else
{
// no convention set/reset: take convention of parent
conventionStack.push(conventionStack.current());
}
}
//if (debug)
// logger.debug("ConventionStack: ", conventionStack);
conv.startElement(xpath, uri, local, raw, atts);
}
public virtual void startElement(CMLStack xpath, System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
System.String name = local;
////logger.debug("StartElement");
currentChars = "";
BUILTIN = "";
DICTREF = "";
for (int i = 0; i < atts.GetLength(); i++)
{
System.String qname = atts.GetFullName(i);
if (qname.Equals("builtin"))
{
BUILTIN = atts.GetValue(i);
////logger.debug(name, "->BUILTIN found: ", atts.GetValue(i));
}
else if (qname.Equals("dictRef"))
{
DICTREF = atts.GetValue(i);
////logger.debug(name, "->DICTREF found: ", atts.GetValue(i));
}
else if (qname.Equals("title"))
{
elementTitle = atts.GetValue(i);
////logger.debug(name, "->TITLE found: ", atts.GetValue(i));
}
else
{
////logger.debug("Qname: ", qname);
}
}
if ("atom".Equals(name))
{
atomCounter++;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
System.String value_Renamed = atts.GetValue(i);
if (att.Equals("id"))
{
// this is supported in CML 1.x
elid.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("elementType"))
{
elsym.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("title"))
{
eltitles.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("x2"))
{
x2.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("xy2"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
x2.Add(tokenizer.NextToken());
y2.Add(tokenizer.NextToken());
}
// this is supported in CML 2.0
else if (att.Equals("xyzFract"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
xfract.Add(tokenizer.NextToken());
yfract.Add(tokenizer.NextToken());
zfract.Add(tokenizer.NextToken());
}
// this is supported in CML 2.0
else if (att.Equals("xyz3"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(value_Renamed);
x3.Add(tokenizer.NextToken());
y3.Add(tokenizer.NextToken());
z3.Add(tokenizer.NextToken());
}
// this is supported in CML 2.0
else if (att.Equals("y2"))
{
y2.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("x3"))
{
x3.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("y3"))
{
y3.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("z3"))
{
z3.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("xFract"))
{
xfract.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("yFract"))
{
yfract.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("zFract"))
{
zfract.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("formalCharge"))
{
formalCharges.Add(value_Renamed);
}
// this is supported in CML 2.0
else if (att.Equals("hydrogenCount"))
{
hCounts.Add(value_Renamed);
}
else if (att.Equals("isotope"))
{
isotope.Add(value_Renamed);
}
else if (att.Equals("dictRef"))
{
atomDictRefs.Add(value_Renamed);
}
else if (att.Equals("spinMultiplicity"))
{
spinMultiplicities.Add(value_Renamed);
}
else
{
////logger.warn("Unparsed attribute: " + att);
}
}
}
else if ("atomArray".Equals(name))
{
bool atomsCounted = false;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
int count = 0;
if (att.Equals("atomID"))
{
count = addArrayElementsTo(elid, atts.GetValue(i));
}
else if (att.Equals("elementType"))
{
count = addArrayElementsTo(elsym, atts.GetValue(i));
}
else if (att.Equals("x2"))
{
count = addArrayElementsTo(x2, atts.GetValue(i));
}
else if (att.Equals("y2"))
{
count = addArrayElementsTo(y2, atts.GetValue(i));
}
else if (att.Equals("x3"))
{
count = addArrayElementsTo(x3, atts.GetValue(i));
}
else if (att.Equals("y3"))
{
count = addArrayElementsTo(y3, atts.GetValue(i));
}
else if (att.Equals("z3"))
{
count = addArrayElementsTo(z3, atts.GetValue(i));
}
else if (att.Equals("xFract"))
{
count = addArrayElementsTo(xfract, atts.GetValue(i));
}
else if (att.Equals("yFract"))
{
count = addArrayElementsTo(yfract, atts.GetValue(i));
}
else if (att.Equals("zFract"))
{
count = addArrayElementsTo(zfract, atts.GetValue(i));
}
else
{
////logger.warn("Unparsed attribute: " + att);
}
if (!atomsCounted)
{
atomCounter += count;
atomsCounted = true;
}
}
}
else if ("bond".Equals(name))
{
bondCounter++;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
////logger.debug("B2 ", att, "=", atts.GetValue(i));
if (att.Equals("id"))
{
bondid.Add(atts.GetValue(i));
////logger.debug("B3 ", bondid);
}
else if (att.Equals("atomRefs") || att.Equals("atomRefs2"))
{
// this is CML 2.0 support
// expect exactly two references
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(atts.GetValue(i));
bondARef1.Add((System.String)st.NextToken());
bondARef2.Add((System.String)st.NextToken());
}
catch (System.Exception e)
{
//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("Error in CML file: ", e.Message);
////logger.debug(e);
}
}
else if (att.Equals("order"))
{
// this is CML 2.0 support
order.Add(atts.GetValue(i).Trim());
}
else if (att.Equals("dictRef"))
{
bondDictRefs.Add(atts.GetValue(i).Trim());
}
}
stereoGiven = false;
curRef = 0;
}
else if ("bondArray".Equals(name))
{
bool bondsCounted = false;
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
int count = 0;
if (att.Equals("bondID"))
{
count = addArrayElementsTo(bondid, atts.GetValue(i));
}
else if (att.Equals("atomRefs1"))
{
count = addArrayElementsTo(bondARef1, atts.GetValue(i));
}
else if (att.Equals("atomRefs2"))
{
count = addArrayElementsTo(bondARef2, atts.GetValue(i));
}
else if (att.Equals("atomRef1"))
{
count = addArrayElementsTo(bondARef1, atts.GetValue(i));
}
else if (att.Equals("atomRef2"))
{
count = addArrayElementsTo(bondARef2, atts.GetValue(i));
}
else if (att.Equals("order"))
{
count = addArrayElementsTo(order, atts.GetValue(i));
}
else
{
////logger.warn("Unparsed attribute: " + att);
}
if (!bondsCounted)
{
bondCounter += count;
bondsCounted = true;
}
}
curRef = 0;
}
else if ("molecule".Equals(name))
{
newMolecule();
BUILTIN = "";
cdo.startObject("Molecule");
for (int i = 0; i < atts.GetLength(); i++)
{
if (atts.GetFullName(i).Equals("id"))
{
cdo.setObjectProperty("Molecule", "id", atts.GetValue(i));
}
else if (atts.GetFullName(i).Equals("dictRef"))
{
cdo.setObjectProperty("Molecule", "dictRef", atts.GetValue(i));
}
}
}
else if ("crystal".Equals(name))
{
newCrystalData();
cdo.startObject("Crystal");
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
if (att.Equals("z"))
{
cdo.setObjectProperty("Crystal", "z", atts.GetValue(i));
}
}
}
else if ("symmetry".Equals(name))
{
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
if (att.Equals("spaceGroup"))
{
cdo.setObjectProperty("Crystal", "spacegroup", atts.GetValue(i));
}
}
}
else if ("scalar".Equals(name))
{
if (xpath.ToString().EndsWith("crystal/scalar/"))
crystalScalar++;
}
else if ("list".Equals(name))
{
cdo.startObject("SetOfMolecules");
}
}
public override void startElement(CMLStack xpath, System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
System.String name = raw;
isELSYM = false;
if ("list".Equals(name))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if (atts.GetFullName(i).Equals("title") && atts.GetValue(i).Equals("sequence"))
{
}
else if (atts.GetFullName(i).Equals("title") && atts.GetValue(i).Equals("connections"))
{
// assume that Atom's have been read
//logger.debug("Assuming that Atom's have been read: storing them");
base.storeAtomData();
connectionTable = true;
//logger.debug("Start Connection Table");
}
else if (atts.GetFullName(i).Equals("title") && atts.GetValue(i).Equals("connect"))
{
//logger.debug("New connection");
isBond = true;
}
else if (atts.GetFullName(i).Equals("id") && isBond)
{
connect_root = atts.GetValue(i);
}
// ignore other list items at this moment
}
}
else
{
base.startElement(xpath, uri, local, raw, atts);
}
}
public override void startElement(CMLStack xpath, System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
if ("reaction".Equals(local))
{
cdo.startObject("Reaction");
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
System.String value_Renamed = atts.GetValue(i);
if (att.Equals("id"))
{
cdo.setObjectProperty("Reaction", "id", value_Renamed);
}
}
}
else if ("reactionList".Equals(local))
{
cdo.startObject("SetOfReactions");
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
System.String value_Renamed = atts.GetValue(i);
if (att.Equals("id"))
{
cdo.setObjectProperty("SetOfReactions", "id", value_Renamed);
}
}
}
else if ("reactant".Equals(local))
{
cdo.startObject("Reactant");
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
System.String value_Renamed = atts.GetValue(i);
if (att.Equals("id"))
{
cdo.setObjectProperty("Reactant", "id", value_Renamed);
}
}
}
else if ("product".Equals(local))
{
cdo.startObject("Product");
for (int i = 0; i < atts.GetLength(); i++)
{
System.String att = atts.GetFullName(i);
System.String value_Renamed = atts.GetValue(i);
if (att.Equals("id"))
{
cdo.setObjectProperty("Product", "id", value_Renamed);
}
}
}
else if ("molecule".Equals(local))
{
// do nothing for now
base.newMolecule();
}
else
{
base.startElement(xpath, uri, local, raw, atts);
}
}
public override void startElement(CMLStack xpath, System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
System.String name = local;
if (name.Equals("list"))
{
//logger.debug("Oke, JMOLANIMATION seems to be kicked in :)");
cdo.startObject("Animation");
base.startElement(xpath, uri, local, raw, atts);
}
else if (name.Equals("molecule"))
{
cdo.startObject("Frame");
//logger.debug("New frame being parsed.");
base.startElement(xpath, uri, local, raw, atts);
}
else if (name.Equals("float"))
{
bool isEnergy = false;
//logger.debug("FLOAT found!");
for (int i = 0; i < atts.GetLength(); i++)
{
//logger.debug(" att: ", atts.GetFullName(i), " -> ", atts.GetValue(i));
if (atts.GetFullName(i).Equals("title") && atts.GetValue(i).Equals("FRAME_ENERGY"))
{
isEnergy = true;
}
}
if (isEnergy)
{
// oke, this is the frames energy!
current = ENERGY;
}
else
{
base.startElement(xpath, uri, local, raw, atts);
}
}
else
{
base.startElement(xpath, uri, local, raw, atts);
}
}