/// Returns the polarity of the bond. This is calculated as the
/// absolute value of the difference in electronegativity between the
/// two atoms in the bond.
Real Bond::polarity() const
{
if(atom1()->atomicNumber() == atom2()->atomicNumber()){
return 0;
}
return std::abs(atom1()->electronegativity() - atom2()->electronegativity());
}
/// Returns the dipole moment for the bond.
Vector3 Bond::dipoleMoment() const
{
Point3 a = atom1()->position();
Point3 b = atom2()->position();
Real qa = atom1()->partialCharge();
Real qb = atom2()->partialCharge();
return (a - b) * (qa - qb);
}
void SolventAccessibleSurface::createEdge(Position j)
{
SASEdge* edge = edges_[j];
edge->index_ = j;
RSEdge* rsedge = reduced_surface_->edges_[j];
if (rsedge->face_[0] != NULL)
{
edge->vertex_[0] = vertices_[rsedge->face_[0]->index_];
edge->vertex_[1] = vertices_[rsedge->face_[1]->index_];
}
else
{
edge->vertex_[0] = NULL;
edge->vertex_[1] = NULL;
}
edge->face_[0] = faces_[rsedge->vertex_[0]->index_];
edge->face_[1] = faces_[rsedge->vertex_[1]->index_];
edge->angle_ = rsedge->angle_;
edge->circle_.p = rsedge->center_of_torus_;
edge->circle_.radius = rsedge->radius_of_torus_;
TSphere3<double> atom1(reduced_surface_->atom_[rsedge->vertex_[0]->atom_]);
TSphere3<double> atom2(reduced_surface_->atom_[rsedge->vertex_[1]->atom_]);
edge->circle_.n = atom1.p-atom2.p;
}
// --- Properties ---------------------------------------------------------- //
/// Returns the atom at \p index in the bond. Index must be either
/// \c 0 or \c 1.
Atom* Bond::atom(size_t index) const
{
return index == 0 ? atom1() : atom2();
}
/// Returns the length of the bond. Length is in Angstroms.
Real Bond::length() const
{
return atom1()->distance(atom2());
}
// --- Geometry ------------------------------------------------------------ //
/// Returns the center point of the bond. The center is equal to the
/// midpoint between the two atoms in the bond.
Point3 Bond::center() const
{
return chemkit::geometry::midpoint(atom1()->position(),
atom2()->position());
}
/// Returns \c true if either of the two atoms in the bond are
/// terminal.
bool Bond::isTerminal() const
{
return atom1()->isTerminal() || atom2()->isTerminal();
}
/// Returns \c true if the bond contains an atom of the element \p a
/// and an atom of the element \p b.
///
/// For example, to check if this is a carbonyl bond you could use:
/// \code
/// if(bond->containsBoth(Atom::Carbon, Atom::Oxygen) && bond->order() == Bond::Double){
/// // it is a carbonyl
/// }
/// \endcode
bool Bond::containsBoth(const Element &a, const Element &b) const
{
return (atom1()->is(a) && atom2()->is(b)) || (atom2()->is(a) && atom1()->is(b));
}
/// Returns \c true if the bond contains an atom of the given
/// \p element.
bool Bond::contains(const Element &element) const
{
return atom1()->is(element) || atom2()->is(element);
}
// --- Structure ----------------------------------------------------------- //
/// Returns \c true if the bond contains atom.
bool Bond::contains(const Atom *atom) const
{
return atom1() == atom || atom2() == atom;
}
