IMPATOM_BEGIN_INTERNAL_NAMESPACE
void add_dihedral_to_list(const CHARMMParameters *param, kernel::Particle *p1,
kernel::Particle *p2, kernel::Particle *p3,
kernel::Particle *p4, kernel::Particles &ps) {
try {
base::Vector<CHARMMDihedralParameters> p = param->get_dihedral_parameters(
CHARMMAtom(p1).get_charmm_type(), CHARMMAtom(p2).get_charmm_type(),
CHARMMAtom(p3).get_charmm_type(), CHARMMAtom(p4).get_charmm_type());
for (base::Vector<CHARMMDihedralParameters>::const_iterator it = p.begin();
it != p.end(); ++it) {
Dihedral dd = Dihedral::setup_particle(
new kernel::Particle(p1->get_model()), core::XYZ(p1), core::XYZ(p2),
core::XYZ(p3), core::XYZ(p4));
dd.set_ideal(it->ideal / 180.0 * PI);
dd.set_multiplicity(it->multiplicity);
if (it->force_constant < 0.0) {
dd.set_stiffness(-std::sqrt(-it->force_constant * 2.0));
} else {
dd.set_stiffness(std::sqrt(it->force_constant * 2.0));
}
ps.push_back(dd);
}
}
catch (const base::IndexException &e) {
// If no parameters, warn, and create an empty dihedral
IMP_WARN(e.what() << std::endl);
Dihedral dd = Dihedral::setup_particle(
new kernel::Particle(p1->get_model()), core::XYZ(p1), core::XYZ(p2),
core::XYZ(p3), core::XYZ(p4));
ps.push_back(dd);
}
}
void CHARMMParameters::add_angle(kernel::Particle *p1, kernel::Particle *p2,
kernel::Particle *p3,
kernel::Particles &ps) const {
IMP_OBJECT_LOG;
Angle ad = Angle::setup_particle(new kernel::Particle(p1->get_model()),
core::XYZ(p1), core::XYZ(p2), core::XYZ(p3));
try {
const CHARMMBondParameters &p = get_angle_parameters(
CHARMMAtom(p1).get_charmm_type(), CHARMMAtom(p2).get_charmm_type(),
CHARMMAtom(p3).get_charmm_type());
ad.set_ideal(p.ideal / 180.0 * PI);
ad.set_stiffness(std::sqrt(p.force_constant * 2.0));
}
catch (const base::IndexException &e) {
// If no parameters, warn only
IMP_WARN(e.what());
}
ps.push_back(ad);
}
String CHARMMParameters::get_force_field_atom_type(Atom atom) const {
IMP_OBJECT_LOG;
// Override base class to use CHARMMAtom decorator
static String empty_atom_type;
if (CHARMMAtom::get_is_setup(atom)) {
return CHARMMAtom(atom).get_charmm_type();
} else {
IMP_WARN_ONCE(atom.get_atom_type().get_string(),
"Atom " << atom << " does not have a known CHARMM type",
warn_context_);
return empty_atom_type;
}
}
