void assign_blame(const RestraintsTemp &rs, const ParticlesTemp &ps, FloatKey attribute) { IMP_FUNCTION_LOG; for (unsigned int i = 0; i < ps.size(); ++i) { if (ps[i]->has_attribute(attribute)) { ps[i]->set_value(attribute, 0); } else { ps[i]->add_attribute(attribute, 0, false); } } Restraints drs; for (unsigned int i = 0; i < rs.size(); ++i) { Pointer<Restraint> rd = rs[i]->create_decomposition(); if (rd) { drs.push_back(rd); } } IMP_NEW(RestraintsScoringFunction, rsf, (drs)); rsf->evaluate(false); DependencyGraph dg = get_dependency_graph(IMP::internal::get_model(rs)); // attempt to get around boost/gcc bug and the most vexing parse DependencyGraphVertexIndex dgi((IMP::get_vertex_index(dg))); ControlledBy controlled_by; for (unsigned int i = 0; i < ps.size(); ++i) { ParticlesTemp cps = get_dependent_particles(ps[i], ps, dg, dgi); IMP_INTERNAL_CHECK(cps.size() > 0, "No dependent particles for " << ps[i]); for (unsigned int j = 0; j < cps.size(); ++j) { controlled_by[cps[j]] = ps[i]; } } for (unsigned int i = 0; i < drs.size(); ++i) { distribute_blame(drs[i], controlled_by, attribute, 1.0); } }
InteractionGraph get_interaction_graph(ScoringFunctionAdaptor rsi, const ParticlesTemp &ps) { if (ps.empty()) return InteractionGraph(); InteractionGraph ret(ps.size()); Restraints rs = create_decomposition(rsi->create_restraints()); // Model *m= ps[0]->get_model(); boost::unordered_map<ModelObject *, int> map; InteractionGraphVertexName pm = boost::get(boost::vertex_name, ret); DependencyGraph dg = get_dependency_graph(ps[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); }*/ 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); } pm[i] = ps[i]; } IMP::Restraints all_rs = IMP::get_restraints(rs); for (Restraints::const_iterator it = all_rs.begin(); it != all_rs.end(); ++it) { ModelObjectsTemp pl = (*it)->get_inputs(); add_edges(ps, pl, map, *it, ret); } /* Make sure that composite score states (eg the normalizer for rigid body rotations) don't induce interactions among unconnected particles.*/ ScoreStatesTemp ss = get_required_score_states(rs); for (ScoreStatesTemp::const_iterator it = ss.begin(); it != ss.end(); ++it) { ModelObjectsTemps interactions = (*it)->get_interactions(); for (unsigned int i = 0; i < interactions.size(); ++i) { add_edges(ps, interactions[i], map, *it, ret); } } IMP_INTERNAL_CHECK(boost::num_vertices(ret) == ps.size(), "Wrong number of vertices " << boost::num_vertices(ret) << " vs " << ps.size()); return ret; }
void RestraintCache::add_restraints(const kernel::RestraintsAdaptor &rs) { IMP_OBJECT_LOG; if (rs.empty()) return; kernel::Model *m = rs[0]->get_model(); DependencyGraph dg = get_dependency_graph(m); ParticleStatesTable *pst = cache_.get_generator().get_particle_states_table(); DepMap dependencies; kernel::ParticlesTemp allps = pst->get_particles(); DependencyGraphVertexIndex index = IMP::get_vertex_index(dg); for (unsigned int i = 0; i < allps.size(); ++i) { kernel::ParticlesTemp depp = get_dependent_particles(allps[i], allps, dg, index); for (unsigned int j = 0; j < depp.size(); ++j) { dependencies[depp[j]].push_back(allps[i]); } dependencies[allps[i]].push_back(allps[i]); IMP_LOG_TERSE("Particle " << Showable(allps[i]) << " controls " << dependencies[allps[i]] << std::endl); } for (unsigned int i = 0; i < rs.size(); ++i) { base::Pointer<kernel::Restraint> r = rs[i]->create_decomposition(); IMP_IF_LOG(TERSE) { IMP_LOG_TERSE("Before:" << std::endl); IMP_LOG_WRITE(TERSE, show_restraint_hierarchy(rs[i])); } if (r) { IMP_LOG_TERSE("after:" << std::endl); IMP_LOG_WRITE(TERSE, show_restraint_hierarchy(r)); add_restraint_internal(r, next_index_, nullptr, std::numeric_limits<double>::max(), Subset(), dependencies); } ++next_index_; } IMP_IF_LOG(TERSE) { IMP_LOG_WRITE(TERSE, show_restraint_information(IMP_STREAM)); } }
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; }