// set the model's bonds using Jmol display.
public void setModelBonds() {
int currModel = 0, prevModel = 0;
Atom atom1, atom2;
Bond bond;
String index1, index2;
ArrayList<Bond> ownbonds = new ArrayList<Bond>();
org.jmol.modelset.Bond[] bonds = viewer.ms.bo;
for (int i = 0; i < bonds.length; i++) {
prevModel = currModel;
currModel = bonds[i].getAtom1().getModelNumber();
Model model = modelList.get(currModel - 1);
if (currModel != prevModel && i != 0) {
modelList.get(prevModel - 1).setBonds(ownbonds);
ownbonds.clear();
}
index1 = model.getModelName() + bonds[i].getAtom1().atomSite;
index2 = model.getModelName() + bonds[i].getAtom2().atomSite;
atom1 = model.getAtomHash().get(index1);
atom2 = model.getAtomHash().get(index2);
if (atom1 == null || atom2 == null) continue;
bond = new Bond(atom1, atom2);
ownbonds.add(bond);
atom1.setBond(bond);
atom2.setBond(bond);
if (i == bonds.length - 1) {
modelList.get(currModel - 1).setBonds(ownbonds);
}
}
}
public void updateViewerCoord() {
for (Atom atm : modelList.get(viewer.getDisplayModelIndex()).getAtomHash().values()) {
viewer.ms.setAtomCoord(
(atm.getAtomSeqNum() - 1),
atm.getCoordinates()[0],
atm.getCoordinates()[1],
atm.getCoordinates()[2]);
}
jmolPanel.getViewer().refresh(3, "minimization step ");
}
public void atomMoved() {
for (Atom atm : modelList.get(viewer.getDisplayModelIndex()).getAtomHash().values()) {
for (int i = 0; i < viewer.ms.at.length; i++) {
if (atm.getAtomSeqNum() == (i + 1)) {
double[] coords = {viewer.ms.at[i].x, viewer.ms.at[i].y, viewer.ms.at[i].z};
atm.setCoordinates(coords);
}
}
}
}
public void notifyUpdated(AbstractParticle[] particles) {
List<Atom> atomsUpdated = new ArrayList<Atom>();
// When the two particles are part of common model
if (modelList.size() != 0) {
for (int i = 0; i < particles.length; i++) {
if (particles[i] instanceof Atom) { // if particle is Atom type
// get the updated atom from model
atomsUpdated.add(
modelList
.get(0)
.getAtomHash()
.get(modelList.get(0).getModelName() + ((Atom) particles[i]).getChainSeqNum()));
}
}
// update atoms in jmol display
for (int i = 0; i < atomsUpdated.size(); i++) {
Atom atom = atomsUpdated.get(i);
float xOffset =
(float) atom.getPosition().x - viewer.getAtomPoint3f(atom.getChainSeqNum() - 1).x;
float yOffset =
(float) atom.getPosition().y - viewer.getAtomPoint3f(atom.getChainSeqNum() - 1).y;
float zOffset =
(float) atom.getPosition().z - viewer.getAtomPoint3f(atom.getChainSeqNum() - 1).z;
viewer.evalString("select atomno=" + atom.getChainSeqNum());
viewer.evalString("translateSelected {" + xOffset + " " + yOffset + " " + zOffset + "}");
}
}
}
// paste copied/cut atoms, not applicable when copied atoms are paste to same model.
public void pasteSavedAtoms(int modelIndex) {
if (savedAtoms == null)
JOptionPane.showMessageDialog(
jmolPanel,
"You have not copied or cut any atoms to paste!",
"Warning",
JOptionPane.WARNING_MESSAGE);
else {
boolean error = false;
for (int i = 0; i < savedAtoms.size(); i++) {
for (Atom atm : modelList.get(modelIndex).getAtomHash().values()) {
if (savedAtoms.get(i).getCoordinates()[0] == atm.getCoordinates()[0]
&& savedAtoms.get(i).getCoordinates()[1] == atm.getCoordinates()[1]
&& savedAtoms.get(i).getCoordinates()[2] == atm.getCoordinates()[2]) {
error = true;
break;
}
}
if (error) {
JOptionPane.showMessageDialog(
jmolPanel,
"You are trying to paste atoms in location occupied!",
"Warning",
JOptionPane.WARNING_MESSAGE);
break;
} else {
addAtom(modelIndex, savedAtoms.get(i));
}
}
String pdb = DataManager.modelToPDB(modelList);
System.out.println(pdb);
viewer.openStringInline(pdb);
viewer.setCurrentModelIndex(modelIndex);
}
toolPanel.setModelText(modelList);
}
public void displayParticles(ArrayList<AbstractParticle> list) {
String pdb = "MODEL 1\n";
for (int i = 0; i < list.size(); i++) {
// String index = String.format("%4d", list.get(i).getGUID());
String index = String.format("%4d", i);
if (list.get(i) instanceof Atom) {
double scale = Math.pow(10, 10 + list.get(i).getPosition().metric);
Vector3D position = list.get(i).getPosition();
double x = capCoord(position.x * scale);
double y = capCoord(position.y * scale);
double z = capCoord(position.z * scale);
String coords = String.format("%8.3f%8.3f%8.3f", x, y, z);
String elementSymbol =
String.format("%-4s", ((Atom) list.get(i)).getElementSymbol().toUpperCase());
pdb +=
"HETATM " + index + " " + elementSymbol + " 1 " + coords + " 1.00 0.00\n";
} else if (list.get(i) instanceof Molecule) {
Molecule m = (Molecule) list.get(i);
if (World.simulationLvlAtomic == true) {
for (Atom a : m.getChains().get(0).atomSeq) {
double scale = Math.pow(10, 10 + list.get(i).getPosition().metric);
Vector3D position = a.getPosition();
double x = capCoord(position.x * scale);
double y = capCoord(position.y * scale);
double z = capCoord(position.z * scale);
String coords = String.format("%8.3f%8.3f%8.3f", x, y, z);
String elementSymbol = String.format("%-4s", a.getElementSymbol().toUpperCase());
pdb +=
"HETATM "
+ index
+ " "
+ elementSymbol
+ " 1 "
+ coords
+ " 1.00 0.00\n";
}
/*
pdb += "HETATM 1 NA TST A 1 5.000 5.000 5.000 1.00 0.00\n"+
"HETATM 2 CL TST A 1 6.400 6.400 6.400 1.00 0.00\n"+
"CONECT 1 2\n" +
"CONECT 2 1\n";
*/
} else {
double scale = Math.pow(10, 10 + list.get(i).getPosition().metric);
Vector3D position = list.get(i).getPosition();
double x = capCoord(position.x * scale);
double y = capCoord(position.y * scale);
double z = capCoord(position.z * scale);
String coords = String.format("%8.3f%8.3f%8.3f", x, y, z);
pdb += "HETATM 1 CS TST A 1 " + coords + " 1.00 0.00\n";
}
}
}
pdb += "ENDMDL";
if (World.displayUI) viewer.openStringInline(pdb);
try {
BufferedWriter writer = new BufferedWriter(new FileWriter("output.pdb"));
writer.write(pdb);
writer.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
World.simulationStatus = "restart";
}
if (World.displayUI) {
createUserModel(DataManager.readFile("output.pdb"));
}
}