void load_particle_states(const Subset &s,
const Assignment &ss,
const ParticleStatesTable *pst) {
load_particle_states(s.begin(), s.end(), ss, pst);
if (s.size()!=0) {
s[0]->get_model()->update();
}
}
/**
* Compute the Kramer-Mesner matrix.
*
* Precondition: t < k
*/
KramerMesnerMatrix computeKMMatrix(const Group& G, unsigned int t, unsigned int k) {
std::vector<KMBuilderOutput> builderOutputs; // stores the relevant data for k = 2 onwards
Matrix A;
for (int i = 2; i <= k; i++) {
boost::scoped_ptr<KMBuilder> builder;
// Get orbit representatives of (i - 1)-subsets
std::vector<Subset> orbitReps;
if (i == 2) {
// As it is the first time, we have to compute the orbit representatives of singleton subsets...
Subset pointsRemaining = generateX(G.getNumPoints());
while (!pointsRemaining.empty()) {
typedef OrbitSet<Permutation, unsigned long>::const_iterator OrbitSetIterator;
unsigned long point = *(pointsRemaining.begin()); // A new representative...
Subset singletonSet = makeSingletonSet(point); // ...as a set
orbitReps.push_back(singletonSet);
// Compute the orbit of the point, and remove it from the remaining points
OrbitSet<Permutation, unsigned long> orbit = G.orbit(point, Transversal::TrivialAction());
for (OrbitSetIterator it = orbit.begin(); it != orbit.end(); it++) {
pointsRemaining.erase(pointsRemaining.find(*it));
}
}
builder.reset(new KMBuilder(G, i, orbitReps));
} else {
// We get them from what we computed earlier
KMBuilderOutput& input = builderOutputs[i - 3];
orbitReps = input.getNewReps();
builder.reset(new KMBuilder(G, i, orbitReps, input.getPrunerData()));
}
KMBuilderOutput builderOutput = builder->build();
builderOutputs.push_back(builderOutput);
// From the identity that A[t][k] = A[t][s] * A[s][k] / combinat(k - t, k - s) for any s
// between t and k, we get the following:
if (i == t + 1) {
assignMatrix(A, builderOutput.getNewMatrix());
} else if (i > t + 1) {
assignMatrix(A, matrixMultiply(A, builderOutput.getNewMatrix()));
scalarDivide(i - t, A);
}
}
return KramerMesnerMatrix(G, builderOutputs[t - 2].getNewReps(), builderOutputs[k - 2].getNewReps(), A);
}
Ints get_partial_index(const ParticlesTemp &particles,
const Subset &subset, const Subsets &excluded) {
for (unsigned int i=0; i< excluded.size(); ++i) {
bool all=true;
for (unsigned int j=0; j< particles.size(); ++j) {
if (!std::binary_search(excluded[i].begin(), excluded[i].end(),
particles[j])) {
all=false;
break;
}
}
if (all) {
return Ints();
}
}
Ints ret(particles.size(), -1);
for (unsigned int i=0; i< particles.size(); ++i) {
Subset::const_iterator it= std::lower_bound(subset.begin(),
subset.end(), particles[i]);
if (it!= subset.end() && *it == particles[i]) {
ret[i]= it-subset.begin();
}
}
IMP_IF_LOG(VERBOSE) {
IMP_LOG(VERBOSE, "Returning ");
for (unsigned int i=0; i< ret.size(); ++i) {
IMP_LOG(VERBOSE, ret[i] << " ");
}
IMP_LOG(VERBOSE, "for ");
for (unsigned int i=0; i< particles.size(); ++i) {
IMP_LOG(VERBOSE, particles[i]->get_name() << " ");
}
IMP_LOG(VERBOSE, " subset " << subset << std::endl);
}
return ret;
}
Subset MinRepPruner::minRep(const Subset& candidate) {
typedef boost::dynamic_bitset<unsigned long> dset;
dset candidateBitset(G->getNumPoints());
for (Subset::const_iterator it = candidate.begin(); it != candidate.end(); ++it) {
candidateBitset[*it] = true;
}
dset resultBitset = search.lexMin(candidateBitset);
Subset result;
for (dset::size_type i = resultBitset.find_first(); i != dset::npos; i = resultBitset.find_next(i)) {
result.insert(i);
}
return result;
}
RestraintsTemp get_restraints(const Subset &s,
const ParticleStatesTable *pst,
const DependencyGraph &dg,
RestraintSet *rs) {
RestraintsTemp rw= get_restraints(RestraintsTemp(1, rs));
Subset other=pst->get_subset();
ParticlesTemp oms;
std::set_difference(other.begin(), other.end(),
s.begin(), s.end(),
std::back_inserter(oms));
IMP::compatibility::map<Restraint*, int> index
= IMP::base::internal::get_graph_index<Restraint>(dg);
Ints to_remove;
for (unsigned int i=0; i< rw.size(); ++i) {
if (IMP::internal::get_has_ancestor(dg, index[rw[i]], oms)) {
to_remove.push_back(i);
}
}
for (int i=to_remove.size()-1; i >=0; --i) {
rw.erase(rw.begin()+to_remove[i]);
}
return rw;
}
int S(const Subset &v) {
return accumulate(v.begin(), v.end(), 0);
}
SubsetGraph get_restraint_graph(ScoringFunctionAdaptor in,
const ParticleStatesTable *pst) {
RestraintsTemp rs =
IMP::create_decomposition(in->create_restraints());
// ScoreStatesTemp ss= get_required_score_states(rs);
SubsetGraph ret(rs.size()); // + ss.size());
IMP_LOG_TERSE("Creating restraint graph on " << rs.size() << " restraints."
<< std::endl);
boost::unordered_map<Particle *, int> map;
SubsetGraphVertexName pm = boost::get(boost::vertex_name, ret);
DependencyGraph dg = get_dependency_graph(rs[0]->get_model());
DependencyGraphVertexIndex index = IMP::get_vertex_index(dg);
/*IMP_IF_LOG(VERBOSE) {
IMP_LOG_VERBOSE( "dependency graph is \n");
IMP::internal::show_as_graphviz(dg, std::cout);
}*/
Subset ps = pst->get_subset();
for (unsigned int i = 0; i < ps.size(); ++i) {
ParticlesTemp t = get_dependent_particles(
ps[i], ParticlesTemp(ps.begin(), ps.end()), dg, index);
for (unsigned int j = 0; j < t.size(); ++j) {
IMP_USAGE_CHECK(map.find(t[j]) == map.end(),
"Currently particles which depend on more "
<< "than one particle "
<< "from the input set are not supported."
<< " Particle \"" << t[j]->get_name()
<< "\" depends on \"" << ps[i]->get_name()
<< "\" and \""
<< ps[map.find(t[j])->second]->get_name() << "\"");
map[t[j]] = i;
}
IMP_IF_LOG(VERBOSE) {
IMP_LOG_VERBOSE("Particle \"" << ps[i]->get_name() << "\" controls ");
for (unsigned int i = 0; i < t.size(); ++i) {
IMP_LOG_VERBOSE("\"" << t[i]->get_name() << "\" ");
}
IMP_LOG_VERBOSE(std::endl);
}
}
for (unsigned int i = 0; i < rs.size(); ++i) {
ParticlesTemp pl = IMP::get_input_particles(rs[i]->get_inputs());
std::sort(pl.begin(), pl.end());
pl.erase(std::unique(pl.begin(), pl.end()), pl.end());
Subset os(pl);
for (unsigned int j = 0; j < pl.size(); ++j) {
pl[j] = ps[map[pl[j]]];
}
std::sort(pl.begin(), pl.end());
pl.erase(std::unique(pl.begin(), pl.end()), pl.end());
Subset s(pl);
IMP_LOG_VERBOSE("Subset for restraint " << rs[i]->get_name() << " is " << s
<< " from " << os << std::endl);
pm[i] = s;
}
/*ScoreStatesTemp ss= get_required_score_states(rs);
for (ScoreStatesTemp::const_iterator it= ss.begin();
it != ss.end(); ++it) {
ParticlesTemp pl= (*it)->get_input_particles();
add_edges(ps, pl, map, *it, ret);
ParticlesTemp opl= (*it)->get_output_particles();
add_edges(ps, opl, map, *it, ret);
}
IMP_INTERNAL_CHECK(boost::num_vertices(ret) == ps.size(),
"Wrong number of vertices "
<< boost::num_vertices(ret)
<< " vs " << ps.size());*/
for (unsigned int i = 0; i < boost::num_vertices(ret); ++i) {
for (unsigned int j = 0; j < i; ++j) {
if (get_intersection(pm[i], pm[j]).size() > 0) {
boost::add_edge(i, j, ret);
IMP_LOG_VERBOSE("Connecting " << rs[i]->get_name() << " with "
<< rs[j]->get_name() << std::endl);
}
}
}
return ret;
}
