/* Return all particles whose attributes are read by the restraints. To
do this, ask the pair score what particles it uses.*/
IMP::ModelObjectsTemp UniformBoundedRestraint::do_get_inputs() const {
ParticlesTemp ret;
ret.push_back(p_);
ret.push_back(a_);
ret.push_back(b_);
return ret;
}
ParticlesTemp CHARMMStereochemistryRestraint::get_input_particles() const
{
ParticlesTemp ps;
for (Particles::const_iterator b = bonds_.begin(); b != bonds_.end(); ++b) {
ps.push_back(*b);
ParticlesTemp bps = bond_score_->get_input_particles(*b);
ps.insert(ps.end(), bps.begin(), bps.end());
}
for (Particles::const_iterator a = angles_.begin();
a != angles_.end(); ++a) {
ps.push_back(*a);
ParticlesTemp bps = angle_score_->get_input_particles(*a);
ps.insert(ps.end(), bps.begin(), bps.end());
}
for (Particles::const_iterator d = dihedrals_.begin();
d != dihedrals_.end(); ++d) {
ps.push_back(*d);
ParticlesTemp bps = dihedral_score_->get_input_particles(*d);
ps.insert(ps.end(), bps.begin(), bps.end());
}
for (Particles::const_iterator i = impropers_.begin();
i != impropers_.end(); ++i) {
ps.push_back(*i);
ParticlesTemp bps = improper_score_->get_input_particles(*i);
ps.insert(ps.end(), bps.begin(), bps.end());
}
return ps;
}
ModelObjectsTemp NOERestraint::do_get_inputs() const {
ParticlesTemp ret;
ret.push_back(p0_);
ret.push_back(p1_);
ret.push_back(sigma_);
ret.push_back(gamma_);
return ret;
}
/* Return all particles whose attributes are read by the restraints. To
do this, ask the pair score what particles it uses.*/
ModelObjectsTemp SigmoidRestraintSphere::do_get_inputs() const
{
ParticlesTemp ret;
ret.push_back(get_model()->get_particle(p1_));
ret.push_back(get_model()->get_particle(p2_));
return ret;
}
const ParticlesTemp
FixedRefiner::get_refined(Particle *) const
{
ParticlesTemp ps;
for(unsigned int i=0; i < pis_.size(); i++){
ps.push_back(m_->get_particle(pis_[i]));
}
return ps;
}
ParticlesTemp RadiusOfGyrationRestraint::get_input_particles() const
{
ParticlesTemp pt;
for (ParticleConstIterator it= particles_begin();
it != particles_end(); ++it) {
pt.push_back(*it);
}
return pt;
}
/* Return all particles whose attributes are read by the restraints. To
do this, ask the pair score what particles it uses.*/
ModelObjectsTemp CrossLinkMSRestraint::do_get_inputs() const {
ParticlesTemp ret;
for (unsigned int k = 0; k < get_number_of_contributions(); ++k) {
if (ppis_[k][0] == ppis_[k][1]) {
ret.push_back(get_model()->get_particle(ppis_[k][0]));
} else {
ret.push_back(get_model()->get_particle(ppis_[k][0]));
ret.push_back(get_model()->get_particle(ppis_[k][1]));
}
if ( sigmass_[k][0] == sigmass_[k][1]) {
ret.push_back(get_model()->get_particle(sigmass_[k][0]));
} else {
ret.push_back(get_model()->get_particle(sigmass_[k][0]));
ret.push_back(get_model()->get_particle(sigmass_[k][1]));
}
ret.push_back(get_model()->get_particle(psis_[k]));
}
return ret;
}
const ParticlesTemp RigidLeavesRefiner::get_refined(Particle *p) const {
ParticlesTemp members = core::RigidBody(p).get_rigid_members();
ParticlesTemp ret;
for (ParticlesTemp::const_iterator it = members.begin(); it != members.end();
++it) {
if (atom::Hierarchy::get_is_setup(*it)
&& atom::Hierarchy(*it).get_number_of_children() == 0) {
ret.push_back(*it);
}
}
return ret;
}
ParticlesTemp get_output_particles(const ModelObjectsTemp &mo) {
ParticlesTemp ret;
for (unsigned int i = 0; i < mo.size(); ++i) {
ModelObject *o = mo[i];
Particle *p = dynamic_cast<Particle *>(o);
if (p)
ret.push_back(p);
else {
ret += get_output_particles(o->get_inputs());
}
}
return ret;
}
core::MonteCarloMoverResult BallMover::do_propose() {
IMP_OBJECT_LOG;
// random displacement
algebra::Vector3D displacement = algebra::get_random_vector_in(
algebra::Sphere3D(algebra::Vector3D(0.0, 0.0, 0.0), max_tr_));
// store old coordinates of master particle
oldcoord_ = core::XYZ(p_).get_coordinates();
// master particle coordinates after displacement
algebra::Vector3D nc = oldcoord_ + displacement;
// find center of the closest cell
double mindist = 1.0e+24;
unsigned icell = 0;
for (unsigned i = 0; i < ctrs_.size(); ++i) {
// calculate distance between nc and cell center
double dist = algebra::get_l2_norm(nc - ctrs_[i]);
// find minimum distance
if (dist < mindist) {
mindist = dist;
icell = i;
}
}
// find inverse transformation
algebra::Transformation3D cell_tr = trs_[icell].get_inverse();
// set new coordinates for master particle
core::XYZ(p_).set_coordinates(cell_tr.get_transformed(nc));
// set new coordinates for slave particles
oldcoords_.clear();
for (unsigned i = 0; i < ps_.size(); ++i) {
core::XYZ xyz = core::XYZ(ps_[i]);
algebra::Vector3D oc = xyz.get_coordinates();
// store old coordinates
oldcoords_.push_back(oc);
// apply transformation
algebra::Vector3D nc = cell_tr.get_transformed(oc);
xyz.set_coordinates(nc);
}
ParticlesTemp ret;
ret.push_back(p_);
ret.insert(ret.end(), ps_.begin(), ps_.end());
return core::MonteCarloMoverResult(get_indexes(ret), 1.0);
}
/* Return all particles whose attributes are read by the restraints. To
do this, ask the pair score what particles it uses.*/
ParticlesTemp MarginalHBondRestraint::get_input_particles() const
{
ParticlesTemp ret;
for (unsigned i=0; i<volumes_.size(); ++i)
{
int npairs = contribs_[i]->get_number_of_particle_pairs();
for (int j=0; j < npairs; ++j)
{
ret.push_back(contribs_[i]->get_particle_pair(j)[0]);
ret.push_back(contribs_[i]->get_particle_pair(j)[1]);
}
}
return ret;
}
IMPDOMINOEXPORT CliqueGraph get_clique_graph(const InteractionGraph& cig) {
InteractionGraphConstVertexName pm= boost::get(boost::vertex_name, cig);
typedef base::Vector<InteractionGraphVertex> Clique;
base::Vector<Clique> cliques;
internal::maximal_cliques(cig, std::back_inserter(cliques));
for (unsigned int i=0; i< cliques.size(); ++i) {
/*std::cout << "Clique is ";
for (unsigned int j=0; j< cliques[i].size(); ++j) {
std::cout << cliques[i][j] << " ";
}*/
std::sort(cliques[i].begin(), cliques[i].end());
}
CliqueGraph cg(cliques.size());
CliqueGraphVertexName cm
= boost::get(boost::vertex_name, cg);
for (unsigned int i=0; i< cliques.size(); ++i) {
ParticlesTemp cur;
for (unsigned int j=0; j< cliques[i].size(); ++j) {
cur.push_back(pm[cliques[i][j]]);
}
Subset ss(cur);
cm[i]=ss;
}
for (unsigned int i=0; i< cliques.size(); ++i) {
for (unsigned int j=0; j< i; ++j) {
Subset intersection= get_intersection(cm[i], cm[j]);
if (intersection.size() >0) {
double minus_weight=intersection.size();
/*std::cout << "edge " << i << " " << j
<< " has weight "
<< -static_cast<int>(intersection.size()) << std::endl;*/
boost::add_edge(i, j,
CliqueGraph::edge_property_type(-minus_weight),
cg);
}
}
}
return cg;
}
ModelObjectsTemp DummyRestraint::do_get_inputs() const {
ParticlesTemp ret;
ret.push_back(p0_);
ret.push_back(p1_);
return ret;
}
ModelObjectsTemp DummyRestraint::do_get_inputs() const {
ParticlesTemp pt;
pt.push_back(p1_);
pt.push_back(p2_);
return pt;
}
ParticlesTemp SameResiduePairFilter::get_input_particles( Particle* t) const {
ParticlesTemp ret;
ret.push_back(t);
ret.push_back(Hierarchy(t).get_parent());
return ret;
}
/* Return all particles whose attributes are read by the restraints. To
do this, ask the pair score what particles it uses.*/
ModelObjectsTemp WeightRestraint::do_get_inputs() const {
ParticlesTemp ret;
ret.push_back(w_);
return ret;
}
ModelObjectsTemp BallMover::do_get_inputs() const {
ParticlesTemp ret;
ret.push_back(p_);
ret.insert(ret.end(), ps_.begin(), ps_.end());
return ret;
}