Hierarchy
create_simplified_along_backbone(Chain in,
const IntRanges& residue_segments,
bool keep_detailed) {
IMP_USAGE_CHECK(in.get_is_valid(true), "Chain " << in
<< " is not valid.");
if (in.get_number_of_children() ==0 || residue_segments.empty()) {
IMP_LOG_TERSE( "Nothing to simplify in " << (in? in->get_name(): "nullptr")
<< " with " << residue_segments.size() << " segments.\n");
return Hierarchy();
}
for (unsigned int i=0; i< residue_segments.size(); ++i) {
IMP_USAGE_CHECK(residue_segments[i].first < residue_segments[i].second,
"Residue intervals must be non-empty");
}
IMP_IF_LOG(VERBOSE) {
for (unsigned int i=0; i < residue_segments.size(); ++i) {
IMP_LOG_VERBOSE( "[" << residue_segments[i].first
<< "..." << residue_segments[i].second << ") ");
}
IMP_LOG_VERBOSE( std::endl);
}
unsigned int cur_segment=0;
Hierarchies cur;
Hierarchy root=create_clone_one(in);
for (unsigned int i=0; i< in.get_number_of_children(); ++i) {
Hierarchy child=in.get_child(i);
int index= Residue(child).get_index();
IMP_LOG_VERBOSE( "Processing residue " << index
<< " with range " << residue_segments[cur_segment].first
<< " " << residue_segments[cur_segment].second << std::endl);
if (index >= residue_segments[cur_segment].first
&& index < residue_segments[cur_segment].second) {
} else if (!cur.empty()) {
IMP_LOG_VERBOSE( "Added particle for "
<< residue_segments[cur_segment].first
<< "..." << residue_segments[cur_segment].second
<< std::endl);
Hierarchy cur_approx=create_approximation_of_residues(cur);
root.add_child(cur_approx);
if (keep_detailed) {
for (unsigned int j=0; j< cur.size(); ++j) {
cur[j].get_parent().remove_child(cur[j]);
cur_approx.add_child(cur[j]);
}
}
cur.clear();
++cur_segment;
}
cur.push_back(child);
}
if (!cur.empty()) {
root.add_child(create_approximation_of_residues(cur));
}
/*#ifdef IMP_ATOM_USE_IMP_CGAL
double ov= get_volume(in);
double cv= get_volume(root);
double scale=1;
ParticlesTemp rt= get_by_type(root, XYZR_TYPE);
Floats radii(rt.size());
for (unsigned int i=0; i< rt.size(); ++i) {
core::XYZR d(rt[i]);
radii[i]=d.get_radius();
}
do {
show(root);
double f= ov/cv*scale;
scale*=.95;
IMP_LOG_TERSE( "Bumping radius by " << f << std::endl);
for (unsigned int i=0; i< rt.size(); ++i) {
core::XYZR d(rt[i]);
d.set_radius(radii[i]*f);
}
double nv=get_volume(root);
IMP_LOG_TERSE( "Got volume " << nv << " " << ov << std::endl);
if (nv < ov) {
break;
}
} while (true);
#else
#endif*/
IMP_INTERNAL_CHECK(root.get_is_valid(true),
"Invalid hierarchy produced " << root);
return root;
}
int _test_intranges(const IntRanges &ips) { return ips.size(); }
