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;
}
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);
}
}
RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(kernel::Particles ps,
int num_residues,
Float scale):
kernel::Restraint(IMP::internal::get_model(ps),
"RadiusOfGyrationRestraint"){
if (ps.size()==0) return;
add_particles(ps);
mdl_=ps[0]->get_model();
predicted_rog_ = get_approximated_radius_of_gyration(num_residues);
scale_=scale;
hub_=new core::HarmonicUpperBound(predicted_rog_*scale_,1);
}
Particles CHARMMParameters::create_dihedrals(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 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) {
kernel::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) {
kernel::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;
}
SimpleDistance create_simple_distance(const kernel::Particles &ps)
{
IMP_USAGE_CHECK(ps.size() == 2, "Two particles should be given");
/****** Set the restraint ******/
IMP_NEW(core::HarmonicUpperBound, h, (0, 1));
IMP_NEW(core::DistanceRestraint, dr, (h, ps[0], ps[1]));
/****** Add restraint to the model ******/
//Model *mdl = (*ps)[0]->get_model();
//mdl->add_restraint(dr);
/****** Return a SimpleDistance object ******/
return SimpleDistance(dr, h);
}
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);
}
SimpleDiameter create_simple_diameter(const kernel::Particles &ps, Float diameter)
{
IMP_USAGE_CHECK(ps.size() >= 2, "At least two particles should be given");
/****** Set the restraint ******/
IMP_NEW(core::HarmonicUpperBound, h, (0, 1));
IMP_NEW(container::ListSingletonContainer, lsc, (get_as<kernel::ParticlesTemp>(ps)));
IMP_NEW(core::DiameterRestraint, dr, (h, lsc, diameter));
/****** Add restraint to the model ******/
//Model *mdl = (*ps)[0]->get_model();
//mdl->add_restraint(dr);
/****** Return a SimpleDiameter object ******/
return SimpleDiameter(dr, h);
}