AtomSetCollection readAtomSetCollection(BufferedReader reader) throws Exception {
this.reader = reader;
atomSetCollection = new AtomSetCollection("mol2");
setFractionalCoordinates(false);
readLine();
modelNumber = 0;
while (line != null) {
if (line.equals("@<TRIPOS>MOLECULE")) {
if (++modelNumber == desiredModelNumber || desiredModelNumber <= 0) {
try {
processMolecule();
} catch (Exception e) {
Logger.error("Could not read file at line: " + line, e);
}
if (desiredModelNumber > 0) break;
continue;
}
}
readLine();
}
return atomSetCollection;
}
void setProperty(String propertyName, Object value, BitSet bs) {
Logger.debug("MeshCollection.setProperty(" + propertyName + "," + value + ")");
/*
Logger.debug("meshCount=" + meshCount +
" currentMesh=" + currentMesh);
for (int i = 0; i < meshCount; ++i) {
Mesh mesh = meshes[i];
Logger.debug("i=" + i +
" mesh.thisID=" + mesh.thisID +
" mesh.visible=" + mesh.visible +
" mesh.translucent=" + mesh.translucent +
" mesh.colix=" + mesh.meshColix);
}
*/
if ("thisID" == propertyName) {
setMesh((String) value);
return;
}
if ("reset" == propertyName) {
String thisID = (String) value;
if (setMesh(thisID) == null) return;
deleteMesh();
setMesh(thisID);
return;
}
if ("on" == propertyName) {
if (currentMesh != null) currentMesh.visible = true;
else {
for (int i = meshCount; --i >= 0; ) meshes[i].visible = true;
}
return;
}
if ("off" == propertyName) {
if (currentMesh != null) currentMesh.visible = false;
else {
for (int i = meshCount; --i >= 0; ) meshes[i].visible = false;
}
return;
}
if ("background" == propertyName) {
boolean doHide = !((Boolean) value).booleanValue();
if (currentMesh != null) currentMesh.hideBackground = doHide;
else {
for (int i = meshCount; --i >= 0; ) meshes[i].hideBackground = doHide;
}
return;
}
if ("title" == propertyName) {
if (currentMesh != null) {
currentMesh.title = (String[]) value;
}
return;
}
if ("color" == propertyName) {
if (value == "sets") {
currentMesh.allocVertexColixes();
for (int i = 0; i < currentMesh.surfaceSet.length; i++)
for (int j = 0; j < currentMesh.vertexCount; j++)
if (currentMesh.surfaceSet[i].get(j))
currentMesh.vertexColixes[j] = Graphics3D.getColix(Graphics3D.colorNames[i]);
return;
}
if (value != null) {
colix = Graphics3D.getColix(value);
if (currentMesh != null) {
currentMesh.colix = colix;
currentMesh.vertexColixes = null;
} else {
for (int i = meshCount; --i >= 0; ) {
Mesh mesh = meshes[i];
mesh.colix = colix;
mesh.vertexColixes = null;
}
}
}
return;
}
if ("translucency" == propertyName) {
boolean isTranslucent = ("translucent" == value);
if (currentMesh != null) currentMesh.setTranslucent(isTranslucent);
else {
for (int i = meshCount; --i >= 0; ) meshes[i].setTranslucent(isTranslucent);
}
return;
}
if ("dots" == propertyName) {
boolean showDots = value == Boolean.TRUE;
if (currentMesh != null) currentMesh.showPoints = showDots;
else {
for (int i = meshCount; --i >= 0; ) meshes[i].showPoints = showDots;
}
return;
}
if ("mesh" == propertyName) {
boolean showMesh = value == Boolean.TRUE;
if (currentMesh != null) currentMesh.drawTriangles = showMesh;
else {
for (int i = meshCount; --i >= 0; ) meshes[i].drawTriangles = showMesh;
}
return;
}
if ("fill" == propertyName) {
boolean showFill = value == Boolean.TRUE;
if (currentMesh != null) currentMesh.fillTriangles = showFill;
else {
for (int i = meshCount; --i >= 0; ) meshes[i].fillTriangles = showFill;
}
return;
}
if ("delete" == propertyName) {
deleteMesh();
return;
}
}