void Chemistry::Bond::cycleBondOrder()
{
quint8 order = bondOrder();
if (order == 3)
setBondOrder(1);
else
setBondOrder(order + 1);
}
bool UffBondStrechCalculation::setup()
{
const UffAtomParameters *pa = parameters(atom(0));
const UffAtomParameters *pb = parameters(atom(1));
if(!pa || !pb){
return false;
}
// n = bondorder (1.5 for aromatic, 1.366 for amide)
chemkit::Real bondorder = bondOrder(atom(0), atom(1));
chemkit::Real r0 = bondLength(pa, pb, bondorder);
// parameter(1) = k_ij = 664.12 * (Z*_i * Z*_j) / r_ij^3
chemkit::Real za = pa->Z;
chemkit::Real zb = pb->Z;
chemkit::Real kb = 664.12 * (za * zb) / pow(r0, 3);
setParameter(0, kb);
setParameter(1, r0);
return true;
}
bool UffTorsionCalculation::setup()
{
UffForceField *forceField = static_cast<UffForceField *>(this->forceField());
const chemkit::ForceFieldAtom *b = atom(1);
const chemkit::ForceFieldAtom *c = atom(2);
if(b->type().length() < 3 || c->type().length() < 3){
return false;
}
const UffAtomParameters *pb = parameters(b);
const UffAtomParameters *pc = parameters(c);
chemkit::Real V = 0;
chemkit::Real n = 0;
chemkit::Real phi0 = 0;
// sp3-sp3
if(b->type()[2] == '3' && c->type()[2] == '3'){
// exception for two group six atoms
if(forceField->isGroupSix(b) && forceField->isGroupSix(c)){
if(b->atom()->is(chemkit::Atom::Oxygen) && c->atom()->is(chemkit::Atom::Oxygen)){
V = 2; // sqrt(2*2)
}
else if(b->atom()->is(chemkit::Atom::Oxygen) || c->atom()->is(chemkit::Atom::Oxygen)){
V = sqrt(2 * 6.8);
}
else{
V = sqrt(6.8 * 6.8);
}
n = 2;
phi0 = 90;
}
// general case
else{
// equation 16
V = sqrt(pb->V * pc->V);
n = 3;
phi0 = 180 * chemkit::constants::DegreesToRadians;
}
}
// sp2-sp2
else if((b->type()[2] == '2' || b->type()[2] == 'R') && (c->type()[2] == '2' || c->type()[2] == 'R')){
chemkit::Real bondorder = bondOrder(b, c);
// equation 17
V = 5 * sqrt(pb->U * pc->U) * (1 + 4.18 * log(bondorder));
n = 2;
phi0 = 180 * chemkit::constants::DegreesToRadians;
}
// group 6 sp3 - any sp2 or R
else if((forceField->isGroupSix(b) && (c->type()[2] == '2' || c->type()[2] == 'R')) ||
(forceField->isGroupSix(c) && (b->type()[2] == '2' || b->type()[2] == 'R'))){
chemkit::Real bondorder = bondOrder(b, c);
// equation 17
V = 5 * sqrt(pb->U * pc->U) * (1 + 4.18 * log(bondorder));
n = 2;
phi0 = 90 * chemkit::constants::DegreesToRadians;
}
// sp3-sp2
else if((b->type()[2] == '3' && (c->type()[2] == '2' || c->type()[2] == 'R')) ||
(c->type()[2] == '3' && (b->type()[2] == '2' || b->type()[2] == 'R'))){
V = 1;
n = 6;
phi0 = 0;
}
else{
return false;
}
setParameter(0, V);
setParameter(1, n);
setParameter(2, phi0);
return true;
}
