public override void endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
System.String name = local;
if (current == ENERGY)
{
cdo.setObjectProperty("Frame", "energy", frame_energy);
// + " " + units);
current = UNKNOWN;
frame_energy = "";
}
else if (name.Equals("list"))
{
base.endElement(xpath, uri, local, raw);
cdo.endObject("Animation");
}
else if (name.Equals("molecule"))
{
base.endElement(xpath, uri, local, raw);
cdo.endObject("Frame");
}
else
{
base.endElement(xpath, uri, local, raw);
}
}
public override void endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
if ("reaction".Equals(local))
{
cdo.endObject("Reaction");
}
else if ("reactionList".Equals(local))
{
cdo.endObject("SetOfReactions");
}
else if ("reactant".Equals(local))
{
cdo.endObject("Reactant");
}
else if ("product".Equals(local))
{
cdo.endObject("Product");
}
else if ("molecule".Equals(local))
{
//logger.debug("Storing Molecule");
base.storeData();
// do nothing else but store atom/bond information
}
else
{
base.endElement(xpath, uri, local, raw);
}
}
/// <summary> Constructor for the CMLHandler.
///
/// </summary>
/// <param name="cdo">The Chemical Document Object in which data is stored
///
/// </param>
public CMLHandler(IChemicalDocumentObject cdo)
{
//logger = new LoggingTool(this);
conv = new CMLCoreModule(cdo);
userConventions = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
xpath = new CMLStack();
conventionStack = new CMLStack();
}
/// <summary> Constructor for the CMLHandler.
///
/// </summary>
/// <param name="cdo">The Chemical Document Object in which data is stored
///
/// </param>
public CMLHandler(IChemicalDocumentObject cdo)
{
//logger = new LoggingTool(this);
conv = new CMLCoreModule(cdo);
userConventions = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
xpath = new CMLStack();
conventionStack = new CMLStack();
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
System.String s = new System.String(ch, start, length).Trim();
//logger.debug("Start PMP chardata (" + CurrentElement + ") :" + s);
//logger.debug(" ElTitle: " + elementTitle);
if (xpath.ToString().EndsWith("string/") && BUILTIN.Equals("spacegroup"))
{
System.String sg = "P1";
// standardize space group names (see Crystal.java)
if ("P 21 21 21 (1)".Equals(s))
{
sg = "P 2_1 2_1 2_1";
}
cdo.setObjectProperty("Crystal", "spacegroup", sg);
}
else
{
if (xpath.ToString().EndsWith("floatArray/") && (elementTitle.Equals("a") || elementTitle.Equals("b") || elementTitle.Equals("c")))
{
System.String axis = elementTitle + "-axis";
cdo.startObject(axis);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(s);
//logger.debug("Tokens: " + st.Count);
if (st.Count > 2)
{
System.String token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "x", token);
token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "y", token);
token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "z", token);
}
else
{
//logger.debug("PMP Convention error: incorrect number of cell axis fractions!\n");
}
}
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'"
//logger.debug("PMP Convention error: " + e.ToString());
}
cdo.endObject(axis);
}
else
{
base.characterData(xpath, ch, start, length);
}
}
//logger.debug("End PMP chardata");
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
if (current == ENERGY)
{
frame_energy = new System.String(ch, start, length);
}
else
{
base.characterData(xpath, ch, start, length);
}
}
public override void endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
System.String name = raw;
if (name.Equals("list") && connectionTable && !isBond)
{
//logger.debug("End Connection Table");
connectionTable = false;
}
isELSYM = false;
isBond = false;
base.endElement(xpath, uri, local, raw);
}
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);
}
}
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);
}
}
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);
}
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
System.String s = new System.String(ch, start, length).Trim();
if (xpath.ToString().EndsWith("string/") && BUILTIN.Equals("stereo"))
{
stereoGiven = true;
if (s.Trim().Equals("W"))
{
//logger.debug("CML W stereo found");
bondStereo.Add("1");
}
else if (s.Trim().Equals("H"))
{
//logger.debug("CML H stereo found");
bondStereo.Add("6");
}
}
else
{
base.characterData(xpath, ch, start, length);
}
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
System.String s = new System.String(ch, start, length).Trim();
if (xpath.ToString().EndsWith("string/") && BUILTIN.Equals("stereo"))
{
stereoGiven = true;
if (s.Trim().Equals("W"))
{
//logger.debug("CML W stereo found");
bondStereo.Add("1");
}
else if (s.Trim().Equals("H"))
{
//logger.debug("CML H stereo found");
bondStereo.Add("6");
}
}
else
{
base.characterData(xpath, ch, start, length);
}
}
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 characterData(CMLStack xpath, char[] ch, int start, int length)
{
if (current == ENERGY)
{
frame_energy = new System.String(ch, start, length);
}
else
{
base.characterData(xpath, ch, start, length);
}
}
public override void endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
base.endElement(xpath, uri, local, raw);
}
public override void startElement(CMLStack xpath, System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
////logger.debug("MDLMol element: name");
base.startElement(xpath, uri, local, raw, atts);
}
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 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 virtual void characterData(CMLStack xpath, char[] ch, int start, int length)
{
currentChars = currentChars + new System.String(ch, start, length);
////logger.debug("CD: ", currentChars);
}
public override void endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
if ("reaction".Equals(local))
{
cdo.endObject("Reaction");
}
else if ("reactionList".Equals(local))
{
cdo.endObject("SetOfReactions");
}
else if ("reactant".Equals(local))
{
cdo.endObject("Reactant");
}
else if ("product".Equals(local))
{
cdo.endObject("Product");
}
else if ("molecule".Equals(local))
{
//logger.debug("Storing Molecule");
base.storeData();
// do nothing else but store atom/bond information
}
else
{
base.endElement(xpath, uri, local, raw);
}
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
System.String s = new System.String(ch, start, length).Trim();
//logger.debug("Start PMP chardata (" + CurrentElement + ") :" + s);
//logger.debug(" ElTitle: " + elementTitle);
if (xpath.ToString().EndsWith("string/") && BUILTIN.Equals("spacegroup"))
{
System.String sg = "P1";
// standardize space group names (see Crystal.java)
if ("P 21 21 21 (1)".Equals(s))
{
sg = "P 2_1 2_1 2_1";
}
cdo.setObjectProperty("Crystal", "spacegroup", sg);
}
else
{
if (xpath.ToString().EndsWith("floatArray/") && (elementTitle.Equals("a") || elementTitle.Equals("b") || elementTitle.Equals("c")))
{
System.String axis = elementTitle + "-axis";
cdo.startObject(axis);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(s);
//logger.debug("Tokens: " + st.Count);
if (st.Count > 2)
{
System.String token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "x", token);
token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "y", token);
token = st.NextToken();
//logger.debug("FloatArray (Token): " + token);
cdo.setObjectProperty(axis, "z", token);
}
else
{
//logger.debug("PMP Convention error: incorrect number of cell axis fractions!\n");
}
}
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'"
//logger.debug("PMP Convention error: " + e.ToString());
}
cdo.endObject(axis);
}
else
{
base.characterData(xpath, ch, start, length);
}
}
//logger.debug("End PMP chardata");
}
public override void endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
base.endElement(xpath, uri, local, raw);
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
base.characterData(xpath, ch, start, length);
}
public override void characterData(CMLStack xpath, char[] ch, int start, int length)
{
base.characterData(xpath, ch, start, length);
}
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);
}
}
public override void endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
System.String name = raw;
if (name.Equals("list") && connectionTable && !isBond)
{
//logger.debug("End Connection Table");
connectionTable = false;
}
isELSYM = false;
isBond = false;
base.endElement(xpath, uri, local, raw);
}
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 = 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 endElement(CMLStack xpath, System.String uri, System.String local, System.String raw)
{
System.String name = local;
if (current == ENERGY)
{
cdo.setObjectProperty("Frame", "energy", frame_energy);
// + " " + units);
current = UNKNOWN;
frame_energy = "";
}
else if (name.Equals("list"))
{
base.endElement(xpath, uri, local, raw);
cdo.endObject("Animation");
}
else if (name.Equals("molecule"))
{
base.endElement(xpath, uri, local, raw);
cdo.endObject("Frame");
}
else
{
base.endElement(xpath, uri, local, raw);
}
}
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)
{
//logger.debug("PMP element: name");
base.startElement(xpath, uri, local, raw, atts);
}
