Particles CHARMMParameters::create_angles(kernel::Particles bonds) const {
IMP_OBJECT_LOG;
kernel::Particles ps;
BondMap particle_bonds;
make_bond_map(bonds, particle_bonds);
// Iterate over all bonds
for (kernel::Particles::const_iterator bit1 = bonds.begin();
bit1 != bonds.end(); ++bit1) {
IMP::atom::Bond bd = IMP::atom::Bond(*bit1);
kernel::Particle *p2 = bd.get_bonded(0).get_particle();
kernel::Particle *p3 = bd.get_bonded(1).get_particle();
// Extend along each adjoining p2 bond to get candidate p1-p2-p3 angles
for (base::Vector<IMP::atom::Bond>::const_iterator bit2 =
particle_bonds[p2].begin();
bit2 != particle_bonds[p2].end(); ++bit2) {
kernel::Particle *p1 = get_other_end_of_bond(p2, *bit2);
// Avoid making angles where p1 == p3, and avoid double-counting
if (p3 > p1) {
add_angle(p1, p2, p3, ps);
}
}
// Do the same for p2-p3-p4 angles
for (base::Vector<IMP::atom::Bond>::const_iterator bit2 =
particle_bonds[p3].begin();
bit2 != particle_bonds[p3].end(); ++bit2) {
kernel::Particle *p4 = get_other_end_of_bond(p3, *bit2);
if (p4 < p2) {
add_angle(p2, p3, p4, ps);
}
}
}
return ps;
}
Particles CHARMMParameters::create_dihedrals(Particles bonds) const
{
IMP_OBJECT_LOG;
Particles ps;
BondMap particle_bonds;
make_bond_map(bonds, particle_bonds);
// Iterate over all bonds
for (Particles::const_iterator bit1 = bonds.begin();
bit1 != bonds.end(); ++bit1) {
IMP::atom::Bond bd = IMP::atom::Bond(*bit1);
Particle *p2 = bd.get_bonded(0).get_particle();
Particle *p3 = bd.get_bonded(1).get_particle();
// Extend along each bond from p2 and p3 to get candidate
// p1-p2-p3-p4 dihedrals
for (base::Vector<IMP::atom::Bond>::const_iterator bit2
= particle_bonds[p2].begin();
bit2 != particle_bonds[p2].end(); ++bit2) {
Particle *p1 = get_other_end_of_bond(p2, *bit2);
if (p1 != p3) {
for (base::Vector<IMP::atom::Bond>::const_iterator bit3
= particle_bonds[p3].begin();
bit3 != particle_bonds[p3].end(); ++bit3) {
Particle *p4 = get_other_end_of_bond(p3, *bit3);
// Avoid generating dihedrals for three-membered rings
if (p1 != p4 && p2 != p4) {
internal::add_dihedral_to_list(this, p1, p2, p3, p4, ps);
}
}
}
}
}
return ps;
}