CnSymmAxisDetector::CnSymmAxisDetector(int symm_deg,
const atom::Hierarchies &mhs)
: symm_deg_(symm_deg) {
// create a density map
kernel::Particles ps;
for (atom::Hierarchies::const_iterator it = mhs.begin(); it != mhs.end();
it++) {
kernel::Particles temp_ps = core::get_leaves(*it);
ps.insert(ps.end(), temp_ps.begin(), temp_ps.end());
}
// TODO - check the number of particles!!
IMP_NEW(em::SampledDensityMap, sampled_dmap, (ps, 3., 1.));
sampled_dmap->resample();
sampled_dmap->calcRMS();
dmap_ = new em::DensityMap(*(sampled_dmap->get_header()));
dmap_->copy_map(sampled_dmap);
double top_20_den_val = get_top_density_value(dmap_,
dmap_->get_header()->dmin, 0.8);
vecs_ = em::density2vectors(dmap_, top_20_den_val);
// calculate pca
pca_ = algebra::get_principal_components(vecs_);
// calculate transformation from the native axes system to the one
// defined by the pca
from_native_ = algebra::get_rotation_from_x_y_axes(
pca_.get_principal_component(0), pca_.get_principal_component(1));
to_native_ = from_native_.get_inverse();
sampled_dmap = nullptr;
}
SimpleExcludedVolume create_simple_excluded_volume_on_molecules(
atom::Hierarchies const &mhs)
{
IMP_CHECK_CODE(size_t mhs_size = mhs.size());
IMP_USAGE_CHECK(mhs_size > 0, "At least one hierarchy should be given");
kernel::ParticlesTemp ps;
for ( size_t i=0; i<mhs.size(); ++i )
{
kernel::ParticlesTemp leaves= IMP::atom::get_leaves(mhs[i]);
ps.insert(ps.end(), leaves.begin(), leaves.end());
}
/****** Set the restraint ******/
IMP_NEW(container::ListSingletonContainer, lsc, (ps));
IMP_NEW(core::ExcludedVolumeRestraint, evr, (lsc));
/****** Add restraint to the model ******/
//Model *mdl = mhs[0].get_particle()->get_model();
//mdl->add_restraint(evr);
/****** Return a SimpleExcludedVolume object ******/
return SimpleExcludedVolume(evr);
}
atom::Hierarchies create_coarse_molecules_from_molecules(
const atom::Hierarchies &mhs, int frag_len, kernel::Model *mdl,
float bead_radius, bool add_conn_restraint) {
atom::Hierarchies ret;
for (int i = 0; i < (int)mhs.size(); i++) {
// decide the number of beads for the molecule
int num_beads = std::max(
1,
(int)(atom::get_by_type(mhs[i], atom::RESIDUE_TYPE).size()) / frag_len);
ret.push_back(create_coarse_molecule_from_molecule(
mhs[i], num_beads, mdl, bead_radius, add_conn_restraint));
}
return ret;
}
core::RigidBodies set_rigid_bodies(atom::Hierarchies const &mhs)
{
IMPRESTRAINER_DEPRECATED_FUNCTION_DEF(2.1,
"Use atom::create_rigid_body() instead.");
size_t mhs_size = mhs.size();
IMP_USAGE_CHECK(mhs_size > 0, "At least one hierarchy should be given");
kernel::Particles rbps;
for ( size_t i=0; i<mhs_size; ++i )
{
// The rigid body is set to be optimized
IMP::atom::setup_as_rigid_body(mhs[i]);
rbps.push_back(mhs[i].get_particle());
}
return (core::RigidBodies(rbps));
}
SimpleEMFit create_simple_em_fit(atom::Hierarchies const &mhs,
em::DensityMap *dmap)
{
size_t mhs_size = mhs.size();
IMP_USAGE_CHECK(mhs_size > 0, "At least one hierarchy should be given");
kernel::ParticlesTemp ps;
for ( size_t i=0; i<mhs_size; ++i )
{
kernel::ParticlesTemp pss = core::get_leaves(mhs[i]);
ps.insert(ps.end(),pss.begin(),pss.end());
}
IMP_NEW(em::FitRestraint, fit_rs, (ps, dmap,
FloatPair(0.,0.),
atom::Mass::get_mass_key(),
1.0));
return SimpleEMFit(fit_rs);
}
SimpleConnectivity create_simple_connectivity_on_molecules(
const atom::Hierarchies &mhs)
{
size_t mhs_size = mhs.size();
IMP_USAGE_CHECK(mhs_size > 0, "At least one hierarchy should be given");
kernel::ParticlesTemp ps;
for ( size_t i=0; i<mhs_size; ++i )
{
ps.push_back(mhs[i].get_particle());
}
/****** Define Refiner ******/
// Use LeavesRefiner for the hierarchy leaves under a particle
IMP_NEW(core::LeavesRefiner, lr, (atom::Hierarchy::get_traits()));
/****** Define PairScore ******/
// Score on the lowest of the pairs defined by refining the two particles.
IMP_NEW(core::HarmonicUpperBound, h, (0, 1));
IMP_NEW(core::SphereDistancePairScore, sdps, (h));
IMP_NEW(core::KClosePairsPairScore, lrps, (sdps, lr));
/****** Set the restraint ******/
IMP_NEW(core::ConnectivityRestraint, cr, (lrps));
cr->set_particles((ps));
/****** Add restraint to the model ******/
//Model *mdl = mhs[0].get_particle()->get_model();
//mdl->add_restraint(cr);
/****** Return a SimpleConnectivity object ******/
return SimpleConnectivity(cr, h, sdps);
}