void Fragment::set_residue_indexes(kernel::Model *m, kernel::ParticleIndex pi,
Ints o) {
if (o.empty()) {
set_residue_indexes(m, pi, IntPairs());
return;
}
std::sort(o.begin(), o.end());
o.erase(std::unique(o.begin(), o.end()), o.end());
IntPairs pairs;
int begin = 0;
for (unsigned int i = 1; i < o.size(); ++i) {
if (o[i] != o[i - 1] + 1) {
pairs.push_back(IntPair(o[begin], o[i - 1] + 1));
begin = i;
}
}
pairs.push_back(IntPair(o[begin], o.back() + 1));
set_residue_indexes(m, pi, pairs);
using IMP::operator<<;
IMP_IF_CHECK(USAGE) {
for (unsigned int i = 0; i < o.size(); ++i) {
IMP_INTERNAL_CHECK(Fragment(m, pi).get_contains_residue(o[i]),
"Residue index not found after addition: "
<< o << " became " << pairs);
}
}
}
IntPairs Fragment::get_residue_index_ranges() const {
if (!get_model()->get_has_attribute(get_begins_key(), get_particle_index())) {
return IntPairs();
}
Ints begins =
get_model()->get_attribute(get_begins_key(), get_particle_index());
Ints ends = get_model()->get_attribute(get_ends_key(), get_particle_index());
IMP_INTERNAL_CHECK(begins.size() == ends.size(),
"The fragment residues are corrupted.");
IntPairs ret(begins.size());
for (unsigned int i = 0; i < ret.size(); ++i) {
ret[i] = IntPair(begins[i], ends[i]);
}
return ret;
}
/// For algorithm details, see http://wiki.openstreetmap.org/wiki/Relation:multipolygon/Algorithm
void MultipolygonProcessor::process() {
bool allClosed = true;
// NOTE do not count multipolygon tag itself
bool hasNoTags = relation_.tags.size() < 2;
Ints outerIndecies;
Ints innerIndecies;
CoordinateSequences sequences;
for (const auto &member : members_) {
if (member.type!="w")
continue;
Coordinates coordinates;
auto wayPair = context_.wayMap.find(member.refId);
if (wayPair!=context_.wayMap.end()) {
coordinates = wayPair->second->coordinates;
} else {
auto areaPair = context_.areaMap.find(member.refId);
if (areaPair!=context_.areaMap.end()) {
coordinates = areaPair->second->coordinates;
// NOTE make coordinates to be closed ring
coordinates.push_back(coordinates[0]);
// NOTE merge tags to relation
// hasNoTags prevents the case where relation has members with their own tags
// which should be processed independently (geometry reusage)
if (member.role=="outer" && hasNoTags)
mergeTags(areaPair->second->tags);
} else {
auto relationPair = context_.relationMap.find(member.refId);
if (relationPair==context_.relationMap.end())
return; // NOTE cannot fill relation: incomplete data
resolve_(*relationPair->second);
}
}
if (coordinates.empty())
continue;
if (member.role=="outer")
outerIndecies.push_back(static_cast<int>(sequences.size()));
else if (member.role=="inner")
innerIndecies.push_back(static_cast<int>(sequences.size()));
else
continue;
auto sequence = std::make_shared<CoordinateSequence>(member.refId, coordinates);
if (!sequence->isClosed())
allClosed = false;
sequences.push_back(sequence);
}
if (outerIndecies.size()==1 && allClosed)
simpleCase(sequences, outerIndecies, innerIndecies);
else
complexCase(sequences);
}
void AnchorsData::set_secondary_structure_probabilities(
const Particles &ssres_ps, const Ints &indices) {
IMP_USAGE_CHECK(secondary_structure_ps_.size() == points_.size(),
"Secondary structure has not been set up, "
"run AnchorsData::setup_secondary_structure() first");
int anum;
for (int ssnum = 0; ssnum < (int)ssres_ps.size(); ssnum++) {
IMP_USAGE_CHECK(
atom::SecondaryStructureResidue::get_is_setup(ssres_ps[ssnum]),
"SSE Particles must be decorated as"
"SecondaryStructureResidues");
if (indices.size() == 0)
anum = ssnum;
else
anum = indices[ssnum];
atom::SecondaryStructureResidue(secondary_structure_ps_[anum])
.set_prob_helix(
atom::SecondaryStructureResidue(ssres_ps[ssnum]).get_prob_helix());
atom::SecondaryStructureResidue(secondary_structure_ps_[anum])
.set_prob_strand(atom::SecondaryStructureResidue(ssres_ps[ssnum])
.get_prob_strand());
atom::SecondaryStructureResidue(secondary_structure_ps_[anum])
.set_prob_coil(
atom::SecondaryStructureResidue(ssres_ps[ssnum]).get_prob_coil());
}
}
void KMCentersTree::skeleton_tree(const Ints &p_id,
KMPoint *bb_lo,KMPoint *bb_hi) {
//TODO: where do get n from ?
IMP_INTERNAL_CHECK(data_points_ != nullptr,
"Points must be supplied to construct tree.");
if (p_id.size() == 0) {
for (int i = 0; i < data_points_->get_number_of_points(); i++)
p_id_.push_back(i);
}
else {
for (int i = 0; i < data_points_->get_number_of_points(); i++)
p_id_.push_back(p_id[i]);
}
if (bb_lo == nullptr || bb_hi == nullptr) {
bnd_box_ = bounding_rectangle(0,data_points_->get_number_of_points()-1);;
}
// if points are provided, use it
if (bb_lo != nullptr) {
copy_point(bb_lo,bnd_box_->get_point(0));
}
if (bb_hi != nullptr) {
copy_point(bb_hi,bnd_box_->get_point(1));
}
root_ = nullptr;
}
void KMCentersNodeSplit::get_neighbors(const Ints &cands, KMPointArray *sums,
KMPoint *sum_sqs, Ints *weights) {
if (cands.size() == 1) {
IMP_LOG_VERBOSE("KMCentersNodeSplit::get_neighbors the data points are"
<< " associated to center : " << cands[0] << std::endl);
// post points as neighbors
post_neighbor(sums, sum_sqs, weights, cands[0]);
}
// get cloest candidate to the box represented by the node
else {
Ints new_cands;
IMP_LOG_VERBOSE(
"KMCentersNodeSplit::get_neighbors compute close centers for node:\n");
IMP_LOG_WRITE(VERBOSE, show(IMP_STREAM));
compute_close_centers(cands, &new_cands);
for (unsigned int i = 0; i < new_cands.size(); i++) {
IMP_LOG_VERBOSE(new_cands[i] << " | ");
}
IMP_LOG_VERBOSE("\nKMCentersNodeSplit::get_neighbors call left child with "
<< new_cands.size() << " candidates\n");
children_[0]->get_neighbors(new_cands, sums, sum_sqs, weights);
IMP_LOG_VERBOSE("KMCentersNodeSplit::get_neighbors call right child with "
<< new_cands.size() << " candidates\n");
children_[1]->get_neighbors(new_cands, sums, sum_sqs, weights);
}
}
FrameHandles FrameHandle::get_children() const {
Ints children = get_shared_data()->get_children(get_frame_id());
FrameHandles ret(children.size());
for (unsigned int i = 0; i < ret.size(); ++i) {
ret[i] = FrameHandle(children[i], get_shared_data());
}
return ret;
}
bool PymolWriter::handle_surface(SurfaceMeshGeometry *g, Color color,
std::string name) {
setup(name, TRIANGLES);
if (!open_type_) {
get_stream() << "BEGIN, TRIANGLES, ";
open_type_ = TRIANGLES;
}
Ints triangles = internal::get_triangles(g);
algebra::Vector3Ds normals =
internal::get_normals(triangles, g->get_vertexes());
IMP_INTERNAL_CHECK(triangles.size() % 3 == 0,
"The returned triangles aren't triangles");
for (unsigned int i = 0; i < triangles.size() / 3; ++i) {
write_triangle(triangles.begin() + 3 * i, triangles.begin() + 3 * i + 3,
g->get_vertexes(), normals, color, get_stream());
}
return true;
}
// see http://wiki.openstreetmap.org/wiki/Relation:multipolygon/Algorithm
void MultipolygonProcessor::process()
{
bool allClosed = true;
Ints outerIndecies;
Ints innerIndecies;
CoordinateSequences sequences;
for (const auto& member : members_) {
if (member.type != "way")
continue;
Coordinates coordinates;
auto wayPair = context_.wayMap.find(member.refId);
if (wayPair != context_.wayMap.end()) {
coordinates = wayPair->second->coordinates;
}
else {
auto areaPair = context_.areaMap.find(member.refId);
if (areaPair != context_.areaMap.end()) {
coordinates = areaPair->second->coordinates;
// NOTE merge tags to relation
if (member.role == "outer")
mergeTags(areaPair->second->tags);
}
else {
auto relationPair = context_.relationMap.find(member.refId);
if (relationPair == context_.relationMap.end())
return; // NOTE cannot fill relation: incomplete data
resolve_(*relationPair->second);
}
}
if (coordinates.empty())
continue;
if (member.role == "outer")
outerIndecies.push_back(static_cast<int>(sequences.size()));
else if (member.role == "inner")
innerIndecies.push_back(static_cast<int>(sequences.size()));
else
continue;
auto sequence = std::make_shared<CoordinateSequence>(member.refId, coordinates);
if (!sequence->isClosed())
allClosed = false;
sequences.push_back(sequence);
}
if (outerIndecies.size() == 1 && allClosed)
simpleCase(sequences, outerIndecies, innerIndecies);
else
complexCase(sequences);
}
Assignment get_merged_assignment(const Subset &s, const Assignment &ss0,
const Ints &i0, const Assignment &ss1,
const Ints &i1) {
Ints ret(s.size(), -1);
IMP_USAGE_CHECK(ss0.size() == i0.size(),
"The size of the subset and "
<< "the index don't match: " << ss0.size() << " vs "
<< i0.size());
IMP_USAGE_CHECK(ss1.size() == i1.size(),
"The size of the subset and "
<< "the index don't match: " << ss1.size() << " vs "
<< i1.size());
for (unsigned int i = 0; i < i0.size(); ++i) {
ret[i0[i]] = ss0[i];
}
for (unsigned int i = 0; i < i1.size(); ++i) {
ret[i1[i]] = ss1[i];
}
IMP_IF_CHECK(USAGE) {
for (unsigned int i = 0; i < ret.size(); ++i) {
IMP_USAGE_CHECK(ret[i] >= 0, "Not all set");
}
}
return Assignment(ret);
}
void KMCentersNodeSplit::get_assignments(const Ints &cands,
Ints &close_center) {
if (cands.size() == 1) {
children_[0]->get_assignments(cands, close_center);
children_[1]->get_assignments(cands, close_center);
} else { // get closest cand to box
Ints new_cands;
compute_close_centers(cands, &new_cands);
// apply to children
children_[0]->get_assignments(new_cands, close_center);
children_[1]->get_assignments(new_cands, close_center);
}
}
NNGraph MSConnectivityScore::build_subgraph_from_assignment(
NNGraph &G, Assignment const &assignment) const {
unsigned int num_particles = restraint_.particle_matrix_.size();
Ints vertices;
for (unsigned int i = 0; i < assignment.size(); ++i)
if (!assignment[i].empty()) {
Ints const &conf = assignment[i].get_tuple();
for (unsigned int j = 0; j < conf.size(); ++j)
vertices.push_back(conf[j]);
}
boost::property_map<NNGraph, boost::vertex_name_t>::type vertex_id =
boost::get(boost::vertex_name, G);
boost::property_map<NNGraph, boost::edge_weight_t>::type dist =
boost::get(boost::edge_weight, G);
NNGraph ng(vertices.size());
boost::property_map<NNGraph, boost::vertex_name_t>::type new_vertex_id =
boost::get(boost::vertex_name, ng);
boost::property_map<NNGraph, boost::edge_weight_t>::type new_dist =
boost::get(boost::edge_weight, ng);
for (unsigned int i = 0; i < vertices.size(); ++i)
boost::put(new_vertex_id, i, vertices[i]);
Ints vertex_id_to_idx(num_particles, -1);
for (unsigned int i = 0; i < vertices.size(); ++i)
vertex_id_to_idx[vertices[i]] = i;
NNGraph::edge_iterator e, end;
for (boost::tie(e, end) = edges(G); e != end; ++e) {
unsigned int source_id = boost::get(vertex_id, source(*e, G));
unsigned int dest_id = boost::get(vertex_id, target(*e, G));
unsigned int p_src = vertex_id_to_idx[source_id];
unsigned int p_dst = vertex_id_to_idx[dest_id];
if (p_src == static_cast<unsigned int>(-1) ||
p_dst == static_cast<unsigned int>(-1))
continue;
NNGraph::edge_descriptor ed = boost::add_edge(p_src, p_dst, ng).first;
double d = boost::get(dist, *e);
boost::put(new_dist, ed, d);
}
return ng;
}
algebra::Vector3Ds get_normals(const Ints &faces,
const algebra::Vector3Ds &vertices) {
IMP_INTERNAL_CHECK(faces.size() % 3 == 0, "Not triangles");
IMP_INTERNAL_CHECK(faces.size() > 0, "No faces");
Ints count(vertices.size());
algebra::Vector3Ds sum(vertices.size(), algebra::get_zero_vector_d<3>());
for (unsigned int i = 0; i < faces.size() / 3; ++i) {
algebra::Vector3D n =
get_normal(faces.begin() + 3 * i, faces.begin() + 3 * i + 3, vertices);
IMP_INTERNAL_CHECK(!IMP::isnan(n[0]), "Nan found");
for (unsigned int j = 0; j < 3; ++j) {
int v = faces[3 * i + j];
sum[v] += n;
count[v] += 1;
}
}
for (unsigned int i = 0; i < count.size(); ++i) {
sum[i] /= count[i];
IMP_INTERNAL_CHECK(!IMP::isnan(sum[i][0]),
"Nan found at end:" << count[i] << " on " << i);
}
return sum;
}
void Changer::remainingActionsDecrement(
Ints& actions_vect,
int bacterium_index
) {
bool less = bacterium_index < 0;
bool greater = bacterium_index >= actions_vect.size();
if (less || greater) {
throw Exception("Changer: invalid bacterium index.");
}
actions_vect[bacterium_index]--;
if (actions_vect[bacterium_index] < 0) {
throw Exception("Changer: too many commands for one move.");
}
}
domino::SubsetFilter* ExampleSubsetFilterTable::get_subset_filter(
const domino::Subset& cur_subset,
const domino::Subsets& prior_subsets) const {
IMP_OBJECT_LOG;
Ints its = get_indexes(cur_subset, prior_subsets);
if (its.size() != ps_.size()) {
// either the subset doesn't contain the needed particles or the prior does
return nullptr;
} else {
IMP_NEW(ExampleSubsetFilter, ret, (its, max_diff_));
// remember to release
return ret.release();
}
}
InferenceStatistics::Data InferenceStatistics::get_data(
const Subset &, AssignmentContainer *iss) const {
Assignments ss =
iss->get_assignments(IntRange(0, iss->get_number_of_assignments()));
Data ret;
ret.size = iss->get_number_of_assignments();
Ints sample;
for (int i = 0; i < ret.size; ++i) {
if (sample.size() < sample_size) {
sample.push_back(i);
} else {
double prob = static_cast<double>(sample_size) / i;
if (select_(base::random_number_generator) < prob) {
int replace = place_(base::random_number_generator);
sample[replace] = i;
}
}
}
ret.sample.resize(sample.size());
for (unsigned int i = 0; i < sample.size(); ++i) {
ret.sample[i] = iss->get_assignment(sample[i]);
}
return ret;
}
bool PymolWriter::handle_polygon(PolygonGeometry *g, Color color,
std::string name) {
setup(name, TRIANGLES);
if (!open_type_) {
get_stream() << "BEGIN, TRIANGLES, ";
open_type_ = TRIANGLES;
}
Ints tris = internal::get_triangles(g);
algebra::Vector3Ds normals = internal::get_normals(tris, g->get_geometry());
for (unsigned int i = 0; i < tris.size() / 3; ++i) {
write_triangle(tris.begin() + 3 * i, tris.begin() + 3 * i + 3,
g->get_geometry(), normals, color, get_stream());
}
return true;
}
void RestraintCache::save_cache(const kernel::ParticlesTemp &particle_ordering,
const kernel::RestraintsTemp &restraints,
RMF::HDF5::Group group,
unsigned int max_entries) {
RMF::HDF5::FloatDataSet1Ds scores;
RMF::HDF5::IntDataSet2Ds assignments;
base::map<kernel::Restraint *, int> restraint_index;
ParticleIndex particle_index = get_particle_index(particle_ordering);
Orders orders = get_orders(known_restraints_, restraints, particle_ordering);
// create data sets for restraints
for (unsigned int i = 0; i < restraints.size(); ++i) {
kernel::Restraint *r = restraints[i];
RestraintID rid =
get_restraint_id(particle_index, known_restraints_.find(r)->second,
restraint_index_.find(r)->second);
RMF::HDF5::Group g = group.add_child_group(r->get_name());
g.set_attribute<RMF::HDF5::IndexTraits>(
"restraint", RMF::HDF5::Indexes(1, rid.get_restraint_index()));
g.set_attribute<RMF::HDF5::IndexTraits>(
"particles", RMF::HDF5::Indexes(rid.get_particle_indexes().begin(),
rid.get_particle_indexes().end()));
scores.push_back(g.add_child_data_set<RMF::HDF5::FloatTraits, 1>("scores"));
assignments.push_back(
g.add_child_data_set<RMF::HDF5::IntTraits, 2>("assignments"));
restraint_index[r] = i;
}
// finally start saving them
unsigned int count = 0;
for (Cache::ContentIterator it = cache_.contents_begin();
it != cache_.contents_end(); ++it) {
int ri = restraint_index.find(it->key.get_restraint())->second;
Ints ord = orders[ri].get_list_ordered(it->key.get_assignment());
double score = it->value;
RMF::HDF5::DataSetIndexD<2> asz = assignments[ri].get_size();
RMF::HDF5::DataSetIndexD<1> row(asz[0]);
asz[1] = ord.size();
++asz[0];
assignments[ri].set_size(asz);
assignments[ri].set_row(row, RMF::HDF5::Ints(ord.begin(), ord.end()));
RMF::HDF5::DataSetIndexD<1> ssz = scores[ri].get_size();
RMF::HDF5::DataSetIndexD<1> nsz = ssz;
++nsz[0];
scores[ri].set_size(nsz);
scores[ri].set_value(ssz, score);
++count;
if (count > max_entries) break;
}
}
Hierarchy create_protein(Model *m, std::string name, double resolution,
const Ints db) {
Hierarchy root = Hierarchy::setup_particle(new Particle(m));
Domain::setup_particle(root, IntRange(db.front(), db.back()));
for (unsigned int i = 1; i < db.size(); ++i) {
std::ostringstream oss;
oss << name << "-" << i - 1;
Hierarchy cur = create_protein(
m, oss.str(), resolution, db[i] - db[i - 1], db[i - 1],
atom::get_volume_from_mass(
atom::get_mass_from_number_of_residues(db[i] - db[i - 1])),
false);
root.add_child(cur);
}
Molecule::setup_particle(root);
root->set_name(name);
return root;
}
PartitionalClustering *
RecursivePartitionalClusteringMetric::create_full_clustering(
PartitionalClustering *center_cluster) {
IMP::base::Vector<Ints> clusters(center_cluster->get_number_of_clusters());
Ints reps(clusters.size());
for (unsigned int i = 0; i < clusters.size(); ++i) {
Ints outer = center_cluster->get_cluster(i);
reps[i] = clustering_->get_cluster_representative(
center_cluster->get_cluster_representative(i));
for (unsigned int j = 0; j < outer.size(); ++j) {
Ints inner = clustering_->get_cluster(outer[j]);
clusters[i].insert(clusters[i].end(), inner.begin(), inner.end());
}
}
IMP_NEW(internal::TrivialPartitionalClustering, ret, (clusters, reps));
validate_partitional_clustering(ret, metric_->get_number_of_items());
return ret.release();
}
bool ChimeraWriter::handle_polygon(PolygonGeometry *g, Color color,
std::string name) {
cleanup(name, false, true);
Ints triangles = internal::get_triangles(g);
get_stream() << "v=[";
for (unsigned int i = 0; i < g->get_geometry().size(); ++i) {
get_stream() << "(" << commas_io(g->get_geometry()[i]) << "), ";
}
get_stream() << "]\n";
get_stream() << "vi=[";
for (unsigned int i = 0; i < triangles.size() / 3; ++i) {
get_stream() << "(" << triangles[3 * i] << ", " << triangles[3 * i + 1]
<< ", " << triangles[3 * i + 2] << "), ";
}
get_stream() << "]\n";
get_stream() << "m.addPiece(v, vi, (" << commas_io(color) << ", 1))\n";
return true;
}
ParticleIndexPairs NearestNeighborsClosePairsFinder::get_close_pairs(
kernel::Model *m, const kernel::ParticleIndexes &pai) const {
kernel::ParticlesTemp c = IMP::get_particles(m, pai);
IMP_NEW(algebra::NearestNeighborD<3>, nn, (c.begin(), c.end(), 0));
double rm = max_radius(c.begin(), c.end());
kernel::ParticleIndexPairs ret;
for (unsigned int i = 0; i < c.size(); ++i) {
XYZR d(c[i]);
Ints cur = nn->get_in_ball(d.get_coordinates(),
rm + get_distance() + d.get_radius());
for (unsigned int j = 0; j < cur.size(); ++j) {
if (d < c[cur[j]]) {
ret.push_back(
kernel::ParticleIndexPair(pai[cur[j]], d.get_particle_index()));
}
}
}
return ret;
}
int KMCentersNode::mid_center(const Ints &cands) {
KMPoint *lo, *hi, mid;
lo = bnd_box_.get_point(0);
hi = bnd_box_.get_point(1);
// get the mid point of the bounding box
for (int d = 0; d < bnd_box_.get_dim(); d++) {
mid.push_back(((*lo)[d] + (*hi)[d]) / 2);
}
// the closest center will be the closest to the middle of the bounding box
double min_dist = km_distance2(mid, *((*centers_)[cands[0]]));
int min_ind = 0;
for (unsigned int j = 1; j < cands.size(); j++) {
double dist = km_distance2(mid, *((*centers_)[cands[j]]));
if (dist < min_dist) {
min_dist = dist;
min_ind = j;
}
}
return cands[min_ind];
}
Ints _pass_ints(Ints in) {
for (unsigned int i = 0; i < in.size(); ++i) {
std::cout << in[i] << " ";
}
return in;
}
double
get_slack_estimate(const ParticlesTemp& ps,
double upper_bound,
double step,
const RestraintsTemp &restraints,
bool derivatives,
Optimizer *opt,
ClosePairContainer *cpc) {
std::vector<Data> datas;
for (double slack=0; slack< upper_bound; slack+= step) {
IMP_LOG(VERBOSE, "Computing for " << slack << std::endl);
datas.push_back(Data());
datas.back().slack=slack;
{
boost::timer imp_timer;
int count=0;
base::SetLogState sl(opt->get_model(), SILENT);
do {
cpc->set_slack(slack);
cpc->update();
++count;
} while (imp_timer.elapsed()==0);
datas.back().ccost= imp_timer.elapsed()/count;
IMP_LOG(VERBOSE, "Close pair finding cost "
<< datas.back().ccost << std::endl);
}
{
boost::timer imp_timer;
double score=0;
int count=0;
int iters=1;
base::SetLogState sl(opt->get_model(), SILENT);
do {
for ( int j=0; j< iters; ++j) {
for (unsigned int i=0; i< restraints.size(); ++i) {
score+=restraints[i]->evaluate(derivatives);
// should restore
}
}
count += iters;
iters*=2;
} while (imp_timer.elapsed()==0);
datas.back().rcost= imp_timer.elapsed()/count;
IMP_LOG(VERBOSE, "Restraint evaluation cost "
<< datas.back().rcost << std::endl);
}
}
int ns=100;
int last_ns=1;
int opt_i=-1;
std::vector<Floats > dists(1, Floats(1,0.0));
std::vector< std::vector<algebra::Vector3D> >
pos(1, std::vector<algebra::Vector3D>(ps.size()));
for (unsigned int j=0; j< ps.size(); ++j) {
pos[0][j]=core::XYZ(ps[j]).get_coordinates();
}
do {
IMP_LOG(VERBOSE, "Stepping from " << last_ns << " to " << ns << std::endl);
dists.resize(ns, Floats(ns, 0.0));
for ( int i=0; i< last_ns; ++i) {
dists[i].resize(ns, 0.0);
}
pos.resize(ns, std::vector<algebra::Vector3D>(ps.size()));
base::SetLogState sl(opt->get_model(), SILENT);
for ( int i=last_ns; i< ns; ++i) {
opt->optimize(1);
for (unsigned int j=0; j< ps.size(); ++j) {
pos[i][j]=core::XYZ(ps[j]).get_coordinates();
}
}
for ( int i=last_ns; i< ns; ++i) {
for ( int j=0; j< i; ++j) {
double md=0;
for (unsigned int k=0; k< ps.size(); ++k) {
md= std::max(md, algebra::get_distance(pos[i][k], pos[j][k]));
}
dists[i][j]=md;
dists[j][i]=md;
}
}
// estimate lifetimes from slack
for (unsigned int i=0; i< datas.size(); ++i) {
Ints deaths;
for ( int j=0; j< ns; ++j) {
for ( int k=j+1; k < ns; ++k) {
if (dists[j][k]> datas[i].slack) {
deaths.push_back(k-j);
break;
}
}
}
std::sort(deaths.begin(), deaths.end());
// kaplan meier estimator
double ml=0;
if (deaths.empty()) {
ml= ns;
} else {
//double l=1;
IMP_INTERNAL_CHECK(deaths.size() < static_cast<unsigned int>(ns),
"Too much death");
double S=1;
for (unsigned int j=0; j< deaths.size(); ++j) {
double n= ns-j;
double t=(n-1.0)/n;
ml+=(S-t*S)*deaths[j];
S*=t;
}
}
datas[i].lifetime=ml;
IMP_LOG(VERBOSE, "Expected life of " << datas[i].slack
<< " is " << datas[i].lifetime << std::endl);
}
/**
C(s) is cost to compute
R(s) is const to eval restraints
L(s) is lifetime of slack
minimize C(s)/L(s)+R(s)
*/
// smooth
for (unsigned int i=1; i< datas.size()-1; ++i) {
datas[i].rcost=(datas[i].rcost+ datas[i-1].rcost+datas[i+1].rcost)/3.0;
datas[i].ccost=(datas[i].ccost+ datas[i-1].ccost+datas[i+1].ccost)/3.0;
datas[i].lifetime=(datas[i].lifetime
+ datas[i-1].lifetime+datas[i+1].lifetime)/3.0;
}
double min= std::numeric_limits<double>::max();
for (unsigned int i=0; i< datas.size(); ++i) {
double v= datas[i].rcost+ datas[i].ccost/datas[i].lifetime;
IMP_LOG(VERBOSE, "Cost of " << datas[i].slack << " is " << v
<< " from " << datas[i].rcost
<< " " << datas[i].ccost << " " << datas[i].lifetime
<< std::endl);
if (v < min) {
min=v;
opt_i=i;
}
}
last_ns=ns;
ns*=2;
IMP_LOG(VERBOSE, "Opt is " << datas[opt_i].slack << std::endl);
// 2 for the value, 2 for the doubling
// if it more than 1000, just decide that is enough
} while (datas[opt_i].lifetime > ns/4.0 && ns <1000);
return datas[opt_i].slack;
}
void write_pdb(const ParticlesTemp& ps, TextOutput out) {
IMP_FUNCTION_LOG;
int last_index = 0;
bool use_input_index = true;
for (unsigned int i = 0; i < ps.size(); ++i) {
if (Atom(ps[i]).get_input_index() != last_index + 1) {
use_input_index = false;
break;
} else {
++last_index;
}
}
for (unsigned int i = 0; i < ps.size(); ++i) {
if (Atom::get_is_setup(ps[i])) {
Atom ad(ps[i]);
Residue rd = get_residue(ad);
// really dumb and slow, fix later
char chain;
Chain c = get_chain(rd);
if (c) {
chain = c.get_id()[0];
} else {
chain = ' ';
}
int inum = i+1;
if (i>=99999) inum=99999;
out.get_stream() << get_pdb_string(
core::XYZ(ps[i]).get_coordinates(),
use_input_index ? ad.get_input_index()
: static_cast<int>(inum),
ad.get_atom_type(), rd.get_residue_type(), chain,
rd.get_index(), rd.get_insertion_code(),
ad.get_occupancy(), ad.get_temperature_factor(),
ad.get_element());
if (!out) {
IMP_THROW("Error writing to file in write_pdb", IOException);
}
}
else if (Residue::get_is_setup(ps[i])) { // if C-alpha residue is available
Residue rd = IMP::atom::Residue(ps[i]);
// comment 1 by SJ - TODO: How to retrieve the correct chain information without an hierarchy?
char chain;
Chain c = get_chain(rd);
if (c) {
chain = c.get_id()[0];
} else {
chain = ' ';
}
// comment 2 by SJ - TODO: The C-alpha residues are not sorted yet. We need to sort the residues similarly to what PMI does.
out.get_stream() << get_pdb_string(
core::XYZ(ps[i]).get_coordinates(),
static_cast<int>(i + 1),
IMP::atom::AT_CA, rd.get_residue_type(), chain,
rd.get_index(), ' ',
1.0, IMP::core::XYZR(ps[i]).get_radius());
}
else { // if a coarse-grained BEAD is available
Ints resindexes = IMP::atom::Fragment(ps[i]).get_residue_indexes();
int resindex = (int)resindexes.front() + (int)(resindexes.size()/2);
// comment 1 by SJ - TODO: How to retrieve the correct chain information without an hierarchy?
char chain = ' ';
// comment 3 by SJ - TODO: The BEADs are not sorted yet. We need to sort the residues similarly to what PMI does.
// comment 4 by SJ - TODO: currently IMP does not allow "BEA" as a residue name, while PMI allows it. Thus "UNK" was used instead.
out.get_stream() << get_pdb_string(
core::XYZ(ps[i]).get_coordinates(),
static_cast<int>(i + 1),
IMP::atom::AT_CA, IMP::atom::UNK, chain,
(int)resindex, ' ',
1.0, IMP::core::XYZR(ps[i]).get_radius());
}
}
}
