bool UffAngleBendCalculation::setup()
{
const UffAtomParameters *pa = parameters(atom(0));
const UffAtomParameters *pb = parameters(atom(1));
const UffAtomParameters *pc = parameters(atom(2));
if(!pa || !pb || !pc){
return false;
}
chemkit::Real theta0 = pb->theta * chemkit::constants::DegreesToRadians;
const chemkit::Bond *bond_ab = atom(0)->atom()->bondTo(atom(1)->atom());
const chemkit::Bond *bond_bc = atom(1)->atom()->bondTo(atom(2)->atom());
chemkit::Real bo_ij = bond_ab->order();
chemkit::Real bo_jk = bond_bc->order();
chemkit::Real r_ab = bondLength(pa, pb, bo_ij);
chemkit::Real r_bc = bondLength(pb, pc, bo_jk);
chemkit::Real r_ac = sqrt(pow(r_ab, 2) + pow(r_bc, 2) - (2.0 * r_ab * r_bc * cos(theta0)));
chemkit::Real beta = 664.12 / (r_ab * r_bc);
chemkit::Real z_a = pa->Z;
chemkit::Real z_c = pc->Z;
// equation 13
chemkit::Real ka = beta * ((z_a * z_c) / pow(r_ac, 5)) * r_ab * r_bc * (3.0 * r_ab * r_bc * (1.0 - pow(cos(theta0), 2.0)) - (pow(r_ac, 2.0) * cos(theta0)));
setParameter(0, ka);
chemkit::Real c2 = 1 / (4 * pow(sin(theta0), 2));
chemkit::Real c1 = -4 * c2 * cos(theta0);
chemkit::Real c0 = c2 * (2 * pow(cos(theta0), 2) + 1);
setParameter(1, c0);
setParameter(2, c1);
setParameter(3, c2);
return true;
}
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;
}
void GraphNodeParameters::decrementBondLength() {
bondLength(bondLength() - bondLengthIncrement);
}
