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#include <iostream>
#include <vector>
#include <string>
#include "coot-utils/atom-selection-container.hh"
#include "ghost-molecule-display.hh"
#include "ncs-ghosts.hh"
// I copied this function over without reading it - I now think that this might not be the function that
// I want.
// fill ncs ghosts: detect exact ncs automatically.
//
std::vector<coot::ghost_molecule_display_t>
fill_ghost_info(atom_selection_container_t *atom_sel, float homology_lev, bool is_from_shelx_ins_flag) {
if (true)
std::cout << "DEBUG:: --------------- in fill_ghost_info ------- with homology_lev "
<< homology_lev << std::endl;
bool do_rtops_flag = true;
std::vector<std::string> chain_ids;
std::vector<std::vector<std::pair<std::string, int> > > residue_types;
std::vector<int> chain_atom_selection_handles;
std::vector<short int> first_chain_of_this_type;
bool allow_offset_flag = 0;
if (is_from_shelx_ins_flag) allow_offset_flag = true;
std::vector<coot::ghost_molecule_display_t> ncs_ghosts;
if (atom_sel->n_selected_atoms > 0) {
int n_models = atom_sel->mol->GetNumberOfModels();
if (n_models > 0) {
int imod = 1; // otherwise madness
mmdb::Model *model_p = atom_sel->mol->GetModel(imod);
// run over chains of the existing mol
int nchains = model_p->GetNumberOfChains();
// std::cout << "DEUBG:: in fill_ghost_info() nchains is " << nchains << std::endl;
if (nchains > 0) {
chain_ids.resize(nchains);
residue_types.resize(nchains);
chain_atom_selection_handles.resize(nchains);
first_chain_of_this_type.resize(nchains, 1);
for (int ichain=0; ichain<nchains; ichain++) {
mmdb::Chain *chain_p = model_p->GetChain(ichain);
if (! chain_p->isSolventChain()) {
chain_ids[ichain] = chain_p->GetChainID();
int iselhnd = atom_sel->mol->NewSelection();
mmdb::PAtom *atom_selection = NULL;
int nSelAtoms;
atom_sel->mol->SelectAtoms(iselhnd, imod,
chain_p->GetChainID(),
mmdb::ANY_RES, "*",
mmdb::ANY_RES, "*",
"*", "*", "*", "*");
atom_sel->mol->GetSelIndex(iselhnd, atom_selection, nSelAtoms);
chain_atom_selection_handles[ichain] = iselhnd;
// debugging the atom selection
if (false) {
mmdb::PPAtom selatoms_1 = NULL;
int n_sel_atoms_1 = 0;
atom_sel->mol->GetSelIndex(iselhnd, selatoms_1, n_sel_atoms_1);
std::cout << "DEBUG:: fill_ghost_info: first atom of " << n_sel_atoms_1
<< " in " << chain_p->GetChainID() << " " << iselhnd
<< " selection " << selatoms_1[0] << std::endl;
}
int nres = chain_p->GetNumberOfResidues();
residue_types[ichain].resize(nres);
// std::cout << "INFO:: residues_types[" << ichain << "] resized to "
// << residue_types[ichain].size() << std::endl;
for (int ires=0; ires<nres; ires++) {
mmdb::PResidue residue_p = chain_p->GetResidue(ires);
std::string resname(residue_p->name);
residue_types[ichain][ires] = std::pair<std::string, int> (resname, residue_p->seqNum);
}
}
}
}
}
// add_ncs_ghosts_no_explicit_master(chain_ids, residue_types, first_chain_of_this_type,
// chain_atom_selection_handles, do_rtops_flag, homology_lev,
// allow_offset_flag);
}
return ncs_ghosts;
}
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