public static double getDist(Atom a, Atom b) {
double xDist = a.getPoint().x - b.getPoint().x;
double yDist = a.getPoint().y - b.getPoint().y;
double dist = Math.sqrt((xDist * xDist) + (yDist * yDist));
return dist;
}
public void draw() {
sketch.send("moveto", coords);
sketch.send("framecircle", new Atom[] {Atom.newAtom(size)});
if (triggered) {
sketch.send("circle", new Atom[] {Atom.newAtom(size)});
} else if (hover) {
sketch.send("circle", new Atom[] {Atom.newAtom(size)});
} else if (selected) {
sketch.send("circle", new Atom[] {Atom.newAtom(size)});
}
}
/* public void fixAtomsOfBond(){ // do fix bonds of Atom first
ArrayList<Atom> temp = new ArrayList<Atom>(atomList.size());
ArrayList<Bond> temp2 = new ArrayList<Bond>(bondList.size());
for(int i = 0; i < temp2.size(); i++){ // iterates bondList
for(int j = 0; j < atomList.size(); j++){//iterates atomlist
temp2 = atomList.get(j).getAdjacentBonds();
for(int k = 0; k < temp2.size(); k++){ //iterates bonds on atomList
if(temp2.get(k).getEdgeNum() == bondList.get(k).getEdgeNum()){
temp.set(k, bondList.get(j));
}
}
bondList.get(i).setAdjacentAtoms(temp);
}
}
} */
public String toString() {
String temp = " ";
if (atomList == null) {
return "Null found for atomList";
}
for (Atom a : atomList) {
temp = temp.concat(a.toString()) + "\n";
}
if (bondList == null) {
return "Null found for bondList";
}
if (bondList.isEmpty()) {
temp += " bondList is empty";
// return "bondList is empty";
}
for (Bond b : bondList) {
temp = temp.concat(b.toString()) + "\n";
}
return temp;
}
private void trigger(double dist) {
triggered = true;
outlet(
0,
new Atom[] {
Atom.newAtom(name),
Atom.newAtom(polar[0]),
Atom.newAtom(polar[1]),
Atom.newAtom(size),
Atom.newAtom(coords[0]),
Atom.newAtom(coords[1]),
Atom.newAtom(coords[2])
});
}
public QTFastStartRAF(FileAccessor accessor, boolean enable) throws IOException {
input = accessor;
if (enable) {
String name = accessor.getName();
boolean log;
String fail = null;
synchronized (tested) {
log = !tested.contains(name);
if (log) {
tested.add(name);
}
}
try {
Atom ah = null;
Atom ftypAtom = null;
boolean gotFtyp = false;
boolean gotMdat = false;
boolean justCopy = false;
while (input.getFilePointer() < input.length()) {
ah = new Atom(input);
// System.out.println( "got " + ah.type +", size=" + ah.size );
if (!isValidTopLevelAtom(ah)) {
throw new IOException("Non top level QT atom found (" + ah.type + "). File invalid?");
}
if (gotFtyp && !gotMdat && ah.type.equalsIgnoreCase(ATOM_MOOV)) {
justCopy = true;
break;
}
// store ftyp atom to buffer
if (ah.type.equalsIgnoreCase(ATOM_FTYP)) {
ftypAtom = ah;
ftypAtom.fillBuffer(input);
gotFtyp = true;
} else if (ah.type.equalsIgnoreCase(ATOM_MDAT)) {
gotMdat = true;
input.skipBytes((int) ah.size);
} else {
input.skipBytes((int) ah.size);
}
}
if (justCopy) {
transparent = true;
return;
}
if (ftypAtom == null) {
throw new IOException("No FTYP atom found");
}
if (ah == null || !ah.type.equalsIgnoreCase(ATOM_MOOV)) {
throw new IOException("Last QT atom was not the MOOV atom.");
}
input.seek(ah.offset);
Atom moovAtom = ah;
moovAtom.fillBuffer(input);
if (isCompressedMoovAtom(moovAtom)) {
throw new IOException("Compressed MOOV qt atoms are not supported");
}
patchMoovAtom(moovAtom);
body_start = ftypAtom.offset + ftypAtom.size;
body_end = moovAtom.offset;
header = new byte[ftypAtom.buffer.length + moovAtom.buffer.length];
System.arraycopy(ftypAtom.buffer, 0, header, 0, ftypAtom.buffer.length);
System.arraycopy(
moovAtom.buffer, 0, header, ftypAtom.buffer.length, moovAtom.buffer.length);
if (accessor.length() != header.length + (body_end - body_start)) {
throw (new IOException("Inconsistent: file size has changed"));
}
} catch (Throwable e) {
// e.printStackTrace();
fail = Debug.getNestedExceptionMessage(e);
transparent = true;
} finally {
input.seek(0);
if (log) {
String message;
if (fail == null) {
message = transparent ? "Not required" : "Required";
} else {
message = "Failed - " + fail;
}
Debug.outNoStack("MOOV relocation for " + accessor.getName() + ": " + message);
}
}
} else {
transparent = true;
}
}
@Override
public void setValue(Atom a, Atom v) {
m_phi.setValue(a, v);
m_variableResolver.put(a.toString(), v.toString());
}
public void writeMeat() {
try {
for (int i = 0; i < aList.size(); i++) {
w.write("{");
w.newLine();
Atom tempA = aList.get(i);
w.write("\t" + "\"" + "vertexNum" + "\":" + tempA.getVertexNum() + "\",");
w.newLine();
w.write("\t" + "\"" + "atomicNum" + "\":" + tempA.getAtomicNum() + "\",");
w.newLine();
w.write("\t" + "\"" + "atomicWeight" + "\":" + tempA.getAtomicWeight() + "\",");
w.newLine();
w.write("\t" + "\"" + "electroNeg" + "\":" + tempA.getElectroNeg() + "\",");
w.newLine();
w.write("\t" + "\"" + "atomName" + "\":" + tempA.getAtomName() + "\",");
w.newLine();
w.write("\t" + "\"" + "adjacentBonds" + "\": {");
w.newLine();
for (int z = 0; z < tempA.getAdjacentBonds().size(); z++) {
w.write("\t\t" + "[");
w.newLine();
w.write(
"\t\t\t"
+ "\""
+ "edgeNum"
+ "\":"
+ tempA.getAdjacentBonds().get(z).getEdgeNum()
+ "\",");
w.newLine();
w.write(
"\t\t\t"
+ "\""
+ "bondType"
+ "\":"
+ tempA.getAdjacentBonds().get(z).getBondType()
+ "\",");
w.newLine();
w.write(
"\t\t\t"
+ "\""
+ "exist"
+ "\":"
+ tempA.getAdjacentBonds().get(z).getExist()
+ "\",");
w.newLine();
w.write("\t\t\t" + "\"" + "weight" + "\":" + tempA.getAdjacentBonds().get(z).getWeight());
w.newLine();
w.write("\t\t" + "]");
w.newLine();
}
w.write("\t" + "}");
w.newLine();
}
for (int p = 0; p < bList.size(); p++) {
Bond tempB = bList.get(p);
w.write("{");
w.newLine();
w.write("\t" + "\"" + "edgeNum" + "\":" + tempB.getEdgeNum() + "\",");
w.newLine();
w.write("\t" + "\"" + "bondType" + "\":" + tempB.getBondType() + "\",");
w.newLine();
w.write("\t" + "\"" + "exist" + "\":" + tempB.getExist() + "\",");
w.newLine();
w.write("\t" + "\"" + "weight" + tempB.getWeight() + "\":");
w.newLine();
w.write("\t" + "\"" + "adjacentAtoms" + "\": {");
w.newLine();
w.write("\t\t" + "\"" + "vertexNum" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "atomicNum" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "atomicWeight" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "electroNeg" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "atomName" + "\":" + "\",");
w.newLine();
}
w.write("\t" + "}");
w.newLine();
} catch (IOException e) {
System.out.println("error writing meat of file");
}
}
public void draw() {
sketch.send(
"moveto",
new Atom[] {Atom.newAtom(coords[0]), Atom.newAtom(coords[1]), Atom.newAtom(coords[2])});
sketch.send(
"lineto",
new Atom[] {Atom.newAtom(origin[0]), Atom.newAtom(origin[1]), Atom.newAtom(origin[2])});
sketch.send(
"lineto",
new Atom[] {
Atom.newAtom(origin[0]), Atom.newAtom(origin[1]), Atom.newAtom(origin[2] + 0.1)
});
sketch.send(
"lineto",
new Atom[] {Atom.newAtom(coords[0]), Atom.newAtom(coords[1]), Atom.newAtom(coords[2])});
}
public static double getRoughDist(Atom a, Atom b) {
double xDist = a.getPoint().x - b.getPoint().x;
double yDist = a.getPoint().y - b.getPoint().y;
return xDist + yDist;
}
public AbrahamGAValue getABGroup(ChemGraph p_chemGraph) {
// #[ operation getGAGroup(ChemGraph)
AbramData result_abram = new AbramData();
Graph g = p_chemGraph.getGraph();
HashMap oldCentralNode = (HashMap) (p_chemGraph.getCentralNode()).clone();
// satuate radical site
int max_radNum_molecule = ChemGraph.getMAX_RADICAL_NUM();
int max_radNum_atom = Math.min(8, max_radNum_molecule);
int[] idArray = new int[max_radNum_molecule];
Atom[] atomArray = new Atom[max_radNum_molecule];
Node[][] newnode = new Node[max_radNum_molecule][max_radNum_atom];
int radicalSite = 0;
Iterator iter = p_chemGraph.getNodeList();
FreeElectron satuated = FreeElectron.make("0");
while (iter.hasNext()) {
Node node = (Node) iter.next();
Atom atom = (Atom) node.getElement();
if (atom.isRadical()) {
radicalSite++;
// save the old radical atom
idArray[radicalSite - 1] = node.getID().intValue();
atomArray[radicalSite - 1] = atom;
// new a satuated atom and replace the old one
Atom newAtom = new Atom(atom.getChemElement(), satuated);
node.setElement(newAtom);
node.updateFeElement();
}
}
// add H to satuate chem graph
Atom H = Atom.make(ChemElement.make("H"), satuated);
Bond S = Bond.make("S");
for (int i = 0; i < radicalSite; i++) {
Node node = p_chemGraph.getNodeAt(idArray[i]);
Atom atom = atomArray[i];
int HNum = atom.getRadicalNumber();
for (int j = 0; j < HNum; j++) {
newnode[i][j] = g.addNode(H);
g.addArcBetween(node, S, newnode[i][j]);
}
node.updateFgElement();
}
// find all the thermo groups
iter = p_chemGraph.getNodeList();
while (iter.hasNext()) {
Node node = (Node) iter.next();
Atom atom = (Atom) node.getElement();
if (!(atom.getType().equals("H"))) {
if (!atom.isRadical()) {
p_chemGraph.resetThermoSite(node);
AbrahamGAValue thisAbrahamValue = thermoLibrary.findAbrahamGroup(p_chemGraph);
if (thisAbrahamValue == null) {
System.err.println("Abraham group not found: " + node.getID());
} else {
// System.out.println(node.getID() + " " + thisGAValue.getName()+ "
// "+thisGAValue.toString());
result_abram.plus(thisAbrahamValue);
}
} else {
System.err.println("Error: Radical detected after satuation!");
}
}
}
// // find the BDE for all radical groups
// for (int i=0; i<radicalSite; i++) {
// int id = idArray[i];
// Node node = g.getNodeAt(id);
// Atom old = (Atom)node.getElement();
// node.setElement(atomArray[i]);
// node.updateFeElement();
//
// // get rid of the extra H at ith site
// int HNum = atomArray[i].getRadicalNumber();
// for (int j=0;j<HNum;j++) {
// g.removeNode(newnode[i][j]);
// }
// node.updateFgElement();
//
// p_chemGraph.resetThermoSite(node);
// ThermoGAValue thisGAValue = thermoLibrary.findRadicalGroup(p_chemGraph);
// if (thisGAValue == null) {
// System.err.println("Radical group not found: " + node.getID());
// }
// else {
// //System.out.println(node.getID() + " radical correction: " +
// thisGAValue.getName() + " "+thisGAValue.toString());
// result.plus(thisGAValue);
// }
//
// //recover the satuated site for next radical site calculation
// node.setElement(old);
// node.updateFeElement();
// for (int j=0;j<HNum;j++) {
// newnode[i][j] = g.addNode(H);
// g.addArcBetween(node,S,newnode[i][j]);
// }
// node.updateFgElement();
//
// }
//
// // recover the chem graph structure
// // recover the radical
// for (int i=0; i<radicalSite; i++) {
// int id = idArray[i];
// Node node = g.getNodeAt(id);
// node.setElement(atomArray[i]);
// node.updateFeElement();
// int HNum = atomArray[i].getRadicalNumber();
// //get rid of extra H
// for (int j=0;j<HNum;j++) {
// g.removeNode(newnode[i][j]);
// }
// node.updateFgElement();
// }
//
// // substrate the enthalphy of H from the result
// int rad_number = p_chemGraph.getRadicalNumber();
// ThermoGAValue enthalpy_H = new ThermoGAValue(ENTHALPY_HYDROGEN * rad_number,
// 0,0,0,0,0,0,0,0,0,0,0,null);
// result.minus(enthalpy_H);
//
// // make the symmetric number correction to entropy
//
// if (p_chemGraph.isAcyclic()){
// int sigma = p_chemGraph.getSymmetryNumber();
// ThermoGAValue symmtryNumberCorrection = new
// ThermoGAValue(0,GasConstant.getCalMolK()*Math.log(sigma),0,0,0,0,0,0,0,0,0,0,null);
// result.minus(symmtryNumberCorrection);
// }
p_chemGraph.setCentralNode(oldCentralNode);
return result_abram;
// #]
}
public static final void pack(List fileList, String destinationFile, final JIPEngine engine)
throws FileNotFoundException, IOException {
InputStream ins = null;
File outf = new File(destinationFile);
if (!outf.isAbsolute()) outf = new File(engine.getSearchPath(), destinationFile);
final ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(outf));
String strPath = null;
int len = fileList.getHeight();
for (int i = 1; i <= len; i++) {
try {
PrologObject path = getRealTerm(fileList.getTerm(i));
if (!(path instanceof Atom))
throw new JIPTypeException(JIPTypeException.ATOM_OR_STRING, path);
strPath = ((Atom) path).getName();
String strFileName[] = new String[1];
String strCurDir[] = new String[1];
ins =
StreamManager.getStreamManager()
.getInputStream(strPath, engine.getSearchPath(), strFileName, strCurDir);
String file = new File(strPath).getName();
final int nPos = file.lastIndexOf('.');
file = new StringBuilder(file.substring(0, nPos)).append(".jip").toString();
PrologParser parser =
new PrologParser(
new ParserReader(new PushbackLineNumberInputStream(ins)),
engine.getOperatorManager(),
engine,
strPath);
try {
PrologObject term;
while ((term = parser.parseNext()) != null) {
out.writeObject(term);
}
ins.close();
ins = null;
} catch (IOException ex) {
ins.close();
ins = null;
out.close();
ex.printStackTrace();
throw new JIPJVMException(ex);
}
} catch (FileNotFoundException ex) {
try {
if (ins != null) ins.close();
out.close();
} catch (IOException ex1) {
}
;
throw JIPExistenceException.createSourceSynkException(Atom.createAtom(strPath));
} catch (IOException ex) {
try {
if (ins != null) ins.close();
} catch (IOException ex1) {
}
throw new JIPJVMException(ex);
} catch (SecurityException ex) {
try {
if (ins != null) ins.close();
} catch (IOException ex1) {
}
throw new JIPPermissionException("access", "source_sink", Atom.createAtom(strPath));
} catch (JIPRuntimeException ex) {
ex.m_strFileName = strPath;
throw ex;
} finally {
try {
if (ins != null) ins.close();
} catch (IOException ex1) {
}
}
}
out.close();
}