protected ArrayList<String> generateHashCodes(Iterable<IAtom> atoms) {
ArrayList<String> hashes = new ArrayList<String>();
for (IAtom atom : atoms) {
hashes.add(Integer.toString(atom.hashCode()));
}
return hashes;
}
/** Converts an Atom to a MSML Atom element */
protected AtomType convertAtom(IAtom atom, String parentID) {
AtomType atomElement = new AtomType();
String id = "";
if (atom.getID() != null) {
id = atom.getID();
} else {
id = Integer.toString(atom.hashCode());
}
String atomID = parentID + PREFIX_ATOM + id;
atomElement.setId(atomID);
atomElement.setCustomId("" + id);
// atom name
atomElement.setTitle(atom.getAtomTypeName());
// element name
atomElement.setElementType(atom.getSymbol());
double x, y, z;
// set choords
if (atom.getPoint3d() != null) {
x = atom.getPoint3d().x;
y = atom.getPoint3d().y;
z = atom.getPoint3d().z;
} else { // what if mol in 2d? -> has to use getPoint2d
x = atom.getPoint2d().x;
y = atom.getPoint2d().y;
z = 0.0;
}
if (atom.getFormalCharge() != null) {
atomElement.setFormalCharge(BigInteger.valueOf(atom.getFormalCharge()));
}
atomElement.setX3(new Float(x));
atomElement.setY3(new Float(y));
atomElement.setZ3(new Float(z));
return atomElement;
}