void FitRestraint::store_particles(ParticlesTemp ps) {
all_ps_=get_as<Particles>(ps);
add_particles(ps);
//sort to rigid and not rigid members
if (use_rigid_bodies_) {
for(Particles::iterator it = all_ps_.begin();it != all_ps_.end(); it++) {
if (core::RigidMember::particle_is_instance(*it)) {
core::RigidBody rb=core::RigidMember(*it).get_rigid_body();
part_of_rb_.push_back(*it);
if (member_map_.find(rb) == member_map_.end()) {
member_map_[rb]=Particles();
rbs_.push_back(rb);
}
member_map_[rb].push_back(*it);
}
else {
not_part_of_rb_.push_back(*it);
}
}
}
else {
not_part_of_rb_=all_ps_;
}
IMP_LOG(TERSE,"number of"
<<" particles that are not rigid bodies is:"
<<not_part_of_rb_.size()<<", "<<part_of_rb_.size()<<" particles "<<
" are part of "<<rbs_.size()<<" rigid bodies"<<std::endl);
}
// arm
void particle_system::explode(thing *th, bool kill)
{
static const unsigned SHOCKWAVE_PARTICLES = 25, DEBRIS_PARTICLES = 75;
if (board::current()->thing_lives(th)) {
boost::array<vec2, 2*(SHOCKWAVE_PARTICLES + DEBRIS_PARTICLES)> explosion;
unsigned i = 0;
while (i < 2*SHOCKWAVE_PARTICLES) {
float rho = rand_between(64.0, 81.0);
float theta = rand_between(0.0, 1.0);
explosion[i++] = polar_vec2(rho, rand_near(theta, 0.0625));
explosion[i++] = polar_vec2(rho, rand_near(theta, 0.0625));
}
while (i < 2*(SHOCKWAVE_PARTICLES + DEBRIS_PARTICLES)) {
float theta = rand_between(0.0, 1.0);
explosion[i++] = polar_vec2(rand_between(3.0, 7.0)*rand_between(3.0, 7.0), theta);
explosion[i++] = polar_vec2(rand_between(3.0, 7.0)*rand_between(3.0, 7.0), theta);
}
add_particles(th->center, make_vec2(1.0, 0.0), explosion);
if (kill)
board::current()->remove_thing(th);
}
}
IMPEM_BEGIN_NAMESPACE
EnvelopePenetrationRestraint::EnvelopePenetrationRestraint(
Particles ps,
DensityMap *em_map,Float threshold
): Restraint("Envelope penetration restraint")
{
IMP_LOG_TERSE("Load envelope penetration with the following input:"<<
"number of particles:"<<ps.size()<<
"\n");
threshold_=threshold;
target_dens_map_ = em_map;
IMP_IF_CHECK(USAGE) {
for (unsigned int i=0; i< ps.size(); ++i) {
IMP_USAGE_CHECK(core::XYZR::particle_is_instance(ps[i]),
"Particle " << ps[i]->get_name()
<< " is not XYZR"
<< std::endl);
}
}
add_particles(ps);
ps_=ps;
IMP_LOG_TERSE("after adding particles"<<std::endl);
IMP_LOG_TERSE( "Finish initialization" << std::endl);
}
RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(Particles ps,
int num_residues,
Float scale):
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);
}
IMPMULTIFIT_BEGIN_NAMESPACE
WeightedExcludedVolumeRestraint::WeightedExcludedVolumeRestraint(
core::RigidBodies rbs, Refiner *refiner, FloatKey weight_key)
: Restraint(IMP::internal::get_model(rbs),
"Weighted Excluded Volume Restraint") {
IMP_LOG_TERSE("Load WeightedExcludedVolumeRestraint \n");
rb_refiner_ = refiner;
add_particles(rbs);
rbs_ = rbs;
initialize_model_density_map(weight_key);
}
