FittingSolutionRecords
convert_transformations_to_multifit_format(
const algebra::Transformation3Ds &trans) {
FittingSolutionRecords ret;
for (unsigned int i=0;i<trans.size();i++) {
FittingSolutionRecord rec;
rec.set_fit_transformation(trans[i]);
ret.push_back(rec);
}
return ret;
}
em::FittingSolutions convert_multifit_to_em_format(
const FittingSolutionRecords &multifit_fits) {
em::FittingSolutions output;
for(FittingSolutionRecords::const_iterator it = multifit_fits.begin();
it != multifit_fits.end();it++) {
for(unsigned int i=0;i<multifit_fits.size();i++)
output.add_solution(it->get_fit_transformation(),
it->get_fitting_score());
}
return output;
}
void ProbabilisticAnchorGraph::set_particle_probabilities_on_anchors(
Particle *p, FittingSolutionRecords sols) {
IMP_USAGE_CHECK(sols.size() > 0, "no solutions provided\n");
IMP_NEW(algebra::NearestNeighborD<3>, nn, (positions_));
Ints anchor_counters;
anchor_counters.insert(anchor_counters.end(), positions_.size(), 0);
for (unsigned int i = 0; i < sols.size(); i++) {
algebra::Vector3D loc = sols[i].get_fit_transformation().get_transformed(
core::XYZ(p).get_coordinates());
anchor_counters[nn->get_nearest_neighbor(loc)]++;
}
Floats probs;
for (unsigned int i = 0; i < anchor_counters.size(); i++) {
probs.push_back(1. * anchor_counters[i] / sols.size());
}
particle_to_anchor_probabilities_[p] = probs;
}
algebra::Transformation3Ds
convert_multifit_format_to_transformations(
const FittingSolutionRecords &recs) {
algebra::Transformation3Ds ret;
for (unsigned int i=0;i<recs.size();i++) {
ret.push_back(recs[i].get_fit_transformation());
}
return ret;
}
FittingSolutionRecords read_fitting_solutions(const char *fitting_fn) {
std::fstream in;
FittingSolutionRecords sols;
in.open(fitting_fn, std::fstream::in);
if (! in.good()) {
IMP_WARN("Problem opening file " << fitting_fn <<
" for reading; returning 0 solutions" << std::endl);
in.close();
return sols;
}
std::string line;
getline(in, line); //skip header line
while (!in.eof()) {
if (!getline(in, line)) break;
sols.push_back(parse_fitting_line(line));
}
in.close();
return sols;
}
IMPMULTIFIT_BEGIN_NAMESPACE
FittingSolutionRecords get_close_to_point(
const FittingSolutionRecords &fit_sols, atom::Hierarchy mh,
IMP::Particle *ap, Float dist) {
FittingSolutionRecords pruned_fit_sols;
Float dist2 = dist * dist;
IMP::algebra::Vector3D ap_centroid = IMP::core::XYZ(ap).get_coordinates();
IMP::algebra::Vector3D mh_centroid =
IMP::core::get_centroid(IMP::core::XYZs(IMP::core::get_leaves(mh)));
for (FittingSolutionRecords::const_iterator it = fit_sols.begin();
it != fit_sols.end(); it++) {
if (IMP::algebra::get_squared_distance(
it->get_fit_transformation().get_transformed(mh_centroid),
ap_centroid) < dist2) {
pruned_fit_sols.push_back(*it);
}
}
return pruned_fit_sols;
}
void write_fitting_solutions(const char *fitting_fn,
const FittingSolutionRecords &fit_sols,
int num_sols) {
if (num_sols==-1) {
num_sols = fit_sols.size();
}
std::fstream out;
out.open(fitting_fn, std::fstream::out);
IMP_USAGE_CHECK(out.good(), "Problem opening file " <<
fitting_fn << " for writing"<<std::endl);
//write header
out<<FittingSolutionRecord::get_record_header();
for(int i=0;i<num_sols;i++) {
fit_sols[i].show(out);
out<<std::endl;
}
out.close();
}
