// for C++
Selection::Selection(Hierarchy h, std::string molname, int residue_index)
: radius_(-1) {
set_hierarchies(h.get_model(),
kernel::ParticleIndexes(1, h.get_particle_index()));
set_molecules(Strings(1, molname));
set_residue_indexes(Ints(1, residue_index));
}
IMPATOM_BEGIN_NAMESPACE
CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint(Hierarchy h,
CHARMMTopology *topology):
Restraint(h->get_model(), "CHARMMStereochemistryRestraint%1%")
{
bonds_ = topology->add_bonds(h);
angles_ = topology->get_parameters()->create_angles(bonds_);
dihedrals_ = topology->get_parameters()->create_dihedrals(bonds_);
impropers_ = topology->add_impropers(h);
bond_score_ = new BondSingletonScore(new core::Harmonic(0., 1.));
angle_score_ = new AngleSingletonScore(new core::Harmonic(0., 1.));
dihedral_score_ = new DihedralSingletonScore();
improper_score_ = new ImproperSingletonScore(new core::Harmonic(0., 1.));
}
Hierarchy create_simplified_along_backbone(Hierarchy in,
int num_res,
bool keep_detailed) {
Hierarchies chains= get_by_type(in, CHAIN_TYPE);
if (chains.size() > 1) {
Hierarchy root= Hierarchy::setup_particle(new Particle(in->get_model(),
in->get_name()));
for (unsigned int i=0; i< chains.size(); ++i) {
Chain chain(chains[i].get_particle());
root.add_child(create_simplified_along_backbone(chain, num_res));
}
return root;
} else if (chains.size()==1) {
// make sure to cast it to chain to get the right overload
return create_simplified_along_backbone(Chain(chains[0]), num_res,
keep_detailed);
} else {
IMP_THROW("No chains to simplify", ValueException);
}
}
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h,
Hierarchy reference) {
ParticlesTemp hl= get_leaves(h);
ParticlesTemp rl= get_leaves(reference);
algebra::Transformation3D tr
= algebra::get_transformation_aligning_first_to_second(rl, hl);
algebra::Transformation3D rtr
= core::RigidMember(reference).get_rigid_body().\
get_reference_frame().get_transformation_to();
algebra::Transformation3D rbtr= tr*rtr;
Particle *rbp= new Particle(h->get_model());
rbp->set_name(h->get_name()+" rigid body");
ParticlesTemp all = rb_process(h);
core::RigidBody rbd
= core::RigidBody::setup_particle(rbp, algebra::ReferenceFrame3D(rbtr));
for (unsigned int i=0; i< all.size(); ++i) {
rbd.add_member(all[i]);
}
rbd.set_coordinates_are_optimized(true);
IMP_INTERNAL_CHECK(h.get_is_valid(true), "Invalid hierarchy produced");
return rbd;
}
Selection::Selection(Hierarchy h) : radius_(-1) {
set_hierarchies(h.get_model(),
kernel::ParticleIndexes(1, h.get_particle_index()));
}
