public String perceiveCDKAtomTypes(IMolecule mol)
throws InvocationTargetException {
ICDKMolecule cdkmol;
try {
cdkmol = cdk.asCDKMolecule(mol);
}
catch ( BioclipseException e ) {
e.printStackTrace();
throw new InvocationTargetException(
e, "Error while creating a ICDKMolecule" );
}
IAtomContainer ac = cdkmol.getAtomContainer();
CDKAtomTypeMatcher cdkMatcher
= CDKAtomTypeMatcher.getInstance(ac.getBuilder());
StringBuffer result = new StringBuffer();
int i = 1;
for (IAtom atom : ac.atoms()) {
IAtomType type = null;
try {
type = cdkMatcher.findMatchingAtomType(ac, atom);
}
catch ( CDKException e ) {}
result.append(i).append(':').append(
type != null ? type.getAtomTypeName() : "null"
).append('\n'); // FIXME: should use NEWLINE here
i++;
}
return result.toString();
}
public String removeTriple(String subject, String predicate, String object, String wikiURL) {
String result = null;
String action = "DELETE";
try {
result = updateTriple(subject, predicate, object, wikiURL, action);
} catch (BioclipseException e) {
e.printStackTrace();
}
return result;
}
/**
* Get
*
* @param wikiURL
* @param limit
* @return resultRDF
*/
public IRDFStore getRDF(String wikiURL, int limit) {
String sparqlQuery = null;
RDFManager myRdfManager = new RDFManager();
IRDFStore resultRDF = null;
if (limit == 0) {
sparqlQuery = "CONSTRUCT { ?s ?p ?o } WHERE { ?s ?p ?o }";
} else {
sparqlQuery =
"CONSTRUCT { ?s ?p ?o } WHERE { ?s ?p ?o }" + "LIMIT " + Integer.toString(limit);
}
// Make some configurations
String serviceURL = wikiURL + "Special:SPARQLEndpoint";
try {
resultRDF = myRdfManager.sparqlConstructRemote(serviceURL, sparqlQuery, null);
} catch (BioclipseException e) {
e.printStackTrace();
}
return resultRDF;
}
public void putRDF(IRDFStore rdfData, String wikiURL) {
// Create a Manager for SPARQLing the rdfData
RDFManager myRdfManager = new RDFManager();
String sparqlInsertTriple;
String sparqlGetAllTriples = "SELECT ?s ?p ?o WHERE { ?s ?p ?o }";
try {
StringMatrix rdfDataMatrix = myRdfManager.sparql(rdfData, sparqlGetAllTriples);
int mxRowsCnt = rdfDataMatrix.getRowCount();
System.out.println("mxRowsCnt: " + mxRowsCnt);
// We skip the first row which just contains column names
for (int i = 1; i < mxRowsCnt; i++) {
sparqlInsertTriple = "INSERT INTO <> {\n";
sparqlInsertTriple +=
"<"
+ rdfDataMatrix.get(i, 1)
+ "> <"
+ rdfDataMatrix.get(i, 2)
+ "> <"
+ rdfDataMatrix.get(i, 3)
+ "> .\n";
sparqlInsertTriple += "}\n";
System.out.println(
"SPARQL INSERT CODE:\n---------------------------------\n" + sparqlInsertTriple);
sparql(sparqlInsertTriple, wikiURL);
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (BioclipseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (CoreException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
public String perceiveSybylAtomTypes(IMolecule mol)
throws InvocationTargetException {
ICDKMolecule cdkmol;
try {
cdkmol = cdk.asCDKMolecule(mol);
}
catch (BioclipseException e) {
System.out.println("Error converting cdk10 to cdk");
e.printStackTrace();
throw new InvocationTargetException(e);
}
IAtomContainer ac = cdkmol.getAtomContainer();
CDKAtomTypeMatcher cdkMatcher
= CDKAtomTypeMatcher.getInstance(ac.getBuilder());
AtomTypeMapper mapper
= AtomTypeMapper.getInstance(
"org/openscience/cdk/dict/data/cdk-sybyl-mappings.owl" );
IAtomType[] sybylTypes = new IAtomType[ac.getAtomCount()];
int atomCounter = 0;
int a=0;
for (IAtom atom : ac.atoms()) {
IAtomType type;
try {
type = cdkMatcher.findMatchingAtomType(ac, atom);
}
catch (CDKException e) {
type = null;
}
if (type==null) {
// logger.debug("AT null for atom: " + atom);
type = atom.getBuilder().newAtomType(atom.getSymbol());
type.setAtomTypeName("X");
}
AtomTypeManipulator.configure(atom, type);
a++;
}
try {
CDKHueckelAromaticityDetector.detectAromaticity(ac);
// System.out.println("Arom: "
// + CDKHueckelAromaticityDetector.detectAromaticity(ac) );
}
catch (CDKException e) {
logger.debug("Failed to perceive aromaticity: " + e.getMessage());
}
for (IAtom atom : ac.atoms()) {
String mappedType = mapper.mapAtomType(atom.getAtomTypeName());
if ("C.2".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "C.ar";
}
else if ("N.pl3".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "N.ar";
}
try {
sybylTypes[atomCounter] = factory.getAtomType(mappedType);
}
catch (NoSuchAtomTypeException e) {
// yes, setting null's here is important
sybylTypes[atomCounter] = null;
}
atomCounter++;
}
StringBuffer result = new StringBuffer();
// now that full perception is finished, we can set atom type names:
for (int i = 0; i < sybylTypes.length; i++) {
if (sybylTypes[i] != null) {
ac.getAtom(i).setAtomTypeName(sybylTypes[i].getAtomTypeName());
}
else {
ac.getAtom(i).setAtomTypeName("X");
}
result.append(i).append(':').append(ac.getAtom(i).getAtomTypeName())
/*.append("\n")*/;
}
return result.toString();
}
