internal virtual Bond addNewBond(int atomIndex1, int atomIndex2, int order)
{
Bond bond = new Bond(atomIndex1, atomIndex2, order);
addBond(bond);
return bond;
}
internal virtual void addBond(Bond bond)
{
/*
System.out.println("I see a bond:" + bond.atomIndex1 + "-" +
bond.atomIndex2 + ":" + bond.order);
*/
if (bond.atomIndex1 < 0 || bond.atomIndex2 < 0 || bond.order <= 0)
{
/*
System.out.println(">>>>>>BAD BOND:" + bond.atomIndex1 + "-" +
bond.atomIndex2 + ":" + bond.order);
*/
return;
}
if (bondCount == bonds.Length)
bonds = (Bond[])AtomSetCollectionReader.setLength(bonds, bondCount + 1024);
bonds[bondCount++] = bond;
}
public override bool hasNext()
{
if (ibond == atomSetCollection.bondCount)
return false;
bond = bonds[ibond++];
return true;
}
