public void bondAtoms(Atom atom1, Atom atom2, short order, BitArray bsA, BitArray bsB)
{
bool atom1InSetA = bsA == null || bsA.Get(atom1.atomIndex);
bool atom1InSetB = bsB == null || bsB.Get(atom1.atomIndex);
bool atom2InSetA = bsA == null || bsA.Get(atom2.atomIndex);
bool atom2InSetB = bsB == null || bsB.Get(atom2.atomIndex);
if (atom1InSetA & atom2InSetB || atom1InSetB & atom2InSetA)
{
addBond(atom1.bondMutually(atom2, order, this));
}
}
public void bondAtoms(Atom atom1, Atom atom2, int order)
{
// skip ht lookup - pointless
if (bondCount == bonds.Length)
{
bonds = (Bond[])Util.setLength(bonds, bondCount + 2 * ATOM_GROWTH_INCREMENT);
}
// note that if the atoms are already bonded then
// Atom.bondMutually(...) will return null
Bond bond = atom1.bondMutually(atom2, (short)order, this);
if (bond != null)
{
bonds[bondCount++] = bond;
if ((order & JmolConstants.BOND_HYDROGEN_MASK) != 0)
{
fileHasHbonds = true;
}
}
}
public void checkValencesAndBond(Atom atomA, Atom atomB, short order)
{
// System.out.println("checkValencesAndBond(" +
// atomA.point3f + "," + atomB.point3f + ")");
if (atomA.CurrentBondCount > JmolConstants.MAXIMUM_AUTO_BOND_COUNT || atomB.CurrentBondCount > JmolConstants.MAXIMUM_AUTO_BOND_COUNT)
{
System.Console.Out.WriteLine("maximum auto bond count reached");
return;
}
int formalChargeA = atomA.FormalCharge;
if (formalChargeA != 0)
{
int formalChargeB = atomB.FormalCharge;
if ((formalChargeA < 0 && formalChargeB < 0) || (formalChargeA > 0 && formalChargeB > 0))
{
return;
}
}
addBond(atomA.bondMutually(atomB, order, this));
}
public void bondAtoms(Atom atom1, Atom atom2, short order, BitArray bsA, BitArray bsB)
{
bool atom1InSetA = bsA == null || bsA.Get(atom1.atomIndex);
bool atom1InSetB = bsB == null || bsB.Get(atom1.atomIndex);
bool atom2InSetA = bsA == null || bsA.Get(atom2.atomIndex);
bool atom2InSetB = bsB == null || bsB.Get(atom2.atomIndex);
if (atom1InSetA & atom2InSetB || atom1InSetB & atom2InSetA)
addBond(atom1.bondMutually(atom2, order, this));
}
public void bondAtoms(Atom atom1, Atom atom2, int order)
{
// skip ht lookup - pointless
if (bondCount == bonds.Length)
bonds = (Bond[])Util.setLength(bonds, bondCount + 2 * ATOM_GROWTH_INCREMENT);
// note that if the atoms are already bonded then
// Atom.bondMutually(...) will return null
Bond bond = atom1.bondMutually(atom2, (short)order, this);
if (bond != null)
{
bonds[bondCount++] = bond;
if ((order & JmolConstants.BOND_HYDROGEN_MASK) != 0)
fileHasHbonds = true;
}
}
public void checkValencesAndBond(Atom atomA, Atom atomB, short order)
{
// System.out.println("checkValencesAndBond(" +
// atomA.point3f + "," + atomB.point3f + ")");
if (atomA.CurrentBondCount > JmolConstants.MAXIMUM_AUTO_BOND_COUNT || atomB.CurrentBondCount > JmolConstants.MAXIMUM_AUTO_BOND_COUNT)
{
System.Console.Out.WriteLine("maximum auto bond count reached");
return;
}
int formalChargeA = atomA.FormalCharge;
if (formalChargeA != 0)
{
int formalChargeB = atomB.FormalCharge;
if ((formalChargeA < 0 && formalChargeB < 0) || (formalChargeA > 0 && formalChargeB > 0))
return;
}
addBond(atomA.bondMutually(atomB, order, this));
}
public void bondAtoms(Atom atom1, Atom atom2, short order)
{
addBond(atom1.bondMutually(atom2, order, this));
}
