ParticlePairsTemp MSConnectivityRestraint::get_connected_pairs() const {
IMP_CHECK_OBJECT(ps_.get());
tree_.finalize();
MSConnectivityScore mcs(tree_, ps_.get(), eps_,
*const_cast<MSConnectivityRestraint *>(this));
EdgeSet edges = mcs.get_connected_pairs();
ParticlePairsTemp ret(edges.size());
unsigned index = 0;
for (EdgeSet::iterator p = edges.begin(); p != edges.end(); ++p) {
ret[index++] = ParticlePair(mcs.get_particle(p->first),
mcs.get_particle(p->second));
}
return ret;
}
inline
bool
CollisionBox<ScalarT, dimN>::addParticle(
const typename CollisionBox<ScalarT, dimN>::Point& newPosition,
const typename CollisionBox<ScalarT, dimN>::Vector& newVelocity)
{
/* Find the cell containing the new particle: */
Point newP=newPosition;
Index cellIndex;
for (int i=0;i<dimension;++i)
{
if (newP[i]<boundaries.min[i]+particleRadius)
newP[i]=boundaries.min[i]+particleRadius;
else if (newP[i]>boundaries.max[i]-particleRadius)
newP[i]=boundaries.max[i]-particleRadius;
cellIndex[i]=int(Math::floor((newP[i]-boundaries.min[i])/cellSize[i]))+1;
}
GridCell* cell=cells.getAddress(cellIndex);
/* Check if there is room to add the new particle: */
for (int i=0;i<numNeighbors;++i)
{
GridCell* neighborCell=cell+neighborOffsets[i];
for (Particle* pPtr=neighborCell->particlesHead;pPtr!=0;pPtr=pPtr->cellSucc)
{
Scalar dist2=Geometry::sqrDist(pPtr->position,newP);
if (dist2<=Scalar(2)*particleRadius2)
return false; // Could not add the particle
}
}
/* Add a new particle to the particle list: */
particles.push_back(Particle());
Particle& p=particles.back();
/* Initialize the new particle: */
p.position=newPosition;
p.velocity=newVelocity;
p.timeStamp=Scalar(0);
cell->addParticle(&p);
for (typename ParticleList::iterator i = particles.begin(); i != particles.end() && &(*i) != &p; ++i) {
if (&(*i) != &p) {
particlePairs.push_back(ParticlePair(&p, &(*i)));
}
}
return true; // Particle succesfully added
}
ParticlePairsTemp get_possible_interactions(const ParticlesTemp &ps,
double max_distance,
ParticleStatesTable *pst) {
if (ps.empty()) return ParticlePairsTemp();
ParticleStatesList psl;
ParticlesTemp all= pst->get_particles();
unsigned int max=0;
for (unsigned int i=0; i< all.size(); ++i) {
psl.push_back( pst->get_particle_states(all[i]));
max= std::max(psl[i]->get_number_of_particle_states(), max);
}
algebra::BoundingBox3Ds bbs(ps.size());
for (unsigned int i=0; i< max; ++i) {
for (unsigned int j=0; j< all.size(); ++j) {
psl[j]->load_particle_state(std::min(i,
psl[j]->get_number_of_particle_states()-1),
all[j]);
}
ps[0]->get_model()->update();
for (unsigned int j=0; j< ps.size(); ++j) {
core::XYZ d(ps[j]);
bbs[j]+= d.get_coordinates();
}
}
for (unsigned int j=0; j< ps.size(); ++j) {
core::XYZR d(ps[j]);
bbs[j]+= d.get_radius() + max_distance;
}
IMP_NEW(core::GridClosePairsFinder, gcpf, ());
gcpf->set_distance(max_distance);
IntPairs ips= gcpf->get_close_pairs(bbs);
ParticlePairsTemp ret(ips.size());
for (unsigned int i=0; i< ips.size(); ++i) {
ret[i]= ParticlePair(ps[ips[i].first], ps[ips[i].second]);
}
return ret;
}
void add(Particle *p1, Particle *p2) {
this->push_back(ParticlePair(p1, p2));
}
