/* coot-utils/coot-coord-utils.cc
 * 
 * Copyright 2006 by The University of York
 * Copyright 2007 by Paul Emsley
 * Copyright 2007, 2008, 2009 by The University of Oxford
 * Copyright 2012, 2013, 2014, 2015, 2016 by Medical Research Council
 * Author: Paul Emsley
 * Author: Bernhard Lohkamp
 * 
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or (at
 * your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
 * 02110-1301, USA
 */

#include <algorithm>
#include <stdexcept>

#include <string.h> // for strcpy

#include <gsl/gsl_cdf.h>
#include <gsl/gsl_statistics_double.h>

#include "utils/coot-utils.hh"
#include "coot-coord-utils.hh"
#include <mmdb2/mmdb_tables.h>  // for mmdb::Get1LetterCode()
#include <mmdb2/mmdb_math_graph.h> // for graph matching

#include "compat/coot-sysdep.h"

#include "clipper/mmdb/clipper_mmdb.h"
#include "geometry/main-chain.hh"
#include "geometry/mol-utils.hh"
#include "geometry/residue-and-atom-specs.hh"

#include "utils/logging.hh"
extern logging logger;

std::vector<std::string>
coot::util::residue_types_in_molecule(mmdb::Manager *mol) { 

   std::vector<std::string> v;

   if (mol) { 

      int n_models = mol->GetNumberOfModels();
      
      for (int imod=1; imod<=n_models; imod++) { 
      
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
   
         mmdb::Chain *chain;
         // run over chains of the existing mol
         int nchains = model_p->GetNumberOfChains();
         if (nchains <= 0) { 
            std::cout << "bad nchains in trim molecule " << nchains
                      << std::endl;
         } else { 
            for (int ichain=0; ichain<nchains; ichain++) {
               chain = model_p->GetChain(ichain);
               if (chain == NULL) {  
                  // This should not be necessary. It seem to be a
                  // result of mmdb corruption elsewhere - possibly
                  // DeleteChain in update_molecule_to().
                  std::cout << "NULL chain in residues_types_in_molecule: "
                            << std::endl;
               } else { 
                  int nres = chain->GetNumberOfResidues();
                  mmdb::Residue *residue_p;
                  for (int ires=0; ires<nres; ires++) { 
                     residue_p = chain->GetResidue(ires);

//                     int n_atoms = residue_p->GetNumberOfAtoms();
//                      for (int iat=0; iat<n_atoms; iat++) {
//                         mmdb::Atom *atom_p = residue_p->GetAtom(iat);
//                      }

                     std::string resname = residue_p->name;

                     if (! is_member_p(v, resname)) { 
                        v.push_back(resname);
                     } 
                  }
               }
            }
         }
      }
   }
   return v;
}

std::vector<std::string>
coot::util::non_standard_residue_types_in_molecule(mmdb::Manager *mol) {

   std::vector<std::string> r;
   if (! mol) return r;
   std::vector<std::string> v = residue_types_in_molecule(mol);
   std::vector<std::string> standards = coot::util::standard_residue_types();
   
   for (unsigned int i=0; i<v.size(); i++)
      if (! is_member_p(standards, v[i]))
         r.push_back(v[i]);
            
   return r; 
}

std::vector<std::string>
coot::util::standard_residue_types() {

   std::vector<std::string> v;
   v.push_back("ALA"); v.push_back("ARG"); v.push_back("ASP");
   v.push_back("ASN"); v.push_back("CYS"); v.push_back("SER");
   v.push_back("PRO"); v.push_back("PHE"); v.push_back("GLY");
   v.push_back("GLU"); v.push_back("GLN"); v.push_back("ILE");
   v.push_back("LEU"); v.push_back("TYR"); v.push_back("TRP");
   v.push_back("HIS"); v.push_back("LYS"); v.push_back("MET");
   v.push_back("VAL"); v.push_back("THR"); v.push_back("MSE"); 
   return v;
}

std::vector<std::string>
coot::util::PDB_standard_residue_types() {

   std::vector<std::string> v = coot::util::standard_residue_types();
   v.push_back("Td"); v.push_back("Tr"); v.push_back("T");
   v.push_back("Gd"); v.push_back("Gr"); v.push_back("G");
   v.push_back("Ad"); v.push_back("Ar"); v.push_back("A");

   v.push_back("DG"); v.push_back("DC"); v.push_back("DA");
   v.push_back("DU"); v.push_back("DT"); v.push_back("DI");

   v.push_back("UNK"); v.push_back("N");

   return v;
}




std::vector<std::pair<int, int> >
coot::util::pair_residue_atoms(mmdb::Residue *a_residue_p,
                               mmdb::Residue *b_residue_p) {

   std::vector<std::pair<int, int> > pv;

   mmdb::PPAtom residue_atoms_1 = NULL;
   mmdb::PPAtom residue_atoms_2 = NULL;
   int n_residue_atoms_1, n_residue_atoms_2;
   a_residue_p->GetAtomTable(residue_atoms_1, n_residue_atoms_1);
   b_residue_p->GetAtomTable(residue_atoms_2, n_residue_atoms_2);

   for (int i=0; i<n_residue_atoms_1; i++) {
      std::string atn1(residue_atoms_1[i]->name);
      std::string alt1(residue_atoms_1[i]->altLoc);
      for (int j=0; j<n_residue_atoms_2; j++) {
         std::string atn2(residue_atoms_2[j]->name);
         std::string alt2(residue_atoms_2[j]->altLoc);
         if (atn1 == atn2) {
            if (alt1 == alt2) {
               std::pair<int, int> p(i,j);
               pv.push_back(p);
               break;
            }
         }
      }
   }
   return pv;
}


mmdb::Manager *
coot::util::copy_molecule(mmdb::Manager *mol) {
   mmdb::Manager *n = new mmdb::Manager;
   n->Copy(mol, mmdb::MMDBFCM_All);
   return n;
}

void
coot::util::translate_close_to_origin(mmdb::Manager *mol) {

   try {
      std::pair<clipper::Cell, clipper::Spacegroup> csp = get_cell_symm(mol);
      clipper::Coord_frac cf = coot::util::shift_to_origin(mol);
      clipper::Coord_orth co = cf.coord_orth(csp.first);
      for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
         mmdb::Chain *chain_p;
         int nchains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<nchains; ichain++) {
            chain_p = model_p->GetChain(ichain);
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            mmdb::Atom *at;
            for (int ires=0; ires<nres; ires++) { 
               residue_p = chain_p->GetResidue(ires);
               int n_atoms = residue_p->GetNumberOfAtoms();
               for (int iat=0; iat<n_atoms; iat++) {
                  at = residue_p->GetAtom(iat);
                  at->x += co.x();
                  at->y += co.y();
                  at->z += co.z();
               }
            }
         }
      }
   } 
   catch (const std::runtime_error &rte) {
      std::cout << rte.what() << std::endl;
   } 
}

void
coot::util::shift(mmdb::Manager *mol, clipper::Coord_orth pt) {

   for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol->GetModel(imod);
      if (! model_p) continue;
      mmdb::Chain *chain_p;
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         chain_p = model_p->GetChain(ichain);
         int nres = chain_p->GetNumberOfResidues();
         mmdb::Residue *residue_p;
         mmdb::Atom *at;
         for (int ires=0; ires<nres; ires++) { 
            residue_p = chain_p->GetResidue(ires);
            int n_atoms = residue_p->GetNumberOfAtoms();
            for (int iat=0; iat<n_atoms; iat++) {
               at = residue_p->GetAtom(iat);
               at->x += pt.x();
               at->y += pt.y();
               at->z += pt.z();
            }
         }
      }
   }
}



void
coot::sort_chains(mmdb::Manager *mol) {

   if (mol) { 
      for (int imod=1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
         model_p->SortChains(mmdb::SORT_CHAIN_ChainID_Asc); // "B" comes after "A"
      }
      mol->PDBCleanup(mmdb::PDBCLEAN_SERIAL|mmdb::PDBCLEAN_INDEX);
      mol->FinishStructEdit();
   }
}
      

bool
coot::sort_chains_util(const std::pair<mmdb::Chain *, std::string> &a,
                       const std::pair<mmdb::Chain *, std::string> &b) {

   return (a.second < b.second); 
}

void
coot::sort_residues(mmdb::Manager *mol) {

   if (mol) { 
      for (int imod=1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (model_p) {
            mmdb::Chain *chain_p;
            // run over chains of the existing mol
            int nchains = model_p->GetNumberOfChains();
            for (int ichain=0; ichain<nchains; ichain++) {
               chain_p = model_p->GetChain(ichain);
               chain_p->SortResidues();
            }
         } else {
            std::cout << "ERROR:: (trapped) sort_residues() Null Model "
                      << imod << " of " << mol->GetNumberOfModels() << std::endl;
         } 
      }
      mol->PDBCleanup(mmdb::PDBCLEAN_SERIAL|mmdb::PDBCLEAN_INDEX);
      mol->FinishStructEdit();
   } else {
      std::cout << "ERROR:: (trapped) sort_residues() called with Null molecule"
                << std::endl;
   } 
}

// return residue specs for residues that have atoms that are
// closer than radius Angstroems to any atom in the residue
// specified by res_in.
// 
std::vector<coot::residue_spec_t>
coot::residues_near_residue(const coot::residue_spec_t &rs,
                            mmdb::Manager *mol,
                            float radius) {

   std::vector<coot::residue_spec_t> r;

   if (mol) { 
      mmdb::Residue *res_p = coot::util::get_residue(rs.chain_id, rs.res_no, rs.ins_code, mol);
      if (!res_p) {
         std::cout << "OOps failed to find " << rs << " in molecule\n";
      } else {
         
         // std::cout << "  Finding contacts of " << rs << " in molecule\n";
         
         std::vector<mmdb::Residue *> close_residues = residues_near_residue(res_p, mol, radius);
         
         for (unsigned int i=0; i<close_residues.size(); i++)
            r.push_back(residue_spec_t(close_residues[i]));
      }
   }
   return r;
}

std::vector<mmdb::Residue *>
coot::residues_near_residue(mmdb::Residue *res_ref,
                            mmdb::Manager *mol,
                            float radius) {

   if (false)
      std::cout << "debug:: residues_near_residue of " << residue_spec_t(res_ref) << std::endl;

   mmdb::PPAtom atom_selection = NULL;
   int n_selected_atoms;
   std::vector<mmdb::Residue *> close_residues;

   if (mol) {

      int SelectionHandle = mol->NewSelection(); // d
      mol->SelectAtoms (SelectionHandle, 0, "*",
                        mmdb::ANY_RES, // starting resno, an int
                        "*", // any insertion code
                        mmdb::ANY_RES, // ending resno
                        "*", // ending insertion code
                        "*", // any residue name
                        "*", // atom name
                        "*", // elements
                        "*"  // alt loc.
                        );

      mol->GetSelIndex(SelectionHandle, atom_selection, n_selected_atoms);

      if (! res_ref)
         return close_residues;

      mmdb::PPAtom res_atom_selection = 0;
      int n_res_atoms = 0;
      res_ref->GetAtomTable(res_atom_selection, n_res_atoms);


      if (n_res_atoms > 0) {

         mmdb::Contact *pscontact = NULL;
         int n_contacts;
         float min_dist = 0.01;
         long i_contact_group = 1;
         mmdb::mat44 my_matt;
         mmdb::SymOps symm;
         for (int i=0; i<4; i++) 
            for (int j=0; j<4; j++) 
               my_matt[i][j] = 0.0;      
         for (int i=0; i<4; i++) my_matt[i][i] = 1.0;

         // by-pass bug noted below (?)
         if (min_dist < radius)
            min_dist = 0.0;
         // bypass a bug when the n_contacts is 11m or so, but
         // pscontact[0] is NULL.  hence crash when we try to get the
         // residue from that atom index.
         // 
         if (radius > 0.0) {

            mol->SeekContacts(res_atom_selection, n_res_atoms, 
                              atom_selection, n_selected_atoms,
                              min_dist, radius, // min, max distances
                              0,        // seqDist 0 -> in same res also
                              pscontact, n_contacts,
                              0, &my_matt, i_contact_group);
         
            //       std::cout << " Found " << n_contacts  << " contacts " << std::endl;

            if (n_contacts > 0) {
               if (pscontact) { 
                  int n_cont_diff = 0; 
                  int n_cont_same = 0; 
                  for (int i=0; i<n_contacts; i++) {
                     //             std::cout << "   comparing " << atom_selection[pscontact[i].id2]
                     //                       << " " << coot::atom_spec_t(atom_selection[pscontact[i].id2])
                     //                       << " " << " to " << rs << " " << res_p << std::endl;
                     if (atom_selection[pscontact[i].id2]->residue != res_ref) {
                        n_cont_diff++;
                        std::vector<mmdb::Residue *>::iterator result =
                           std::find(close_residues.begin(),
                                     close_residues.end(),
                                     atom_selection[pscontact[i].id2]->residue);
                  
                        if (result == close_residues.end()) { 
                           close_residues.push_back(atom_selection[pscontact[i].id2]->residue);
                        }
                     } else {
                        n_cont_same++;
                     }
                  }
               } else {
                  std::cout << "ERROR:: trapped null pscontact in residues_near_residue"
                            << std::endl;
               } 
            }
         }
         mol->DeleteSelection(SelectionHandle);
      }
   }

   return close_residues;
}

// return a map of neighbouring residues, the keys should be in residues_vec
//
// Note, it takes some effort to check that the key is or is not in residues_vec, so
// a faster way still is not to pass residues_vec and get the results for the
// whole molecule: residues_near_residues(mmdb::Manager *mol, float dist_crit)
//
// and then if we want a particular to limit that to a particular set of residues:
//
// std::map<mmdb::Residue *, std::set<mmdb::Residue *> >
// residues_near_residues(std::map<mmdb::Residue *, std::set<mmdb::Residue *> > all_molecule_residue_map,
//                        std::vector<mmdb::Residue *> limit_residues); // or a vector of pairs with a bool
// that should be fast.
//
std::map<mmdb::Residue *, std::set<mmdb::Residue *> >
coot::residues_near_residues(const std::vector<std::pair<bool,mmdb::Residue *> > &residues_vec,
                             mmdb::Manager *mol,
                             float dist_crit) {

   std::map<mmdb::Residue *, std::set<mmdb::Residue *> > m;

   if (mol) {

      if (false) {
         std::cout << "residues_near_residues: debug mol:" << mol << std::endl;
         for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
            std::cout << "debug:: residues_near_residues Model " << imod << std::endl;
            mmdb::Model *model_p = mol->GetModel(imod);
            if (model_p) {
               int n_chains = model_p->GetNumberOfChains();
               for (int ichain=0; ichain<n_chains; ichain++) {
                  mmdb::Chain *chain_p = model_p->GetChain(ichain);
                  std::cout << "  debug:: residues_near_residuesChain " << chain_p->GetChainID() << std::endl;
                  int nres = chain_p->GetNumberOfResidues();
                  for (int ires=0; ires<nres; ires++) {
                     mmdb::Residue *residue_p = chain_p->GetResidue(ires);
                     std::cout << "    debug:: residues_near_residues " << residue_spec_t(residue_p)
                               << " " << residue_p << std::endl;
                     int n_atoms = residue_p->GetNumberOfAtoms();
                     for (int iat=0; iat<n_atoms; iat++) {
                        mmdb::Atom *at = residue_p->GetAtom(iat);
                        std::cout << "        " << atom_spec_t(at) << std::endl;
                     }
                  }
               }
            }
         }
      }

      int SelectionHandle = mol->NewSelection(); // d
      mol->SelectAtoms(SelectionHandle, 0, "*",
                       mmdb::ANY_RES, // starting resno, an int
                       "*", // any insertion code
                       mmdb::ANY_RES, // ending resno
                       "*", // ending insertion code
                       "*", // any residue name
                       "*", // atom name
                       "*", // elements
                       "*"  // alt loc.
                       );

      mmdb::PPAtom atom_selection = 0;
      int n_selected_atoms = 0;
      mol->GetSelIndex(SelectionHandle, atom_selection, n_selected_atoms);

      mmdb::Contact *pscontact = NULL;
      int n_contacts;
      float min_dist = 0.01;
      long i_contact_group = 1;
      mmdb::mat44 my_matt;
      mmdb::SymOps symm;
      for (int i=0; i<4; i++)
         for (int j=0; j<4; j++)
            my_matt[i][j] = 0.0;
      for (int i=0; i<4; i++) my_matt[i][i] = 1.0;

      float radius = dist_crit;
      // by-pass bug noted below (?)
      if (min_dist < radius)
         min_dist = 0.0;
      // bypass a bug when the n_contacts is 11m or so, but
      // pscontact[0] is NULL.  hence crash when we try to get the
      // residue from that atom index.
      //
      if (radius > 0.0) {

         mol->SeekContacts(atom_selection, n_selected_atoms,
                           atom_selection, n_selected_atoms,
                           min_dist, radius, // min, max distances
                           0,        // seqDist 0 -> in same res also
                           pscontact, n_contacts,
                           0, &my_matt, i_contact_group);

         if (n_contacts > 0) {
            if (pscontact) {
               for (int i=0; i<n_contacts; i++) {
                  mmdb::Atom *atom_1 = atom_selection[pscontact[i].id1];
                  mmdb::Atom *atom_2 = atom_selection[pscontact[i].id2];
                  mmdb::Residue *key  = atom_1->residue;
                  mmdb::Residue *data = atom_2->residue;
                  if (data != key) {
                     if (m.find(key) != m.end()) {
                        m[key].insert(data);
                     } else {
                        // make a new key (for residues that are in input vector)
                        bool key_is_in_input_vector = false;
                        for (std::size_t ir=0; ir<residues_vec.size(); ir++) {
                           if (key == residues_vec[ir].second) {
                              key_is_in_input_vector = true;
                              break;
                           }
                        }
                        if (key_is_in_input_vector) {
                           m[key].insert(data);
                        }
                     }
                  }
               }
            }
         }
      }
      delete [] pscontact;
      mol->DeleteSelection(SelectionHandle);
   }
   return m;
}

std::map<mmdb::Residue *, std::set<mmdb::Residue *> >
coot::residues_near_residues(mmdb::Manager *mol, float dist_crit) {

   std::map<mmdb::Residue *, std::set<mmdb::Residue *> > m;

   if (mol) {

      int SelectionHandle = mol->NewSelection(); // d
      mol->SelectAtoms(SelectionHandle, 0, "*",
                       mmdb::ANY_RES, // starting resno, an int
                       "*", // any insertion code
                       mmdb::ANY_RES, // ending resno
                       "*", // ending insertion code
                       "*", // any residue name
                       "*", // atom name
                       "*", // elements
                       "*"  // alt loc.
                       );

      mmdb::PPAtom atom_selection = 0;
      int n_selected_atoms = 0;
      mol->GetSelIndex(SelectionHandle, atom_selection, n_selected_atoms);

      mmdb::Contact *pscontact = NULL;
      int n_contacts;
      float min_dist = 0.01;
      long i_contact_group = 1;
      mmdb::mat44 my_matt;
      mmdb::SymOps symm;
      for (int i=0; i<4; i++)
         for (int j=0; j<4; j++)
            my_matt[i][j] = 0.0;
      for (int i=0; i<4; i++) my_matt[i][i] = 1.0;

      float radius = dist_crit;
      // by-pass bug noted below (?)
      if (min_dist < radius)
         min_dist = 0.0;
      // bypass a bug when the n_contacts is 11m or so, but
      // pscontact[0] is NULL.  hence crash when we try to get the
      // residue from that atom index.
      //
      if (radius > 0.0) {

         mol->SeekContacts(atom_selection, n_selected_atoms,
                           atom_selection, n_selected_atoms,
                           min_dist, radius, // min, max distances
                           0,        // seqDist 0 -> in same res also
                           pscontact, n_contacts,
                           0, &my_matt, i_contact_group);

         if (n_contacts > 0) {
            if (pscontact) {
               for (int i=0; i<n_contacts; i++) {
                  mmdb::Atom *atom_1 = atom_selection[pscontact[i].id1];
                  mmdb::Atom *atom_2 = atom_selection[pscontact[i].id2];
                  mmdb::Residue *key  = atom_1->residue;
                  mmdb::Residue *data = atom_2->residue;
                  if (data != key) {
                     m[key].insert(data);
                  }
               }
            }
         }
      }
      mol->DeleteSelection(SelectionHandle);
   }
   return m;
}

std::map<mmdb::Residue *, std::set<mmdb::Residue *> >
coot::residues_near_residues_for_residues(const std::map<mmdb::Residue *, std::set<mmdb::Residue *> > &all_molecule_map,
                                          const std::set<mmdb::Residue *> &limit_to_these_residues_vec) {

   std::map<mmdb::Residue *, std::set<mmdb::Residue *> > m;
   std::map<mmdb::Residue *, std::set<mmdb::Residue *> >::const_iterator it_map;

   for(it_map=all_molecule_map.begin(); it_map!=all_molecule_map.end(); it_map++) {
      mmdb::Residue *r = it_map->first;
      if (limit_to_these_residues_vec.find(r) != limit_to_these_residues_vec.end())
         m[r] = it_map->second;
   }
   return m;
}


std::vector<mmdb::Residue *>
coot::residues_near_position(const clipper::Coord_orth &pt,
                             mmdb::Manager *mol,
                             double radius) {

   std::vector<mmdb::Residue *> v;
   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (! model_p) return v;
   mmdb::Chain *chain_p;
   int nchains = model_p->GetNumberOfChains();
   for (int ichain=0; ichain<nchains; ichain++) {
      chain_p = model_p->GetChain(ichain);
      int nres = chain_p->GetNumberOfResidues();
      mmdb::PResidue residue_p;
      mmdb::Atom *at;
      for (int ires=0; ires<nres; ires++) { 
         residue_p = chain_p->GetResidue(ires);
         int n_atoms = residue_p->GetNumberOfAtoms();
         for (int iat=0; iat<n_atoms; iat++) {
            at = residue_p->GetAtom(iat);
            clipper::Coord_orth at_pt(at->x, at->y, at->z);
            double d = clipper::Coord_orth::length(pt, at_pt);
            if (d < radius) { 
               v.push_back(residue_p);
               break;
            }
         }
      }
   }
   return v;
}

// Don't include residues that are HOH residues that are not bonded to
// the protein (if bonding to res_ref but not protein, then reject.
// Reject waters that are not within water_dist_max to any atom in
// res_ref.
//
std::vector<mmdb::Residue *>
coot::filter_residues_by_solvent_contact(mmdb::Residue *res_ref,
                                         mmdb::Manager *mol,
                                         const std::vector<mmdb::Residue *> &residues,
                                         const double &water_dist_max) {
   std::vector<mmdb::Residue *> v;
   mmdb::PPAtom lig_residue_atoms = 0;
   int n_lig_residue_atoms;
   res_ref->GetAtomTable(lig_residue_atoms, n_lig_residue_atoms);
   for (unsigned int i=0; i<residues.size(); i++) { 
      std::string res_name = residues[i]->GetResName();
      if (res_name != "HOH") { 
         v.push_back(residues[i]);
      } else {
         mmdb::PPAtom residue_atoms = 0;
         int n_residue_atoms;
         residues[i]->GetAtomTable(residue_atoms, n_residue_atoms);
         bool i_added = 0;
         for (int jat=0; jat<n_lig_residue_atoms; jat++) {
            clipper::Coord_orth lig_pt(lig_residue_atoms[jat]->x,
                                       lig_residue_atoms[jat]->y,
                                       lig_residue_atoms[jat]->z);
            std::string ligand_atom_ele = lig_residue_atoms[jat]->element;
            for (int iat=0; iat<n_residue_atoms; iat++) {
               if (ligand_atom_ele != " C" && ligand_atom_ele != " H") { 
                  clipper::Coord_orth pt(residue_atoms[iat]->x,
                                         residue_atoms[iat]->y,
                                         residue_atoms[iat]->z);
                  if ((lig_pt-pt).lengthsq() < (water_dist_max*water_dist_max)) {
                     if (0) 
                        std::cout << "pushing back " << coot::residue_spec_t(residues[i])
                                  << " with dist "
                                  << sqrt((lig_pt-pt).lengthsq()) << " to "
                                  << coot::atom_spec_t(lig_residue_atoms[jat])
                                  << std::endl;
                     i_added = 1;
                     v.push_back(residues[i]);
                     break;
                  }
               }
            }
            if (i_added)
               break;
         }
      } 
   }
   return v;
}


std::pair<bool,float>
coot::closest_approach(mmdb::Manager *mol,
                       mmdb::Residue *r1, mmdb::Residue *r2) {

    int n_res_1_atoms; 
    int n_res_2_atoms;
    mmdb::PPAtom residue_atoms_1 = 0, residue_atoms_2 = 0;
    double dist_sqrd_best = 9999999.9;
    bool good_d = 0;
       
    r1->GetAtomTable( residue_atoms_1, n_res_1_atoms);
    r2->GetAtomTable( residue_atoms_2, n_res_2_atoms);
    for (int i=0; i<n_res_1_atoms; i++) {
       clipper::Coord_orth pt1(residue_atoms_1[i]->x,
                               residue_atoms_1[i]->y,
                               residue_atoms_1[i]->z);
       for (int j=0; j<n_res_2_atoms; j++) { 
          clipper::Coord_orth pt2(residue_atoms_2[j]->x,
                                  residue_atoms_2[j]->y,
                                  residue_atoms_2[j]->z);
          double d_sqrd = (pt2 - pt1).lengthsq();

          if (d_sqrd < dist_sqrd_best) {
             dist_sqrd_best = d_sqrd;
             good_d = true;
          }
       }
    }

    return std::pair<bool, float> (good_d, sqrt(dist_sqrd_best));
    
          
   // Older, faster method.
   // It doesn't work though
   // 
   // I don't know why this fail, but it always gives 0 ncontacts.
   
//    std::pair<bool,mmdb::realtype> r(0, 0.0);
   
//    int n_res_1_atoms; 
//    int n_res_2_atoms;
//    mmdb::PPAtom residue_atoms_1 = 0, residue_atoms_2 = 0;
//    int ncontacts = 0;
//    mmdb::realtype dist_closest = 9999999999.9;
//    mmdb::Contact *contact = NULL;
//    long i_contact_group = 0;
//    mmdb::mat44 my_matt;
//    for (int i=0; i<4; i++) 
//       for (int j=0; j<4; j++) 
//          my_matt[i][j] = 0.0;      
//    for (int i=0; i<4; i++) my_matt[i][i] = 1.0;
   
//    r1->GetAtomTable( residue_atoms_1, n_res_1_atoms);
//    r2->GetAtomTable( residue_atoms_2, n_res_2_atoms);
//    mol->SeekContacts(residue_atoms_1, n_res_1_atoms,
//                      residue_atoms_2, n_res_2_atoms,
//                      0.01, 10.0, 1, // not in the same residue
//                      contact, ncontacts,
//                      0, &my_matt, i_contact_group);


//    // debug mol
//    if (0) { 
//       int imod = 1;
//       mmdb::Model *model_p = mol->GetModel(imod);
//       mmdb::Chain *chain_p;
//       // run over chains of the existing mol
//       int nchains = model_p->GetNumberOfChains();
//       for (int ichain=0; ichain<nchains; ichain++) {
//          chain_p = model_p->GetChain(ichain);
//          int nres = chain_p->GetNumberOfResidues();
//          mmdb::PResidue residue_p;
//          mmdb::Atom *at;
//          for (int ires=0; ires<nres; ires++) { 
//             residue_p = chain_p->GetResidue(ires);
//             int n_atoms = residue_p->GetNumberOfAtoms();
         
//             for (int iat=0; iat<n_atoms; iat++) {
//                at = residue_p->GetAtom(iat);
//                std::cout << "mol atom "
//                          << at ->name << " " 
//                          << at ->GetSeqNum() << " " 
//                          << at ->GetInsCode() << " " 
//                          << at ->GetChainID() << " "
//                          << at ->z << " "
//                          << at ->y << " "
//                          << at ->z << std::endl;
//             }
//          }
//       }
//    }

   

//    for (int i=0; i<n_res_1_atoms; i++)
//       std::cout << "closest_approach res_1 " << i << " "
//                 << residue_atoms_1[i]->name << " ("
//                 << residue_atoms_1[i]->x << " "
//                 << residue_atoms_1[i]->y << " "
//                 << residue_atoms_1[i]->z << ") "
//                 << std::endl;
//    for (int i=0; i<n_res_2_atoms; i++)
//       std::cout << "closest_approach res_2 " << i << " " 
//                 << residue_atoms_2[i]->name << " ("
//                 << residue_atoms_2[i]->x << " "
//                 << residue_atoms_2[i]->y << " "
//                 << residue_atoms_2[i]->z << ") "
//                 << std::endl;


//    for (int i=0; i<ncontacts; i++) {
      
//       clipper::Coord_orth atom_1(residue_atoms_1[ contact[i].id1 ]->x,
//                                  residue_atoms_1[ contact[i].id1 ]->y,
//                                  residue_atoms_1[ contact[i].id1 ]->z);
//       clipper::Coord_orth atom_2(residue_atoms_2[ contact[i].id2 ]->x,
//                                  residue_atoms_2[ contact[i].id2 ]->y,
//                                  residue_atoms_2[ contact[i].id2 ]->z);
//       float d = clipper::Coord_orth::length(atom_1, atom_2);
//       if (d < dist_closest) {
//          dist_closest = d;
//          r = std::pair<bool,mmdb::realtype>(1, d);
//       } 
//    }
//    std::cout << "DEbug:: closest_approach() d " << r.first << " " << r.second
//              << " using " << ncontacts << " contacts with n_res_atoms "
//              << n_res_1_atoms << " " << n_res_2_atoms << std::endl;
//    return r;
}


// Return dist in Angstroms, can throw an exception if any of the
// atoms is null.
// 
double
coot::distance(mmdb::Atom *at_1, mmdb::Atom *at_2) {

   double d = -1;
   if (at_1 && at_2) {
      clipper::Coord_orth pt_1(at_1->x, at_1->y, at_1->z);
      clipper::Coord_orth pt_2(at_2->x, at_2->y, at_2->z);
      d = clipper::Coord_orth::length(pt_1, pt_2);
   }

   return d;
}

// Return angle in degrees, can throw an exception if any of the
// atoms is null.
// 
double
coot::angle(mmdb::Atom *at_1, mmdb::Atom *at_2, mmdb::Atom *at_3) {

   double ang = -1;

   if (at_1 && at_2 && at_3) {

      clipper::Coord_orth pt_1(at_1->x, at_1->y, at_1->z);
      clipper::Coord_orth pt_2(at_2->x, at_2->y, at_2->z);
      clipper::Coord_orth pt_3(at_3->x, at_3->y, at_3->z);

      ang = clipper::Util::rad2d(clipper::Coord_orth::angle(pt_1, pt_2, pt_3));

   } 
   return ang; 
}


clipper::RTop_orth
coot::util::matrix_convert(mmdb::mat44 mat) {
   
   clipper::Mat33<double> clipper_mat(mat[0][0], mat[0][1], mat[0][2],
                                      mat[1][0], mat[1][1], mat[1][2],
                                      mat[2][0], mat[2][1], mat[2][2]);
   clipper::Coord_orth cco(mat[0][3], mat[1][3], mat[2][3]);
   return clipper::RTop_orth(clipper_mat, cco);
}

// current view has a particular orientation of the mainchain on the screen -
// I want to move to the residue_next (which could be the previous residue)
// for shift-space - what rotation/translation do I need?
//
// @return pair.first false if we don't have a valid RTop.
//
std::pair<bool, clipper::RTop_orth>
coot::util::get_reorientation_matrix(mmdb::Residue *residue_current,
                                     mmdb::Residue *residue_next) {

   bool status = false;
   clipper::RTop_orth rtop;

   if (residue_current) {
      if (residue_next) {
         mmdb::Atom *atoms_this[3];
         mmdb::Atom *atoms_next[3];
         for (unsigned int ii=0; ii<3; ii++) {
            atoms_this[ii] = 0;
            atoms_next[ii] = 0;
         }
         int n_residue_atoms_this;
         int n_residue_atoms_next;
         mmdb::PAtom *residue_atoms_this;
         mmdb::PAtom *residue_atoms_next;
         residue_current->GetAtomTable(residue_atoms_this, n_residue_atoms_this);
         residue_next->GetAtomTable(   residue_atoms_next, n_residue_atoms_next);
         for (int iat=0; iat<n_residue_atoms_this; iat++) {
            mmdb::Atom *at = residue_atoms_this[iat];
            std::string atom_name = at->GetAtomName();
            if (atom_name == " N  ") atoms_this[0] = at;
            if (atom_name == " CA ") atoms_this[1] = at;
            if (atom_name == " C  ") atoms_this[2] = at;
         }
         if (atoms_this[0] && atoms_this[1] && atoms_this[2]) {
            for (int jat=0; jat<n_residue_atoms_next; jat++) {
               mmdb::Atom *at = residue_atoms_next[jat];
               std::string atom_name = at->GetAtomName();
               if (atom_name == " N  ") atoms_next[0] = at;
               if (atom_name == " CA ") atoms_next[1] = at;
               if (atom_name == " C  ") atoms_next[2] = at;
            }
            if (atoms_next[0] && atoms_next[1] && atoms_next[2]) {
               std::vector<clipper::Coord_orth> this_pos;
               std::vector<clipper::Coord_orth> next_pos;
               this_pos.push_back(co(atoms_this[0]));
               this_pos.push_back(co(atoms_this[1]));
               this_pos.push_back(co(atoms_this[2]));
               next_pos.push_back(co(atoms_next[0]));
               next_pos.push_back(co(atoms_next[1]));
               next_pos.push_back(co(atoms_next[2]));
               clipper::RTop_orth lrtop(this_pos, next_pos);
               rtop = lrtop;
               status = true;
            }
         }
      }
   }

   return std::pair<bool, clipper::RTop_orth>(status, rtop);

}


std::ostream&
coot::operator<<(std::ostream&  s, const coot::lsq_range_match_info_t &m) {

   s << "LSQ Match: (" << m.model_number_reference << ") " << m.reference_chain_id << " "
     << m.to_reference_start_resno << "-" << m.to_reference_end_resno
     << " to ("
     << m.model_number_matcher << ") " << m.matcher_chain_id << " "
     << m.from_matcher_start_resno << "-" << m.from_matcher_end_resno
     << " type: " << m.match_type_flag;
   return s;
}

//
float
coot::util::interquartile_range(const std::vector<float> &v_in) {

   float iqr = 0;
   std::vector<float> v = v_in;

   std::sort(v.begin(), v.end());
   unsigned int n = v.size();
   int q_1 = int(0.25 * n);
   int q_3 = int(0.75 * n);
   float v_1 = v[q_1];
   float v_3 = v[q_3];
   iqr = v_3 - v_1;
   return iqr;
}

coot::util::stats_data::stats_data(const std::vector<float> &v) {

   mean = 0;
   sd = 0;
   iqr = 0;
   double sum = 0;
   double sum_sq = 0;
   for (unsigned int i=0; i<v.size(); i++) {
      sum += v[i];
      sum_sq += v[i] * v[i];
   }
   if (v.size() > 0) {
      mean = sum/double(v.size());
      double var = sum_sq/double(v.size()) - mean * mean;
      if (var < 0) var = 0;
      sd = sqrt(var);
      iqr = interquartile_range(v);
   }
}

coot::util::stats_data::stats_data(const std::vector<double> &v) {

   mean = 0;
   sd = 0;
   iqr = 0;
   double sum = 0;
   double sum_sq = 0;
   for (unsigned int i=0; i<v.size(); i++) {
      sum += v[i];
      sum_sq += (v[i] * v[i]);
   }
   if (v.size() > 0) { 
      mean = sum/double(v.size());
      double var = sum_sq/double(v.size()) - mean * mean;
      if (var < 0) var = 0;
      sd = sqrt(var);
      std::vector<float> vf(v.size());
      for (unsigned int i=0; i<v.size(); i++) vf[i] = v[i];
      iqr = interquartile_range(vf);
   }
}

std::vector<std::pair<double, double> >
coot::util::qq_plot_t::qq_norm() {
   
   std::vector<std::pair<double, double> > v;

   std::sort(data.begin(), data.end());
   size_t stride = 1;
   std::vector<double> sorted_data(data.size());
   for (unsigned int i=0; i<data.size(); i++) { 
      sorted_data[i] = data[i];
   }
   stats_data sd = stats_data(data);

   // debugging
   std::vector<double> save_gs;
   std::vector<double> save_qs;
   

   // frac goes between 0 and 1.
   for (double frac=0.01; frac<1; frac+= 0.01) {

      double g = gsl_cdf_gaussian_Pinv(frac, sd.sd);
      double q = gsl_stats_quantile_from_sorted_data(sorted_data.data(), stride,
                                                     data.size(), frac);

      // mean correction (gs would otherwise have mean 0)
      double g_mc = g + sd.mean;
      if (0) 
         std::cout << "debug:: g " << g << " from frac " << frac
                   << " and sd " << sd.sd << std::endl;

      std::pair<double, double> p(g_mc, q);
      v.push_back(p);
      save_gs.push_back(g_mc);
      save_qs.push_back(q);
   }

   stats_data gs_data(save_gs);
   stats_data qs_data(save_qs);
   
   std::cout << "debug:: gs: mean " << gs_data.mean << " sd " <<  gs_data.sd  << std::endl;
   std::cout << "debug:: qs: mean " << qs_data.mean << " sd " <<  qs_data.sd  << std::endl;
   std::cout << "debug:: sd: mean " << sd.mean << " sd " <<  sd.sd  << std::endl;
   
   return v;
}


// -------------------------------------------------------------
//                       quaternions
// -------------------------------------------------------------

clipper::Mat33<double>
coot::util::quaternion::matrix() const {

   clipper::Mat33<double> mat;

   mat(0,0) = 1.0 - 2.0 * (q1 * q1 + q2 * q2);
   mat(0,1) = 2.0 * (q0 * q1 - q2 * q3);
   mat(0,2) = 2.0 * (q2 * q0 + q1 * q3);
   
   mat(1,0) = 2.0 * (q0 * q1 + q2 * q3);
   mat(1,1)= 1.0 - 2.0 * (q2 * q2 + q0 * q0);
   mat(1,2) = 2.0 * (q1 * q2 - q0 * q3);
   
   mat(2,0) = 2.0 * (q2 * q0 - q1 * q3);
   mat(2,1) = 2.0 * (q1 * q2 + q0 * q3);
   mat(2,2) = 1.0 - 2.0 * (q1 * q1 + q0 * q0);
   
   return mat;
}

coot::util::quaternion::quaternion(const clipper::Mat33<double> &m) {

   float pw = 1 + m(0,0) + m(1,1) + m(2,2);
   float px = 1 + m(0,0) - m(1,1) - m(2,2);
   float py = 1 - m(0,0) + m(1,1) - m(2,2); 
   float pz = 1 - m(0,0) - m(1,1) + m(2,2);

   float pr1 = sqrt( (pw>0) ? pw : 0) / 2.0;
   float pr2 = sqrt( (px>0) ? px : 0) / 2.0;
   float pr3 = sqrt( (py>0) ? py : 0) / 2.0;
   float pr4 = sqrt( (pz>0) ? pz : 0) / 2.0;

   q0 = convert_sign(pr2, m(2,1) - m(1,2));
   q1 = convert_sign(pr3, m(0,2) - m(2,0));
   q2 = convert_sign(pr4, m(1,0) - m(0,1));
   q3 = pr1;
   
}

// Return x with the sign of y.
float 
coot::util::quaternion::convert_sign(const float &x, const float &y) const {

   if ((x > 0) && (y > 0)) return  x;
   if ((x < 0) && (y > 0)) return -x; 
   if ((x > 0) && (y < 0)) return -x; 
   return  x; 
}

void
coot::util::quaternion::normalize() {

   double sum_sq = 0.0;
   sum_sq += q0*q0;
   sum_sq += q1*q1;
   sum_sq += q2*q2;
   sum_sq += q3*q3;
   if (sum_sq > 0.0) {
      double f = sqrt(1.0/sum_sq);
      q0 *= f;
      q1 *= f;
      q2 *= f;
      q3 *= f;
   }
} 


coot::util::quaternion
coot::util::quaternion::rotate(double angle, const clipper::Coord_orth &vec) const {

   coot::util::quaternion q(0,0,0,1);

   std::cout << "rotate() just a stub - fill me later!" << std::endl;

   return q;
}

coot::util::quaternion
coot::util::quaternion::inverse() const {

   coot::util::quaternion q(q0, q1, q2, -q3);
   return q;
}


clipper::RTop_orth
coot::util::quaternion::centroid_rtop(const std::vector<std::pair<clipper::RTop_orth,float> > &rtops) {

   if (rtops.size() == 0) { 
      return clipper::RTop_orth(clipper::Mat33<double>(1,0,0,0,1,0,0,0,1), clipper::Vec3<double>(0,0,0));
   } else {
      clipper::Coord_orth sum_trn(0,0,0);
      for (unsigned int i=0; i<rtops.size(); i++) { 
         quaternion q(rtops[i].first.rot());
         q0 += rtops[i].second * q.q0;
         q1 += rtops[i].second * q.q1;
         q2 += rtops[i].second * q.q2;
         q3 += rtops[i].second * q.q3;
         sum_trn += rtops[i].first.trn();
      }
      normalize();
      clipper::Mat33<double> m = matrix();
      double inv_n = 1.0/double(rtops.size());
      clipper::Coord_orth t(sum_trn.x() * inv_n, sum_trn.y() * inv_n, sum_trn.z() * inv_n);
      return clipper::RTop_orth(m, t);
   }
}

clipper::RTop_orth
coot::util::quaternion::centroid_rtop(const std::vector<std::pair<clipper::RTop_orth,float> > &rtops,
                                      bool robust_filter) {

   if (! robust_filter) { 
      return centroid_rtop(rtops);
   } else {
      if (rtops.size() < 2) {
         return centroid_rtop(rtops);
      } else { 
         clipper::Coord_orth sum_trn(0,0,0);
         for (unsigned int i=0; i<rtops.size(); i++) { 
            quaternion q(rtops[i].first.rot());
            q0 += rtops[i].second * q.q0;
            q1 += rtops[i].second * q.q1;
            q2 += rtops[i].second * q.q2;
            q3 += rtops[i].second * q.q3;
            sum_trn += rtops[i].first.trn();
         }
         normalize();

         double inv_n = 1.0/double(rtops.size());
         clipper::Coord_orth t(sum_trn.x() * inv_n, sum_trn.y() * inv_n, sum_trn.z() * inv_n);

         double sum_rotation_distance_sq = 0.0;
         double sum_translation_distance_sq = 0.0;
         std::vector<w_rtop_orth> deviance(rtops.size());
         for (unsigned int i=0; i<rtops.size(); i++) {
            // rotation
            quaternion q(rtops[i].first.rot());
            double d0 = q0 - rtops[i].second * q.q0;
            double d1 = q1 - rtops[i].second * q.q1;
            double d2 = q2 - rtops[i].second * q.q2;
            double d3 = q3 - rtops[i].second * q.q3;
            double d = d0*d0 + d1*d1 + d2*d2 + d3*d3;
            sum_rotation_distance_sq += d;
         
            // translation
            clipper::Coord_orth wpt(rtops[i].second * clipper::Coord_orth(rtops[i].first.trn()));
            double dt = (t-wpt).lengthsq();
            sum_translation_distance_sq += dt;
            if (0)
               std::cout << "for irtop " << i << " added rotation distance_sq " << d 
                         << " and translation distance "<< dt << std::endl;
            deviance[i].rtop   = rtops[i].first;
            deviance[i].weight = rtops[i].second;
            deviance[i].deviance = d * 1.888 + dt;
         }

         std::sort(deviance.begin(), deviance.end(), deviance_sorter);
         for (unsigned int i=0; i<deviance.size(); i++)
            if (0) 
               std::cout << "        deviance " << i << " " << deviance[i].weight << " "
                         << deviance[i].deviance << std::endl;
         std::vector<float> iqr_data(deviance.size());
         for (unsigned int i=0; i<deviance.size(); i++)
            iqr_data[i] = deviance[i].deviance;
         stats_data sd(iqr_data);
      
         clipper::Coord_orth sum_trn_filtered_dev(0,0,0);
         int n = 0;

         for (unsigned int i=0; i<deviance.size(); i++) {
            if (deviance[i].deviance < sd.mean + 0.5 * sd.iqr) {
               n++;
               quaternion q(rtops[i].first.rot());
               q0 += deviance[i].weight * q.q0;
               q1 += deviance[i].weight * q.q1;
               q2 += deviance[i].weight * q.q2;
               q3 += deviance[i].weight * q.q3;
               sum_trn_filtered_dev += deviance[i].weight * deviance[i].rtop.trn();
            }
         }

         //       std::cout << "rejecting deviances more than " << sd.mean + 0.5 * sd.iqr
         //                 << " leaves " << n << " from " << rtops.size() 
         //                 << std::endl;
      
         if (n > 0) {

            normalize();
            double inv_n_local = 1.0/double(n);
            clipper::Mat33<double> m = matrix();
            clipper::Coord_orth td(sum_trn_filtered_dev.x() * inv_n_local,
                                   sum_trn_filtered_dev.y() * inv_n_local,
                                   sum_trn_filtered_dev.z() * inv_n_local);
            return clipper::RTop_orth(m, td);
         } else { 
       
            // unfiltered
            clipper::Mat33<double> m = matrix();
            return clipper::RTop_orth(m, t);
         }
      }
   } 
}

// static
bool
coot::util::quaternion::deviance_sorter(const w_rtop_orth &a,
                                        const w_rtop_orth &b) {
   return a.deviance < a.deviance;
}




// static 
void
coot::util::quaternion::test_quaternion() {

   // currently quaternions are tested in testcootutils
} 

std::ostream&  coot::util::operator<<(std::ostream& s, const coot::util::quaternion &q) {

   s << "(" << q.q0 << ", " << q.q1 << ", " << q.q2 << ", " << q.q3 << ")";
   return s;
}

std::ofstream& coot::util::operator<<(std::ofstream &s, const coot::util::quaternion &q) {

   // s << "(" << q.q0 << ", " << q.q1 << ", " << q.q2 << ", " << q.q3 << ")";
   return s;
} 


// -------------------------------------------------------------

bool
coot::is_hydrogen_atom(mmdb::Atom *at_p) {

   std::string ele = at_p->element;
   if ((ele == "H") || (ele == " H"))
      return true;
   else
      return ((ele == "D") || (ele == " D"));
}


// Urgh.  Should use a template...
bool
coot::is_member_p(const std::vector<mmdb::Residue *> &v, mmdb::Residue *a) {
   
   bool ir = 0;
   unsigned int vsize = v.size();

   for (unsigned int i=0; i<vsize; i++) { 
      if (v[i] == a) { 
         ir = 1;
         break;
      } 
   }
   return ir;
} 

bool
coot::residues_in_order_p(mmdb::Chain *chain_p) {

   bool ordered_flag = 1;

   if (chain_p) {

      int n_residues = chain_p->GetNumberOfResidues();
      int current_resno = -9999999;
      for (int ires=0; ires<n_residues; ires++) {
         mmdb::Residue *res_p = chain_p->GetResidue(ires);
         int seqnum = res_p->GetSeqNum();
         if (seqnum < current_resno) {
            ordered_flag = 0;
            break;
         } else {
            current_resno = seqnum;
         }
      }
   }
   return ordered_flag;
}

// Throw an exception if there is no consistent seg id for the
// atoms in the given residue.
std::string
coot::residue_atoms_segid(mmdb::Residue *residue_p) {

   int n_residue_atoms;
   mmdb::PPAtom residue_atoms;

   std::vector<std::string> seg_ids;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int iat=0; iat<n_residue_atoms; iat++) {
      mmdb::Atom *at = residue_atoms[iat];
      std::string seg_id = at->segID;
      if (seg_ids.size() == 0) {
         seg_ids.push_back(seg_id);
      } else {
         if (!coot::is_member_p(seg_ids, seg_id)) {
            std::string mess = "No consistent segids for residue ";
            mess += coot::util::int_to_string(residue_p->GetSeqNum());
            throw std::runtime_error(mess);
         }
      }
   }

   if (seg_ids.size() == 0) {
      std::string mess = "No segids for residue ";
      mess += coot::util::int_to_string(residue_p->GetSeqNum());
      throw std::runtime_error(mess);
   }
      
   return seg_ids[0]; 
}


// Use the above function the get the segid and insert it into all
// the atoms of receiver.
bool
coot::copy_segid(mmdb::Residue *provider, mmdb::Residue *receiver) {

   try {
      std::string s = coot::residue_atoms_segid(provider);
      int n_residue_atoms;
      mmdb::PPAtom residue_atoms;
      
      receiver->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) {
         mmdb::Atom *at = residue_atoms[iat];
         // BL says:: to set the SegID we just strcpy it, we shouldnt fiddle
         // with GetIndex().
         strcpy(at->segID, s.c_str());
         // we want to set just the segid, but there is no function to
         // do that (there is for others, e.g. element, atom-name etc.).
         //         at->SetAtomName(at->GetIndex(),
         //                 at->serNum,
         //                 at->GetAtomName(),
         //                 at->altLoc,
         //                 s.c_str(),
         //                 at->GetElementName());

      }
   }

   catch (const std::runtime_error &mess) {
      // maybe do this.. not sure.
      std::cout << "   INFO:: " << mess.what() << std::endl;
   }

   return 1;

}

// Throw an exception if there is no consistent seg id for the
// atoms in the given chain.
std::string
coot::chain_atoms_segid(mmdb::Chain *chain_p) {

   int n_residue_atoms;
   mmdb::PPAtom residue_atoms;

   std::vector<std::string> seg_ids;

   int n_residues = chain_p->GetNumberOfResidues();

   for (int ires=0; ires<n_residues; ires++) {
      mmdb::Residue *residue_p = chain_p->GetResidue(ires);
      residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) {
         mmdb::Atom *at = residue_atoms[iat];
         std::string seg_id = at->segID;
         if (seg_ids.size() == 0) {
            seg_ids.push_back(seg_id);
         } else {
            if (!coot::is_member_p(seg_ids, seg_id)) {
               std::string mess = "No consistent segids for chain ";
               mess += chain_p->GetChainID();
               throw std::runtime_error(mess);
            }
         }
      }
   }
   

   if (seg_ids.size() == 0) {
      std::string mess = "No segids for chain ";
      mess += chain_p->GetChainID();
      throw std::runtime_error(mess);
   }
   return seg_ids[0]; 
} 



std::vector<std::string>
coot::util::residue_types_in_chain(mmdb::Chain *chain_p) {

   std::vector<std::string> v;
   
   mmdb::PResidue residue_p;
   int nres = chain_p->GetNumberOfResidues();
   for (int ires=0; ires<nres; ires++) { 
      residue_p = chain_p->GetResidue(ires);
      if (residue_p) {
         std::string n(residue_p->name);
         if (! is_member_p(v, n))
            v.push_back(n);
      }
   }
   return v;
}

std::vector<std::string>
coot::util::residue_types_in_residue_vec(const std::vector<mmdb::Residue *> &residues) {

   std::vector<std::string> v;
   for (unsigned int ires=0; ires<residues.size(); ires++) { 
      if (residues[ires]) {
         std::string n(residues[ires]->name);
         if (! is_member_p(v, n))
            v.push_back(n);
      }
   }
   return v;
} 


// Return -1 on badness 
int
coot::util::max_number_of_residues_in_chain(mmdb::Manager *mol) {

   int max_number_of_residues_in_chain = -1;
   if (mol) { 

      int n_models = mol->GetNumberOfModels();
      
      for (int imod=1; imod<=n_models; imod++) { 
      
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
   
         mmdb::Chain *chain;
         // run over chains of the existing mol
         int nchains = model_p->GetNumberOfChains();
         if (nchains <= 0) { 
            std::cout << "bad nchains in max_number_of_residues_in_chain "
                      << nchains << std::endl;
         } else { 
            for (int ichain=0; ichain<nchains; ichain++) {
               chain = model_p->GetChain(ichain);
               if (chain == NULL) {  
                  // This should not be necessary. It seem to be a
                  // result of mmdb corruption elsewhere - possibly
                  // DeleteChain in update_molecule_to().
                  std::cout << "NULL chain in max_number_of_residues_in_chain: "
                            << std::endl;
               } else { 
                  int nres = chain->GetNumberOfResidues();
                  if (nres > max_number_of_residues_in_chain) {
                     max_number_of_residues_in_chain = nres;
                  }
               }
            }
         }
      }
   }
   return max_number_of_residues_in_chain;
}

// return 9999,-9999 on failure
std::pair<int, int>
coot::util::min_and_max_residues(mmdb::Chain *chain_p) {

   // min and max
   std::pair<int, int> p(9999,-9999);
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      for (int ires=0; ires<nres; ires++) {
         mmdb::Residue *residue_p = chain_p->GetResidue(ires);
         int rn = residue_p->GetSeqNum();
         if (rn < p.first)  p.first  = rn;
         if (rn > p.second) p.second = rn;
      }
   }
   return p;
}

// Return -1 on badness.
// 
// So that we can calculate the lenght of the graph x axis - there may
// be gaps, which is why max_number_of_residues_in_chain would fail.
// 
int
coot::util::max_min_max_residue_range(mmdb::Manager *mol) {

   int max_min_max = -1;
   if (mol) { 

      int n_models = mol->GetNumberOfModels();
      
      for (int imod=1; imod<=n_models; imod++) { 
      
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
   
         // run over chains of the existing mol
         int nchains = model_p->GetNumberOfChains();
         if (nchains <= 0) { 
            std::cout << "bad nchains in max_min_max_residue_range "
                      << nchains << std::endl;
         } else { 
            for (int ichain=0; ichain<nchains; ichain++) {
               mmdb::Chain *chain = model_p->GetChain(ichain);
               if (chain == NULL) {  
                  // This should not be necessary. It seem to be a
                  // result of mmdb corruption elsewhere - possibly
                  // DeleteChain in update_molecule_to().
                  std::cout << "NULL chain in max_min_max_residue_range(): "
                            << std::endl;
               } else { 
                  int nres = chain->GetNumberOfResidues();
                  if (nres > 0) { 
                     int min_resno = 99999;
                     int max_resno = -99999;
                     for (int i=0; i<nres; i++) {
                        int this_resno = chain->GetResidue(i)->GetSeqNum();
                        if (this_resno > max_resno)
                           max_resno = this_resno;
                        if (this_resno < min_resno)
                           min_resno = this_resno;
                     }
                     int range = max_resno - min_resno + 1; // residues 1, 2 -> 2
                     if (range > max_min_max)
                        max_min_max = range;
                  }
               }
            }
         }
      }
   }
   return max_min_max;
}

// this can return an empty list if the residues for resno_start or resnoend  are not found
std::vector<mmdb::Residue *>
coot::util::get_residues_in_range(mmdb::Manager *mol, const std::string &chain_id, int resno_start, int resno_end) {

   std::vector<mmdb::Residue *> v;
   if (resno_end < resno_start) return v;
   residue_spec_t spec_1(chain_id, resno_start);
   residue_spec_t spec_2(chain_id, resno_end);
   mmdb::Residue *r1 = get_residue(spec_1, mol);
   mmdb::Residue *r2 = get_residue(spec_2, mol);

   if (r1) {
      if (r2) {
         v.push_back(r1);
         if (r1 != r2) {
            bool get_next = true;
            mmdb::Residue *r = r1;
            while (get_next) {
               r = next_residue(r);
               if (!r)
                  get_next = false;
               else
                  v.push_back(r);
               if (r == r2)
                  get_next = false;
            }
         }
      }
   }
   return v;
}



// Return a vector of residue that are in this fragment.
// Fragments are marked by consecutively numbered residues.  A
// gap in the sequence numbers marks the end/beginning of a
// fragment.
std::vector<mmdb::PResidue>
coot::util::get_residues_in_fragment(mmdb::Chain *chain_p,
                                     coot::residue_spec_t clicked_residue) {

   std::vector<mmdb::PResidue> r;
   int nSelResidues;
   mmdb::PResidue *SelResidues;

   chain_p->GetResidueTable(SelResidues, nSelResidues);
   for (int i=0; i<nSelResidues; i++)
      r.push_back(SelResidues[i]);

   return r; 
}

std::pair<bool, clipper::Coord_orth>
coot::util::get_residue_centre(mmdb::Residue *residue_p) {

   bool status = 0;
   clipper::Coord_orth centre(0,0,0);

   mmdb::PPAtom residue_atoms = 0;
   int n_residue_atoms;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   if (n_residue_atoms>0) {
      status = 1;
      for (int i=0; i<n_residue_atoms; i++) {
         clipper::Coord_orth pt(residue_atoms[i]->x,
                                residue_atoms[i]->y,
                                residue_atoms[i]->z);
         centre += pt;
      }
      double scale = 1.0/double(n_residue_atoms);
      centre = scale * centre;
   }
   return std::pair<bool, clipper::Coord_orth> (status, centre);
 
}

std::pair<bool, clipper::Coord_orth>
coot::util::get_CA_position_in_residue(mmdb::Residue *residue_p) {

   bool status = 0;
   clipper::Coord_orth pos(0,0,0);
   mmdb::PPAtom residue_atoms = 0;
   int n_residue_atoms;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int i=0; i<n_residue_atoms; i++) {
      std::string atom_name(residue_atoms[i]->GetAtomName());
      if (atom_name == " CA ") { // PDBv3 FIXME
         clipper::Coord_orth pt(residue_atoms[i]->x,
                                residue_atoms[i]->y,
                                residue_atoms[i]->z);
         pos = pt;
         status = true;
         break;
      }
   }
   return std::pair<bool, clipper::Coord_orth> (status, pos);
}

std::pair<bool, clipper::Coord_orth>
coot::util::get_CB_position_in_residue(mmdb::Residue *residue_p) {

   bool status = 0;
   clipper::Coord_orth pos(0,0,0);
   mmdb::PPAtom residue_atoms = 0;
   int n_residue_atoms;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int i=0; i<n_residue_atoms; i++) {
      std::string atom_name(residue_atoms[i]->GetAtomName());
      if (atom_name == " CB ") { // PDBv3 FIXME
         clipper::Coord_orth pt(residue_atoms[i]->x,
                                residue_atoms[i]->y,
                                residue_atoms[i]->z);
         pos = pt;
         status = true;
         break;
      }
   }
   return std::pair<bool, clipper::Coord_orth> (status, pos);
}





// Return -1 on badness (actually, number of chains in the last model)
int
coot::util::number_of_chains(mmdb::Manager *mol) {

   int nchains = -1;

   if (mol) { 

      int n_models = mol->GetNumberOfModels();
      
      for (int imod=1; imod<=n_models; imod++) { 
      
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
   
         // run over chains of the existing mol
         nchains = model_p->GetNumberOfChains();
         if (nchains <= 0) { 
            std::cout << "bad nchains in number_of_chains "
                      << nchains << std::endl;
         }
      }
   }
   return nchains;
}

// Return -1 on badness:
int
coot::get_selection_handle(mmdb::Manager *mol, const coot::atom_spec_t &at) {

   int SelHnd = -1;
   if (mol) { 
      SelHnd = mol->NewSelection();
      const char *chain   =  at.chain_id.c_str();
      const char *inscode =  at.ins_code.c_str();
      const char *atname  =  at.atom_name.c_str(); // atom name
      const char *altconf =  at.alt_conf.c_str();
      mol->SelectAtoms (SelHnd, 0, chain,
                        at.res_no, // starting resno, an int
                        inscode, // any insertion code
                        at.res_no, // ending resno
                        inscode, // ending insertion code
                        "*", // any residue name
                        atname,
                        "*", // elements
                        altconf  // alt loc.
                        );
   }
   return SelHnd;
}

// caller deletes the selection!
int
coot::specs_to_atom_selection(const std::vector<coot::residue_spec_t> &specs,
                              mmdb::Manager *mol,
                              int atom_mask_mode) {

   int SelHnd = -1;
   if (mol) {
      SelHnd = mol->NewSelection();
      for (unsigned int ilocal=0; ilocal<specs.size(); ilocal++) {

         std::string res_name_selection  = "*";
         std::string atom_name_selection = "*";

         if (atom_mask_mode != 0) { // main chain for standard amino acids
            mmdb::Residue *res = util::get_residue(specs[ilocal], mol);
            if (res) {
               std::string residue_name(res->GetResName());
               if (util::is_standard_residue_name(residue_name)) { 

                  // PDBv3 FIXME
                  // 
                  if (atom_mask_mode == 1)
                     atom_name_selection = " N  , H  , HA , CA , C  , O  ";
                  if (atom_mask_mode == 2)
                     atom_name_selection = "!( N  , H  , HA , CA , C  , O  )";
                  if (atom_mask_mode == 3)
                     atom_name_selection = "!( N  , H  , HA , CA , C  , O  , CB )";
               } else {
                  if (atom_mask_mode == 4)
                     atom_name_selection = "%%%%%%"; // nothing (perhaps use "")
                  if (atom_mask_mode == 5)
                     atom_name_selection = "%%%%%%"; // nothing
               }
            }
         }

         mol->SelectAtoms(SelHnd, 1,
                          specs[ilocal].chain_id.c_str(),
                          specs[ilocal].res_no,
                          specs[ilocal].ins_code.c_str(),
                          specs[ilocal].res_no,
                          specs[ilocal].ins_code.c_str(),
                          res_name_selection.c_str(),
                          atom_name_selection.c_str(), 
                          "*", // elements
                          "*", // alt loc.
                          mmdb::SKEY_OR
                          );
      }
   }
   return SelHnd;
}


// deleted by calling process
std::pair<mmdb::Manager *, std::vector<coot::residue_spec_t> >
coot::util::get_fragment_from_atom_spec(const coot::atom_spec_t &atom_spec,
                                        mmdb::Manager *mol_in) {

   mmdb::Manager *mol = 0;
   std::vector<coot::residue_spec_t> v;
   
   // Plan:
   //
   // We only want one model, so take the first.
   // 
   // First we find the residue in mol_in.
   //
   // Then find the top residue that is attached by direct attachment
   // (continuously increasing residue number).
   //
   // Then find the bottom residue that is attached by direct attachment
   // (continuously decreasing residue number).
   //
   // Then use and return create_mmdbmanager_from_res_selection()


   mmdb::Residue *residue_bot = 0;
   mmdb::Residue *residue_top = 0;
   mmdb::Atom *search_atom = 0;

   int resno_top = -999;
   int resno_bot = -999;

   int imod = 1;

   mmdb::Model *model_p = mol_in->GetModel(imod);
   if (! model_p) return std::make_pair(nullptr, v);
   // run over chains of the existing mol
   int nchains = model_p->GetNumberOfChains();
   for (int ichain=0; ichain<nchains; ichain++) {
      mmdb::Chain *chain_p = model_p->GetChain(ichain);
      std::string mol_chain_id = chain_p->GetChainID();
      if (mol_chain_id == atom_spec.chain_id) {
         int nres = chain_p->GetNumberOfResidues();
         mmdb::PResidue residue_p;
         mmdb::Atom *at;
         for (int ires=0; ires<nres; ires++) { 
            residue_p = chain_p->GetResidue(ires);
            if (residue_p->GetSeqNum() == atom_spec.res_no) {
               int n_atoms = residue_p->GetNumberOfAtoms();
            
               for (int iat=0; iat<n_atoms; iat++) {
                  at = residue_p->GetAtom(iat);
                  std::string mol_atom_name = at->name;
                  if (mol_atom_name == atom_spec.atom_name) {
                     std::string alt_conf = at->altLoc;
                     if (alt_conf == atom_spec.alt_conf) {
                        search_atom = at;
                     }
                  }
                  if (search_atom)
                     break;
               }
            }
            if (search_atom)
               break;
         }
      }
      if (search_atom)
         break;
   }

   if (search_atom) {
      bool found_search = false;
      // now try to set res_bot and res_top and their resnos.
      mmdb::Chain *chain_p = search_atom->GetChain();
      int nres = chain_p->GetNumberOfResidues();
      mmdb::PResidue residue_p;
      for (int ires=0; ires<nres; ires++) { 
         residue_p = chain_p->GetResidue(ires);
         if (residue_p == search_atom->GetResidue()) {

            residue_top = residue_p;
            residue_bot = residue_p;
            int resno_this = residue_p->GetSeqNum();
            resno_bot = resno_this;
            resno_top = resno_this;

            // search forwards on this chain
            for (int ires_search=ires+1; ires_search<nres; ires_search++) {
               int ioff = ires_search - ires; 
               mmdb::Residue *residue_search_p = chain_p->GetResidue(ires_search);
               if (residue_search_p->GetSeqNum() == resno_this + ioff) {
                  residue_top = residue_search_p;
                  resno_top = residue_search_p->GetSeqNum();
               } else {
                  break;
               }
            }

            // search backwards on this chain
            for (int ires_search=ires-1; ires_search>=0; ires_search--) {
               int ioff = ires_search - ires; 
               mmdb::Residue *residue_search_p = chain_p->GetResidue(ires_search);
               if (residue_search_p->GetSeqNum() == (resno_this + ioff)) {
                  residue_bot = residue_search_p;
                  resno_bot = residue_search_p->GetSeqNum();
               } else {
                  break;
               }
               
            }
            
            found_search = true;
         }
         
         if (found_search)
            break;
      }
   }

   if (residue_bot && residue_top) {

      mmdb::PResidue *SelResidues = 0; 
      int nSelResidues;
      int selHnd = mol_in->NewSelection();

      mol_in->Select(selHnd, mmdb::STYPE_RESIDUE, 1,
                     atom_spec.chain_id.c_str(),
                     resno_bot, "",
                     resno_top, "",
                     "*",  // residue name
                     "*",  // Residue must contain this atom name?
                     "*",  // Residue must contain this Element?
                     "*",  // altLocs
                     mmdb::SKEY_NEW // selection key
                     );
      mol_in->GetSelIndex(selHnd, SelResidues, nSelResidues);

      std::pair<mmdb::Manager *, int> mol_info = 
         create_mmdbmanager_from_res_selection(mol_in, 
                                               SelResidues, 
                                               nSelResidues, 0, 0, "", atom_spec.chain_id, 0);
      if (mol_info.second) { 
         mol = mol_info.first;
         for (int ires=0; ires<nSelResidues; ires++) {
            v.push_back(coot::residue_spec_t(SelResidues[ires]->GetChainID(),
                                             SelResidues[ires]->GetSeqNum(),
                                             SelResidues[ires]->GetInsCode()));
         }
      }

      mol_in->DeleteSelection(selHnd);                     

   } else {
      if (! residue_top) 
         std::cout << "ERROR:: missing top residue in fragment" << std::endl;
      if (! residue_bot) 
         std::cout << "ERROR:: missing bot residue in fragment" << std::endl;
   }

   return std::pair<mmdb::Manager *, std::vector<coot::residue_spec_t> > (mol, v);
} 


std::vector<mmdb::Atom * >
coot::torsion::matching_atoms(mmdb::Residue *residue) {

   std::vector<mmdb::Atom *> v;
   
   mmdb::Atom *catom_1 = 0;  
   mmdb::Atom *catom_2 = 0; 
   mmdb::Atom *catom_3 = 0; 
   mmdb::Atom *catom_4 = 0;

   mmdb::PPAtom residue_atoms;
   int nResidueAtoms;
   residue->GetAtomTable(residue_atoms, nResidueAtoms);
   for (int iat=0; iat<nResidueAtoms; iat++) {
      if (atom_1.second.matches_spec(residue_atoms[iat]))
         catom_1 = residue_atoms[iat];
      if (atom_2.second.matches_spec(residue_atoms[iat]))
         catom_2 = residue_atoms[iat];
      if (atom_3.second.matches_spec(residue_atoms[iat]))
         catom_3 = residue_atoms[iat];
      if (atom_4.second.matches_spec(residue_atoms[iat]))
         catom_4 = residue_atoms[iat];
   }

   if (! (catom_1 && catom_2 && catom_3 && catom_4)) {
      if (false) { // too noisy
         if (!catom_1)
            std::cout << " atom_1 is null for " << atom_1.second.atom_name << std::endl;
         if (!catom_2)
            std::cout << " atom_2 is null for " << atom_2.second.atom_name << std::endl;
         if (!catom_3)
            std::cout << " atom_3 is null for " << atom_3.second.atom_name << std::endl;
         if (!catom_4)
            std::cout << " atom_4 is null for " << atom_4.second.atom_name << std::endl;
      }
   } else { 
      v.push_back(catom_1);
      v.push_back(catom_2);
      v.push_back(catom_3);
      v.push_back(catom_4);
   }

   return v;
}

// Are these residue one after the other (e.g. ("B" 17 "") and ("B" 18 ""))?
// Have a go at testing for insertion codes too (although
// testing 17 and 18 from a 17-17A-18 will give the incorrect
// answer).  Insertion codes not a problem in reality though
// because this is used to test carbohydrates.
//
// The first is tandem? The second is order-switch-needed? (in
// the case that second is in front of first)
// 
// std::pair<bool, bool>
// coot::tandem_residues_p(const residue_spec_t &first,
//                         const residue_spec_t &second) {



std::vector<std::string>
coot::util::chains_in_molecule(mmdb::Manager *mol) { 

   std::vector<std::string> v;

   if (mol) { 

      int n_models = mol->GetNumberOfModels();
      
      for (int imod=1; imod<=n_models; imod++) { 
      
         mmdb::Model *model_p = mol->GetModel(imod);
         if (model_p) {
            mmdb::Chain *chain;
            // run over chains of the existing mol
            int nchains = model_p->GetNumberOfChains();
            if (nchains <= 0) {
               std::cout << "bad nchains in trim molecule " << nchains
                         << std::endl;
            } else {
               for (int ichain=0; ichain<nchains; ichain++) {
                  chain = model_p->GetChain(ichain);
                  if (chain == NULL) {
                     // This should not be necessary. It seem to be a
                     // result of mmdb corruption elsewhere - possibly
                     // DeleteChain in update_molecule_to().
                     std::cout << "NULL chain in residues_in_molecule: "
                               << std::endl;
                  } else {
                     v.push_back(chain->GetChainID());
                  }
               }
            }
         }
      }
   }
   return v;
}

std::pair<bool, int>
coot::util::min_resno_in_chain(mmdb::Chain *chain_p) {

   bool found_residues = 0;
   int min_resno = 99999999;
   
   if (chain_p == NULL) {  
      // This should not be necessary. It seem to be a
      // result of mmdb corruption elsewhere - possibly
      // DeleteChain in update_molecule_to().
      std::cout << "NULL chain in min_resno_in_chain: "
                << std::endl;
   } else { 
      int nres = chain_p->GetNumberOfResidues();
      mmdb::Residue *residue_p;
      int resno;
      for (int ires=0; ires<nres; ires++) {
         residue_p = chain_p->GetResidue(ires);
         resno = residue_p->seqNum;
         if (resno < min_resno) {
            min_resno = resno;
            found_residues = 1;
         }
      }
   }
   return std::pair<bool, int>(found_residues, min_resno);
}


std::pair<bool, int>
coot::util::max_resno_in_chain(mmdb::Chain *chain_p) {

   bool found_residues = 0;
   int max_resno = -31999;
   
   if (chain_p == NULL) {  
      // This should not be necessary. It seem to be a
      // result of mmdb corruption elsewhere - possibly
      // DeleteChain in update_molecule_to().
      std::cout << "NULL chain in max_resno_in_chain: "
                << std::endl;
   } else { 
      int nres = chain_p->GetNumberOfResidues();
      mmdb::Residue *residue_p;
      int resno;
      if (nres > 0) { 
         for (int ires=0; ires<nres; ires++) {
            residue_p = chain_p->GetResidue(ires);
            resno = residue_p->seqNum;
            if (resno > max_resno) {
               max_resno = resno;
               found_residues = 1;
            }
         }
      } else {
         // there was a chain, but no residues in it. which is what
         // happens in pointer_atom_molecule() when we create a
         // Pointer Atom molecule.
         //
         // In that case, we want the added atom to have residue
         // number 1.
         max_resno = 0;
      } 
   }
//    std::cout << "DEBUG:: max_resno_in_chain returning " << found_residues
//              << " " << max_resno << std::endl;
   return std::pair<bool, int>(found_residues, max_resno);
}

std::pair<bool, std::pair<int, int> >
coot::util::min_max_residues_in_polymer_chain(mmdb::Chain *chain_p) {

   bool found_residues = false;
   int max_resno = -31999;
   int min_resno =  31999;

   if (chain_p == NULL) {
      // This should not be necessary. It seem to be a
      // result of mmdb corruption elsewhere - possibly
      // DeleteChain in update_molecule_to().
      std::cout << "NULL chain in min_max_residues_in_polymer_chain: "
                << std::endl;
   } else {
      int nres = chain_p->GetNumberOfResidues();
      if (nres > 0) {
         for (int ires=0; ires<nres; ires++) {
            mmdb::Residue *residue_p = chain_p->GetResidue(ires);
            int resno = residue_p->seqNum;
            if (resno > max_resno) {
               if (! residue_has_hetatms(residue_p)) {
                  max_resno = resno;
                  found_residues = true;
               }
            }
            if (resno < min_resno) {
               if (! residue_has_hetatms(residue_p)) {
                  min_resno = resno;
                  found_residues = true;
               }
            }
         }
      }
   }
   return std::pair<bool, std::pair<int, int> > (found_residues, std::pair<int, int> (min_resno, max_resno));
}


std::pair<bool, int>
coot::util::max_resno_in_molecule(mmdb::Manager *mol) {

   bool found_residues = 0;
   int current_high = -31999;
   
   int n_models = mol->GetNumberOfModels();
   for (int imod=1; imod<=n_models; imod++) { 
      
      mmdb::Model *model_p = mol->GetModel(imod);
      if (! model_p) continue;
      mmdb::Chain *chain_p;
      // run over chains of the existing mol
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         chain_p = model_p->GetChain(ichain);
         std::pair<bool, int> p = coot::util::max_resno_in_chain(chain_p);
         if (p.first) { 
            if (p.second > current_high) { 
               current_high = p.second;
               found_residues = 1;
            }
         }
      }
   }
   return std::pair<bool, int> (found_residues, current_high);
} 


int
coot::util::number_of_residues_in_molecule(mmdb::Manager *mol) {

   int number_of_residues = 0;
   if (mol) { 

      int n_models = mol->GetNumberOfModels();
      
      for (int imod=1; imod<=n_models; imod++) { 
      
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
   
         mmdb::Chain *chain_p;
         mmdb::Residue *residue_p;
         // run over chains of the existing mol
         int nchains = model_p->GetNumberOfChains();
         if (nchains <= 0) { 
            std::cout << "bad nchains in number_of_residues_in_molecule() " << nchains
                      << std::endl;
         } else { 
            for (int ichain=0; ichain<nchains; ichain++) {
               chain_p = model_p->GetChain(ichain);
               if (chain_p == NULL) {  
                  // This should not be necessary. It seem to be a
                  // result of mmdb corruption elsewhere - possibly
                  // DeleteChain in update_molecule_to().
                  std::cout << "NULL chain in number residues_in_molecule: "
                            << std::endl;
               } else { 
                  int nres = chain_p->GetNumberOfResidues();
                  for (int ires=0; ires<nres; ires++) { 
                     residue_p = chain_p->GetResidue(ires);
                     if (residue_p != NULL) {
                        number_of_residues++;
                     }
                  }
               }
            }
         }
      }
   }
   return number_of_residues;
}

std::vector<mmdb::Residue *>
coot::util::residues_in_molecule_of_type(mmdb::Manager *mol, const std::string &residue_type) {

   std::vector<mmdb::Residue *> v;
   for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol->GetModel(imod);
      if (model_p) {
         int n_chains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<n_chains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int n_res = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<n_res; ires++) {
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               if (residue_p) {
                  std::string res_name = residue_p->GetResName();
                  if (res_name == residue_type) {
                     v.push_back(residue_p);
                  }
               }
            }
         }
      }
   }
   return v;
}


std::vector<mmdb::Chain *>
coot::util::chains_in_atom_selection(mmdb::Manager *mol, int model_number, const std::string &atom_selection) {

   std::vector<mmdb::Chain *> v;

   int selHnd = mol->NewSelection(); // d
   mmdb::Chain **SelChains;
   int nSelChains = 0;
   mol->Select(selHnd, mmdb::STYPE_CHAIN, atom_selection.c_str(), mmdb::SKEY_NEW);
   mol->GetSelIndex(selHnd, SelChains, nSelChains);

   for (int i=0; i<nSelChains; i++)
      v.push_back(SelChains[i]);
   mol->DeleteSelection(selHnd);
   return v;
}


//
// On failure, return "";
std::string
coot::util::single_letter_to_3_letter_code(char code) {

   if (code == 'G') return std::string("GLY");
   if (code == 'A') return std::string("ALA");
   if (code == 'V') return std::string("VAL");
   if (code == 'S') return std::string("SER");
   if (code == 'N') return std::string("ASN");
   if (code == 'P') return std::string("PRO");
   if (code == 'D') return std::string("ASP");
   if (code == 'C') return std::string("CYS");
   if (code == 'Q') return std::string("GLN");
   if (code == 'E') return std::string("GLU");
   if (code == 'H') return std::string("HIS");
   if (code == 'I') return std::string("ILE");
   if (code == 'L') return std::string("LEU");
   if (code == 'K') return std::string("LYS");
   if (code == 'M') return std::string("MET");
   if (code == 'F') return std::string("PHE");
   if (code == 'T') return std::string("THR");
   if (code == 'W') return std::string("TRP");
   if (code == 'Y') return std::string("TYR");
   if (code == 'R') return std::string("ARG");

   return std::string("");
}


std::string
coot::util::single_letter_to_3_letter_code(const std::string &code) {

   if (code == "G") return std::string("GLY");
   if (code == "A") return std::string("ALA");
   if (code == "V") return std::string("VAL");
   if (code == "S") return std::string("SER");
   if (code == "N") return std::string("ASN");
   if (code == "P") return std::string("PRO");
   if (code == "D") return std::string("ASP");
   if (code == "C") return std::string("CYS");
   if (code == "Q") return std::string("GLN");
   if (code == "E") return std::string("GLU");
   if (code == "H") return std::string("HIS");
   if (code == "I") return std::string("ILE");
   if (code == "L") return std::string("LEU");
   if (code == "K") return std::string("LYS");
   if (code == "M") return std::string("MET");
   if (code == "F") return std::string("PHE");
   if (code == "T") return std::string("THR");
   if (code == "W") return std::string("TRP");
   if (code == "Y") return std::string("TYR");
   if (code == "R") return std::string("ARG");

   return std::string("");
}



// Match on graph
// 
// Return the orientation matrix moving res_moving to res_reference
// and a flag letting us know that the match worked OK.
// 
coot::graph_match_info_t
coot::graph_match(mmdb::Residue *res_moving,
                  mmdb::Residue *res_reference,
                  bool apply_rtop_flag,
                  bool match_hydrogens_also) {

  clipper::Mat33<double> m_dum(1,0,0,0,1,0,0,0,1);
  clipper::Coord_orth pt_dum(0,0,0);
  clipper::RTop_orth rtop(m_dum, pt_dum);
   bool success = 0;
   std::vector<std::pair<std::pair<std::string, std::string>, std::pair<std::string, std::string> > > best_matching_atoms;

   mmdb::math::Graph graph1;
   mmdb::math::Graph graph2;

   // These are deleted at the end
   // 
   mmdb::Residue *cleaned_res_moving    = NULL;
   mmdb::Residue *cleaned_res_reference = NULL;

   if (! match_hydrogens_also) { 
      cleaned_res_moving    = coot::util::copy_and_delete_hydrogens(res_moving);
      cleaned_res_reference = coot::util::copy_and_delete_hydrogens(res_reference);
   } else {
      cleaned_res_moving    = coot::util::deep_copy_this_residue(res_moving);
      cleaned_res_reference = coot::util::deep_copy_this_residue(res_reference);
   } 

   // debug 
   if (0) {
      int n_residue_atoms_1;
      mmdb::PPAtom residue_atoms_1;
      cleaned_res_moving->GetAtomTable(residue_atoms_1, n_residue_atoms_1);
      int n_residue_atoms_2;
      mmdb::PPAtom residue_atoms_2;
      cleaned_res_moving->GetAtomTable(residue_atoms_2, n_residue_atoms_2);
      // are these the same atoms?
      for (int i=0; i<4; i++) {
         std::cout << "moving and ref atoms: " << residue_atoms_1[i] <<  " " << residue_atoms_2[i]
                   << std::endl;
      }
   }

   graph1.MakeGraph(cleaned_res_moving);
   graph2.MakeGraph(cleaned_res_reference);

   if (match_hydrogens_also) {
      // 20101206 this stops infinite looping in mmdb_graph.cpp:1898
      // Backtrack1() when we have hydrogens in the match.  It is not
      // clear to my why we don't want to do this all the time.
      // Anyway...
      // 20161008 Now make it true - we are using SRS now.
      // This does need a test
      // 
      // graph1.MakeSymmetryRelief ( false );
      // graph2.MakeSymmetryRelief ( false );
 
      graph1.MakeSymmetryRelief(true);
      graph2.MakeSymmetryRelief(true);
   }

   int build_status1 = graph1.Build(true);
   int build_status2 = graph2.Build(true);
   double best_match_sum = 1e20;
   int best_n_match = -99;

   if (build_status1 != 0) {
      std::cout << "ERROR:: build_status1: " << build_status1 << std::endl;
   } else { 
      if (build_status2 != 0) {
         std::cout << "ERROR:: build_status2: " << build_status2 << std::endl;
      } else {

         int n_atoms_ref = cleaned_res_reference->GetNumberOfAtoms();
         int n_atoms_mov = cleaned_res_moving->GetNumberOfAtoms();

         int minMatch = 4;
         int n_ref_frac = int(0.75*float(n_atoms_ref));
         int n_mov_frac = int(0.75*float(n_atoms_mov));

         int min_n = (n_ref_frac < n_mov_frac) ? n_ref_frac : n_mov_frac;
         if (min_n > minMatch)
            minMatch = min_n;
         
         mmdb::math::GraphMatch match;

         std::cout << "INFO:: match.MatchGraphs must match at least "
                   << minMatch << " atoms."
                   << std::endl;
         bool vertext_type = true;
         match.MatchGraphs(&graph1, &graph2, minMatch, vertext_type);
         int n_match = match.GetNofMatches();
         std::cout << "INFO:: match NumberofMatches (potentially similar graphs) "
                   << n_match << std::endl;
         // match.PrintMatches();

         int best_match = -1;
         clipper::Mat33<double> m_dum(1,0,0,0,1,0,0,0,1);
         clipper::Coord_orth pt_dum(0,0,0);
         clipper::RTop_orth best_rtop(m_dum, pt_dum);
         for (int imatch=0; imatch<n_match; imatch++) {
            std::vector<std::pair<std::pair<std::string, std::string>, std::pair<std::string, std::string> > > matching_atoms; 
            int n;
            mmdb::realtype p1, p2;
            mmdb::ivector FV1, FV2;
            match.GetMatch(imatch, FV1, FV2, n, p1, p2); // n p1 p2 set
//             For understanding only.  
//             std::cout << "Match number: " << imatch << "  " << p1*100 << "% "
//                       << p2*100 << "% "<< std::endl;
            std::vector<clipper::Coord_orth> coords_1_local;
            std::vector<clipper::Coord_orth> coords_2_local;
            for (int ipair=1; ipair<=n; ipair++) {
               mmdb::math::PVertex V1 = graph1.GetVertex ( FV1[ipair] );
               mmdb::math::PVertex V2 = graph2.GetVertex ( FV2[ipair] );
               if ((!V1) || (!V2))  {
                  std::cout << "Can't get vertices for match "
                            << ipair << std::endl;
               } else  {
//                   printf(" %4i.  [%4s] <-> [%4s]\n",
//                          ipair, V1->GetName(), V2->GetName());
                  mmdb::Atom *at1 = cleaned_res_moving->atom[V1->GetUserID()];
                  mmdb::Atom *at2 = cleaned_res_reference->atom[V2->GetUserID()];
                  coords_1_local.push_back(clipper::Coord_orth(at1->x, at1->y, at1->z));
                  coords_2_local.push_back(clipper::Coord_orth(at2->x, at2->y, at2->z));
                  std::pair<std::string, std::string> atom_info_1(at1->name, at1->altLoc);
                  std::pair<std::string, std::string> atom_info_2(at2->name, at2->altLoc);
                  std::pair<std::pair<std::string, std::string>, std::pair<std::string, std::string> > atom_pair(atom_info_1, atom_info_2);
                  matching_atoms.push_back(atom_pair);
               }
            }
            
            double dist_sum = 0.0;
            clipper::RTop_orth rtop_local(clipper::Mat33<double>(0,0,0,0,0,0,0,0,0),
                                          clipper::Coord_orth(0,0,0)); // unset
            if (apply_rtop_flag) {

               rtop_local = clipper::RTop_orth(coords_1_local, coords_2_local);
               for (unsigned int i=0; i<coords_1_local.size(); i++) {
                  dist_sum += clipper::Coord_orth::length(coords_2_local[i],
                                                          coords_1_local[i].transform(rtop_local));
               }
            } else {
               for (unsigned int i=0; i<coords_1_local.size(); i++) {
                  dist_sum += clipper::Coord_orth::length(coords_2_local[i], coords_1_local[i]);
               }
            } 
            if (dist_sum < best_match_sum) {
               
               // Debugging
               // std::cout << "DEBUG:: better dist_sum: " << dist_sum << std::endl;
               
               best_rtop = rtop_local;
               best_match_sum = dist_sum;
               best_match = imatch;
               best_matching_atoms = matching_atoms;
               best_n_match = coords_1_local.size();
            }
         } // imatch loop

         if (best_match != -1) {
            rtop = best_rtop;
            success = 1;
         }
      }
   }
   delete cleaned_res_reference;
   delete cleaned_res_moving;
   coot::graph_match_info_t gmi;
   gmi.success = success;
   gmi.rtop = rtop;
   gmi.dist_score = best_match_sum;
   gmi.matching_atom_names = best_matching_atoms;
   gmi.n_match = best_n_match;
   return gmi;
}

// Change the names in res_moving_names to match those in
// res_reference as much as possible.  When there is a name collision
// (i.e. the name maped from the res_reference is already in the
// res_moving_names (and that is not to be replace by anything)),
// invent a new name for the atom.  Use the internal
// matching_atom_names.
void
coot::graph_match_info_t::match_names(mmdb::Residue *res_with_moving_names) {

   bool debug = false;
   if (!success) {
      std::cout << "Can't do name remapping, graph match failed" << std::endl;
   } else { 

      // non-mapped and not the same, that is.
      std::vector<std::string> orig_moving_atom_names_non_mapped_non_same;

      // not in the set of graph matched pairs, not changing (presumably).
      std::vector<std::string> orig_moving_atom_names_non_mapped_same;
   
      std::vector<std::string> residue_atom_names;
   

      // fill orig_moving_atom_names_non_mapped_non_same
      mmdb::PPAtom residue_atoms = 0;
      int n_residue_atoms;
      res_with_moving_names->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) {
         std::string atom_name(residue_atoms[iat]->name);
         // add the name if is not already there.
         if (std::find(residue_atom_names.begin(), residue_atom_names.end(), atom_name)
             == residue_atom_names.end())
            residue_atom_names.push_back(atom_name);
         bool found_match = 0;
         for (unsigned int j_pair=0; j_pair<matching_atom_names.size(); j_pair++) {
            // first is working atom spec
            if (matching_atom_names[j_pair].first.first == atom_name) {
               found_match = 1;
               break;
            }
         }

         // std::cout << ".... atom name: " << atom_name << ": found_match "
         // << found_match << std::endl;
         
         if (! found_match) {
            // this atom name was not in the list of working atoms that were matched.

            // now, was this atom name in the list of matched target atoms?
            // If so, it is a collision-atom
            bool found_match_2 = 0;
            for (unsigned int j_pair=0; j_pair<matching_atom_names.size(); j_pair++) {
               // second is reference atom spec
               if (matching_atom_names[j_pair].second.first == atom_name) {
                  found_match_2 = 1;
                  break;
               }
            }
            // std::cout << "      found_match_2 " << found_match_2 << std::endl;
            if (found_match_2)
               orig_moving_atom_names_non_mapped_non_same.push_back(atom_name);
            else
               orig_moving_atom_names_non_mapped_same.push_back(atom_name);
            
         }
      }

      if (debug) {
         std::cout << "Mapped atom names: " << matching_atom_names.size() << std::endl;
         // according to header ref is first, work is second.
         for (unsigned int i=0; i<matching_atom_names.size(); i++) { 
            std::cout << "   " << i << " :" << matching_atom_names[i].first.first 
                      << ": -> :" << matching_atom_names[i].second.first << ":"
                      << std::endl;
         }
         std::cout << "Non-mapped non-same atom names: " << orig_moving_atom_names_non_mapped_non_same.size()
                   << std::endl;
         for (unsigned int i=0; i<orig_moving_atom_names_non_mapped_non_same.size(); i++) { 
            std::cout << "   " << i << " :" << orig_moving_atom_names_non_mapped_non_same[i] << ":" << std::endl;
         }
         std::cout << "Non mapped same atom names: " << orig_moving_atom_names_non_mapped_same.size()
                   << std::endl;
         for (unsigned int i=0; i<orig_moving_atom_names_non_mapped_same.size(); i++) { 
            std::cout << "   " << i << " :" << orig_moving_atom_names_non_mapped_same[i] << ":" << std::endl;
         }
      }

      for (int iat=0; iat<n_residue_atoms; iat++) {

         // check for a collision.  Is the reference name in existing
         // atom names that are not due to be replaced?
         std::string this_atom_name(residue_atoms[iat]->name);

         bool replace_name = 0;
         std::string new_atom_name = "";
      
      
         if (std::find(orig_moving_atom_names_non_mapped_non_same.begin(),
                       orig_moving_atom_names_non_mapped_non_same.end(),
                       this_atom_name) !=
             orig_moving_atom_names_non_mapped_non_same.end()) {
            // OK, this atom name is in the list of atoms non-mapped needing a name change
            std::string ele = residue_atoms[iat]->element;
            new_atom_name = invent_new_name(this_atom_name, ele, residue_atom_names);
            residue_atom_names.push_back(new_atom_name);
            replace_name = 1;
            // std::cout << ":" << this_atom_name << ": non-mapped..." << std::endl;
         } else {

            // OK, this moving residue atom is not non-mapped and needing a name change.

            // Is it non-mapped and not needing a name change?
            //
            //   If it is, don't set replace name,
            ///  If is not, then it should be in the (graph) matching atom names, so
            //      check there if the atom names are the same and if they are, do not
            //      set the replace_name flag

            if (std::find(orig_moving_atom_names_non_mapped_same.begin(),
                          orig_moving_atom_names_non_mapped_same.end(),
                          this_atom_name) !=
                orig_moving_atom_names_non_mapped_same.end()) {

               // no change to replace_name.

            } else { 

               // std::cout << ":" << this_atom_name << ": mapped" << std::endl;
               replace_name = 1;
               for (unsigned int j_pair=0; j_pair<matching_atom_names.size(); j_pair++) {
                  if (matching_atom_names[j_pair].first.first == this_atom_name) { 
                     // if the atom name is the same the reference atom name, then
                     // nothing to do.
                     if (matching_atom_names[j_pair].second.first ==
                         matching_atom_names[j_pair].first.first) {
                        replace_name = 0;
                        break;
                     } else {
                        new_atom_name = matching_atom_names[j_pair].second.first;
                     } 
                  }
               }
            }
         }

         if (false)
            std::cout << "debug atom name :" << this_atom_name
                      << ": replace status: " << replace_name
                      << " new name :" << new_atom_name << ":" << std::endl;
         if (replace_name) {
            residue_atoms[iat]->SetAtomName(new_atom_name.c_str());
         } 
      
      }
   }
} 

std::string
coot::graph_match_info_t::invent_new_name(const std::string &name_in,
                                          const std::string &ele,
                                          const std::vector<std::string> &residue_atom_name) const {
   std::string a("ABCDEFGHIJKLMNOPQRSTUVWXYZ");
   bool found = 0;
   std::string new_name("XXXX");
   for (unsigned int i=0; i<a.size(); i++) { 
      for (unsigned int j=0; j<a.size(); j++) {
         std::string test_atom_name = "";
         if (ele.length() == 1) { 
            test_atom_name = " ";
            test_atom_name += ele;
         } else {
            test_atom_name = ele;
         }
         test_atom_name += a[i];
         test_atom_name += a[j];
         if (std::find(residue_atom_name.begin(), residue_atom_name.end(), test_atom_name)
             == residue_atom_name.end()) {
            found = 1;
            new_name = test_atom_name;
         }
         if (found)
            break;
      }
      if (found)
         break;
   }
   return new_name;
} 



float
coot::util::median_temperature_factor(mmdb::PPAtom atom_selection,
                                      int n_atoms,
                                      float low_cutoff,
                                      float high_cutoff,
                                      bool apply_low_cutoff,
                                      bool apply_high_cutoff) {

   float this_b;
   float median = 0;
   std::vector<float> b;
   for (int i=0; i<n_atoms; i++) {
      this_b = atom_selection[i]->tempFactor;
      if ((apply_low_cutoff && (this_b > low_cutoff)) ||
          !apply_low_cutoff) {
         if ((apply_high_cutoff && (this_b > high_cutoff)) ||
             !apply_high_cutoff) {
            b.push_back(this_b);
         }
      }
   }

   if (b.size() > 0) { 
      std::sort(b.begin(), b.end());
      int mid_pos = b.size()/2;
      median = b[mid_pos];
   }
   return median;
} 

float
coot::util::average_temperature_factor(mmdb::PPAtom atom_selection,
                                       int n_atoms,
                                       float low_cutoff,
                                       float high_cutoff,
                                       short int apply_low_cutoff,
                                       short int apply_high_cutoff) {

   float this_b = 0.0;
   float b_sum = 0.0;
   int n_sum = 0;

   for (int i=0; i<n_atoms; i++) {
      this_b = atom_selection[i]->tempFactor;
      if ((apply_low_cutoff && (this_b > low_cutoff)) ||
          !apply_low_cutoff) {
         if ((apply_high_cutoff && (this_b > high_cutoff)) ||
             !apply_high_cutoff) {
            b_sum += this_b;
            n_sum++;
         }
      }
   }

   float mean = 0.0;
   if (n_atoms > 0)
      mean = b_sum/float(n_atoms);
   return mean;
} 

float
coot::util::standard_deviation_temperature_factor(mmdb::PPAtom atom_selection,
                                                  int n_atoms,
                                                  float low_cutoff,
                                                  float high_cutoff,
                                                  short int apply_low_cutoff,
                                                  short int apply_high_cutoff) {

   double this_b = 0.0;
   double b_sum = 0.0;
   double b_sum_sqs = 0.0;
   int n_sum = 0;

   for (int i=0; i<n_atoms; i++) {
      this_b = atom_selection[i]->tempFactor;
      if ((apply_low_cutoff && (this_b > low_cutoff)) ||
          !apply_low_cutoff) {
         if ((apply_high_cutoff && (this_b > high_cutoff)) ||
             !apply_high_cutoff) {
            b_sum += this_b;
            b_sum_sqs += this_b * this_b;
            n_sum++;
         }
      }
   }

   double mean = 0.0;
   double var  = 0.0;
   float sd = 0.0;
   if (n_atoms > 0) { 
      mean = b_sum/double(n_atoms);
      var = b_sum_sqs/double(n_atoms) - mean * mean;
      if (var < 0.0)
         var = 0.0;
      sd = sqrt(var);
   } 
   return sd;
}


// adjust the atoms of residue_p
void
coot::util::delete_alt_confs_except(mmdb::Residue *residue_p, const std::string &alt_conf) {

   // we make a big list and then delete them all at once.  Deleting
   // them in place (inside the residue block crashes?).
   // 
   std::vector<mmdb::Atom *> atoms_to_be_deleted;
   
   mmdb::PPAtom residue_atoms = 0;
   int n_residue_atoms;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int i=0; i<n_residue_atoms; i++) { 
      std::string atom_alt_conf(residue_atoms[i]->altLoc);
      if (atom_alt_conf != alt_conf) {
         atoms_to_be_deleted.push_back(residue_atoms[i]);
      }
   }
   for (unsigned int iat=0; iat<atoms_to_be_deleted.size(); iat++) { 
      delete atoms_to_be_deleted[iat];
      atoms_to_be_deleted[iat] = NULL;
   }
} 


// Return NULL on residue not found in this molecule. Only look in
// MODEL 1.
// 
mmdb::Residue *
coot::util::get_residue(const std::string &chain_id,
                        int reso, const std::string &insertion_code,
                        mmdb::Manager *mol) {

   mmdb::Residue *res = NULL;
   bool found_res = 0;

   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      if (model_p) { 
         mmdb::Chain *chain_p;
         int n_chains = model_p->GetNumberOfChains(); 
         for (int i_chain=0; i_chain<n_chains; i_chain++) {
            chain_p = model_p->GetChain(i_chain);
            std::string mol_chain(chain_p->GetChainID());
            if (mol_chain == chain_id) {
               int nres = chain_p->GetNumberOfResidues();
               for (int ires=0; ires<nres; ires++) { // ires is a serial number
                  mmdb::Residue *residue_p = chain_p->GetResidue(ires);
                  if (residue_p->GetSeqNum() == reso) {
                     std::string ins_code(residue_p->GetInsCode());
                     if (insertion_code == ins_code) {
                        res = residue_p;
                        found_res = 1;
                        break;
                     }
                  }
                  if (found_res) break;
               }
            }
            if (found_res) break;
         }
      }
   }
   return res;
}

// return first false on failure to find reseidue
std::pair<bool, clipper::Coord_orth>
coot::util::get_residue_mid_point(mmdb::Manager *mol, const coot::residue_spec_t &rs) {
   bool status = false;
   clipper::Coord_orth co(0,0,0);
   if (mol) {
      mmdb::Residue *residue_p = get_residue(rs, mol);
      if (residue_p) {
         unsigned int n = 0;
         double sum_x = 0;
         double sum_y = 0;
         double sum_z = 0;
         mmdb::Atom **residue_atoms = 0;
         int n_residue_atoms = 0;
         residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
         for (int iat=0; iat<n_residue_atoms; iat++) {
            mmdb::Atom *at = residue_atoms[iat];
            if (! at->isTer()) {
               sum_x += at->x;
               sum_y += at->y;
               sum_z += at->z;
               n += 1;
            }
         }
         if (n > 0) {
            double nn = static_cast<double>(n);
            clipper::Coord_orth pt(sum_x/nn, sum_y/nn, sum_z/nn);
            co = pt;
            status = true;
         }
      }
   }
   return std::make_pair(status, co);
}


// Return NULL on residue not found in this molecule. Only look in
// MODEL 1.
//
mmdb::Residue *
coot::util::get_residue_by_binary_search(const std::string &chain_id,
                                         int res_no, const std::string &insertion_code,
                                         mmdb::Manager *mol) {

   // std::cout << "start search for " << chain_id << " " << res_no << " :" << insertion_code
   // << ":" << std::endl;
   mmdb::Residue *res = NULL;
   bool found_res = 0;

   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      if (model_p) {
         int n_chains = model_p->GetNumberOfChains();
         for (int i_chain=0; i_chain<n_chains; i_chain++) {
            mmdb::Chain *chain_p = model_p->GetChain(i_chain);
            std::string mol_chain_id(chain_p->GetChainID());
            if (mol_chain_id == chain_id) {
               // std::cout << "----- found chain id " << mol_chain_id << std::endl;
               int nres = chain_p->GetNumberOfResidues();
               int top_idx = nres-1;
               int idx_trial_prev = -999;
               int bottom_idx = 0;
               // std::cout << "starting with top_idx " << top_idx << std::endl;

               while (! found_res) {
                  int idx_delta = top_idx - bottom_idx;
                  // int idx_trial = std::lround(std::floor(bottom_idx + idx_delta * 0.5));
                  int idx_trial = bottom_idx + idx_delta/2;
                  if (false)
                     std::cout << "   idx_bottom " << bottom_idx
                               << " idx_top " << top_idx
                               << " idx_delta " << idx_delta << " "
                               << " idx_trial " << idx_trial << std::endl;
                  mmdb::Residue *residue_this = chain_p->GetResidue(idx_trial);

                  if (!residue_this) break;

                  if (residue_this->GetSeqNum() == res_no) {
                     std::string ins_code(residue_this->GetInsCode());
                     if (insertion_code == ins_code) {
                        res = residue_this;
                        found_res = true;
                        // std::cout << "found!" << std::endl;
                        break;
                     }
                  }

                  if (! found_res) {
                     if (top_idx == bottom_idx) {
                        // std::cout << "give up " << res_no << " " << insertion_code << std::endl;
                        break; // give up
                     }
                     if (idx_trial == bottom_idx) {
                        // std::cout << "give up " << res_no << " " << insertion_code << std::endl;
                        break; // give up
                     }
                     if (residue_this->GetSeqNum() > res_no) {
                        top_idx = idx_trial;
                     }
                     if (residue_this->GetSeqNum() < res_no) {
                        bottom_idx = idx_trial;
                     }
                     if (idx_trial == idx_trial_prev) {
                        // give up, - insertion code nightmare
                        break;
                     }
                  }

                  // setup for next round
                  idx_trial_prev = idx_trial;

               } // while

               if (! found_res) {
                  // try all

                  for (int ires=0; ires<nres; ires++) { // ires is a serial number
                     mmdb::Residue *residue_p = chain_p->GetResidue(ires);
                     if (residue_p->GetSeqNum() == res_no) {
                        std::string ins_code(residue_p->GetInsCode());
                        if (insertion_code == ins_code) {
                           res = residue_p;
                           found_res = true;
                           // std::cout << "found res " << residue_spec_t(res) << std::endl;
                           break;
                        }
                     } else {
                        // std::cout << "    was not " << residue_spec_t(residue_p) << std::endl;
                     }
                     if (found_res) break;
                  }
               }
            }
            if (found_res) break;
         }
      }
   }

   if (false)
      std::cout << "binary-search returns res " << res << " get_residue() returns "
                << get_residue(chain_id, res_no, insertion_code, mol) << " "
                << residue_spec_t(res) << std::endl;
   return res;
}


mmdb::Residue *
coot::util::get_residue(const residue_spec_t &rs, mmdb::Manager *mol) {

   // return get_residue(rs.chain_id, rs.res_no, rs.ins_code, mol);

   return get_residue_by_binary_search(rs.chain_id, rs.res_no, rs.ins_code, mol);

}

// get this and next residue - either can be null - both need testing
std::pair<mmdb::Residue *, mmdb::Residue *>
coot::util::get_this_and_next_residues(const residue_spec_t &rs, mmdb::Manager *mol) {

   // this function can be optimized if needed

   mmdb::Residue *r2 = 0;
   mmdb::Residue *r1 = get_residue(rs, mol);
   if (r1) {
      r2 = get_following_residue(residue_spec_t(r1), mol);
   }
   return std::pair<mmdb::Residue *, mmdb::Residue *> (r1, r2);
}


// Return NULL on residue not found in this molecule.
// 
mmdb::Residue *
coot::util::get_following_residue(const residue_spec_t &rs, 
                                  mmdb::Manager *mol) {

   mmdb::Residue *res = NULL;
   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      if (! model_p) return res;
      mmdb::Chain *chain_p;
      mmdb::Chain *chain_this_res = NULL;
      bool found_this_res = false;
      
      int n_chains = model_p->GetNumberOfChains();
      for (int i_chain=0; i_chain<n_chains; i_chain++) {
         chain_p = model_p->GetChain(i_chain);
         std::string mol_chain_id(chain_p->GetChainID());
         if (mol_chain_id == rs.chain_id) {
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            for (int ires=0; ires<nres; ires++) {
               residue_p = chain_p->GetResidue(ires);
               if (found_this_res == 0) {
                  if (rs.res_no == residue_p->GetSeqNum()) {
                     std::string ins_code = residue_p->GetInsCode();
                     if (ins_code == rs.ins_code) {
                        found_this_res = true;
                        chain_this_res = chain_p;
                     }
                  }
               } else {
                  // previous was our residue
                  if (chain_p == chain_this_res) {
                     // next residue in the same chain
                     res = residue_p;
                     break;
                  } 
               }
            }
         }
         if (res) break;
      }
   }
   return res;
}

// Return NULL on residue not found in this molecule.
// 
mmdb::Residue *
coot::util::get_previous_residue(const residue_spec_t &rs, 
                                 mmdb::Manager *mol) {
   mmdb::Residue *res = NULL;
   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      mmdb::Chain *chain_p;
      mmdb::Chain *chain_this_res = NULL;
      bool found_this_res = 0;
      if (! model_p) return res;

      int n_chains = model_p->GetNumberOfChains();
      for (int i_chain=0; i_chain<n_chains; i_chain++) {
         chain_p = model_p->GetChain(i_chain);
         std::string mol_chain_id(chain_p->GetChainID());
         if (mol_chain_id == rs.chain_id) {
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *prev_residue = 0;
            for (int ires=0; ires<nres; ires++) {
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               if (residue_spec_t(residue_p) == rs) {
                  res = prev_residue;
                  break;
               }
               // next round
               prev_residue = residue_p;
            }
         }
         if (res) break;
      }
   }
   return res;

}


mmdb::Residue *
coot::util::get_first_residue(mmdb::Manager *mol) {

   mmdb::Residue *res = NULL;
   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      if (model_p) { 
         mmdb::Chain *chain_p;
      
         int n_chains = model_p->GetNumberOfChains();
         for (int i_chain=0; i_chain<n_chains; i_chain++) {
            chain_p = model_p->GetChain(i_chain);
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            for (int ires=0; ires<nres; ires++) {
               residue_p = chain_p->GetResidue(ires);
               if (residue_p) {
                  res = residue_p;
                  break;
               }
            }
            if (res)
               break;
         }
      }
   }
   return res;
}

mmdb::Residue *
coot::util::get_first_residue_in_chain(mmdb::Chain *chain_p) {

   mmdb::Residue *r = 0;
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      for (int ires=0; ires<nres; ires++) {
         mmdb::Residue *residue_p = chain_p->GetResidue(ires);
         if (residue_p) {
            r = residue_p;
            break;
         }
      }
   }
   return r;
}

mmdb::Residue *
coot::util::get_last_residue_in_chain(mmdb::Chain *chain_p) {

   mmdb::Residue *r = 0;
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      for (int ires=(nres-1); ires>=0; ires--) {
         mmdb::Residue *residue_p = chain_p->GetResidue(ires);
         if (residue_p) {
            r = residue_p;
            break;
         }
      }
   }
   return r;
}

mmdb::Residue *
coot::util::get_second_residue_in_chain(mmdb::Chain *chain_p) {

   mmdb::Residue *r = nullptr;
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      if (nres > 1) {
         r = chain_p->GetResidue(1);
      }
   }
   return r;
}

mmdb::Residue *
coot::util::get_penultimate_residue_in_chain(mmdb::Chain *chain_p) {

   mmdb::Residue *r = nullptr;
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      if (nres > 1) {
         int idx = nres-2;
         r = chain_p->GetResidue(idx);
      }
   }
   return r;
}



std::vector<mmdb::Residue *>
coot::util::get_hetgroups(mmdb::Manager *mol, bool include_waters) {

   std::vector<mmdb::Residue *> het_residues;
   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      if (model_p) {
         int n_chains = model_p->GetNumberOfChains();
         for (int i_chain=0; i_chain<n_chains; i_chain++) {
            mmdb::Chain *chain_p = model_p->GetChain(i_chain);
            int nres = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<nres; ires++) {
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               if (residue_p) {
                  std::string res_name = residue_p->GetResName();
                  if (include_waters || res_name != "HOH") {
                     int n_atoms = residue_p->GetNumberOfAtoms();
                     for (int iat=0; iat<n_atoms; iat++) {
                        mmdb::Atom *atom_p = residue_p->GetAtom(iat);
                        if (atom_p->Het) {
                           het_residues.push_back(residue_p);
                           break;
                        }
                     }
                  }
               }
            }
         }
      }
   }
   return het_residues;
}


mmdb::Residue *
coot::util::get_biggest_hetgroup(mmdb::Manager *mol) {

   mmdb::Residue *res = NULL;

   std::vector<std::pair<mmdb::Residue *, int> > het_residues;
   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      if (model_p) { 
         mmdb::Chain *chain_p;
         int n_chains = model_p->GetNumberOfChains();
         for (int i_chain=0; i_chain<n_chains; i_chain++) {
            chain_p = model_p->GetChain(i_chain);
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            for (int ires=0; ires<nres; ires++) {
               residue_p = chain_p->GetResidue(ires);
               if (residue_p) {
                  mmdb::Atom *atom_p;
                  int n_atoms = residue_p->GetNumberOfAtoms();
                  for (int iat=0; iat<n_atoms; iat++) {
                     atom_p = residue_p->GetAtom(iat);
                     if (atom_p->Het) {
                        std::pair<mmdb::Residue *, int> p(residue_p, n_atoms);
                        het_residues.push_back(p);
                        break;
                     }
                  }
               }
            }
         }
      }
   }
   int biggest_n = 0;
   for (unsigned int ires=0; ires<het_residues.size(); ires++) { 
      if (het_residues[ires].second > biggest_n) {
         res = het_residues[ires].first;
         biggest_n = het_residues[ires].second;
      }
   }
   return res;
}


// Can return NULL.
// Typically called with nth is 1, 2 or 3.  Will return 0 if called with nth is 0.
mmdb::Residue *
coot::util::get_nth_residue(int nth, mmdb::Manager *mol) {

   int count = 0; 
   mmdb::Residue *res = NULL;
   if (mol) {
      mmdb::Model *model_p = mol->GetModel(1);
      if (model_p) { 
         mmdb::Chain *chain_p;
      
         int n_chains = model_p->GetNumberOfChains();
         for (int i_chain=0; i_chain<n_chains; i_chain++) {
            chain_p = model_p->GetChain(i_chain);
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            for (int ires=0; ires<nres; ires++) {
               residue_p = chain_p->GetResidue(ires);
               if (residue_p) {
                  count++;
                  if (count == nth) {
                     res = residue_p;
                     break;
                  }
               }
            }
            if (res)
               break;
         }
      }
   }
   return res;
} 


// Return NULL on atom not found in this molecule
//
mmdb::Atom *
coot::util::get_atom(const atom_spec_t &spec, mmdb::Manager *mol) {

   mmdb::Atom *at = 0;
   mmdb::Residue *res = get_residue(residue_spec_t(spec), mol);

   if (res) {
      mmdb::PPAtom residue_atoms = 0;
      int n_residue_atoms;
      res->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) { 
         mmdb::Atom *test_at = residue_atoms[iat];
         std::string at_name = test_at->name;
         std::string at_alt_conf = test_at->altLoc;
         if (spec.atom_name == at_name) {
            if (spec.alt_conf == at_alt_conf) {
               if (! test_at->isTer()) {
                  at = test_at;
                  break;
               }
            }
         } 
      }
   } 
   return at;
}

// Return NULL on atom not found in this residue
// 
mmdb::Atom*
coot::util::get_atom(const atom_spec_t &spec, mmdb::Residue *res) {

   mmdb::Atom *at = 0;
   if (res) {
      mmdb::PPAtom residue_atoms = 0;
      int n_residue_atoms;
      res->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) { 
         mmdb::Atom *test_at = residue_atoms[iat];
         std::string at_name = test_at->name;
         std::string at_alt_conf = test_at->altLoc;
         if (spec.atom_name == at_name) {
            if (spec.alt_conf == at_alt_conf) {
               if (! test_at->isTer()) {
                  at = test_at;
                  break;
               }
            }
         } 
      }
   } 
   return at;
} 



// can throw an exception if atom_p is NULL
clipper::Coord_orth
coot::util::get_coords(mmdb::Atom *at) {

   clipper::Coord_orth pt(at->x, at->y, at->z);
   return pt;
} 


// return success status, 1 is good, 0 is fail.  Use clipper::Coord_orth constructor
// 
bool
coot::util::add_atom(mmdb::Residue *res,
                     const std::string &atom_name_1,
                     const std::string &atom_name_2,
                     const std::string &atom_name_3,
                     const std::string &alt_conf,
                     double length,
                     double angle, // degrees
                     double torsion, // degrees
                     const std::string &new_atom_name,
                     const std::string &new_atom_ele,
                     float new_atom_occ,
                     float new_atom_b_factor) {

   bool added_status = 0;
   int n_found = 0; 
   mmdb::Atom *a = NULL;
   mmdb::Atom *b = NULL;
   mmdb::Atom *c = NULL;

   int nResidueAtoms;
   mmdb::PPAtom residue_atoms;
   if (res) { 
      res->GetAtomTable(residue_atoms, nResidueAtoms);
      for (int i=0; i<nResidueAtoms; i++) {
         std::string atom_name(residue_atoms[i]->name);
         std::string atom_alt_conf(residue_atoms[i]->altLoc);
         if (atom_alt_conf == alt_conf) { 
            if (atom_name == atom_name_1) {
               a = residue_atoms[i];
            } 
            if (atom_name == atom_name_2) {
               b = residue_atoms[i];
            } 
            if (atom_name == atom_name_3) {
               c = residue_atoms[i];
            }
         }
      }

      if (a && b && c) {
         clipper::Coord_orth ac(a->x, a->y, a->z);
         clipper::Coord_orth bc(b->x, b->y, b->z);
         clipper::Coord_orth cc(c->x, c->y, c->z);
         double ang  = clipper::Util::d2rad(angle);
         double tors = clipper::Util::d2rad(torsion);
         clipper::Coord_orth pos(ac, bc, cc, length, ang, tors);
         mmdb::Atom *new_atom = new mmdb::Atom();
         new_atom->SetCoordinates(pos.x(), pos.y(), pos.z(), new_atom_occ, new_atom_b_factor);
         new_atom->SetAtomName(new_atom_name.c_str());
         new_atom->SetElementName(new_atom_ele.c_str());
         res->AddAtom(new_atom);
         added_status = 1;
      
      } else {
         std::cout << "Failed to find all reference atoms : "
                   << atom_name_1 << " " 
                   << atom_name_2 << " " 
                   << atom_name_3 << ". Found " << n_found << " out of 3" << std::endl;
      }
   }
   return added_status;
} 


        #if 0 // we already have one of these in geometry

std::vector<std::string>
coot::util::get_residue_alt_confs(mmdb::Residue *res) {

   std::vector<std::string> v;
   mmdb::PPAtom residue_atoms;
   int nResidueAtoms;
   res->GetAtomTable(residue_atoms, nResidueAtoms);
   bool ifound = 0;
   for (int iat=0; iat<nResidueAtoms; iat++) {
      ifound = 0;
      for(unsigned int i=0; i<v.size(); i++) { 
         if (std::string(residue_atoms[iat]->altLoc) == v[i]) {
            ifound = 1;
            break;
         }
      }
      if (! ifound) 
         v.push_back(std::string(residue_atoms[iat]->altLoc));
   }
   return v;
} 

#endif
      




// The flanking residues (if any) are in the residue selection (SelResidues).
// The flags are not needed now we have made adjustments in the calling
// function.
// 
// create_mmdbmanager_from_res_selection must make adjustments
// 
// Note: there is now a molecule-class-info version of this - perhaps
// we should call it?  Next bug fix here: move over to the function call.
// 
// We need to pass orig_mol because of atom index transfer
std::pair<mmdb::Manager *, int>
coot::util::create_mmdbmanager_from_res_selection(mmdb::Manager *orig_mol,
                                                  mmdb::PResidue *SelResidues, 
                                                  int nSelResidues, 
                                                  int have_flanking_residue_at_start,
                                                  int have_flanking_residue_at_end, 
                                                  const std::string &altconf,
                                                  const std::string &chain_id_1,
                                                  short int residue_from_alt_conf_split_flag) {

   int start_offset = 0;
   int end_offset = 0;
   
//    if (have_flanking_residue_at_start)
//       start_offset = -1;
//    if (have_flanking_residue_at_end)
//       end_offset = +1; 

   mmdb::Manager *residues_mol = new mmdb::Manager;
   mmdb::Model *model = new mmdb::Model;
   mmdb::Chain *chain = new mmdb::Chain;
   short int whole_res_flag = 0; // not all alt confs, only this one ("A") and "".

   // For the active residue range (i.e. not the flanking residues) we only want
   // to refine the atoms that have the alt conf the same as the picked atom
   // (and that is altconf, passed here).
   // 
   // However, for *flanking residues* it's different.  Say we are refining a
   // non-split residue with alt conf "": Say that residue has a flanking
   // residue that is completely split, into A and B.  In that case we want
   // either "" or "A" for the flanking atoms.
   // 
   // And say we want to refine the A alt conf of a completely split residue
   // that has a flanking neighbour that is completely unsplit (""), we want
   // atoms that are either "A" or "".
   // 
   // So let's try setting whole_res_flag to 1 for flanking residues.

   mmdb::Residue *r;
   int atom_index_handle = residues_mol->RegisterUDInteger(mmdb::UDR_ATOM, "mol's atom index");
   int afix_handle_orig = orig_mol->GetUDDHandle(mmdb::UDR_ATOM, "shelx afix");
   int afix_handle_new_mol = -1;
   if (afix_handle_orig >= 0)
      afix_handle_new_mol = residues_mol->RegisterUDInteger(mmdb::UDR_ATOM, "shelx afix");

   for (int ires=start_offset; ires<(nSelResidues + end_offset); ires++) { 

      if ( (ires == 0) || (ires == nSelResidues -1) ) { 
         if (! residue_from_alt_conf_split_flag)
            whole_res_flag = 1;
      } else { 
         whole_res_flag = 0;
      }

      if (altconf == "*") whole_res_flag = 1;

      r = coot::util::deep_copy_this_residue_with_atom_index_and_afix_transfer(orig_mol, SelResidues[ires], altconf, whole_res_flag, atom_index_handle, afix_handle_new_mol);
      
      chain->AddResidue(r);
      // r->seqNum = SelResidues[ires]->GetSeqNum();
      // r->SetResName(SelResidues[ires]->GetResName());
      // 
      // 20101208, we need to copy across the ins code too (for
      // rot/transing).  This is the mmdb approved way of doing this.
      // 
      r->SetResID(SelResidues[ires]->GetResName(),
                  SelResidues[ires]->GetSeqNum(),
                  SelResidues[ires]->GetInsCode());
   }
   chain->SetChainID(chain_id_1.c_str());
   model->AddChain(chain);
   residues_mol->AddModel(model);
   residues_mol->PDBCleanup(mmdb::PDBCLEAN_SERIAL|mmdb::PDBCLEAN_INDEX);
   residues_mol->FinishStructEdit();

   if (afix_handle_orig >= 0) { 
      afix_handle_new_mol = residues_mol->GetUDDHandle(mmdb::UDR_ATOM, "shelx afix");
      int imod = 1;
      
      mmdb::Model *model_p = residues_mol->GetModel(imod);
      if (model_p) {
         mmdb::Chain *chain_p;
         // run over chains of the existing mol
         int nchains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<nchains; ichain++) {
            chain_p = model_p->GetChain(ichain);
            int nres = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<nres; ires++) { 
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               //             int n_atoms = residue_p->GetNumberOfAtoms();
            
               //             for (int iat=0; iat<n_atoms; iat++) {
               //                at = residue_p->GetAtom(iat);
               //                int check_afix_number;
               //                if (at->GetUDData(afix_handle_new_mol, check_afix_number) == mmdb::UDDATA_Ok) {
               //                   std::cout << "atom " << at << " has afix handle " << check_afix_number
               //                             << std::endl;
               //                } else {
               //                   std::cout << "Failed to get afix number right after set! "
               //                             << at << std::endl;
               //               }
               //          }
            }
         }
      }
   }


//    int udd_afix_handle_inter = residues_mol->GetUDDHandle(mmdb::UDR_ATOM, "shelx afix");
//    std::cout << "DEBUG:: about to return from create_mmdbmanager_from_res_selection, "
//              << "udd_afix_handle_inter : " << udd_afix_handle_inter << std::endl;

   return std::pair<mmdb::Manager *, int>(residues_mol, atom_index_handle);
}

// More complex than above because res_vec is not sorted on chain or residue number.
//
// The residues are added in order, the chains are added in order.
// The returned mol has the same chain ids as do the input residues.
//
std::pair<bool, mmdb::Manager *>
coot::util::create_mmdbmanager_from_residue_vector(const std::vector<mmdb::Residue *> &res_vec,
                                                   mmdb::Manager *old_mol,
                                                   const std::pair<bool,std::string> &use_alt_conf) {

   if (false) {

      // Have I added new atoms to the molecule?
      //
      // On creating an asc, the "atom index" UDD is created but new atoms don't have an atom index
      // unless asc.regen_atom_selection() has been called.

      for (auto &r : res_vec) {
         coot::residue_spec_t spec(r);
         std::cout << "create_mmdbmanager_from_residue_vector() input residue " << spec << std::endl;
      }
   }

   if (false) {
      int udd_atom_index_handle = old_mol->GetUDDHandle(mmdb::UDR_ATOM, "atom index");
      std::cout << "in create_mmdbmanager_from_residue_vector() udd_atom_index_handle for old_mol "
                << old_mol << " is " << udd_atom_index_handle << std::endl;
   }

   if (false) {
      int udd_atom_index_handle = old_mol->GetUDDHandle(mmdb::UDR_ATOM, "atom index");
      for(int imod = 1; imod<=old_mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = old_mol->GetModel(imod);
         if (model_p) {
            int n_chains = model_p->GetNumberOfChains();
            for (int ichain=0; ichain<n_chains; ichain++) {
               mmdb::Chain *chain_p = model_p->GetChain(ichain);
               int n_res = chain_p->GetNumberOfResidues();
               for (int ires=0; ires<n_res; ires++) {
                  mmdb::Residue *residue_p = chain_p->GetResidue(ires);
                  if (residue_p) {
                     int n_atoms = residue_p->GetNumberOfAtoms();
                     for (int iat=0; iat<n_atoms; iat++) {
                        mmdb::Atom *at = residue_p->GetAtom(iat);
                        if (! at->isTer()) {
                           int idx;
                           if (at->GetUDData(udd_atom_index_handle, idx) == mmdb::UDDATA_Ok) {
                              idx = -999;
                           }
                           std::cout << "input at " << at << "atom index " << idx
                                     << " using udd_atom_index_handle " << udd_atom_index_handle << std::endl;
                        }
                     }
                  }
               }
            }
         }
      }
   }



   // If use_alt_conf first is true then
   //    if use_alt_conf second is not blank
   // then copy atoms that have blank alt conf and those
   // with altconfs that match use_alt_conf.second.

   // So, first make a vector of residue sets, one residue set for each chain.
   std::vector<chain_id_residue_vec_helper_t> residues_of_chain;

   for (unsigned int i=0; i<res_vec.size(); i++) {
      mmdb::Residue *residue_p = res_vec[i];
      if (residue_p == nullptr) {
         logger.log(log_t::ERROR, logging::function_name_t(__FUNCTION__),
                    { "residue A idx:", i, "of", res_vec.size(), "is null"});
         continue;
      } else {
         if (false) { // debugging
            std::stringstream ss;
            ss << residue_p;
            std::string s = ss.str();
            logger.log(log_t::INFO, logging::function_name_t(__FUNCTION__),
                       { "residue A idx:", i, "of", res_vec.size(), "is", s });
         }
      }
      std::string chain_id = residue_p->GetChainID();

      // is chain_id already in residues_of_chain?  Do it in line here
      //
      bool found = false;
      for (unsigned int ich=0; ich<residues_of_chain.size(); ich++) { 
         if (residues_of_chain[ich].chain_id == chain_id) { 
            found = 1;
            break;
         }
      }
      if (! found) { 
         coot::util::chain_id_residue_vec_helper_t chir;
         chir.chain_id = chain_id;
         residues_of_chain.push_back(chir);
      } 
   }

   // now residues_of_chain is full of containers that have the chain_id specified.
   for (unsigned int i=0; i<res_vec.size(); i++) { 
      mmdb::Residue *residue_p = res_vec[i];
      if (residue_p == nullptr) {
         logger.log(log_t::ERROR, logging::function_name_t(__FUNCTION__),
                    { "residue B idx:", i, "of", res_vec.size(), "is null"});
         continue;
      } else {
         if (false) { // debugging
            std::stringstream ss;
            ss << residue_p;
            std::string s = ss.str();
            logger.log(log_t::ERROR, logging::function_name_t(__FUNCTION__),
                       { "residue B idx:", i, "of", res_vec.size(), "is", s });
         }
      }
      std::string chain_id = residue_p->GetChainID();
      for (unsigned int ich=0; ich<residues_of_chain.size(); ich++) { 
         if (residues_of_chain[ich].chain_id == chain_id) { 
            residues_of_chain[ich].residues.push_back(res_vec[i]);
            break;
         } 
      }
   }

   for (unsigned int ich=0; ich<residues_of_chain.size(); ich++) { 
      residues_of_chain[ich].sort_residues();
   }

   if (false) {  // debug sorting
      for (unsigned int ich=0; ich<residues_of_chain.size(); ich++) { 
         std::cout << "chain idx: " << ich << " create_mmdbmanager_from_residue_vector() "
                   << residues_of_chain[ich].chain_id << std::endl;
         for (unsigned int ii=0; ii<residues_of_chain[ich].residues.size(); ii++) { 
            std::cout << "   " << ii << " " << residues_of_chain[ich].residues[ii]->GetSeqNum()
                      << std::endl;
         }
      }
   }

   std::sort(residues_of_chain.begin(), residues_of_chain.end());

   if (false) {  // debug sorting
      for (unsigned int ich=0; ich<residues_of_chain.size(); ich++) { 
         std::cout << "chain idx: " << ich << " create_mmdbmanager_from_residue_vector() "
                   << residues_of_chain[ich].chain_id << std::endl;
         for (unsigned int ii=0; ii<residues_of_chain[ich].residues.size(); ii++) { 
            std::cout << "   post sort " << ii << " "
                      << residues_of_chain[ich].residues[ii]->GetSeqNum()
                      << std::endl;
         }
      }
   }

   mmdb::Manager *mol = new mmdb::Manager;
   mmdb::Model *model_p = new mmdb::Model;
   int index_from_reference_residue_handle = mol->RegisterUDInteger(mmdb::UDR_RESIDUE,
                                                                    "index from reference residue");
   int udd_atom_index_handle = - 1;
   if (old_mol) {
      udd_atom_index_handle = old_mol->GetUDDHandle(mmdb::UDR_ATOM, "atom index");
      if (false)
         std::cout << "debug:: create_mmdbmanager_from_residue_vector(): udd_atom_index_handle "
                   << udd_atom_index_handle << std::endl;
   }
   int udd_old_atom_index_handle = mol->RegisterUDInteger(mmdb::UDR_ATOM, "old atom index");
   mol->AddModel(model_p);

   for (unsigned int ich=0; ich<residues_of_chain.size(); ich++) {
      mmdb::Chain *chain_p = new mmdb::Chain;
      chain_p->SetChainID(residues_of_chain[ich].chain_id.c_str());
      for (unsigned int ires=0; ires<residues_of_chain[ich].residues.size(); ires++) {
         mmdb::Residue *residue_new_p =
            coot::util::deep_copy_this_residue(residues_of_chain[ich].residues[ires], use_alt_conf);

         if (residue_new_p) {

            // deep_copy_this_residue() doesn't copy TER atoms
            mmdb::Residue *residue_old_p = residues_of_chain[ich].residues[ires];
            residue_new_p->PutUDData(index_from_reference_residue_handle, residue_old_p->index);
            mmdb::Atom **new_residue_atoms = 0;
            mmdb::Atom **old_residue_atoms = 0;
            int n_old_residue_atoms;
            int n_new_residue_atoms;
            residue_old_p->GetAtomTable(old_residue_atoms, n_old_residue_atoms);
            residue_new_p->GetAtomTable(new_residue_atoms, n_new_residue_atoms);

            // transfer the atom indices
            if  (old_mol) {
               // residue_new_p doesn't have TER atoms, but residue_old_p might,
               // so deal with that here.

               if (n_old_residue_atoms == n_new_residue_atoms) {

                  // easy path, no need to deal with altconfs in one residue but not in the other

                  for (int iat=0; iat<n_old_residue_atoms; iat++) {
                     if (iat < n_new_residue_atoms) {
                        mmdb::Atom *at_old = old_residue_atoms[iat];
                        mmdb::Atom *at_new = new_residue_atoms[iat];
                        std::string at_name_old = at_old->GetAtomName();
                        std::string at_name_new = at_new->GetAtomName();
                        if (at_name_old == at_name_new) {
                           std::string alt_conf_old = at_old->altLoc;
                           std::string alt_conf_new = at_new->altLoc;
                           if (alt_conf_new == alt_conf_old) {
                              int idx = -1;
                              if (at_old->GetUDData(udd_atom_index_handle, idx) == mmdb::UDDATA_Ok) {
                                 at_new->PutUDData(udd_old_atom_index_handle, idx);
                              } else {
                                 std::cout << "WARNING:: " <<  __FUNCTION__ << "(): oops extracting idx from input old_mol atom "
                                           << at_old << " " << coot::atom_spec_t(at_old)  << " old_mol " << old_mol
                                           << " and udd_atom_index_handle " << udd_atom_index_handle << std::endl;
                              }
                           } else {
                              std::cout << "DEBUG:: oops " << __FUNCTION__ << "(): mismatch altconf reject "
                                        << atom_spec_t(at_old) << std::endl;
                           }
                        }
                     } else {
                        std::cout << "debug:: oops " << __FUNCTION__ << " indexing reject "
                                  << atom_spec_t(old_residue_atoms[iat]) << std::endl;
                     }
                  }
               } else {

                  // this happens when the old residue has alt confs on atoms and new residue
                  // does not have both A and B alt confs

                  for (int iat=0; iat<n_new_residue_atoms; iat++) {
                     mmdb::Atom *at_new = new_residue_atoms[iat];
                     std::string at_name_new = at_new->GetAtomName();
                     std::string alt_conf_new = at_new->altLoc;
                     for (int jat=0; jat<n_old_residue_atoms; jat++) {
                        mmdb::Atom *at_old = old_residue_atoms[jat];
                        std::string at_name_old = at_old->GetAtomName();
                        if (at_name_old == at_name_new) {
                           std::string alt_conf_old = at_old->altLoc;
                           if (alt_conf_new == alt_conf_old) {
                              int idx = -1;
                              if (at_old->GetUDData(udd_atom_index_handle, idx) == mmdb::UDDATA_Ok) {
                                 at_new->PutUDData(udd_old_atom_index_handle, idx);
                                 break;
                              }
                           }
                        }
                     }
                  }
               }
            }
            chain_p->AddResidue(residue_new_p);
         }
      }
      model_p->AddChain(chain_p);
   }

   if (old_mol) {
      int imodel = 1;
      mmdb::Model *mol_old_model_p = old_mol->GetModel(imodel);
      if (mol_old_model_p) {
         int n_links = mol_old_model_p->GetNumberOfLinks();
         if (n_links > 0) {
            for (int i_link=1; i_link<=n_links; i_link++) {
               mmdb::Link *link = mol_old_model_p->GetLink(i_link);
               std::pair<atom_spec_t, atom_spec_t> linked_atoms = link_atoms(link, mol_old_model_p);
               // are those atoms in (new) mol?
               mmdb::Atom *at_1 = get_atom(linked_atoms.first,  mol);
               mmdb::Atom *at_2 = get_atom(linked_atoms.second, mol);
               if (at_1 && at_2) {
                  // add this link to mol
                  mmdb::Link *link = new mmdb::Link; // sym ids default to 1555 1555

                  strcpy(link->atName1,  at_1->GetAtomName());
                  strcpy(link->aloc1,    at_1->altLoc);
                  strcpy(link->resName1, at_1->GetResName());
                  strcpy(link->chainID1, at_1->GetChainID());
                  strcpy(link->insCode1, at_1->GetInsCode());
                  link->seqNum1         = at_1->GetSeqNum();

                  strcpy(link->atName2,  at_2->GetAtomName());
                  strcpy(link->aloc2,    at_2->altLoc);
                  strcpy(link->resName2, at_2->GetResName());
                  strcpy(link->chainID2, at_2->GetChainID());
                  strcpy(link->insCode2, at_2->GetInsCode());
                  link->seqNum2         = at_2->GetSeqNum();

                  model_p->AddLink(link);
               }
            }
         }
      }
   }

   pdbcleanup_serial_residue_numbers(mol);
   mol->FinishStructEdit();


   bool debug_return_molecule = false;
   if (debug_return_molecule) {
      int imod = 1;
      mmdb::Model *model_p = mol->GetModel(imod);
      if (model_p) {
         int n_chains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<n_chains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int nres = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<nres; ires++) {
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               int n_atoms = residue_p->GetNumberOfAtoms();
               for (int iat=0; iat<n_atoms; iat++) {
                  mmdb::Atom *at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     std::cout << "debug:: mol atom " << atom_spec_t(at) << std::endl;
                  }
               }
            }
         }
      }
   }



   return std::pair<bool, mmdb::Manager *> (true, mol);
}


mmdb::Manager *
coot::util::create_mmdbmanager_from_residue_specs(const std::vector<coot::residue_spec_t> &r1,
                                                  mmdb::Manager *mol) {
   std::vector<mmdb::Residue *> residues;

   for (unsigned int ires=0; ires<r1.size(); ires++) {
      mmdb::Residue *res = coot::util::get_residue(r1[ires], mol);
      if (res) {
         residues.push_back(res);
      }
   }
   mmdb::Manager *new_mol = coot::util::create_mmdbmanager_from_residue_vector(residues, mol).second;
   return new_mol;
}



// a new residue for each point
mmdb::Manager *coot::util::create_mmdbmanager_from_points(const std::vector<clipper::Coord_orth> &pts, float b_factor) {

   mmdb::Manager *new_mol = new mmdb::Manager;
   mmdb::Model *model_p = new mmdb::Model;
   mmdb::Chain *chain_p = new mmdb::Chain;
   chain_p->SetChainID("A");

   for (unsigned int i=0; i<pts.size(); i++) {
      mmdb::Atom *at = new mmdb::Atom;
      at->SetCoordinates(pts[i].x(), pts[i].y(), pts[i].z(), 1.0, b_factor);
      at->SetAtomName(" CA ");
      at->SetElementName(" C");
      mmdb::Residue *residue_p = new mmdb::Residue;
      residue_p->SetResName("ALA");
      residue_p->seqNum = i;
      residue_p->AddAtom(at);
      chain_p->AddResidue(residue_p);
   }
   model_p->AddChain(chain_p);
   new_mol->AddModel(model_p);
   return new_mol;
}

void
coot::util::pdbcleanup_serial_residue_numbers(mmdb::Manager *mol) {

   if (mol) {
      for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (model_p) {
            int n_chains = model_p->GetNumberOfChains();
            for (int ichain=0; ichain<n_chains; ichain++) {
               mmdb::Chain *chain_p = model_p->GetChain(ichain);
               int nres = chain_p->GetNumberOfResidues();
               for (int ires=0; ires<nres; ires++) {
                  mmdb::Residue *residue_p = chain_p->GetResidue(ires);
                  residue_p->index = ires;
               }
            }
         }
      }
   }
}

void 
coot::util::chain_id_residue_vec_helper_t::sort_residues() { 

   std::sort(residues.begin(), residues.end(), residues_sort_func);
}


bool
coot::util::chain_id_residue_vec_helper_t::operator<(const chain_id_residue_vec_helper_t &c) const { 

   return (chain_id < c.chain_id);
}

// static 
bool
coot::util::chain_id_residue_vec_helper_t::residues_sort_func(mmdb::Residue *first, mmdb::Residue *second) { 

   if (! first) {
      if (! second) {
         return false;
      } else {
         return true;
      }
   } else {
     if (! second) {
        return true; // check? - perverse case.
     }
   }
   
   if (first->GetSeqNum() < second->GetSeqNum()) { 
      return true;
   } else { 
      if (first->GetSeqNum() > second->GetSeqNum()) { 
         return false; 
      } else { 
         std::string inscode_1 = first->GetInsCode();
         std::string inscode_2 = second->GetInsCode(); 
         if (inscode_1 < inscode_2) 
            return true; 
         else 
            return false;
      }
   }
   return false; // not reached.
}


// chain-split the residues, dont just rely on the sequence number
bool
coot::util::residues_sort_function(mmdb::Residue *r1, mmdb::Residue *r2) {

   if (!r1) {
      if (!r2) {
         return false;
      } else {
         return true;
      }
   } else {
      if (!r2) {
         return false;
      }
   }

   if (r1->chain < r2->chain) {
      return true;
   } else {
      if (r1->chain > r2->chain) {
         return false;
      } else {
         if (r1->GetSeqNum() < r2->GetSeqNum()) {
            return true;
         } else {
            if (r1->GetSeqNum() > r2->GetSeqNum()) {
                return false;
            } else {
               std::string inscode_1 = r1->GetInsCode();
               std::string inscode_2 = r1->GetInsCode();
               return (inscode_1 < inscode_2);
            }
         }
      }
   }
}

// return true if something was removed from header info
//
 bool
    coot::util::delete_residue_references_in_header_info(mmdb::Residue *residue_p, mmdb::Manager *mol) {

    bool was_deleted = false;
    if (residue_p) {
       residue_spec_t residue_for_deletion_spec(residue_p);

       // ----------------------------------------------------------------------------------
       //                             Links
       // ----------------------------------------------------------------------------------

       for (int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
          mmdb::Model *model_p = mol->GetModel(imod);
          if (model_p) {
             std::vector<mmdb::Link *> saved_links;
             unsigned int n_links = model_p->GetNumberOfLinks();
             for (unsigned int ilink=1; ilink<=n_links; ilink++) {
                mmdb::Link *link = model_p->GetLink(ilink);
                std::pair<atom_spec_t, atom_spec_t> la = link_atoms(link, model_p);
                residue_spec_t r1(la.first);
                residue_spec_t r2(la.second);
                if (r1 == residue_for_deletion_spec)
                   continue;
                if (r2 == residue_for_deletion_spec)
                   continue;
                mmdb::Link *link_copy = new mmdb::Link(*link);
                saved_links.push_back(link_copy);
             }
             if (saved_links.size() < n_links) {
                was_deleted = true;
                model_p->RemoveLinks();
                for (unsigned int i=0; i<saved_links.size(); i++)
                   model_p->AddLink(saved_links[i]);
             }
          }
       }

       // ------------------------------------------------------------------------------------
       //                Others :-) CisPeps, HetCompounds, (Helix, Strand, Turn)
       // ------------------------------------------------------------------------------------

    }
    return was_deleted;
 }



bool
coot::mol_has_symmetry(mmdb::Manager *mol) {
   mmdb::mat44 test_mat;
   int i_symm_err = mol->GetTMatrix(test_mat, 0, 0, 0, 0);
   return (i_symm_err == 0); // 0 is OK
}

// (if it has any atom that is anisotropic, return true)
bool
coot::mol_is_anisotropic(mmdb::Manager *mol) {

   bool is_aniso = false;

   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (! model_p) return false;

   mmdb::Chain *chain_p;
   int n_chains = model_p->GetNumberOfChains();
   for (int ichain=0; ichain<n_chains; ichain++) {
      chain_p = model_p->GetChain(ichain);
      int nres = chain_p->GetNumberOfResidues();
      mmdb::Residue *residue_p;
      mmdb::Atom *at;
      for (int ires=0; ires<nres; ires++) {
         residue_p = chain_p->GetResidue(ires);
         int n_atoms = residue_p->GetNumberOfAtoms();
         for (int iat=0; iat<n_atoms; iat++) {
            at = residue_p->GetAtom(iat);
            if (at->WhatIsSet & mmdb::ASET_Anis_tFac) {
               is_aniso = true;
               break;
            }
         }
         if (is_aniso)
            break;
      }
      if (is_aniso)
         break;
   }
   return is_aniso;
}




// We don't mess with the chain ids, give as we get, but also
// return the handle for the atom index transfer.
std::pair<mmdb::Manager *, int>
coot::util::create_mmdbmanager_from_mmdbmanager(mmdb::Manager *mol_in) { 

   mmdb::Manager *residues_mol = new mmdb::Manager;
   int atom_index_handle = residues_mol->RegisterUDInteger(mmdb::UDR_ATOM, "mol's atom index");
   int afix_handle_orig = mol_in->GetUDDHandle(mmdb::UDR_ATOM, "shelx afix");
   int afix_handle_new_mol = -1;
   if (afix_handle_orig >= 0)
      afix_handle_new_mol = residues_mol->RegisterUDInteger(mmdb::UDR_ATOM, "shelx afix");

   std::string altconf = ""; // dummy
   short int whole_res_flag = 1;

   for(int imod = 1; imod<=mol_in->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol_in->GetModel(imod);
      if (! model_p) continue;
      mmdb::Model *new_model_p = new mmdb::Model;
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         mmdb::Chain *new_chain_p = new mmdb::Chain;
         new_chain_p->SetChainID(chain_p->GetChainID());
         int nres = chain_p->GetNumberOfResidues();
         for (int ires=0; ires<nres; ires++) {
            mmdb::Residue *residue_p = chain_p->GetResidue(ires);
            mmdb::Residue *r = coot::util::deep_copy_this_residue_with_atom_index_and_afix_transfer(mol_in, residue_p, altconf, whole_res_flag, atom_index_handle, afix_handle_new_mol);
            new_chain_p->AddResidue(r);
         }
         new_model_p->AddChain(new_chain_p);
      }
      residues_mol->AddModel(new_model_p);
   }

   return std::pair<mmdb::Manager *, int> (residues_mol, atom_index_handle);
}


// ignore atom index transfer
mmdb::Manager *
coot::util::create_mmdbmanager_from_atom_selection(mmdb::Manager *orig_mol,
                                                   int SelectionHandle,
                                                   bool invert_seletion) {

   if (invert_seletion)
      return coot::util::create_mmdbmanager_from_inverted_atom_selection(orig_mol, SelectionHandle);
   else
      return coot::util::create_mmdbmanager_from_atom_selection_straight(orig_mol, SelectionHandle);
}

// 20240201-PE now atom index transfer is applied
mmdb::Manager *
coot::util::create_mmdbmanager_from_atom_selection_straight(mmdb::Manager *orig_mol,
                                                            int SelectionHandle) {

   // std::cout << "----------------- create_mmdbmanager_from_atom_selection_straight() " << std::endl;

   mmdb::Manager *atoms_mol = new mmdb::Manager;

   int orig_atom_index_handle = orig_mol->GetUDDHandle(mmdb::UDR_ATOM, "atom index");
   // std::cout << "orig_atom_index_handle: " << orig_atom_index_handle << std::endl;

   // 20240201-PE used in api replace_fragment()
   int transfered_atom_index_handle = atoms_mol->RegisterUDInteger(mmdb::UDR_ATOM, "transfer atom index");

   // the short version from Eugene. Is it going wrong for cifs? Maybe.
   mmdb::PPAtom atoms = nullptr;
   int n_selected_atoms = 0;
   orig_mol->GetSelIndex(SelectionHandle, atoms, n_selected_atoms);
   for (int iatom=0; iatom<n_selected_atoms; iatom++) {
      mmdb:: Atom *at = atoms[iatom];
      int idx = -1;
      int ierr = at->GetUDData(orig_atom_index_handle, idx);
      if (ierr == mmdb::UDDATA_Ok) {
         if (false)
            std::cout << "atom " << coot::atom_spec_t(at) << " had atom index " << idx << std::endl;
      } else {
         std::cout << "wrong handle for UDD atom-index " << orig_atom_index_handle << std::endl;
      }
      int index = 0; // make a new atom at the nAtoms+1 position
      int new_index = iatom + 1;
      atoms_mol->PutAtom(index, at, iatom+1);
      mmdb::Atom *atn = atoms_mol->GetAtomI(new_index);
      // std::cout << " in atom " << atom_spec_t(at) << " new atoms: " << atom_spec_t(atn) << std::endl;
      atn->PutUDData(transfered_atom_index_handle, idx);
   }

   // now call OrderAtoms()
   // atoms_mol->OrderAtoms();

#if 0
   orig_mol->GetSelIndex(SelectionHandle, atoms, n_selected_atoms);
   for (int iatom=0; iatom<n_selected_atoms; iatom++) {
      mmdb::Atom *at = atoms[iatom];
      mmdb::Residue *res = at->residue;
      std::string res_name(res->GetResName());
      mmdb::Atom *at_new = new mmdb::Atom;
      int imodel = at->GetModelNum();
      std::string chain_id = res->GetChainID();
      std::string ins_code = res->GetInsCode();
      int seq_num = res->GetSeqNum();

      bool added = false;
      at_new->Copy(at);
      for(int imod = 1; imod<=atoms_mol->GetNumberOfModels(); imod++) {
         if (imod == imodel) {
            mmdb::Model *model_p = atoms_mol->GetModel(imod);
            if (model_p) {
               int n_chains = model_p->GetNumberOfChains();
               for (int ichain=0; ichain<n_chains; ichain++) {
                  mmdb::Chain *chain_p = model_p->GetChain(ichain);
                  std::string chain_id_mol = chain_p->GetChainID();
                  if (chain_id == chain_id_mol) {
                     int nres = chain_p->GetNumberOfResidues();
                     for (int ires=0; ires<nres; ires++) {
                        mmdb::Residue *residue_p = chain_p->GetResidue(ires);
                        int res_no_mol = residue_p->GetSeqNum();
                        std::string ins_code_mol = residue_p->GetInsCode();
                        if (res_no_mol == seq_num) {
                           if (ins_code_mol == ins_code)  {
                              residue_p->AddAtom(at_new);
                              added = true;
                           }
                        }
                        if (added) break;
                     }
                  }
                  if (added) break;
               }
            }
         }
      }

      if (! added) {
         // OK, we need to make a new model, chain, residue
         // or  new chain, residue
         // or resdiue

         mmdb::Model *this_model = 0;
         mmdb::Chain *this_chain = 0;
         mmdb::Residue *this_residue = 0;
         bool found_chain = false;
         bool found_model = false;
         bool found_residue = false;
         for (int imod = 1; imod<=atoms_mol->GetNumberOfModels(); imod++) {
            if (imod == imodel) {
               found_model = true;
               this_model = atoms_mol->GetModel(imod);
               break;
            }
         }

         for (int imod = 1; imod<=atoms_mol->GetNumberOfModels(); imod++) {
            if (imod == imodel) {
               mmdb::Model *model_p = atoms_mol->GetModel(imod);
               if (model_p) {
                  int n_chains = model_p->GetNumberOfChains();
                  for (int ichain=0; ichain<n_chains; ichain++) {
                     mmdb::Chain *chain_p = model_p->GetChain(ichain);
                     std::string chain_id_mol = chain_p->GetChainID();
                     if (chain_id_mol == chain_id) {
                        found_chain = true;
                        this_chain = chain_p;
                     }
                  }
               }
            }
         }

         if (false)
            std::cout << "atom " << at << " found_model " << found_model
                      << " found_chain " << found_chain
                      << " found_residue " << found_residue << std::endl;

         if (! found_model) {

            mmdb::Model *new_model = new mmdb::Model;
            mmdb::Chain *new_chain = new mmdb::Chain;
            new_chain->SetChainID(chain_id.c_str());
            new_model->AddChain(new_chain);
            mmdb::Residue *new_residue = new mmdb::Residue;
            new_residue->SetResID(res_name.c_str(), seq_num, ins_code.c_str());
            new_chain->AddResidue(new_residue);
            new_residue->AddAtom(at_new);
            atoms_mol->AddModel(new_model);

         } else {
            // model was found but the chain was not
            if (! found_chain) {
               mmdb::Chain *new_chain = new mmdb::Chain;
               new_chain->SetChainID(chain_id.c_str());
               this_model->AddChain(new_chain);
               mmdb::Residue *new_residue = new mmdb::Residue;
               new_residue->SetResID(res_name.c_str(), seq_num, ins_code.c_str());
               new_chain->AddResidue(new_residue);
               new_residue->AddAtom(at_new);
            } else {
               mmdb::Residue *new_residue = new mmdb::Residue;
               new_residue->SetResID(res_name.c_str(), seq_num, ins_code.c_str());
               this_chain->AddResidue(new_residue);
               new_residue->AddAtom(at_new);
            }
         }
      }
   }
   pdbcleanup_serial_residue_numbers(atoms_mol);
#endif



   /*   mmdb::Model *model = new mmdb::Model;
   atoms_mol->AddModel(model);

   mmdb::PAtom *atoms = 0;
   int n_selected_atoms;
   orig_mol->GetSelIndex(SelectionHandle, atoms, n_selected_atoms);
   
   for (int iatom=0; iatom<n_selected_atoms; iatom++) {

      int atom_residue_selection_handle = atoms_mol->NewSelection();
      mmdb::Atom *at = atoms[iatom];

      // Does this new atoms residue exist in new atoms_mol?
      // if yes,
      //   add a copy of this atom to that residue
      // else
      //   does this new atom's chain exist in new atoms_mol?
      //   if yes
      //      create a new residue in that chain
      //      add a copy of this atom to that new residue
      //   else
      //      create a new chain
      //      create a new residue in that chain
      //      add a copy of this atom to that new residue
      // 
      atoms_mol->Select (atom_residue_selection_handle,
                        mmdb::STYPE_RESIDUE, 0, // .. TYPE, iModel
                        at->GetChainID(), // Chain(s)
                        at->GetSeqNum(), at->GetInsCode(),  // starting res
                        at->GetSeqNum(), at->GetInsCode(),  // ending res
                        at->GetResName(),  // residue name
                        "*",  // Residue must contain this atom name?
                        "*",  // Residue must contain this Element?
                        "*",  // altLocs
                        mmdb::SKEY_NEW // selection key
                        );
      mmdb::PResidue *sel_residues;
      int n_sel_residues;
      atoms_mol->GetSelIndex(atom_residue_selection_handle,
                             sel_residues, n_sel_residues);

      if (n_sel_residues > 0) {
         mmdb::Atom *new_atom = new mmdb::Atom;
         new_atom->Copy(at);
         sel_residues[0]->AddAtom(new_atom);
      } else {
         // residue was not found!
         // Now we select on the chain
         int atom_chain_selection_handle = atoms_mol->NewSelection();
         atoms_mol->Select (atom_chain_selection_handle,
                           STYPE_CHAIN, 0, // .. TYPE, iModel
                            at->GetChainID(), // Chain(s)
                            mmdb::ANY_RES, "*",  // starting res
                            mmdb::ANY_RES, "*",  // ending res
                            "*",  // residue name
                            "*",  // Residue must contain this atom name?
                            "*",  // Residue must contain this Element?
                            "*",  // altLocs
                            mmdb::SKEY_NEW // selection key
                            );
         mmdb::PChain *sel_chains;
         int n_sel_chains;
         atoms_mol->GetSelIndex(atom_chain_selection_handle, sel_chains,
                                n_sel_chains);

         if (n_sel_chains > 0) {
            mmdb::Residue *residue = new mmdb::Residue(sel_chains[0],
                                             at->GetResName(),
                                             at->GetSeqNum(),
                                             at->GetInsCode());
            mmdb::Atom *new_atom = new mmdb::Atom; 
            new_atom->Copy(at);
            residue->AddAtom(new_atom);
         } else {
            // There was not even a chain...
            mmdb::Chain *chain = new mmdb::Chain(model, at->GetChainID());
            mmdb::Residue *residue = new mmdb::Residue(chain,
                                             at->GetResName(),
                                             at->GetSeqNum(),
                                             at->GetInsCode());
            mmdb::Atom *new_atom = new mmdb::Atom; 
            new_atom->Copy(at);
            residue->AddAtom(new_atom);
//             std::cout << "DEBUG:: straight: added atom (and res, chains) :"
//                       << new_atom->GetAtomName()
//                       << ": to "
//                       << residue->GetChainID() << " " 
//                       << residue->GetSeqNum()  << " " 
//                       << residue->GetResName() << " " 
//                       << std::endl;
//             std::cout << "DEBUG:: straight: added    residue " << residue->GetSeqNum()
//                       << std::endl;
//             std::cout << "DEBUG:: straight: added       chain " << chain->GetChainID()
//                       << std::endl;
         } 
      }
      atoms_mol->DeleteSelection(atom_residue_selection_handle);
   }
   */
   mmdb::realtype a[6];
   mmdb::realtype vol;
   int orthcode;
   orig_mol->GetCell(a[0], a[1], a[2], a[3], a[4], a[5], vol, orthcode);
   atoms_mol->SetCell(a[0], a[1], a[2], a[3], a[4], a[5]);
   mmdb::cpstr sg = orig_mol->GetSpaceGroup();
   if (sg) { 
     atoms_mol->SetSpaceGroup(sg);
   }

   transfer_links(orig_mol ,atoms_mol);
   atoms_mol->FinishStructEdit();
   return atoms_mol;
}

// transfer links from mol_orig to mol_new
void
coot::util::transfer_links(mmdb::Manager *mol_orig, mmdb::Manager *mol_new) {

   // c.f. create_mmdbmanager_from_residue_vector

   if (! mol_orig) return;
   if (! mol_new) return;

   int n_models = mol_orig->GetNumberOfModels();
   for (int imod=1; imod <= n_models; imod++) {
      mmdb::Model *model_p = mol_orig->GetModel(imod);
      if (model_p) {
         mmdb::Model *new_model_p = mol_new->GetModel(imod);
         if (new_model_p) {
            int n_links = model_p->GetNumberOfLinks();
            for (int i=1; i<=n_links; i++) {
               mmdb::Link *ref_link = model_p->GetLink(i);
               if (ref_link) {
                  // If there is an atom in new_mol that corresponds to this link,
                  // then copy the link and add it to new_mol
                  std::pair<atom_spec_t, atom_spec_t> linked_atoms = link_atoms(ref_link, model_p);
                  // are those atoms in (new) mol?
                  mmdb::Atom *at_1 = get_atom(linked_atoms.first,  mol_new);
                  mmdb::Atom *at_2 = get_atom(linked_atoms.second, mol_new);
                  if (at_1 && at_2) {
                     // add this link to mol
                     mmdb::Link *link = new mmdb::Link; // sym ids default to 1555 1555

                     strncpy(link->atName1,  at_1->GetAtomName(), 20);
                     strncpy(link->aloc1,    at_1->altLoc, 20);
                     strcpy(link->resName1, at_1->GetResName());
                     strcpy(link->chainID1, at_1->GetChainID());
                     strcpy(link->insCode1, at_1->GetInsCode());
                     link->seqNum1         = at_1->GetSeqNum();

                     strncpy(link->atName2,  at_2->GetAtomName(), 20);
                     strncpy(link->aloc2,    at_2->altLoc, 20);
                     strcpy(link->resName2, at_2->GetResName());
                     strcpy(link->chainID2, at_2->GetChainID());
                     strcpy(link->insCode2, at_2->GetInsCode());
                     link->seqNum2         = at_2->GetSeqNum();

                     new_model_p->AddLink(link);
                  }
               }
            }
         }
      }
   }
}


// Beware This destroys (inverts) the atom selection as passed.
mmdb::Manager *
coot::util::create_mmdbmanager_from_inverted_atom_selection(mmdb::Manager *orig_mol,
                                                            int SelectionHandle) {

   std::cout << "----------------- create_mmdbmanager_from_inverted_atom_selection() " << std::endl;

   // The idea here is that we want to have a selection that is
   // logical NOT of the SelectionHandle selection.
   // 
   // So we need to select everything in orig_mol and then use
   // mmdb::SKEY_XOR to get a selection that is the NOT ofthe
   // SelectionHandle selection.

   orig_mol->Select(SelectionHandle, mmdb::STYPE_ATOM, 0, "*", mmdb::ANY_RES, "*", mmdb::ANY_RES, "*",
                    "*", "*", "*", "*", mmdb::SKEY_XOR);
   mmdb::Manager *new_mol =
      coot::util::create_mmdbmanager_from_atom_selection(orig_mol, SelectionHandle);
   return new_mol;
}


// ignore atom index transfer, return NULL on error.
mmdb::Manager *
coot::util::create_mmdbmanager_from_residue(mmdb::Residue *res) {

   mmdb::Manager *mol = NULL;

   if (res) { 
      mol = new mmdb::Manager;
      mmdb::Residue *r = coot::util::deep_copy_this_residue(res);
      mmdb::Model *model_p = new mmdb::Model;
      mmdb::Chain *chain_p = new mmdb::Chain;
      chain_p->AddResidue(r);
      model_p->AddChain(chain_p);
      mol->AddModel(model_p);
      if (mol) {
         chain_p->SetChainID(res->GetChainID());
      } else {
         chain_p->SetChainID("");
      }
   }
   return mol;
}

mmdb::Manager *
coot::util::create_mmdbmanager_from_atom(mmdb::Atom *at) {
   mmdb::Residue *res = new mmdb::Residue;
   res->AddAtom(at);
   mmdb::Chain *chain_p = new mmdb::Chain;
   chain_p->AddResidue(res);
   chain_p->SetChainID("A");
   mmdb::Model *model_p = new mmdb::Model;
   model_p->AddChain(chain_p);
   mmdb::Manager *mol = new mmdb::Manager;
   mol->AddModel(model_p);
   return mol;
} 


// Note, we also create a chain and add this residue to that chain.
// We do this so that we have a holder for the segid.
// 
// whole_residue_flag: only copy atoms that are either in this altLoc,
// or has an altLoc of "".
// 
mmdb::Residue *
coot::util::deep_copy_this_residue_add_chain(mmdb::Residue *residue,
                                             const std::string &altconf,
                                             bool whole_residue_flag,
                                             bool attach_to_new_chain_flag) {

   mmdb::Residue *rres = NULL;
   if (residue) {
      rres = new mmdb::Residue;
      mmdb::Chain   *chain_p = NULL;
      if (attach_to_new_chain_flag) { 
         chain_p = new mmdb::Chain;
         chain_p->SetChainID(residue->GetChainID());
      }
      rres->seqNum = residue->GetSeqNum();
      strcpy(rres->name, residue->name);
      // BL says:: should copy insCode too, maybe more things...
      strncpy(rres->insCode, residue->GetInsCode(), 3);

      mmdb::PPAtom residue_atoms;
      int nResidueAtoms;
      residue->GetAtomTable(residue_atoms, nResidueAtoms);
      mmdb::Atom *atom_p;
      for(int iat=0; iat<nResidueAtoms; iat++) {
         if (! residue_atoms[iat]->isTer()) {
            std::string this_atom_alt_loc(residue_atoms[iat]->altLoc);
            if (whole_residue_flag ||
                this_atom_alt_loc  == altconf || this_atom_alt_loc == "") {
               atom_p = new mmdb::Atom;
               atom_p->Copy(residue_atoms[iat]);
               rres->AddAtom(atom_p);
            }
         }
      }
      if (attach_to_new_chain_flag)
         chain_p->AddResidue(rres);
   }
   return rres;
}

mmdb::Residue *
coot::util::deep_copy_this_residue(mmdb::Residue *residue) { 

   mmdb::Residue *rres = NULL;

   if (residue) {
      rres = new mmdb::Residue;
      rres->seqNum = residue->GetSeqNum();
      strcpy(rres->name, residue->name);
      strncpy(rres->insCode, residue->GetInsCode(), 3);

      mmdb::PPAtom residue_atoms = 0;
      int nResidueAtoms;
      residue->GetAtomTable(residue_atoms, nResidueAtoms);
   
      for(int iat=0; iat<nResidueAtoms; iat++) {
         if (! residue_atoms[iat]->isTer()) {
            mmdb::Atom *atom_p = new mmdb::Atom;
            atom_p->Copy(residue_atoms[iat]);
            rres->AddAtom(atom_p);
         }
      }
   }
   return rres;
}

// As above but use the alt conf flags to filter copied atoms.
// Can return 0 if there are no atoms copied
//
// If use_alt_conf first is true then
//    if use_alt_conf second is not blank
// then copy atoms that have blank alt conf and those
// with altconfs that match use_alt_conf.second.
mmdb::Residue *
coot::util::deep_copy_this_residue(mmdb::Residue *residue,
                                   const std::pair<bool,std::string> &use_alt_conf) {

   mmdb::Residue *rres = NULL;

   if (residue) {
      rres = new mmdb::Residue;
      rres->seqNum = residue->GetSeqNum();
      strcpy(rres->name, residue->name);
      // BL says:: should copy insCode too, maybe more things...
      strncpy(rres->insCode, residue->GetInsCode(), 3);

      mmdb::PPAtom residue_atoms = 0;
      int nResidueAtoms;
      residue->GetAtomTable(residue_atoms, nResidueAtoms);
      mmdb::Atom *atom_p;

      for(int iat=0; iat<nResidueAtoms; iat++) {
         mmdb::Atom *at = residue_atoms[iat];
         if (! at->isTer()) {

            if (use_alt_conf.first) {
               std::string alt_conf(at->altLoc);
               if (! alt_conf.empty())
                  if (alt_conf != use_alt_conf.second)
                     continue;
            }
            atom_p = new mmdb::Atom;
            atom_p->Copy(residue_atoms[iat]);
            rres->AddAtom(atom_p);
         }
      }

      // should I check the number of added atoms before returning rres? Hmm.
   }

   return rres;
}



// Note, we also create a chain and add this residue to that chain.
// We do this so that we have a holder for the segid.
// 
// whole_residue_flag: only copy atoms that are either in this altLoc,
// or has an altLoc of "".
//
//
// Don't transfer afix number if afix_udd_handle (for the new atoms) is -1;
mmdb::Residue *
coot::util::deep_copy_this_residue_with_atom_index_and_afix_transfer(mmdb::Manager *std_mol, 
                                                                     const mmdb::Residue *residue,
                                                                     const std::string &altconf,
                                                                     short int whole_residue_flag,
                                                                     int atom_index_udd_handle,
                                                                     int afix_udd_handle) {

   // Note we pass the atom_index_udd_handle from the new residues
   // molecule and get the old one by using GetUDDHandle on the
   // old/std mol.

   // Horrible casting to mmdb::Residue because GetSeqNum and GetAtomTable
   // are not const functions.
   // 
   mmdb::Residue *rres = new mmdb::Residue;
   mmdb::Chain   *chain_p = new mmdb::Chain;
   chain_p->SetChainID(((mmdb::Residue *)residue)->GetChainID());
   rres->seqNum = ((mmdb::Residue *)residue)->GetSeqNum();
   strcpy(rres->name, residue->name);
   // BL says:: should copy insCode too, maybe more things...
   strncpy(rres->insCode, ((mmdb::Residue *)residue)->GetInsCode(), 3);

   mmdb::PPAtom residue_atoms;
   int nResidueAtoms;
   ((mmdb::Residue *)residue)->GetAtomTable(residue_atoms, nResidueAtoms);
   mmdb::Atom *atom_p;

   // We are not passed the handle, we have to look it up.
   int mol_atom_index_handle = std_mol->GetUDDHandle(mmdb::UDR_ATOM, "atom index");
   int mol_afix_handle = -1;
   int afix_number;
   if (afix_udd_handle >= 0) {
      mol_afix_handle = std_mol->GetUDDHandle(mmdb::UDR_ATOM, "shelx afix");
   }
      
   for(int iat=0; iat<nResidueAtoms; iat++) {
      std::string this_atom_alt_loc(residue_atoms[iat]->altLoc);
      if (whole_residue_flag ||
          this_atom_alt_loc  == altconf || this_atom_alt_loc == "") { 
         atom_p = new mmdb::Atom;
         atom_p->Copy(residue_atoms[iat]);
         int mol_atom_index = -1;
         residue_atoms[iat]->GetUDData(mol_atom_index_handle, mol_atom_index);
         atom_p->PutUDData(atom_index_udd_handle, mol_atom_index);
         // and shelx afix data:
         if (mol_afix_handle >= 0) {
            if (residue_atoms[iat]->GetUDData(mol_afix_handle, afix_number) == mmdb::UDDATA_Ok) { 
//                std::cout << "DEBUG:: Transfering udd afix: " << afix_number
//                          << " using std mol_udd_handle " << mol_afix_handle
//                          << " to new atom with afix_udd_handle: " << afix_udd_handle
//                          << std::endl;
               atom_p->PutUDData(afix_udd_handle, afix_number);
//             } else {
//                std::cout << "Ooops! Can get afix number from original atom"
//                          << std::endl;
            } 
         } 
         rres->AddAtom(atom_p);
      }
   }
   chain_p->AddResidue(rres);
   return rres;
}

mmdb::Residue *coot::util::copy_and_delete_hydrogens(mmdb::Residue *residue_in) {

   mmdb::Residue *copy = coot::util::deep_copy_this_residue(residue_in);
   mmdb::PPAtom residue_atoms;
   int nResidueAtoms;
   copy->GetAtomTable(residue_atoms, nResidueAtoms);

   for(int i=0; i<nResidueAtoms; i++) {
      std::string element(residue_atoms[i]->element);
      if (element == " H" || element == " D") {
         copy->DeleteAtom(i);
      }
   }
   copy->TrimAtomTable();
   return copy;
} 


// transform the atoms in mol that are in moving_chain.
// 
void
coot::util::transform_chain(mmdb::Manager *mol,
                            mmdb::Chain *moving_chain,
                            int n_atoms, mmdb::PAtom *atom_selection,
                            mmdb::mat44 &my_matt) {

   for (int iat=0; iat<n_atoms; iat++) {
      mmdb::Atom *at = atom_selection[iat];
      if (at->residue->chain == moving_chain) { 
         at->Transform(my_matt);
      }
   }
}

void
coot::util::transform_chain(mmdb::Chain *chain_p, const clipper::RTop_orth &rtop) {

   int nres = chain_p->GetNumberOfResidues();
   for (int ires=0; ires<nres; ires++) {
      mmdb::Residue *residue_p = chain_p->GetResidue(ires);
      int n_atoms = residue_p->GetNumberOfAtoms();
      for (int iat=0; iat<n_atoms; iat++) {
         mmdb::Atom *at = residue_p->GetAtom(iat);
         clipper::Coord_orth pt(co(at));
         clipper::Coord_orth new_pt(rtop * pt);
         at->x = new_pt.x();
         at->y = new_pt.y();
         at->z = new_pt.z();
      }
   }
}


// transform atoms in residue
void
coot::util::transform_atoms(mmdb::Residue *res, const clipper::RTop_orth &rtop) {

   mmdb::PPAtom residue_atoms;
   int natoms;
   clipper::Coord_orth co;
   clipper::Coord_orth trans_pos; 
   res->GetAtomTable(residue_atoms, natoms);
   for (int iatom=0; iatom<natoms; iatom++) {
      co = clipper::Coord_orth(residue_atoms[iatom]->x, 
                               residue_atoms[iatom]->y, 
                               residue_atoms[iatom]->z);
      trans_pos = co.transform(rtop);
      residue_atoms[iatom]->x = trans_pos.x();
      residue_atoms[iatom]->y = trans_pos.y();
      residue_atoms[iatom]->z = trans_pos.z();
   }
}

// transform all the atom in mol
void
coot::util::transform_mol(mmdb::Manager *mol, const clipper::RTop_orth &rtop) {

   int n_models = mol->GetNumberOfModels();
   for (int imod=1; imod<=n_models; imod++) { 
      
      mmdb::Model *model_p = mol->GetModel(imod);
      if (! model_p) continue;
      mmdb::Chain *chain_p;
      // run over chains of the existing mol
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         chain_p = model_p->GetChain(ichain);
         int nres = chain_p->GetNumberOfResidues();
         mmdb::PResidue residue_p;
         mmdb::Atom *at;
         for (int ires=0; ires<nres; ires++) { 
            residue_p = chain_p->GetResidue(ires);
            int n_atoms = residue_p->GetNumberOfAtoms();
            for (int iat=0; iat<n_atoms; iat++) {
               at = residue_p->GetAtom(iat);
               clipper::Coord_orth co(at->x, at->y, at->z);
               clipper::Coord_orth trans_pos = co.transform(rtop);
               at->x = trans_pos.x();
               at->y = trans_pos.y();
               at->z = trans_pos.z();
            }
         }
      }
   }
   mol->FinishStructEdit();
}

// transform the atom selection (provided by handle SelHnd) in mol
void
coot::util::transform_selection(mmdb::Manager *mol, int SelHnd, const clipper::RTop_orth &rtop) {

   mmdb::PAtom *atoms = NULL;
   int n_selected_atoms;
   double sum_dist = 0.0l;
   mol->GetSelIndex(SelHnd, atoms, n_selected_atoms);
   for (int iat=0; iat<n_selected_atoms; iat++) {
      mmdb::Atom *at = atoms[iat];
      clipper::Coord_orth co(at->x, at->y, at->z);
      clipper::Coord_orth trans_pos = co.transform(rtop);
      at->x = trans_pos.x();
      at->y = trans_pos.y();
      at->z = trans_pos.z();
      sum_dist += (trans_pos - co).lengthsq();
   }
   if (0) // for debugging
      std::cout << ".... transformed " << n_selected_atoms << " selected atoms "
                << "by rms distance of "
                << sqrt(sum_dist/double(n_selected_atoms))
                << std::endl;
   mol->FinishStructEdit();
}


// a function to find the previous (next) residue.  Find residue
// by previous (next) serial number.
// Return NULL if prevous (next) resiude not found.
// 
mmdb::Residue *
coot::util::previous_residue(mmdb::Residue *this_residue) {

   mmdb::Residue *prev_res = NULL;
   if (this_residue) { 
      mmdb::Chain *chain_p = this_residue->GetChain();
      if (chain_p) { 
         int nres = chain_p->GetNumberOfResidues();
         mmdb::Residue *residue_p;
         for (int ires=0; ires<nres; ires++) { 
            residue_p = chain_p->GetResidue(ires);
            if (this_residue == residue_p) {
               if (ires>0)
                  prev_res = chain_p->GetResidue(ires-1);
               break;
            }
         }
      }
   }
   return prev_res;
}

// a function to find the previous (next) residue.  Find residue
// by previous (next) serial number.
// Return NULL if prevous (next) resiude not found.
// 
mmdb::Residue *
coot::util::next_residue(mmdb::Residue *this_residue) {

   mmdb::Residue *prev_res = NULL;
   if (this_residue) { 
      mmdb::Chain *chain_p = this_residue->GetChain();
      if (chain_p) { 
         int nres = chain_p->GetNumberOfResidues();
         mmdb::Residue *residue_p;
         for (int ires=0; ires<nres; ires++) { 
            residue_p = chain_p->GetResidue(ires);
            if (this_residue == residue_p) {
               if (ires < (nres-1))
                  prev_res = chain_p->GetResidue(ires+1);
               break;
            } 
         }
      }
   }
   return prev_res;
}


mmdb::Atom *
coot::util::intelligent_this_residue_mmdb_atom(mmdb::Residue *res_p) {

   mmdb::PAtom *residue_atoms;
   int nResidueAtoms;
   
   res_p->GetAtomTable(residue_atoms, nResidueAtoms);
   for (int i=0; i<nResidueAtoms; i++) {
      std::string atom_name(residue_atoms[i]->name);
      if (atom_name == " CA ") {
         return residue_atoms[i];
      }
      if (atom_name == " C1'") {
         return residue_atoms[i];
      }
   }

   if (nResidueAtoms > 0) {
      return residue_atoms[0];
   }

   // failure
   return NULL;

}

float
coot::util::occupancy_sum(mmdb::PAtom *atoms, int n_atoms) {

   float os = 0.0;

   for (int i=0; i<n_atoms; i++) {
      os += atoms[i]->occupancy;
   }
   return os;
} 

short int
coot::util::is_nucleotide(mmdb::Residue *residue_p) {

   // Ancient function!

   short int nuc = 0;

   if (residue_p) { 
      std::string type(residue_p->name); // all spaces cut

      if (type == "A") {
         nuc = 1;
      } else {
         if (type == "C") {
            nuc = 1;
         } else {
            if (type == "G") {
               nuc = 1;
            } else {
               if (type == "T") {
                  nuc = 1;
               } else {
                  if (type == "U") {
                     nuc = 1;
                  }
               }
            }
         }
      }
      if (nuc) return nuc;
      
      if (type == "Ad") { 
         nuc = 1;
      } else { 
         if (type == "Cd") { 
            nuc = 1;
         } else { 
            if (type == "Gd") { 
               nuc = 1;
            } else { 
               if (type == "Td") { 
                  nuc = 1;
               } else { 
                  if (type == "Ar") { 
                     nuc = 1;
                  } else { 
                     if (type == "Cr") { 
                        nuc = 1;
                     } else { 
                        if (type == "Gr") { 
                           nuc = 1;
                        } else { 
                           if (type == "Ur") { 
                              nuc = 1;
                           } else { 
                              if (type == "DG") { 
                                 nuc = 1;
                              } else { 
                                 if (type == "DC") { 
                                    nuc = 1;
                                 } else { 
                                    if (type == "DA") { 
                                       nuc = 1;
                                    } else { 
                                       if (type == "DU") { 
                                          nuc = 1;
                                       } else { 
                                          if (type == "DT") { 
                                             nuc = 1;
                                          } else { 
                                             if (type == "DI") { 
                                                nuc = 1;
                                             } else {
                                                if (type == "Ud") {  // happens sometimes, e.g. brna.pdb
                                                   nuc = 1;
                                                } else {
                                                   if (type == "Tr") {  // not very likely
                                                      nuc = 1;
                                                   }
                                                }
                                             }
                                          }
                                       }
                                    }
                                 }
                              }
                           }
                        }
                     }
                  }
               }
            }
         }
      }
   }
   return nuc;
}

// test for presence of O2'
bool
coot::util::nucleotide_is_DNA(mmdb::Residue *r) {

   bool has_o2_prime = 0;
   mmdb::PPAtom residue_atoms = NULL;
   int n_residue_atoms;
   r->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int i=0; i<n_residue_atoms; i++) {
      std::string atom_name = residue_atoms[i]->name;
      if (atom_name == " O2'") {
         has_o2_prime = 1;
         break;
      }
      if (atom_name == " O2*") {
         has_o2_prime = 1;
         break;
      }
   }

   if (has_o2_prime)
      return 0;
   else
      return 1;
}



// Return NULL on no such chain:
// 
mmdb::Chain *
coot::util::chain_only_of_type(mmdb::Manager *mol, const std::string &residue_type) {

   mmdb::Chain *chain_p = NULL;
   mmdb::Chain *single_type_chain_p = NULL;
   mmdb::Model *model_p = mol->GetModel(1);
   mmdb::Residue *residue_p;
   
   if (model_p) { 
      int nchains = model_p->GetNumberOfChains();
      for (int ich=0; ich<nchains; ich++) {
         chain_p = model_p->GetChain(ich);
         int nres = chain_p->GetNumberOfResidues();
         if (nres) { 
            bool all_same_type_flag = true; 
            for (int ires=0; ires<nres; ires++) { 
               residue_p = chain_p->GetResidue(ires);
               std::string resname(residue_p->name);
               if (! (resname == residue_type)) {
                  all_same_type_flag = false;
                  break;
               }
            }
            if (all_same_type_flag) { 
               single_type_chain_p = chain_p;
               break;
            }
         }
      }
   }
   return single_type_chain_p;
}


std::string
coot::util::three_letter_to_one_letter(const std::string &resname) {

   std::string n;
   char r[10];
   //    std::cout << "DEBUG:: resname length: " << resname << " " << resname.length() << std::endl;

   short int done_locally = 0;
   if (resname.length() == 2) {
      if ((resname[1] == 'd') ||
          (resname[1] == 'r')) {
         n = resname.substr(0, 1);
         done_locally = 1;
      }
      if (resname == "DT") {
         n = "T";
         done_locally = 1;
      } 
      if (resname == "DG") {
         n = "G";
         done_locally = 1;
      } 
      if (resname == "DA") {
         n = "A";
         done_locally = 1;
      } 
      if (resname == "DC") {
         n = "C";
         done_locally = 1;
      } 
   }
   
   if (! done_locally) { 
      mmdb::Get1LetterCode(resname.c_str(), r);
      n = r[0];
   }
   return n;
}

std::string
coot::util::three_letter_to_one_letter_with_specials(const std::string &resname) {

   std::string n;
   if (resname == "HOH") {
      n = "~";
   } else {
      n = coot::util::three_letter_to_one_letter(resname);
   } 
   return n;
}



std::pair<clipper::Coord_orth, clipper::Coord_orth>
coot::util::extents(mmdb::Manager *mol) {

   if (! mol) return std::pair<clipper::Coord_orth, clipper::Coord_orth>
                       (clipper::Coord_orth(0,0,0), clipper::Coord_orth(0,0,0));

   int selHnd = mol->NewSelection();
   mol->SelectAtoms(selHnd, 0, "*", mmdb::ANY_RES, "*", mmdb::ANY_RES, "*",
                    "*", "*", "*", "*");
   std::pair<clipper::Coord_orth, clipper::Coord_orth> p =
      coot::util::extents(mol, selHnd);
   mol->DeleteSelection(selHnd);
   return p;
}

std::pair<clipper::Coord_orth, clipper::Coord_orth>
coot::util::extents(mmdb::Manager *mol,
                     int SelectionHandle) {

   mmdb::PAtom *atoms = NULL;
   int n_selected_atoms;
   mol->GetSelIndex(SelectionHandle, atoms, n_selected_atoms);
   float most_x = -99999;
   float most_y = -99999;
   float most_z = -99999;
   float least_x = 99999;
   float least_y = 99999;
   float least_z = 99999;
   for (int i=0; i<n_selected_atoms; i++) {
      if (atoms[i]->x > most_x) most_x = atoms[i]->x;
      if (atoms[i]->y > most_y) most_y = atoms[i]->y;
      if (atoms[i]->z > most_z) most_z = atoms[i]->z;

      if (atoms[i]->x < least_x) least_x = atoms[i]->x;
      if (atoms[i]->y < least_y) least_y = atoms[i]->y;
      if (atoms[i]->z < least_z) least_z = atoms[i]->z;
   }

   clipper::Coord_orth p1( most_x,  most_y,  most_z);
   clipper::Coord_orth p2(least_x, least_y, least_z);

   return std::pair<clipper::Coord_orth, clipper::Coord_orth> (p2, p1);
}

std::pair<clipper::Coord_orth, clipper::Coord_orth>
coot::util::extents(mmdb::Manager *mol,
                    const std::vector<residue_spec_t> &specs) {

   float most_x = -99999;
   float most_y = -99999;
   float most_z = -99999;
   float least_x = 99999;
   float least_y = 99999;
   float least_z = 99999;
   for (unsigned int ispec=0; ispec<specs.size(); ispec++) { 
      mmdb::Residue *residue_p = get_residue(specs[ispec], mol);
      if (residue_p) {
         mmdb::PPAtom residue_atoms = 0;
         int n_residue_atoms;
         residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
         for (int iat=0; iat<n_residue_atoms; iat++) { 
            mmdb::Atom *at = residue_atoms[iat];
            if (at->x < least_x) least_x = at->x;
            if (at->y < least_y) least_y = at->y;
            if (at->z < least_z) least_z = at->z;
            if (at->x >  most_x)  most_x = at->x;
            if (at->y >  most_y)  most_y = at->y;
            if (at->z >  most_z)  most_z = at->z;
         }
      }
   }
   clipper::Coord_orth p1( most_x,  most_y,  most_z);
   clipper::Coord_orth p2(least_x, least_y, least_z);
   return std::pair<clipper::Coord_orth, clipper::Coord_orth> (p2, p1);
}



// pair.second = 0 for failure
// pair.first  = 1 for success
// 
std::map<std::string, clipper::RTop_orth>
coot::util::get_ori_to_this_res(mmdb::Residue *residue_p) {

   std::map<std::string, clipper::RTop_orth> orientations;

   mmdb::PPAtom residue_atoms = 0;
   int n_residue_atoms;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   std::map<std::string, std::vector<mmdb::Atom *> > atoms;
   // first size up the vectors in the atom map
   for (int iat=0; iat<n_residue_atoms; iat++) { 
      std::string alt_conf  = residue_atoms[iat]->altLoc;
      atoms[alt_conf].resize(3,0);
   }
   for (int iat=0; iat<n_residue_atoms; iat++) { 
      std::string alt_conf  = residue_atoms[iat]->altLoc;
      std::string atom_name = residue_atoms[iat]->name;
      int name_index = -1; 
      if (atom_name == " N  ") name_index = 0;
      if (atom_name == " CA ") name_index = 1;
      if (atom_name == " C  ") name_index = 2;
      if (name_index != -1) {
         // this atom was a main chain reference atom
         atoms[alt_conf][name_index] = residue_atoms[iat];
      }
   }

   std::map<std::string, std::vector<mmdb::Atom *> >::const_iterator it;
   for(it=atoms.begin(); it!=atoms.end(); ++it) {
      if (it->second[0] && it->second[1] && it->second[2]) {
         clipper::Coord_orth  n(it->second[0]->x, it->second[0]->y, it->second[0]->z);
         clipper::Coord_orth ca(it->second[1]->x, it->second[1]->y, it->second[1]->z);
         clipper::Coord_orth  c(it->second[2]->x, it->second[2]->y, it->second[2]->z);

         clipper::Coord_orth can_unit = clipper::Coord_orth((n - ca).unit());
         clipper::Coord_orth cac_unit = clipper::Coord_orth((c - ca).unit());
         
         clipper::Coord_orth bisector ((can_unit + cac_unit).unit());
         clipper::Coord_orth diff_unit((can_unit - cac_unit).unit());
         
         clipper::Coord_orth cross_prod(clipper::Coord_orth::cross(diff_unit,bisector));
         clipper::Coord_orth cpu = clipper::Coord_orth(cross_prod.unit());

//          std::cout << "   n " <<  n.format() << std::endl;
//          std::cout << "  ca " << ca.format() << std::endl;
//          std::cout << "   c " <<  c.format() << std::endl;
//          std::cout << "bisector   " <<   bisector.format() << std::endl;
//          std::cout << "diff_unit  " <<  diff_unit.format() << std::endl;
//          std::cout << "cross prod " << cross_prod.format() << std::endl;

         // bisector   -> new x axis
         // diff_unit  -> new z axis
         // cross_prod -> new y axis
         
         clipper::Mat33<double> m(bisector.x(),  bisector.y(),  bisector.z(),
                                  cpu.x(),       cpu.y(),       cpu.z(),
                                  diff_unit.x(), diff_unit.y(), diff_unit.z());
         clipper::RTop_orth rtop(m.transpose(), ca);
         orientations[it->first] = rtop;
      }
   }

   // debug return value
   //    std::map<std::string, clipper::RTop_orth>::const_iterator ori_it;
   //    for(ori_it=orientations.begin(); ori_it!=orientations.end(); ori_it++) {
   //       std::cout << "get_ori_to_this_res :" << ori_it->first << ":" << std::endl;
   //       std::cout << ori_it->second.format() << std::endl;
   //    } 
   
   return orientations;
} 


// For sequence/sequence alignment


// Take into account the insertion code too:
std::vector<std::pair<mmdb::Residue *, int> >
coot::util::sort_residues_by_seqno(mmdb::PResidue *residues,
                                   int nResidues) {

   std::vector<std::pair<mmdb::Residue *, int> > v;

   // construct the vector
   for (int i=0; i<nResidues; i++)
      v.push_back(std::pair<mmdb::Residue *, int> (residues[i], i));

//    // test
//    std::vector<int> vi;
//    vi.push_back(10);
//    vi.push_back(1);
//    vi.push_back(0);

//    std::vector<int>::iterator start = vi.begin();
//    std::vector<int>::iterator end   = vi.end();

//    sort(start, end);

   // and now with our lovely data (not int)
   // 
   std::vector<std::pair<mmdb::Residue *, int> >::iterator start = v.begin();
   std::vector<std::pair<mmdb::Residue *, int> >::iterator end   = v.end();
   std::sort(start, end, util::compare_residues);
   // sort(start, end) for things that have implicit comparison function.

   if (false) {
      for (unsigned int i=0; i<v.size(); i++)
         std::cout << " sorted " << residue_spec_t(v[i].first) << " " << v[i].second << std::endl;
   }

   return v;
}

bool
coot::util::compare_residues(const std::pair<mmdb::Residue *, int> &a,
                             const std::pair<mmdb::Residue *, int> &b) {

   int r1 = a.first->GetSeqNum();
   int r2 = b.first->GetSeqNum();

   if (r1 < r2) {
      return 1;
   } else {
      if (r1 > r2) {
         return 0;
      } else {
         std::string ins1(a.first->GetInsCode());
         std::string ins2(b.first->GetInsCode());
         if (ins1 > ins2) {
            return 1;
         } else {
            return 0; // now checked
         }
      }
   }

   return 1;
} 


// Use the results of the above to give us a sequence string:
std::string
coot::util::model_sequence(const std::vector<std::pair<mmdb::Residue *, int> > &sa,
                           bool allow_ligands) {

   std::string s;
   char r[10];
   for (unsigned int i=0; i<sa.size(); i++) {
      std::string this_residue = "X";
      std::string res_name = sa[i].first->GetResName();
      if (is_standard_amino_acid_name(res_name) || allow_ligands) {
         mmdb::Get1LetterCode(res_name.c_str(), r);
         this_residue = r[0];
         s += this_residue;
      }
   }
   return s;
}


// residues with insertion codes
std::vector<mmdb::Residue *>
coot::util::residues_with_insertion_codes(mmdb::Manager *mol) {

   std::vector<mmdb::Residue *> v;
   
   int imod = 1;
      
   mmdb::Model *model_p = mol->GetModel(imod);
   if (! model_p) return v;
   mmdb::Chain *chain_p;
   // run over chains of the existing mol
   int nchains = model_p->GetNumberOfChains();
   for (int ichain=0; ichain<nchains; ichain++) {
      chain_p = model_p->GetChain(ichain);
      int nres = chain_p->GetNumberOfResidues();
      mmdb::PResidue residue_p;
      for (int ires=0; ires<nres; ires++) { 
         residue_p = chain_p->GetResidue(ires);
         std::string inscode(residue_p->GetInsCode());
         if (inscode != "") {
            v.push_back(residue_p);
         }
      }
   }
   return v;
}

// return the status too, torsion in radians.
std::pair<bool, double>
coot::util::omega_torsion(mmdb::Residue *C_residue, mmdb::Residue *N_residue, const std::string &altconf) {

   double omega = 0.0;
   bool istatus = false; // initially unset

   if (! C_residue) return std::make_pair(false, 0.0);
   if (! N_residue) return std::make_pair(false, 0.0);

   mmdb::PPAtom C_residue_atoms = NULL;
   int nCResidueAtoms;
   C_residue->GetAtomTable(C_residue_atoms, nCResidueAtoms);
   mmdb::Atom *C_residue_CA_atom_p = NULL;
   mmdb::Atom *C_residue_C_atom_p = NULL; 

   mmdb::PPAtom N_residue_atoms = NULL;
   int nNResidueAtoms;
   N_residue->GetAtomTable(N_residue_atoms, nNResidueAtoms);
   mmdb::Atom *N_residue_CA_atom_p = NULL;
   mmdb::Atom *N_residue_N_atom_p = NULL;

   for (int i=0; i<nCResidueAtoms; i++) {
      std::string atom_name = C_residue_atoms[i]->name;
      std::string altconf_atom = C_residue_atoms[i]->altLoc;
      if (atom_name == " CA ")
         if (altconf_atom == altconf)
            C_residue_CA_atom_p = C_residue_atoms[i];
      if (atom_name == " C  ")
         if (altconf_atom == altconf)
            C_residue_C_atom_p = C_residue_atoms[i];
   }

   for (int i=0; i<nNResidueAtoms; i++) {
      std::string atom_name = N_residue_atoms[i]->name;
      std::string altconf_atom = N_residue_atoms[i]->altLoc;
      if (atom_name == " CA ")
         if (altconf_atom == altconf)
            N_residue_CA_atom_p = N_residue_atoms[i];
      if (atom_name == " N  ")
         if (altconf_atom == altconf)
            N_residue_N_atom_p = N_residue_atoms[i];
   }

   if (C_residue_CA_atom_p && C_residue_C_atom_p && N_residue_N_atom_p && N_residue_CA_atom_p) {
      clipper::Coord_orth ca1(C_residue_CA_atom_p->x,
                              C_residue_CA_atom_p->y,
                              C_residue_CA_atom_p->z);
      clipper::Coord_orth c1(C_residue_C_atom_p->x,
                             C_residue_C_atom_p->y,
                             C_residue_C_atom_p->z);
      clipper::Coord_orth ca2(N_residue_CA_atom_p->x,
                              N_residue_CA_atom_p->y,
                              N_residue_CA_atom_p->z);
      clipper::Coord_orth n2(N_residue_N_atom_p->x,
                             N_residue_N_atom_p->y,
                             N_residue_N_atom_p->z);

      omega = clipper::Coord_orth::torsion(ca1, c1, n2, ca2);
      istatus = true;

      // std::cout << "omega from clipper function: " << omega << " "
      //           << ca1.format() << " " << c1.format() << " " << n2.format() << " " << ca2.format() << "\n      "
      //           << atom_spec_t(C_residue_CA_atom_p) << " " << atom_spec_t(C_residue_C_atom_p) << " "
      //           << atom_spec_t(N_residue_N_atom_p) << " " << atom_spec_t(N_residue_CA_atom_p) << std::endl;

   }
   return std::pair<bool, double> (istatus, omega);
}


// in radians
bool
coot::util::is_cis(const double &omega_torsion) {

   // -90 to +90
   bool is_cis_flag = false;
   if ((omega_torsion < 1.57) && (omega_torsion > -1.57))
      is_cis_flag = true;
   return is_cis_flag;
}


// This function is based on mmdb's CATom::MakePDBAtomName(), so we share
// the copyright (with Eugene/EBI).
//
// 
// 
std::string
coot::pad_atom_name(const std::string &atom_id, const std::string &element) { 

   std::string name = atom_id;
   std::string new_name; // = atom_id;

   // std::cout << "DEBUG:: :" << atom_id << ": :" << element << ":" << std::endl;

   if (name.length() == 4) {

      new_name = name;

   } else {
   
      if (element == "") {
         if (name.length() == 1) {
            new_name = " ";
            new_name += name;
            new_name += "  ";
         }
      
      } else { // element was defined

         // consider the following cases of 
         // atom_id and element:
         //   "CA"  "C"  -> " CA "
         //   "AC8" "C"  -> "AC8 " : in this case we post apply
         //                          the space because the second char of
         //                          the atom_id is equal to the
         //                          element
         //   "NN1" "N"  -> "NN1 " :
         //   "NP"  "P"  -> "NP  "
         
         if (element.length() == 1) {
            int k = atom_id.length();
            if (k == 3) {
               // std::cout << "comparing " << atom_id.substr(1,1) << " and " << element << std::endl;
               if (atom_id.substr(1,1) == element) {
                  new_name = atom_id + " ";
               } else {
                  new_name = " " + atom_id;
               }
            } else { 
               // promote the characters one space
               if (k==2) {
                  // e.g "NP" "P", or "CA" "C"
                  if ((atom_id.substr(1,1) == element) && (element != "H")) {
                     new_name = atom_id + "  ";
                  } else {
                     new_name = " " + atom_id;
                     new_name += " ";
                  }
               } else {
                  new_name = " ";
                  new_name += atom_id;
                  // fill the rest with spaces
                  new_name += "  ";
               }
            }

         } else {
            // element was 2 (or more) characters
            if (element[0] == ' ') { // unusual from dict, but usual for SHELXL reading
               if (element[1] != name[1]) {
                  // promote the characters one space
                  new_name = " ";
                  new_name += atom_id;
                  int k = atom_id.length();
                  // fill the rest with spaces
                  if (k == 1) 
                     new_name += "  ";
                  if (k == 2)
                     new_name += " ";
               } else {
                  int k = atom_id.length();
                  new_name = " ";
                  new_name += atom_id;
                  if (k == 1) 
                     new_name += "  ";
                  if (k == 2)
                     new_name += " ";
               } 
            } else {
               // This is the usual case, there is no leading space
               //
               // left justify the name and pad with spaces
               new_name = atom_id;
               if (atom_id.size() == 1) // never happens?
                  new_name += "   ";
               if (atom_id.size() == 2)
                  new_name += "  ";
               if (atom_id.size() == 3)
                  new_name += " ";
               
            }
         }
      }
   }

   // debug
//    mmdb::Atom at;
//    at.SetAtomName(atom_id.c_str());
//    at.SetElementName(type_symbol.c_str());
//    at.MakePDBAtomName();
//    if (new_name != std::string(at.name)) {
//       std::cout << "name pad failure, mmdb coot :" << at.name << ": :"
//                 << new_name << ": for in_atom :" << atom_id.c_str()
//                 << ": element :" << type_symbol.c_str() << ":" << std::endl;
//    } else {
//       std::cout << "name pad match " << new_name << std::endl;
//    }

//    std::cout << "new atom name :" << new_name << ": from :"
//              << atom_id << ": :" << element << ":" << std::endl;
   
   return new_name;
}

std::pair<double, double>
coot::lsq_plane_deviation(const std::vector<clipper::Coord_orth> &v,
                          const clipper::Coord_orth &pt) {

   coot::lsq_plane_info_t lpd(v);
   double val = lpd.plane_deviation(pt);
   double rms = lpd.plane_atoms_rms();
   return std::pair<double, double> (val, rms);
}

coot::lsq_plane_info_t::lsq_plane_info_t(const std::vector<clipper::Coord_orth> &v) {

   int n_atoms = v.size();
   clipper::Coord_orth sum(0,0,0);
   for (int i=0; i<n_atoms; i++)
      sum += v[i];
   double factor = 1/double(n_atoms);
   clipper::Coord_orth midpoint(sum.x()*factor, sum.y()*factor, sum.z()*factor);
   centre_ = midpoint;

   clipper::Matrix<double> mat(3,3);
   for (int i=0; i<n_atoms; i++) {
      mat(0,0) += (v[i].x() - midpoint.x()) * (v[i].x() - midpoint.x());
      mat(1,1) += (v[i].y() - midpoint.y()) * (v[i].y() - midpoint.y());
      mat(2,2) += (v[i].z() - midpoint.z()) * (v[i].z() - midpoint.z());
      mat(0,1) += (v[i].x() - midpoint.x()) * (v[i].y() - midpoint.y());
      mat(0,2) += (v[i].x() - midpoint.x()) * (v[i].z() - midpoint.z());
      mat(1,2) += (v[i].y() - midpoint.y()) * (v[i].z() - midpoint.z());
   }
   mat(1,0) = mat(0,1);
   mat(2,0) = mat(0,2);
   mat(2,1) = mat(1,2);

   if (0) { 
      std::cout << "  mat for eigens: " << std::endl;
      std::cout << "     " << mat(0,0) << "   " << mat(0,1) << "   " << mat(0,2) << std::endl;
      std::cout << "     " << mat(1,0) << "   " << mat(1,1) << "   " << mat(1,2) << std::endl;
      std::cout << "     " << mat(2,0) << "   " << mat(2,1) << "   " << mat(2,2) << std::endl;
   }
   std::vector<double> eigens = mat.eigen(true);
   // Let's now extract the values of a,b,c normalize them
   abcd.resize(4);
   
   abcd[0] = mat(0,0);
   abcd[1] = mat(1,0);
   abcd[2] = mat(2,0);

   if (0) 
      std::cout << " abcd - pre-values "
                << abcd[0] << " "
                << abcd[1] << " "
                << abcd[2] << " "
                << std::endl;
   
   double sqsum = 1e-20;
   
   for (int i=0; i<3; i++)
      sqsum += abcd[i] * abcd[i];
   for (int i=0; i<3; i++)
      abcd[i] /= sqsum;
   
   // set D, recall di = Axi+Byi+Czi-D, so when
   // xi = x_cen, yi = y_cen, zi = z_cen, d is 0,
   // so we can set D.
   // 
   abcd[3] = abcd[0]*midpoint.x() + abcd[1]*midpoint.y() + abcd[2]*midpoint.z();

   if (0) 
      std::cout << " abcd "
                << abcd[0] << " "
                << abcd[1] << " "
                << abcd[2] << " "
                << abcd[3] << std::endl;

   double var = 0;
   for (unsigned int i_plane_at=0; i_plane_at<v.size(); i_plane_at++) {
      double d =
         abcd[0]*v[i_plane_at].x() +
         abcd[1]*v[i_plane_at].y() +
         abcd[2]*v[i_plane_at].z() - abcd[3];
      var += d*d;
   }
   rms = 0;
   if (v.size() > 0)
      rms = sqrt(var/double(v.size()));

}


bool
coot::compare_atom_specs_user_float(const coot::atom_spec_t &a1, const coot::atom_spec_t &a2) {

   return a1.float_user_data < a2.float_user_data ? 1 : 0;

} 


// For use with interesting-things-gui, make the list argument
// from a vector of atom specs.
// 
// use the user data in the atom spec to give us the molecule number
// and the button label
// 
std::string
coot::util::interesting_things_list(const std::vector<atom_spec_t> &v) {

#ifdef USE_GUILE
   // e.g. (list) for empty v
   // (list (list "button label" imol-no chain-id resno atom-name)
   //       (list "button label" imol-no chain-id resno atom-name)
   // )

   std::string r = " (list ";

   for (unsigned int i=0; i<v.size(); i++) {

      std::string atom_str("\"");
      atom_str += v[i].chain_id;
      atom_str += "\" ";
      atom_str += int_to_string(v[i].res_no);
      atom_str += " \"";
      atom_str += v[i].ins_code;
      atom_str += "\" \"";
      atom_str += v[i].atom_name;
      atom_str += "\" \"";
      atom_str += v[i].alt_conf;
      atom_str += " \"";

      std::string button_label("Clash gap: ");
      button_label += float_to_string(v[i].float_user_data);
      button_label += " : ";
      button_label += v[i].chain_id;
      button_label += " ";
      button_label += int_to_string(v[i].res_no);
      button_label += " ";
      if (v[i].ins_code != "") {
         button_label += v[i].ins_code;
          button_label += " ";
      }
      button_label += v[i].atom_name;
      if (v[i].alt_conf != "") {
         button_label += ",";
    button_label += v[i].alt_conf;
         button_label += " ";
      }

      std::string s = "(list ";
      s += single_quote(button_label);
      s += " ";
      s += int_to_string(v[i].int_user_data);
      s += " ";
      s += atom_str;
      s += ")\n";
      
      r += s;
   }

   r += ")";
   return r;
#else
#ifdef USE_PYTHON
// BL says:: we want to have [] lists in python, separated by commas (,)
   // e.g. [] for empty v
   // [["button label",imol-no,chain-id,resno,atom-name],
   //  ["button label",imol-no,chain-id,resno,atom-name]
   // ]

   std::string r = "[";

   for (unsigned int i=0; i<v.size(); i++) {

      std::string atom_str("\"");
      atom_str += v[i].chain_id;
      atom_str += "\",";
      atom_str += int_to_string(v[i].res_no);
      atom_str += ",\"";
      atom_str += v[i].ins_code;
      atom_str += "\",\"";
      atom_str += v[i].atom_name;
      atom_str += "\",\"";
      atom_str += v[i].alt_conf;
      atom_str += " \"";

      std::string button_label("Clash gap: ");
      button_label += float_to_string(v[i].float_user_data);
      button_label += " : ";
      button_label += v[i].chain_id;
      button_label += " ";
      button_label += int_to_string(v[i].res_no);
      button_label += " ";
      if (v[i].ins_code != "") {
         button_label += v[i].ins_code;
         button_label += " ";
      }
      button_label += v[i].atom_name;
      if (v[i].alt_conf != "") {
         button_label += ",";
         button_label += v[i].alt_conf;
         button_label += " ";
      }

      std::string s = "[";
      s += single_quote(button_label);
      s += ",";
      s += int_to_string(v[i].int_user_data);
      s += ",";
      s += atom_str;
      s += "],\n";

      r += s;
   }

   r += "]";
   return r;
#else    
   return "";
#endif // PYTHON
   
#endif // GUILE
}

// we shall have an extra python version (as well)
std::string
coot::util::interesting_things_list_py(const std::vector<atom_spec_t> &v) {

#ifdef USE_PYTHON
   // BL says:: we want to have [] lists in python, separated by commas (,)
   // e.g. [] for empty v
   // [["button label",imol-no,chain-id,resno,atom-name],
   //  ["button label",imol-no,chain-id,resno,atom-name]
   // ]

   std::string r = "[";

   for (unsigned int i=0; i<v.size(); i++) {

      std::string atom_str("\"");
      atom_str += v[i].chain_id;
      atom_str += "\",";
      atom_str += int_to_string(v[i].res_no);
      atom_str += ",\"";
      atom_str += v[i].ins_code;
      atom_str += "\",\"";
      atom_str += v[i].atom_name;
      atom_str += "\",\"";
      atom_str += v[i].alt_conf;
      atom_str += " \"";

      std::string button_label("Clash gap: ");
      button_label += float_to_string(v[i].float_user_data);
      button_label += " : ";
      button_label += v[i].chain_id;
      button_label += " ";
      button_label += int_to_string(v[i].res_no);
      button_label += " ";
      if (v[i].ins_code != "") {
         button_label += v[i].ins_code;
         button_label += " ";
      }
      button_label += v[i].atom_name;
      if (v[i].alt_conf != "") {
         button_label += ",";
         button_label += v[i].alt_conf;
         button_label += " ";
      }

      std::string s = "[";
      s += single_quote(button_label);
      s += ",";
      s += int_to_string(v[i].int_user_data);
      s += ",";
      s += atom_str;
      s += "],\n";

      r += s;
   }

   r += "]";
   return r;
#else
   return "";
#endif // PYTHON
}

// error_type is e.g. "Z score", "Clash gap"
// 
std::string
coot::util::interesting_things_list_with_fix(const std::vector<coot::util::atom_spec_and_button_info_t> &v,
                                             const std::string &error_type) {

#ifdef USE_GUILE
   // e.g. (list) for empty v
   // (list (list "button label" imol-no chain-id resno atom-name)
   //       (list "button label" imol-no chain-id resno atom-name)
   // )
   //
   // if we have a fix, the callback function is not "" and then the
   // returned thing becomes:
   // 
   // (list (list "button label" imol-no chain-id resno atom-name callback-func)
   //       (list "button label" imol-no chain-id resno atom-name callback-func)
   // )
   //
   // where callback-func is e.g. (lambda() (do-180-degree-side-chain-flip 0 "A" 45 "" ""))

   std::string r = " (list ";

   for (unsigned int i=0; i<v.size(); i++) {

      std::string atom_str("\"");
      atom_str += v[i].as.chain_id;
      atom_str += "\" ";
      atom_str += int_to_string(v[i].as.res_no);
      atom_str += " \"";
      atom_str += v[i].as.ins_code;
      atom_str += "\" \"";
      atom_str += v[i].as.atom_name;
      atom_str += "\" \"";
      atom_str += v[i].as.alt_conf;
      atom_str += " \"";

      std::string button_label = v[i].button_label;

      std::string s = "(list ";
      s += single_quote(button_label);
      s += " ";
      s += int_to_string(v[i].as.int_user_data);
      s += " ";
      s += atom_str;

      if (v[i].callback_func != "") {
         s += " ";
         s +=  v[i].callback_func;
      }
      
      s += ")\n";
      
      r += s;
   }

   r += ")";
   return r;
#else
#ifdef USE_PYTHON
// BL says:: here again we need a [] list in python 
   std::string r = "[";

   for (unsigned int i=0; i<v.size(); i++) {

      std::string atom_str("\"");
      atom_str += v[i].as.chain_id;
      atom_str += "\",";
      atom_str += int_to_string(v[i].as.res_no);
      atom_str += ",\"";
      atom_str += v[i].as.ins_code;
      atom_str += "\",\"";
      atom_str += v[i].as.atom_name;
      atom_str += "\",\"";
      atom_str += v[i].as.alt_conf;
      atom_str += " \"";

      std::string button_label = v[i].button_label;

      std::string s = "[";
      s += single_quote(button_label);
      s += ",";
      s += int_to_string(v[i].as.int_user_data);
      s += ",";
      s += atom_str;

      if (v[i].callback_func != "") {
         s += ",";
         s +=  v[i].callback_func;
      }

      if (i<(v.size()-1)) {
         s += "],\n";
      } else {
         s += "]\n";
      }

      r += s;
   }

   r += "]";
   return r;
#else
   return "";
#endif // PYTHON
#endif // GUILE
}

// python version
std::string
coot::util::interesting_things_list_with_fix_py(const std::vector<coot::util::atom_spec_and_button_info_t> &v,
                                                const std::string &error_type) {
#ifdef USE_PYTHON
// BL says:: here again we need a [] list in python 
   std::string r = "[";

   for (unsigned int i=0; i<v.size(); i++) {

      std::string atom_str("\"");
      atom_str += v[i].as.chain_id;
      atom_str += "\",";
      atom_str += int_to_string(v[i].as.res_no);
      atom_str += ",\"";
      atom_str += v[i].as.ins_code;
      atom_str += "\",\"";
      atom_str += v[i].as.atom_name;
      atom_str += "\",\"";
      atom_str += v[i].as.alt_conf;
      atom_str += " \"";

      std::string button_label = v[i].button_label;

      std::string s = "[";
      s += single_quote(button_label);
      s += ",";
      s += int_to_string(v[i].as.int_user_data);
      s += ",";
      s += atom_str;

      if (v[i].callback_func != "") {
         s += ",";
         s +=  v[i].callback_func;
      }

      if (i<(v.size()-1)) {
         s += "],\n";
      } else {
         s += "]\n";
      }

      r += s;
   }

   r += "]";
   return r;
#else
   return "";
#endif // PYTHON
}



// Return the RTop that matches moving to reference.  Include the base
// atoms, *AND* the furanose and phosphate atoms.
//
// reference is residue
// moving is std_base
// 
std::pair<bool, clipper::RTop_orth>
coot::util::nucleotide_to_nucleotide(mmdb::Residue *residue,
                                     mmdb::Residue *std_base,
                                     bool use_old_style_naming) {

   bool good_rtop_flag = 0;
   clipper::Mat33<double> m_dum(1,0,0,0,1,0,0,0,1);
   clipper::Coord_orth pt_dum(0,0,0);
   clipper::RTop_orth rtop(m_dum, pt_dum);
   
   std::vector<std::string> adenine;  // Pirimidine
   adenine.push_back(" N9 ");
   adenine.push_back(" C8 ");
   adenine.push_back(" N7 ");
   adenine.push_back(" C5 ");
   adenine.push_back(" C4 ");
   // 
   adenine.push_back(" N1 ");
   adenine.push_back(" C2 ");
   adenine.push_back(" N3 ");
   adenine.push_back(" C6 ");
   adenine.push_back(" N6 ");

   std::vector<std::string> guanine; // Pirimidine
   guanine.push_back(" N9 ");
   guanine.push_back(" C8 ");
   guanine.push_back(" N7 ");
   guanine.push_back(" C5 ");
   guanine.push_back(" C4 ");
   //
   guanine.push_back(" N1 ");
   guanine.push_back(" C2 ");
   guanine.push_back(" N3 ");
   guanine.push_back(" C6 ");
   guanine.push_back(" O6 ");
   guanine.push_back(" N2 "); // No matcher for this in adenine

   std::vector<std::string> thymine;  // Purine
   thymine.push_back(" N1 ");
   thymine.push_back(" C2 ");
   thymine.push_back(" N3 ");
   thymine.push_back(" C4 ");
   thymine.push_back(" C5 ");
   thymine.push_back(" C6 ");
   // 
   thymine.push_back(" O2 ");
   thymine.push_back(" O4 ");
   if (use_old_style_naming)
      thymine.push_back(" C5M");
   else 
      thymine.push_back(" C7 ");
   
   std::vector<std::string> cytosine;  // Purine
   cytosine.push_back(" N1 ");
   cytosine.push_back(" C2 ");
   cytosine.push_back(" N3 ");
   cytosine.push_back(" C4 ");
   cytosine.push_back(" C5 ");
   cytosine.push_back(" C6 ");
   // 
   cytosine.push_back(" O2 ");
   cytosine.push_back(" N4 ");
   
   std::vector<std::string> uracil;  // Purine
   uracil.push_back(" N1 ");
   uracil.push_back(" C2 ");
   uracil.push_back(" N3 ");
   uracil.push_back(" C4 ");
   uracil.push_back(" C5 ");
   uracil.push_back(" C6 ");
   // 
   uracil.push_back(" O2 ");
   uracil.push_back(" O4 ");
   

   // These next 2 are in match order, don't change it.
   std::vector<std::string> purine; // A and G
   purine.push_back(" N9 ");
   purine.push_back(" C4 ");
   purine.push_back(" C5 ");
   purine.push_back(" N7 ");
   purine.push_back(" C8 ");

   std::vector<std::string> pyrimidine; // T, U and C
   pyrimidine.push_back(" N1 ");
   pyrimidine.push_back(" C2 ");
   pyrimidine.push_back(" N3 ");
   pyrimidine.push_back(" C5 ");
   pyrimidine.push_back(" C6 ");
   pyrimidine.push_back(" C4 ");

   // We need to know whether we have purine or pyrimidine for both
   // the molecule base and the std_base.
   //
   // We need to get all (5 for pyrimidine, 6 for purine) the
   // coordinates for both bases.
   // 
   // If they are either or both are pyrimidine we match 5 atoms,
   // If they are both purine we match 6 atoms.


   // So what are the input base types?
   //
   // These for flags should be set to something after our test
   short int mol_base_is_pyrimidine = -1;
   short int mol_base_is_purine     = -1;
   short int std_base_is_pyrimidine = -1;
   short int std_base_is_purine     = -1;

   std::string mol_base_name = residue->GetResName();
   std::string std_base_name = std_base->GetResName();

   if (mol_base_name == "Ar" || mol_base_name == "Ad" ||
       mol_base_name == "Gr" || mol_base_name == "Gd" ||
       mol_base_name == "A"  || mol_base_name == "G"  ||
       mol_base_name == "DA" || mol_base_name == "DG") {
      mol_base_is_purine = 1;
      mol_base_is_pyrimidine = 0;
   }

   if (mol_base_name == "Cr" || mol_base_name == "Cd" ||
       mol_base_name == "Ur" || mol_base_name == "Ud" ||
       mol_base_name == "Tr" || mol_base_name == "Td" ||
       mol_base_name == "T"  || mol_base_name == "U"  ||
       mol_base_name == "C"  || mol_base_name == "DC" ||
       mol_base_name == "DT" || mol_base_name == "DU" ) {
      mol_base_is_pyrimidine = 1;
      mol_base_is_purine = 0;
   }

   if (std_base_name == "Ar" || std_base_name == "Ad" ||
       std_base_name == "Gr" || std_base_name == "Gd" ||
       std_base_name == "G"  || std_base_name == "DG" ||
       std_base_name == "A"  || std_base_name == "DA" ) {
      std_base_is_purine = 1;
      std_base_is_pyrimidine = 0;
   }

   if (std_base_name == "Cr" || std_base_name == "Cd" ||
       std_base_name == "Tr" || std_base_name == "Td" ||
       std_base_name == "Ur" || std_base_name == "Ud" ||
       std_base_name == "U"  || std_base_name == "DT" ||
       std_base_name == "C"  || std_base_name == "DC" ) {
      std_base_is_pyrimidine = 1;
      std_base_is_purine = 0;
   }

   if ((mol_base_is_pyrimidine == -1) || (mol_base_is_purine == -1) || 
       (std_base_is_pyrimidine == -1) || (std_base_is_purine == -1) ) {

      std::cout << "ERROR:: nucleotide_to_nucleotide() unassigned type "
                << "mol_base_is_pyrimidine:" << " "
                << mol_base_is_pyrimidine << " "
                << "mol_base_is_purine: " << " "
                << mol_base_is_purine << " "
                << "std_base_is_pyrimidine: " << " "
                << std_base_is_pyrimidine << " "
                << "std_base_is_purine: " << " "
                << std_base_is_purine << " mol_res_name: "
                << residue->GetResName() << " std_base_name: " << std_base->GetResName()
                << std::endl;

      
   } else {
   
//       std::cout << "DEBUG:: assigned types "
//                 << "mol_base_is_pyrimidine:" << " "
//                 << mol_base_is_pyrimidine << " "
//                 << "mol_base_is_purine: " << " "
//                 << mol_base_is_purine << " "
//                 << "std_base_is_pyrimidine: " << " "
//                 << std_base_is_pyrimidine << " "
//                 << "std_base_is_purine: " << " "
//                 << std_base_is_purine << " "
//                 << residue->GetResName() << " " << std_base->GetResName()
//                 << std::endl;

      int n_match_atoms = 5;
      if (mol_base_is_pyrimidine && std_base_is_pyrimidine)
         n_match_atoms = 6;

      std::vector<std::string> moving_name_vector;
      std::vector<std::string> refrce_name_vector;

      if (std_base_is_purine)
         moving_name_vector = purine;
      else
         moving_name_vector = pyrimidine;

      if (mol_base_is_purine)
         refrce_name_vector = purine;
      else
         refrce_name_vector = pyrimidine;
      
      mmdb::PAtom *std_base_atoms;
      int n_std_base_atoms;

      mmdb::PAtom *mol_base_atoms;
      int n_mol_base_atoms;
      
      residue->GetAtomTable( mol_base_atoms, n_mol_base_atoms);
      std_base->GetAtomTable(std_base_atoms, n_std_base_atoms);

      std::vector<clipper::Coord_orth> refrce_atom_positions;
      std::vector<clipper::Coord_orth> moving_atom_positions;

      if (0) { 
         for (unsigned int i=0; i<refrce_name_vector.size(); i++)
            std::cout << "ref base search atom :" << refrce_name_vector[i]
                      << ":" << std::endl;
         for (unsigned int i=0; i<moving_name_vector.size(); i++)
            std::cout << "mov base search atom :" << moving_name_vector[i]
                      << ":" << std::endl;
      }
      
      for (int j=0; j<n_match_atoms; j++) {
         for (int i=0; i<n_mol_base_atoms; i++) {
            std::string atom_name = mol_base_atoms[i]->name;
            if (refrce_name_vector[j] == atom_name) {
               refrce_atom_positions.push_back(clipper::Coord_orth(mol_base_atoms[i]->x,
                                                                   mol_base_atoms[i]->y,
                                                                   mol_base_atoms[i]->z));
               if (0) 
                  std::cout << "Found " << atom_name << " in reference " << std::endl;
            }
         }
      }

      for (int j=0; j<n_match_atoms; j++) {
         for (int i=0; i<n_std_base_atoms; i++) {
         std::string atom_name = std_base_atoms[i]->name;
            if (moving_name_vector[j] == atom_name) {
               moving_atom_positions.push_back(clipper::Coord_orth(std_base_atoms[i]->x,
                                                                   std_base_atoms[i]->y,
                                                                   std_base_atoms[i]->z));
               if (0) 
                  std::cout << "Found " << atom_name << " in moving (std) base " << std::endl;
            }
         }
      }

      if (int(refrce_atom_positions.size()) != n_match_atoms) {
         std::cout << "ERROR:: wrong number of reference atoms found! "
                   << refrce_atom_positions.size() << std::endl;
      } else {

         if (int(moving_atom_positions.size()) != n_match_atoms) {
            std::cout << "ERROR:: wrong number of moving atoms found! "
                   << moving_atom_positions.size() << std::endl;

         } else {

            // all nucleodites have these atoms, use them to do a match:
            // 
            std::vector<std::string> const_nuc_atoms;
            std::string prime_char = "'";
            if (use_old_style_naming)
               prime_char = "*";
            const_nuc_atoms.push_back(std::string(" C1")+prime_char);
            const_nuc_atoms.push_back(std::string(" C2")+prime_char);
            const_nuc_atoms.push_back(std::string(" C3")+prime_char);
            const_nuc_atoms.push_back(std::string(" C4")+prime_char);
            const_nuc_atoms.push_back(std::string(" C5")+prime_char);
            const_nuc_atoms.push_back(std::string(" O3")+prime_char);
            const_nuc_atoms.push_back(std::string(" O4")+prime_char);
            const_nuc_atoms.push_back(std::string(" O5")+prime_char);
            const_nuc_atoms.push_back(std::string(" P ")+prime_char);

            // We want to match the bases too, don't we?
//             moving_atom_positions.clear();
//             refrce_atom_positions.clear(); 

            for (unsigned int inuc=0; inuc<const_nuc_atoms.size(); inuc++) {
               for (int istd=0; istd<n_std_base_atoms; istd++) {
                  std::string std_base_atom_name = std_base_atoms[istd]->name;
                  if (std_base_atom_name == const_nuc_atoms[inuc]) { 
                     for (int imol=0; imol<n_mol_base_atoms; imol++) {
                        std::string mol_base_atom_name = mol_base_atoms[imol]->name;
                        if (mol_base_atom_name == std_base_atom_name) {
                           std::string altconf1 = std_base_atoms[istd]->altLoc;
                           std::string altconf2 = mol_base_atoms[imol]->altLoc;
                           if (altconf1 == altconf2) {
                              clipper::Coord_orth s(std_base_atoms[istd]->x,
                                                    std_base_atoms[istd]->y,
                                                    std_base_atoms[istd]->z);
                              clipper::Coord_orth m(mol_base_atoms[imol]->x,
                                                    mol_base_atoms[imol]->y,
                                                    mol_base_atoms[imol]->z);
                           
//                               std::cout << "---" << std::endl;
//                               std::cout << std_base_atoms[istd]->GetSeqNum() << " "
//                                         << std_base_atoms[istd]->name << " ("
//                                         << std_base_atoms[istd]->x << ","
//                                         << std_base_atoms[istd]->y << ","
//                                         << std_base_atoms[istd]->z << ")" << std::endl;

//                               std::cout << mol_base_atoms[imol]->GetSeqNum() << " "
//                                         << mol_base_atoms[imol]->name << " ("
//                                         << mol_base_atoms[imol]->x << ","
//                                         << mol_base_atoms[imol]->y << ","
//                                         << mol_base_atoms[imol]->z << ")" << std::endl;

                              refrce_atom_positions.push_back(m);
                              moving_atom_positions.push_back(s);
                           }
                        }
                     }
                  }
               }
            }

//             std::cout << "debug:: matching "
//                       << moving_atom_positions.size() << " atoms" << std::endl;
            
            rtop = clipper::RTop_orth (moving_atom_positions, refrce_atom_positions);
            good_rtop_flag = 1;
         }
      }
   }
   return std::pair<bool, clipper::RTop_orth> (good_rtop_flag, rtop);
}


std::vector<std::pair<coot::atom_spec_t, std::string> >
coot::util::gln_asn_b_factor_outliers(mmdb::Manager *mol) {

   std::vector<std::pair<coot::atom_spec_t, std::string> > v;
   int imod = 1;
      
   mmdb::Model *model_p = mol->GetModel(imod);
   if (! model_p) return v;
   mmdb::Chain *chain_p;

   int nchains = model_p->GetNumberOfChains();
   for (int ichain=0; ichain<nchains; ichain++) {
      chain_p = model_p->GetChain(ichain);
      int nres = chain_p->GetNumberOfResidues();
      mmdb::PResidue residue_p;
      mmdb::Atom *at;
      for (int ires=0; ires<nres; ires++) { 
         residue_p = chain_p->GetResidue(ires);
         int n_atoms = residue_p->GetNumberOfAtoms();
         std::string residue_name(residue_p->GetResName());
         if ((residue_name == "ASN") ||
             (residue_name == "GLN")) {
            float b_sum = 0.0;
            float b_sum_sq = 0.0;
            mmdb::Atom *oatom = NULL;
            mmdb::Atom *natom = NULL;
            mmdb::Atom *go_to_atom = NULL;
            int n_residue_atoms = 0;
            for (int iat=0; iat<n_atoms; iat++) {
               at = residue_p->GetAtom(iat);
               std::string altloc(at->altLoc);
               if (altloc == "") {
                  std::string atom_name(at->GetAtomName());
                  
                  if (((residue_name == "GLN") &&
                       ((atom_name == " OE1") ||
                        (atom_name == " NE2"))) ||
                      ((residue_name == "ASN") &&
                       ((atom_name == "OD1") ||
                        (atom_name == "ND2")))) {
                     
                     if (residue_name == "GLN") { 
                        if (atom_name == " OE1") {
                           oatom = at;
                        }
                        if (atom_name == " NE2") {
                           natom = at;
                        }
                     }
                     if (residue_name == "ASN") { 
                        if (atom_name == " OD1") {
                           oatom = at;
                        }
                        if (atom_name == " ND2") {
                           natom = at;
                        }
                     }
                  } else {
                     // is a normal atom of the residue:
                     b_sum += at->tempFactor;
                     b_sum_sq += at->tempFactor * at->tempFactor;
                     n_residue_atoms++;
                  }
                  // find the atom to centre on when the button is
                  // clicked (that's why we need an atom spec vector,
                  // not a residue spec.
                  if (residue_name == "GLN") {
                     if (atom_name == " CD ")
                        go_to_atom = at;
                  }
                  if (residue_name == "ASN") {
                     if (atom_name == " CG ")
                        go_to_atom = at;
                  }
               }
            }
            // end of residue atoms loop
            if (oatom) {
               if (natom) {
                  if (n_residue_atoms > 2) {
                     float mean = b_sum/float(n_residue_atoms);
                     float var = b_sum_sq/float(n_residue_atoms) - mean*mean;
                     float std_dev = sqrt(var);
                     float diff = (oatom->tempFactor - natom->tempFactor)/2.0;
                     // we are only interested in cases that have the
                     // O atom B-factor greater than the N atom
                     // B-factor because only they can be fixed by
                     // flipping.
                     if (diff > 0.0) { 
                        float z = fabs(diff/std_dev);
                        // std::cout << z << std::endl;
                        //                      std::cout << diff << "/sqrt(" << var << ") = " << z
                        //                                << "           " << b_sum << " " << b_sum_sq << " "
                        //                                << n_residue_atoms << std::endl;
                        
                        if (go_to_atom) { 
                           if (z > 2.25) {
                              coot::atom_spec_t as(go_to_atom);
                              std::string button_label = "Z score = ";
                              button_label += coot::util::float_to_string(z);
                              button_label += "   ";
                              button_label += go_to_atom->GetChainID();
                              button_label += " ";
                              button_label += int_to_string(go_to_atom->GetSeqNum());
                              button_label += " ";
                              button_label += go_to_atom->GetResName();
                              as.float_user_data = z;
                              std::pair<coot::atom_spec_t, std::string> p(as, button_label);
                              v.push_back(p);
                           }
                        }
                     }
                  }
               }
            }
         }
      }
   }
   if (v.size() > 1) {
      // sort v;
      std::sort(v.begin(), v.end(), coot::compare_atom_specs_user_float_in_pair);
   }
   return v;
}

bool
coot::compare_atom_specs_user_float_in_pair(const std::pair<coot::atom_spec_t, std::string> &a,
                                            const std::pair<coot::atom_spec_t, std::string> &b) {

   return b.first.float_user_data < a.first.float_user_data ? 1 : 0;
}

bool
coot::util::residue_has_hydrogens_p(mmdb::Residue *res) {

   bool result = 0;

   if (res) { 
      mmdb::PPAtom residue_atoms;
      int natoms;
      res->GetAtomTable(residue_atoms, natoms);
      for (int iat=0; iat<natoms; iat++) {
         mmdb::Atom *at = residue_atoms[iat];
         if (! at->isTer()) {
            std::string ele(at->element);
            if ((ele == " H") || (ele == " D")) {
               result = 1;
               break;
            }
         }
      }
   }
   return result;
}

// return 0 for no, 1 for yes, -1 for NULL residue or 0 atoms;
int
coot::util::residue_has_hetatms(mmdb::Residue *residue_p) {

   int result = -1;
   if (residue_p) { 
      mmdb::PPAtom residue_atoms = 0;
      int natoms;
      residue_p->GetAtomTable(residue_atoms, natoms);
      if (natoms) {
         result = 0;
         for (int iat=0; iat<natoms; iat++) {
            if (residue_atoms[iat]->Het) {
               result = 1;
               break;
            }
         }
      }
   }
   return result;
} 


// angle in radians.
clipper::Coord_orth
coot::util::rotate_around_vector(const clipper::Coord_orth &direction,
                                 const clipper::Coord_orth &position,
                                 const clipper::Coord_orth &origin_shift,
                                 double angle) {
   
   clipper::Coord_orth unit_vec = clipper::Coord_orth(direction.unit());
   
   double l = unit_vec[0];
   double m = unit_vec[1];
   double n = unit_vec[2];

   double ll = l*l;
   double mm = m*m;
   double nn = n*n;
   double cosk = cos(angle);
   double sink = sin(angle);
   double I_cosk = 1.0 - cosk;
   
   // The Rotation matrix angle w about vector with direction cosines l,m,n.
   // 
   // ( l**2+(m**2+n**2)cos k     lm(1-cos k)-nsin k        nl(1-cos k)+msin k   )
   // ( lm(1-cos k)+nsin k        m**2+(l**2+n**2)cos k     mn(1-cos k)-lsin k   )
   // ( nl(1-cos k)-msin k        mn(1-cos k)+lsin k        n*2+(l**2+m**2)cos k )
   //
   // (Amore documentation) Thanks for that pointer EJD :).
   
   clipper::Mat33<double> r( ll+(mm+nn)*cosk,    l*m*I_cosk-n*sink,  n*l*I_cosk+m*sink,
                             l*m*I_cosk+n*sink,  mm+(ll+nn)*cosk,    m*n*I_cosk-l*sink,
                             n*l*I_cosk-m*sink,  m*n*I_cosk+l*sink,  nn+(ll+mm)*cosk );
   clipper::RTop_orth rtop(r, clipper::Coord_orth(0,0,0));
   return origin_shift + (position-origin_shift).transform(rtop);
}


// angle in radians
// 
void
coot::util::rotate_residue(mmdb::Residue *residue_p,
                           const clipper::Coord_orth &direction,
                           const clipper::Coord_orth &origin_shift,
                           double angle) {

   if (residue_p) {
      mmdb::PPAtom residue_atoms = 0;
      int n_residue_atoms;
      residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) {
         mmdb::Atom *at = residue_atoms[iat];
         if (at) {
            if (! at->isTer()) {
               clipper::Coord_orth pt(at->x, at->y, at->z);
               clipper::Coord_orth pt_new = rotate_around_vector(direction, pt, origin_shift, angle);
               at->x = pt_new.x();
               at->y = pt_new.y();
               at->z = pt_new.z();
            }
         }
      }
   }
}

// move the coordinates of at:
// angle in radians
void
coot::util::rotate_atom_about(const clipper::Coord_orth &direction,
                              const clipper::Coord_orth &origin_shift,
                              double angle, mmdb::Atom *at) {

   if (at) {
      clipper::Coord_orth pos(at->x, at->y, at->z);
      clipper::Coord_orth new_pos = rotate_around_vector(direction, pos, origin_shift, angle);
      at->x = new_pos.x();
      at->y = new_pos.y();
      at->z = new_pos.z();
   }
} 





std::string
coot::util::cis_peptide_info_t::string() const {

   std::string s;
   s += chain_id_1;
   s += " ";
   s += int_to_string(resno_1);
   if (! ins_code_1.empty()) { 
      s += " ";
      s += ins_code_1;
   }
   s += " - ";
   s += chain_id_2;
   s += " ";
   s += int_to_string(resno_2);
   if (! ins_code_2.empty()) { 
      s += " ";
      s += ins_code_2;
   }
   return s;
}

void
coot::util::standardize_peptide_C_N_distances(const std::vector<std::pair<mmdb::Atom *, mmdb::Atom *> > &C_N_pairs) {

   for (std::size_t i=0; i<C_N_pairs.size(); i++) {
      mmdb::Atom *c_at = C_N_pairs[i].first;
      mmdb::Atom *n_at = C_N_pairs[i].second;
      if (c_at) {
         if (n_at) {
            clipper::Coord_orth pt_1 = co(c_at);
            clipper::Coord_orth pt_2 = co(n_at);
            double d = clipper::Coord_orth::length(pt_1, pt_2);
            if (d > 1.32) {
               clipper::Coord_orth delta = pt_2 - pt_1;
               clipper::Coord_orth uv(delta.unit());
               double shift = 0.5 * (d - 1.32);
               c_at->x += shift * uv.x();
               c_at->y += shift * uv.y();
               c_at->z += shift * uv.z();
               n_at->x -= shift * uv.x();
               n_at->y -= shift * uv.y();
               n_at->z -= shift * uv.z();
            }
         }
      }
   }
}

std::vector<std::pair<mmdb::Atom *, mmdb::Atom *> >
coot::util::peptide_C_N_pairs(mmdb::Chain *chain_p) {

   double dist_crit = 2.5;

   std::vector<std::pair<mmdb::Atom *, mmdb::Atom *> > v;
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      for (int ires=0; ires<(nres-1); ires++) {
         mmdb::Atom *c_first = NULL, *n_next = NULL;
         mmdb::Residue *residue_p_1 = chain_p->GetResidue(ires);
         int n_atoms_1 = residue_p_1->GetNumberOfAtoms();
         mmdb::Residue *residue_p_2 = chain_p->GetResidue(ires+1);
         int n_atoms_2 = residue_p_2->GetNumberOfAtoms();
         int seq_num_1 = residue_p_1->GetSeqNum();
         int seq_num_2 = residue_p_2->GetSeqNum();
         // just test for tandem residues, insertion codes will cause a mess
         if (seq_num_2 == (seq_num_1+1)) {
            for (int iat=0; iat<n_atoms_1; iat++) {
               mmdb::Atom *at_1 = residue_p_1->GetAtom(iat);
               if (std::string(at_1->GetAtomName()) == " C  ") {
                  c_first = at_1;
                  break;
               }
            }
            // this could go inside the c_first test if speed is needed
            for (int iat=0; iat<n_atoms_2; iat++) {
               mmdb::Atom *at_2 = residue_p_2->GetAtom(iat);
               if (std::string(at_2->GetAtomName()) == " N  ") {
                  n_next = at_2;
                  break;
               }
            }
            if (c_first) {
               if (n_next) {
                  if (! c_first->isTer() && ! n_next->isTer()) {
                     std::string alt_conf_1(c_first->altLoc);
                     std::string alt_conf_2(n_next->altLoc);
                     if (alt_conf_1.empty() || alt_conf_2.empty() || alt_conf_1 == alt_conf_2) {
                        clipper::Coord_orth pt_1 = co(c_first);
                        clipper::Coord_orth pt_2 = co(n_next);
                        double d = clipper::Coord_orth::length(pt_1, pt_2);
                        if (d < dist_crit) {
                           std::string rn_1(residue_p_1->GetResName());
                           std::string rn_2(residue_p_2->GetResName());
                           if (is_standard_amino_acid_name(rn_1)) {
                              if (is_standard_amino_acid_name(rn_2)) {
                                 std::pair<mmdb::Atom *, mmdb::Atom *> p(c_first, n_next);
                                 v.push_back(p);
                              }
                           }
                        }
                     }
                  }
               }
            }
         }
      }
   }
   return v;
}






// We ignore the issue of alt confs because from refinement/reg we
// will be only looking at a single stretch of amino acids, of a given
// alt conf (or blank).
// 
int
coot::util::count_cis_peptides(mmdb::Manager *mol) {

   return cis_peptides_info_from_coords(mol).size();
}

std::vector<coot::util::cis_peptide_info_t>
coot::util::cis_peptides_info_from_coords(mmdb::Manager *mol) {

   std::vector<coot::util::cis_peptide_info_t> v;

   if (!mol) return v;
   
   int n_models = mol->GetNumberOfModels();
   if (n_models== 0) {
      return v;
   }
   
   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (! model_p)
      return v;
   
   mmdb::Chain *chain_p;
   int nchains = model_p->GetNumberOfChains();
   for (int ichain=0; ichain<nchains; ichain++) {
      chain_p = model_p->GetChain(ichain);
      if (chain_p) { 
         // std::cout << "DEBUGG:: in cis_peptides_info_from_coords ichain " << ichain
         // << " chain id " << chain_p->GetChainID() << std::endl;
         int nres = chain_p->GetNumberOfResidues();
         mmdb::Residue *residue_p_1 = 0;
         mmdb::Residue *residue_p_2 = 0;
         mmdb::Atom *at_1 = 0;
         mmdb::Atom *at_2 = 0;
         for (int ires=0; ires<(nres-1); ires++) { 
   
            int n_atoms_1 = 0;
            int n_atoms_2 = 0;
            mmdb::Atom *ca_first = NULL, *c_first = NULL, *n_next = NULL, *ca_next = NULL;
            residue_p_1 = chain_p->GetResidue(ires);
            residue_p_2 = chain_p->GetResidue(ires+1);

            if (residue_p_1 && residue_p_2) { 

               n_atoms_1 = residue_p_1->GetNumberOfAtoms();
               n_atoms_2 = residue_p_2->GetNumberOfAtoms();

               for (int iat=0; iat<n_atoms_1; iat++) {
                  at_1 = residue_p_1->GetAtom(iat);
                  if (std::string(at_1->GetAtomName()) == " CA ")
                     ca_first = at_1;
                  if (std::string(at_1->GetAtomName()) == " C  ")
                     c_first = at_1;
               }

               for (int iat=0; iat<n_atoms_2; iat++) {
                  at_2 = residue_p_2->GetAtom(iat);
                  if (std::string(at_2->GetAtomName()) == " CA ")
                     ca_next = at_2;
                  if (std::string(at_2->GetAtomName()) == " N  ")
                     n_next = at_2;
               }
            }
         
            if (ca_first && c_first && n_next && ca_next) {

               // we don't want to include CISPEPs for residues that
               // have a TER card between them.
               // 
               bool is_ter = false;
               for (int iat=0; iat<n_atoms_1; iat++) { 
                  mmdb::Atom *at = residue_p_1->GetAtom(iat);
                  if (at->isTer()) {
                     is_ter = true;
                     break;
                  }
               }
               if (! is_ter) {
                  clipper::Coord_orth caf(ca_first->x, ca_first->y, ca_first->z);
                  clipper::Coord_orth  cf( c_first->x,  c_first->y,  c_first->z);
                  clipper::Coord_orth can( ca_next->x,  ca_next->y,  ca_next->z);
                  clipper::Coord_orth  nn(  n_next->x,   n_next->y,   n_next->z);
                  double tors = clipper::Coord_orth::torsion(caf, cf, nn, can);
                  double torsion = clipper::Util::rad2d(tors);
                  double pos_torsion = (torsion > 0.0) ? torsion : 360.0 + torsion;
                  double distortion = fabs(180.0 - pos_torsion);
                  double d = sqrt((cf - nn).lengthsq());
                  if (d<3.0) { // the residues were close in space, not just close in sequence
                     if (distortion > 90.0) {
                        coot::residue_spec_t rs1(residue_p_1);
                        coot::residue_spec_t rs2(residue_p_2);
                        coot::util::cis_peptide_info_t cpi(chain_p->GetChainID(), rs1, rs2, imod, torsion);
                        cpi.residue_name_1 = residue_p_1->GetResName();
                        cpi.residue_name_2 = residue_p_2->GetResName();
                        v.push_back(cpi);
                     }
                  }
               }
            }
         } 
      }
   }
   return v;
}


int
coot::util::cis_trans_conversion(mmdb::Residue *res_first, mmdb::Residue *res_second,
                                 mmdb::Manager *mol, mmdb::Manager *standard_residues_mol) {

   int count = 0;

   if (standard_residues_mol) {
      mmdb::PResidue *trans_residues = NULL;
      mmdb::PResidue *cis_residues = NULL;
      int selHnd_trans = standard_residues_mol->NewSelection();
      int ntrans_residues;
      standard_residues_mol->Select(selHnd_trans, mmdb::STYPE_RESIDUE, 0,
                                    "*",
                                    mmdb::ANY_RES, "*",
                                    mmdb::ANY_RES, "*",
                                    "TNS", // residue name
                                    "*",   // Residue must contain this atom name?
                                    "*",   // Residue must contain this Element?
                                    "*",   // altLocs
                                    mmdb::SKEY_NEW // selection key
                                    );
      standard_residues_mol->GetSelIndex(selHnd_trans, trans_residues, ntrans_residues);
      if (ntrans_residues >= 2) {

         int selHnd_cis = standard_residues_mol->NewSelection(); // d
         int ncis_residues;
         standard_residues_mol->Select(selHnd_cis, mmdb::STYPE_RESIDUE, 0,
                                       "*",
                                       mmdb::ANY_RES, "*",
                                       mmdb::ANY_RES, "*",
                                       "CIS", // residue name
                                       "*",   // Residue must contain this atom name?
                                       "*",   // Residue must contain this Element?
                                       "*",   // altLocs
                                       mmdb::SKEY_NEW // selection key
                                       );
         standard_residues_mol->GetSelIndex(selHnd_cis, cis_residues, ncis_residues);

         if (ncis_residues >= 2) {

            auto mol_residues_pair = std::make_pair(res_first, res_second);
            int istatus = cis_trans_convert(mol_residues_pair, trans_residues, cis_residues);
            if (istatus) count = 1; // snicker.
         }
         standard_residues_mol->DeleteSelection(selHnd_cis);
      }
      standard_residues_mol->DeleteSelection(selHnd_trans);
   }
   return count;
}


// ---- cis <-> trans conversion
int
coot::util::cis_trans_conversion(mmdb::Atom *at, bool is_N_flag, mmdb::Manager *mol, mmdb::Manager *standard_residues_mol) {

   // These 3 are pointers, each of which are of size 2
   mmdb::PResidue *trans_residues = NULL;
   mmdb::PResidue *cis_residues = NULL;
   mmdb::PResidue *mol_residues = NULL;

   int offset = 0;
   if (is_N_flag)
      offset = -1;

   int resno_1 = at->GetSeqNum() + offset;
   int resno_2 = resno_1 + 1; // i.e. *this* residue, if N clicked.
   char *chain_id = at->GetChainID();

   int selHnd = mol->NewSelection(); //
   int nSelResidues;

   mol->Select(selHnd, mmdb::STYPE_RESIDUE, 0,
                        chain_id,
                        resno_1, "*",
                        resno_2, "*",
                        "*",  // residue name
                        "*",  // Residue must contain this atom name?
                        "*",  // Residue must contain this Element?
                        "*",  // altLocs
                        mmdb::SKEY_NEW // selection key
                        );
   mol->GetSelIndex(selHnd, mol_residues, nSelResidues);

   int istat = 0;
   if (nSelResidues >= 2) {

      if (standard_residues_mol) {
         int selHnd_trans = standard_residues_mol->NewSelection();
         int ntrans_residues;
         standard_residues_mol->Select(selHnd_trans, mmdb::STYPE_RESIDUE, 0,
                                             "*",
                                             mmdb::ANY_RES, "*",
                                             mmdb::ANY_RES, "*",
                                             "TNS", // residue name
                                             "*",   // Residue must contain this atom name?
                                             "*",   // Residue must contain this Element?
                                             "*",   // altLocs
                                             mmdb::SKEY_NEW // selection key
                                             );
         standard_residues_mol->GetSelIndex(selHnd_trans,
                                                  trans_residues, ntrans_residues);
         if (ntrans_residues >= 2) {

            int selHnd_cis = standard_residues_mol->NewSelection(); // d
            int ncis_residues;
            standard_residues_mol->Select(selHnd_cis, mmdb::STYPE_RESIDUE, 0,
                                                "*",
                                                mmdb::ANY_RES, "*",
                                                mmdb::ANY_RES, "*",
                                                "CIS", // residue name
                                                "*",   // Residue must contain this atom name?
                                                "*",   // Residue must contain this Element?
                                                "*",   // altLocs
                                                mmdb::SKEY_NEW // selection key
                                                );
            standard_residues_mol->GetSelIndex(selHnd_cis, cis_residues, ncis_residues);

            if (ncis_residues >= 2) {

               mmdb::PPAtom residue_atoms = NULL;
               int n_residue_atoms;
               trans_residues[0]->GetAtomTable(residue_atoms, n_residue_atoms);
               trans_residues[1]->GetAtomTable(residue_atoms, n_residue_atoms);

               std::pair<mmdb::Residue *, mmdb::Residue *> mol_residues_pair(mol_residues[0], mol_residues[1]);
               istat = cis_trans_convert(mol_residues_pair, trans_residues, cis_residues);

            } else {
               std::cout << "ERROR:: failed to get cis residues in cis_trans_convert "
                         << ncis_residues << std::endl;
            }
            standard_residues_mol->DeleteSelection(selHnd_cis);
         } else {
            // std::cout << "ERROR:: failed to get trans residues in cis_trans_convert "
            // << ntrans_residues << std::endl;
            logger.log(log_t::ERROR, logging::function_name_t("cis_trans_conversion"),
                       "failed to get trans residues");
         }
         standard_residues_mol->DeleteSelection(selHnd_trans);
      } else {
         // std::cout << "ERROR:: NULL standard residues molecule" << std::endl;
         logger.log(log_t::ERROR, logging::function_name_t("cis_trans_conversion"),
                    "NULL standard residues molecule");
      }
   } else {
      // std::cout << "ERROR:: failed to get mol residues in cis_trans_convert" << std::endl;
      logger.log(log_t::ERROR, logging::function_name_t("cis_trans_conversion"),
                 "failed to get mol residues in cis_trans_convert");
   }
   mol->DeleteSelection(selHnd);

   return istat;
}


// mol_residues, trans_residues, cis_residues must be at least of length 2.
// return status (1 for success)
int
coot::util::cis_trans_convert(std::pair<mmdb::Residue *, mmdb::Residue *> mol_residues, // for mc conversion
                              mmdb::PResidue *trans_residues,
                              mmdb::PResidue *cis_residues) {


   // First of all, are we cis or trans?
   //
   // mol_residues is guaranteed to have at least 2 residues.
   //
   int istatus = 0;
   if (! mol_residues.first)  return 0;
   if (! mol_residues.second) return 0;
   std::string altconf("");
   std::pair<short int, double> omega =
      coot::util::omega_torsion(mol_residues.first, mol_residues.second, altconf);

   std::cout << "INFO:: omega: " << omega.first << " " << omega.second*180.0/3.14159
             << " degrees " << std::endl;

   if (omega.first) {
      short int is_cis_flag = 0;
      mmdb::PResidue *cis_trans_init_match = trans_residues;
      mmdb::PResidue *converted_residues   = cis_residues;
      if ((omega.second < 1.57) && (omega.second > -1.57)) {
         std::cout << "INFO:: This is a CIS peptide - making it TRANS" << std::endl;
         is_cis_flag = 1;
         cis_trans_init_match = cis_residues;
         converted_residues = trans_residues;
      } else {
         std::cout << "INFO:: This is a TRANS peptide - making it CIS" << std::endl;
      }

      // Now match cis_trans_init_match petide atoms onto the peptide
      // atoms of mol_residues and give us a transformation matrix.
      // That matrix will be applied to the converted_residues to give
      // new position of peptide atoms of the mol_residues.

      // we need to set these:
      mmdb::Atom *mol_residue_CA_1 = NULL;
      mmdb::Atom *mol_residue_C_1  = NULL;
      mmdb::Atom *mol_residue_O_1  = NULL;
      mmdb::Atom *mol_residue_CA_2 = NULL;
      mmdb::Atom *mol_residue_N_2  = NULL;
      mmdb::Atom *mol_residue_H_2  = NULL;

      mmdb::PPAtom mol_residue_atoms = NULL;
      int n_residue_atoms;
      mol_residues.first->GetAtomTable(mol_residue_atoms, n_residue_atoms);
      for (int i=0; i<n_residue_atoms; i++) {
         std::string atom_name = mol_residue_atoms[i]->name;
         if (atom_name == " CA ") {
            mol_residue_CA_1 = mol_residue_atoms[i];
         }
         if (atom_name == " C  ") {
            mol_residue_C_1 = mol_residue_atoms[i];
         }
         if (atom_name == " O  ") {
            mol_residue_O_1 = mol_residue_atoms[i];
         }
      }
      mol_residue_atoms = NULL;
      mol_residues.second->GetAtomTable(mol_residue_atoms, n_residue_atoms);
      for (int i=0; i<n_residue_atoms; i++) {
         std::string atom_name = mol_residue_atoms[i]->name;
         if (atom_name == " CA ") {
            mol_residue_CA_2 = mol_residue_atoms[i];
         }
         if (atom_name == " N  ") {
            mol_residue_N_2 = mol_residue_atoms[i];
         }
         if (atom_name == " H  ") {
            mol_residue_H_2 = mol_residue_atoms[i];
         }
      }

      if (mol_residue_CA_1 && mol_residue_C_1 && mol_residue_O_1 &&
          mol_residue_CA_2 && mol_residue_N_2) {

         // So we have this molecules atoms.
         // Now do something similar to get the atoms of cis_trans_init_match

         // we need to set these:
         mmdb::Atom *cis_trans_init_match_residue_CA_1 = NULL;
         mmdb::Atom *cis_trans_init_match_residue_C_1  = NULL;
         mmdb::Atom *cis_trans_init_match_residue_O_1  = NULL;
         mmdb::Atom *cis_trans_init_match_residue_CA_2 = NULL;
         mmdb::Atom *cis_trans_init_match_residue_N_2  = NULL;

         mmdb::PPAtom cis_trans_init_match_residue_atoms = NULL;
         cis_trans_init_match[0]->GetAtomTable(cis_trans_init_match_residue_atoms,
                                               n_residue_atoms);
         for (int i=0; i<n_residue_atoms; i++) {
            std::string atom_name = cis_trans_init_match_residue_atoms[i]->name;
            if (atom_name == " CA ") {
               cis_trans_init_match_residue_CA_1 = cis_trans_init_match_residue_atoms[i];
            }
            if (atom_name == " C  ") {
               cis_trans_init_match_residue_C_1 = cis_trans_init_match_residue_atoms[i];
            }
            if (atom_name == " O  ") {
               cis_trans_init_match_residue_O_1 = cis_trans_init_match_residue_atoms[i];
            }
         }
         cis_trans_init_match_residue_atoms = NULL;
         cis_trans_init_match[1]->GetAtomTable(cis_trans_init_match_residue_atoms,
                                               n_residue_atoms);
         for (int i=0; i<n_residue_atoms; i++) {
            std::string atom_name = cis_trans_init_match_residue_atoms[i]->name;
            if (atom_name == " CA ") {
               cis_trans_init_match_residue_CA_2 = cis_trans_init_match_residue_atoms[i];
            }
            if (atom_name == " N  ") {
               cis_trans_init_match_residue_N_2 = cis_trans_init_match_residue_atoms[i];
            }
         }

         if (cis_trans_init_match_residue_CA_1 &&
             cis_trans_init_match_residue_C_1 &&
             cis_trans_init_match_residue_O_1 &&
             cis_trans_init_match_residue_CA_2 &&
             cis_trans_init_match_residue_N_2) {

            // Now do the same other:

            // we need to set these:
            mmdb::Atom *converted_residues_residue_CA_1 = NULL;
            mmdb::Atom *converted_residues_residue_C_1  = NULL;
            mmdb::Atom *converted_residues_residue_O_1  = NULL;
            mmdb::Atom *converted_residues_residue_CA_2 = NULL;
            mmdb::Atom *converted_residues_residue_N_2  = NULL;

            mmdb::PPAtom converted_residues_residue_atoms = NULL;
            int n_residue_atoms_converted;
            converted_residues[0]->GetAtomTable(converted_residues_residue_atoms,
                                                n_residue_atoms_converted);
            for (int i=0; i<n_residue_atoms_converted; i++) {
               std::string atom_name = converted_residues_residue_atoms[i]->name;
               if (atom_name == " CA ") {
                  converted_residues_residue_CA_1 = converted_residues_residue_atoms[i];
               }
               if (atom_name == " C  ") {
                  converted_residues_residue_C_1 = converted_residues_residue_atoms[i];
               }
               if (atom_name == " O  ") {
                  converted_residues_residue_O_1 = converted_residues_residue_atoms[i];
               }
            }

            converted_residues_residue_atoms = NULL;
            converted_residues[1]->GetAtomTable(converted_residues_residue_atoms,
                                                n_residue_atoms_converted);
            for (int i=0; i<n_residue_atoms_converted; i++) {
               std::string atom_name = converted_residues_residue_atoms[i]->name;
               if (atom_name == " CA ") {
                  converted_residues_residue_CA_2 = converted_residues_residue_atoms[i];
               }
               if (atom_name == " N  ") {
                  converted_residues_residue_N_2 = converted_residues_residue_atoms[i];
               }
            }

            if (converted_residues_residue_CA_1 &&
                converted_residues_residue_C_1 &&
                converted_residues_residue_O_1 &&
                converted_residues_residue_CA_2 &&
                converted_residues_residue_N_2) {

               std::vector<clipper::Coord_orth> current;
               std::vector<clipper::Coord_orth> cis_trans_init;
               std::vector<clipper::Coord_orth> converted;

               current.push_back(clipper::Coord_orth(mol_residue_CA_1->x,
                                                     mol_residue_CA_1->y,
                                                     mol_residue_CA_1->z));
               current.push_back(clipper::Coord_orth(mol_residue_C_1->x,
                                                     mol_residue_C_1->y,
                                                     mol_residue_C_1->z));
               current.push_back(clipper::Coord_orth(mol_residue_O_1->x,
                                                     mol_residue_O_1->y,
                                                     mol_residue_O_1->z));
               current.push_back(clipper::Coord_orth(mol_residue_CA_2->x,
                                                     mol_residue_CA_2->y,
                                                     mol_residue_CA_2->z));
               current.push_back(clipper::Coord_orth(mol_residue_N_2->x,
                                                     mol_residue_N_2->y,
                                                     mol_residue_N_2->z));

               cis_trans_init.push_back(clipper::Coord_orth(cis_trans_init_match_residue_CA_1->x,
                                                            cis_trans_init_match_residue_CA_1->y,
                                                            cis_trans_init_match_residue_CA_1->z));

               cis_trans_init.push_back(clipper::Coord_orth(cis_trans_init_match_residue_C_1->x,
                                                            cis_trans_init_match_residue_C_1->y,
                                                            cis_trans_init_match_residue_C_1->z));

               cis_trans_init.push_back(clipper::Coord_orth(cis_trans_init_match_residue_O_1->x,
                                                            cis_trans_init_match_residue_O_1->y,
                                                            cis_trans_init_match_residue_O_1->z));

               cis_trans_init.push_back(clipper::Coord_orth(cis_trans_init_match_residue_CA_2->x,
                                                            cis_trans_init_match_residue_CA_2->y,
                                                            cis_trans_init_match_residue_CA_2->z));

               cis_trans_init.push_back(clipper::Coord_orth(cis_trans_init_match_residue_N_2->x,
                                                            cis_trans_init_match_residue_N_2->y,
                                                            cis_trans_init_match_residue_N_2->z));

               converted.push_back(clipper::Coord_orth(converted_residues_residue_CA_1->x,
                                                       converted_residues_residue_CA_1->y,
                                                       converted_residues_residue_CA_1->z));

               converted.push_back(clipper::Coord_orth(converted_residues_residue_C_1->x,
                                                       converted_residues_residue_C_1->y,
                                                       converted_residues_residue_C_1->z));

               converted.push_back(clipper::Coord_orth(converted_residues_residue_O_1->x,
                                                       converted_residues_residue_O_1->y,
                                                       converted_residues_residue_O_1->z));

               converted.push_back(clipper::Coord_orth(converted_residues_residue_CA_2->x,
                                                       converted_residues_residue_CA_2->y,
                                                       converted_residues_residue_CA_2->z));

               converted.push_back(clipper::Coord_orth(converted_residues_residue_N_2->x,
                                                       converted_residues_residue_N_2->y,
                                                       converted_residues_residue_N_2->z));

               clipper::RTop_orth lsq_mat(cis_trans_init, current);

               // now move the current atoms in mol_residues to the
               // positions of converted (after converted atoms have
               // been shifted by lsq_mat)

               clipper::Coord_orth newpos;

               newpos = converted[0].transform(lsq_mat);
               mol_residue_CA_1->x = newpos.x();
               mol_residue_CA_1->y = newpos.y();
               mol_residue_CA_1->z = newpos.z();

               newpos = converted[1].transform(lsq_mat);
               mol_residue_C_1->x = newpos.x();
               mol_residue_C_1->y = newpos.y();
               mol_residue_C_1->z = newpos.z();

               newpos = converted[2].transform(lsq_mat);
               mol_residue_O_1->x = newpos.x();
               mol_residue_O_1->y = newpos.y();
               mol_residue_O_1->z = newpos.z();

               newpos = converted[3].transform(lsq_mat);
               mol_residue_CA_2->x = newpos.x();
               mol_residue_CA_2->y = newpos.y();
               mol_residue_CA_2->z = newpos.z();

               newpos = converted[4].transform(lsq_mat);
               mol_residue_N_2->x = newpos.x();
               mol_residue_N_2->y = newpos.y();
               mol_residue_N_2->z = newpos.z();

               if (mol_residue_H_2) {
                  // 20180510 place H on N as a riding atom, not using transformation
                  clipper::Coord_orth at_c_pos  = coot::co(mol_residue_C_1);
                  clipper::Coord_orth at_n_pos  = coot::co(mol_residue_N_2);
                  clipper::Coord_orth at_ca_pos = coot::co(mol_residue_CA_1);
                  double bl = 0.86;
                  double angle = clipper::Util::d2rad(125.0);
                  clipper::Coord_orth H_pos(at_ca_pos, at_c_pos, at_n_pos, bl, angle, M_PI);
                  mol_residue_H_2->x = H_pos.x();
                  mol_residue_H_2->y = H_pos.y();
                  mol_residue_H_2->z = H_pos.z();
               }
               istatus = 1;
            }
         }
      }
   }
   return istatus;
}





// remove wrong cis_peptides from the header records
void
coot::util::remove_wrong_cis_peptides(mmdb::Manager *mol) {

   std::vector<cis_peptide_info_t> v_coords = cis_peptides_info_from_coords(mol);

   if (mol) {
      int n_models = mol->GetNumberOfModels();
      for (int imod=1; imod<=n_models; imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (model_p) {
            std::vector<mmdb::CisPep> bad_cis_peptides;
            std::vector<mmdb::CisPep> good_cis_peptides;
            int ncp = model_p->GetNumberOfCisPeps();
            for (int icp=1; icp<=ncp; icp++) {
               mmdb::CisPep *CisPep = model_p->GetCisPep(icp);
               if (CisPep)  {
                  //             std::cout << "mmdb:: " << " :" << CisPep->chainID1 << ": "
                  // << CisPep->seqNum1 << " :"
                  // << CisPep->chainID2 << ": " << CisPep->seqNum2 << std::endl;
                  coot::util::cis_peptide_info_t cph(CisPep);

                  // Does that match any of the coordinates cispeps?
                  bool ifound = false;
                  for (unsigned int iccp=0; iccp<v_coords.size(); iccp++) {
                     if (cph == v_coords[iccp]) {
                        ifound = true;
                        break;
                     }
                  }
                  if (ifound == false) {
                     // needs to be removed
                     std::cout << "INFO:: Removing CIS peptide from PDB header: "
                               << cph.chain_id_1 << " "
                               << cph.resno_1 << " "
                               << cph.chain_id_2 << " "
                               << cph.resno_2 << " "
                               << std::endl;
                     bad_cis_peptides.push_back(*CisPep);
                  } else {
                     good_cis_peptides.push_back(*CisPep);
                     //                std::cout << "This CIS peptide was real: "
                     //                          << cph.chain_id_1 << " "
                     //                          << cph.resno_1 << " "
                     //                          << cph.chain_id_2 << " "
                     //                          << cph.resno_2 << " "
                     //                          << std::endl;
                  }
               }
            }
            if (bad_cis_peptides.size() > 0) {
               // delete all CISPEPs and add back the good ones
               model_p->RemoveCisPeps();
               for (unsigned int igood=0; igood<good_cis_peptides.size(); igood++) {
                  mmdb::CisPep *good = new mmdb::CisPep;
                  *good = good_cis_peptides[igood];
                  model_p->AddCisPep(good);
               }
            }
         } else {
            std::cout << "WARNING:: null model for model " << imod << std::endl;
         }
      }
   }
}

void
coot::util::correct_link_distances(mmdb::Manager *mol) {

#ifdef MMDB_HAS_LINK_DISTANCE
   if (mol) {
      int n_models = mol->GetNumberOfModels();
      for (int imod=1; imod<=n_models; imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
         int n_links = model_p->GetNumberOfLinks();
         if (n_links > 0) { 
            for (int i_link=1; i_link<=n_links; i_link++) {
               mmdb::Link *link = model_p->GetLink(i_link);
               std::pair<atom_spec_t, atom_spec_t> lp = link_atoms(link, model_p);
               mmdb::Atom *at_1 = get_atom(lp.first,  mol);
               mmdb::Atom *at_2 = get_atom(lp.second, mol);
               if (at_1) {
                  if (at_2) {
                     double link_dist = link->dist;
                     double atom_dist = distance(at_1, at_2);
                     double d = fabs(link_dist - atom_dist);
                     if (d < 0.01) {
                        // std::cout << i_link << " link is fine " << link_dist << " " << atom_dist
                        // << std::endl;
                     } else {
                        if (0)
                           std::cout << "link " << i_link << " needs adjusting to "
                                     << atom_dist << std::endl;
                        link->dist = atom_dist;
                     } 
                  } else {
                     std::cout << "WARNING:: Missing link atom " << lp.second << std::endl;
                  }
               } else {
                  std::cout << "WARNING:: Missing link atom " << lp.first << std::endl;
               }
            }
         }
      }
   }
#endif // MMDB_HAS_LINK_DISTANCE   
}

void
coot::util::remove_long_links(mmdb::Manager *mol, mmdb::realtype dist_max) {

   // Bob Nolte want to remove links to atoms that have moved far away
   // 
   if (mol) {
      for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (model_p) {
            int n_links = model_p->GetNumberOfLinks();
            for (int ilink=1; ilink<=n_links; ilink++) {
               mmdb::Link *link = model_p->GetLink(ilink);
               std::pair<atom_spec_t, atom_spec_t> la = link_atoms(link, model_p);
               mmdb::Atom *at_1 = get_atom(la.first,  mol);
               mmdb::Atom *at_2 = get_atom(la.second, mol);
               if (at_1) {
                  if (at_2) {
                     clipper::Coord_orth pos_1 = co(at_1);
                     clipper::Coord_orth pos_2 = co(at_2);
                     double dsq = clipper::Coord_orth::length(pos_1, pos_2);
                     double d = sqrt(dsq);
                     if (d > dist_max) {
                //        delete link; mmdb crash
                     }
                  }
               }
            }

            n_links = model_p->GetNumberOfLinkRs();
            for (int ilink=1; ilink<=n_links; ilink++) {
               mmdb::LinkR *link = model_p->GetLinkR(ilink);
               std::pair<atom_spec_t, atom_spec_t> la = link_atoms(link, model_p);
               mmdb::Atom *at_1 = get_atom(la.first,  mol);
               mmdb::Atom *at_2 = get_atom(la.second, mol);
               if (at_1) {
                  if (at_2) {
                     clipper::Coord_orth pos_1 = co(at_1);
                     clipper::Coord_orth pos_2 = co(at_2);
                     double dsq = clipper::Coord_orth::length(pos_1, pos_2);
                     double d = sqrt(dsq);
                     if (d > dist_max) {
                //        delete link;
                     }
                  }
               }
            }
         }
      }
   }
}

// return the number of changed links
unsigned int
coot::util::change_chain_in_links(mmdb::Model *model_p, 
                                  const std::string &from_chain_id,
                                  const std::string &to_chain_id) {
   unsigned int n_changed = 0;
   if (model_p) {
      int n_links = model_p->GetNumberOfLinks();
      for (int ilink=1; ilink<=n_links; ilink++) {
         mmdb::Link *link = model_p->GetLink(ilink);
         std::string cid1 = link->chainID1;
         std::string cid2 = link->chainID2;
         if (from_chain_id == cid1) {
            // std::cout << "changing to " << to_chain_id << std::endl;
            strncpy(link->chainID1, to_chain_id.c_str(), 9);
            n_changed++;
         }
         if (from_chain_id == cid2) {
            // std::cout << "changing to " << to_chain_id << std::endl;
            strncpy(link->chainID2, to_chain_id.c_str(), 9);
            n_changed++;
         }
      }
   }
   return n_changed;
}



mmdb::Manager *
coot::mol_by_symmetry(mmdb::Manager *mol, 
                      clipper::Cell cell, 
                      clipper::RTop_frac rtop_frac,
                      std::vector<int> pre_shift_to_origin_abc) {

   bool verbose_output = 0; // should be a passed param?
   
   mmdb::Manager *mol2 = new mmdb::Manager;
   mol2->Copy(mol, mmdb::MMDBFCM_All);

   // Usually gets filled by GetTMatrix().
   mmdb::mat44 mat_origin_shift; // shift needed to get close to the origin.
   for (int i=0; i<4; i++) 
      for (int j=0; j<4; j++) 
         mat_origin_shift[i][j] = 0.0;
   for (int i=0; i<4; i++) mat_origin_shift[i][i] = 1.0;
   
   if (pre_shift_to_origin_abc.size() == 3) { 
      mol2->GetTMatrix(mat_origin_shift, 0,
                       pre_shift_to_origin_abc[0],
                       pre_shift_to_origin_abc[1],
                       pre_shift_to_origin_abc[2]);
   }
      
   // mol2->GetTMatrix(mat, symop_no, shift_a, shift_b, shift_c);

   clipper::Coord_orth origin_shift_orth(mat_origin_shift[0][3],
                                         mat_origin_shift[1][3],
                                         mat_origin_shift[2][3]);
   clipper::RTop_orth to_origin_rtop(clipper::Mat33<double>(1,0,0,0,1,0,0,0,1),
                                     origin_shift_orth);

   clipper::RTop_orth rtop = rtop_frac.rtop_orth(cell);
   for(int imod = 1; imod<=mol2->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol2->GetModel(imod);
      if (! model_p) continue;
      mmdb::Chain *chain_p;
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         chain_p = model_p->GetChain(ichain);
         int nres = chain_p->GetNumberOfResidues();
         mmdb::Residue *residue_p;
         mmdb::Atom *at;
         for (int ires=0; ires<nres; ires++) { 
            residue_p = chain_p->GetResidue(ires);
            int n_atoms = residue_p->GetNumberOfAtoms();
            for (int iat=0; iat<n_atoms; iat++) {
               at = residue_p->GetAtom(iat);
               clipper::Coord_orth co(at->x, at->y, at->z);
               co -= origin_shift_orth;
               clipper::Coord_orth to = co.transform(rtop);
               to += origin_shift_orth;
//                std::cout << " atom from " 
//                          << at->x << " " << at->y << " " << at->z << " " 
//                          << " to " << to.format() << std::endl;
               at->x = to.x(); at->y = to.y(); at->z = to.z(); 
            }
         }
      }
   }

   if (verbose_output) { 
      std::cout << "symmetry rtop_orth:\n" << rtop.format() << std::endl;
      std::cout << "symmetry rtop_frac:\n" << rtop_frac.format() << std::endl;
   }
   
   return mol2;
} 


// Perhaps this should be a class function of a class derived from mmdb::Manager?
int
coot::write_coords_pdb(mmdb::Manager *mol, const std::string &file_name) {

   util::remove_wrong_cis_peptides(mol);
   util::correct_link_distances(mol);
   int r = mol->WritePDBASCII(file_name.c_str());
   return r;
}

// Perhaps this should be a class function of a class derived from mmdb::Manager?
int
coot::write_coords_cif(mmdb::Manager *mol, const std::string &file_name) {

   util::remove_wrong_cis_peptides(mol);
   // util::correct_link_distances(mol);  // this duplicates the molecule.  Needs investigation - GetLink()?
   int r = mol->WriteCIFASCII(file_name.c_str());
   return r;
}


// convert atoms in residue to HETATMs
// 
int
coot::hetify_residue_atoms(mmdb::Residue *res) {

   int n = 0;
   if (res) { 
      mmdb::PPAtom residue_atoms;
      int natoms;
      res->GetAtomTable(residue_atoms, natoms);
      for (int iat=0; iat<natoms; iat++) {
         mmdb::Atom *at = residue_atoms[iat];
         at->Het = 1;
         n++;
      } 
   }
   return n;
}

// convert atoms in residue to HETATMs
// 
int
coot::hetify_residue_atoms_as_needed(mmdb::Residue *res) {

   int r = 0;
   if (res) { 
      std::string resname = res->GetResName();
      if (! is_member_p(coot::util::PDB_standard_residue_types(), resname))
         r = hetify_residue_atoms(res);
   }
   return r;
}


int
coot::hetify_residues_as_needed(mmdb::Manager *mol) {

   int r = 0;
   if (mol) {
      for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
         int n_chains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<n_chains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            for (int ires=0; ires<nres; ires++) { 
               residue_p = chain_p->GetResidue(ires);
               coot::hetify_residue_atoms_as_needed(residue_p);
            }
         }
      }
   }
   return r;
}

void
coot::put_amino_acid_residue_atom_in_standard_order(mmdb::Residue *residue_p) {

   // This function doesn't do what it says. For the moment
   // it just puts the N at the start if the residue has an N
   // (or multiple Ns)
   // Function should do what it says, but this is good enough
   // for now.
   //
   mmdb::Atom **residue_atoms = 0;
   int n_residue_atoms;
   std::vector<mmdb::Atom *> N_ats;
   std::vector<mmdb::Atom *> other_ats;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int i=0; i<n_residue_atoms; i++) {
      mmdb::Atom *at = residue_atoms[i];
      std::string atom_name(at->GetAtomName());
      if (atom_name == " N  ") { // PDBv3 FIXME
         N_ats.push_back(at);
      } else {
         other_ats.push_back(at);
      }
   }

   // shove around the pointers

   int idx = 0;
   for (std::size_t i=0; i<N_ats.size(); i++) {
      mmdb::Atom *at = N_ats[i];
      residue_atoms[idx] = at;
      idx++;
   }
   for (std::size_t i=0; i<other_ats.size(); i++) {
      mmdb::Atom *at = other_ats[i];
      residue_atoms[idx] = at;
      idx++;
   }

}


// Interacting Residues: Return all residues of mol1, mol2 that
// have atoms that are closer that dist to atoms of mol2/mol1.
//
// Slightly horrifically, we have to create a new molecule from the 2
// given molecules so that we can run SeekContacts().  So we choose
// the first (non-blank) model of each of the molecules to go into
// MODEL 1 and MODEL 2 of the combined/new molecule.
//
// The returned mmdb::Residues are not in mol1 and mol2 - they are in combined_mol.
// 
std::pair<std::vector<mmdb::Residue *>, std::vector<mmdb::Residue *> >
coot::close_residues_from_different_molecules_t::close_residues(mmdb::Manager *mol1,
                                                                mmdb::Manager *mol2, float dist) {

   std::vector<mmdb::Residue *> v1;
   std::vector<mmdb::Residue *> v2;

   if (mol1 && mol2) {

      combined_mol = new mmdb::Manager;
      
      // combined_mol MODEL number 1 
      int n_models_mol_1 = mol1->GetNumberOfModels();
      for (int imod=1; imod<=n_models_mol_1; imod++) {
         mmdb::Model *model_p = mol1->GetModel(imod);
         if (model_p) {
            mmdb::Model *new_model = new mmdb::Model;
            new_model->Copy(model_p);
            combined_mol->AddModel(new_model);
            break;
         } 
      } 

      // combined_mol MODEL number 2
      int n_models_mol_2 = mol2->GetNumberOfModels();
      for (int imod=1; imod<=n_models_mol_2; imod++) {
         mmdb::Model *model_p = mol2->GetModel(imod);
         if (model_p) {
            mmdb::Model *new_model = new mmdb::Model;
            new_model->Copy(model_p);
            combined_mol->AddModel(new_model);
            break;
         } 
      } 

      int SelectionHandle_1 = combined_mol->NewSelection();
      mmdb::PPAtom atom_selection_1 = NULL;
      combined_mol->SelectAtoms (SelectionHandle_1, 1, "*",
                                 mmdb::ANY_RES, // starting resno, an int
                                 "*", // any insertion code
                                 mmdb::ANY_RES, // ending resno
                                 "*", // ending insertion code
                                 "*", // any residue name
                                 "*", // atom name
                                 "*", // elements
                                 "*"  // alt loc.
                                 );
      int n_selected_atoms_1;
      combined_mol->GetSelIndex(SelectionHandle_1, atom_selection_1, n_selected_atoms_1);
      
      int SelectionHandle_2 = combined_mol->NewSelection();
      mmdb::PPAtom atom_selection_2;
      combined_mol->SelectAtoms (SelectionHandle_2, 2, "*",
                                 mmdb::ANY_RES, // starting resno, an int
                                 "*", // any insertion code
                                 mmdb::ANY_RES, // ending resno
                                 "*", // ending insertion code
                                 "*", // any residue name
                                 "*", // atom name
                                 "*", // elements
                                 "*"  // alt loc.
                                 );
      int n_selected_atoms_2;
      combined_mol->GetSelIndex(SelectionHandle_2, atom_selection_2, n_selected_atoms_2);

      std::cout << "INFO:: selected " << n_selected_atoms_1
                << " from (copy of) 1st interaction molecule\n";
      std::cout << "INFO:: selected " << n_selected_atoms_2
                << " from (copy of) 2nd interaction molecule\n";
      
      
      // (Sigh (of relief))...
      //
      // OK, now we can run SeekContacts();

      mmdb::Contact *pscontact = NULL;
      int n_contacts;
      long i_contact_group = 1;
      mmdb::mat44 my_matt;
      mmdb::SymOps symm;
      for (int i=0; i<4; i++) 
         for (int j=0; j<4; j++) 
            my_matt[i][j] = 0.0;      
      for (int i=0; i<4; i++) my_matt[i][i] = 1.0;

      std::cout << "... SeekContacts() on " << n_selected_atoms_1
                << " and " << n_selected_atoms_2 << " atoms" << std::endl;
      combined_mol->SeekContacts(atom_selection_1, n_selected_atoms_1,
                                 atom_selection_2, n_selected_atoms_2,
                                 0.0, dist,
                                 1, pscontact, n_contacts,
                                 0, &my_matt, i_contact_group);

      std::cout << "INFO:: Contacts between 2 molecules: found "
                << n_contacts << " contacts" << std::endl;
      
      if (n_contacts > 0) {
         if (pscontact) {
            for (int i_contact=0; i_contact<n_contacts; i_contact++) {

               mmdb::Residue *r1 = atom_selection_1[pscontact[i_contact].id1]->GetResidue();
               mmdb::Residue *r2 = atom_selection_2[pscontact[i_contact].id2]->GetResidue();

               mmdb::Model *model_1 = r1->GetModel();
               mmdb::Model *model_2 = r2->GetModel();

               if (model_1 != model_2) { 
               
                  if (! coot::is_member_p(v1, r1))
                     v1.push_back(r1);
                  if (! coot::is_member_p(v2, r2))
                     v2.push_back(r2);
               }
            }
         }
      } 
   }
   std::cout << "INFO:: interacting residues from molecules: "
             << v1.size() << " and " << v2.size() << std::endl;
   return std::pair<std::vector<mmdb::Residue *>, std::vector<mmdb::Residue *> > (v1, v2);
}


// move waters round protein, fiddle with mol.
// return the number of moved waters.
int
coot::util::move_waters_around_protein(mmdb::Manager *mol) {

   int n_moved = 0;
   std::vector<clipper::Coord_orth> protein_coords;
   std::vector<std::pair<mmdb::Atom*, clipper::Coord_orth> > water_atoms;

   // First we fill protein_atoms and water_atoms (water atoms are not
   // part of protein atoms)

   if (mol) { 
      int imod = 1;
      mmdb::Model *model_p = mol->GetModel(imod);
      mmdb::Chain *chain_p;
      // run over chains of the existing mol
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         chain_p = model_p->GetChain(ichain);
         int nres = chain_p->GetNumberOfResidues();
         mmdb::Residue *residue_p;
         mmdb::Atom *at = 0;
         for (int ires=0; ires<nres; ires++) {
            residue_p = chain_p->GetResidue(ires);
            int n_atoms = residue_p->GetNumberOfAtoms();
            std::string residue_name(residue_p->name);
            if (residue_name == "WAT" ||
                residue_name == "HOH") {

               for (int iat=0; iat<n_atoms; iat++) {
                  at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     at = residue_p->GetAtom(iat);
                     clipper::Coord_orth c(at->x, at->y, at->z);
                     std::pair <mmdb::Atom *, clipper::Coord_orth> pair(at, c);
                     water_atoms.push_back(pair);
                  }
               }
            } else {
               for (int iat=0; iat<n_atoms; iat++) {
                  at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     std::string ele(at->element);
                     if (ele  != " C") { 
                        clipper::Coord_orth pt(at->x, at->y, at->z);
                        protein_coords.push_back(pt);
                     }
                  }
               }
            } 
         }
      }
   }

   // OK, so waters_atoms and protein atoms are filled.

   try { 
      // Now clipperize the variables.
      std::pair<clipper::Cell,clipper::Spacegroup> csp = get_cell_symm(mol);
      clipper::Cell cell = csp.first;
      clipper::Spacegroup spacegroup = csp.second;

      if (cell.is_null()) {
         std::cout << "WARNING:: null cell in move_waters_around_protein" << std::endl;
      } else {
         if (spacegroup.is_null()) { 
            std::cout << "WARNING:: null spgr in move_waters_around_protein" << std::endl;
         } else {

            std::vector<std::pair<mmdb::Atom*, clipper::Coord_orth> > water_atoms_moved =
               symmetry_move_atoms(protein_coords, water_atoms, cell, spacegroup);

            for (unsigned int iw=0; iw<water_atoms_moved.size(); iw++) {
               if (water_atoms_moved[iw].first) {
                  water_atoms_moved[iw].first->x = water_atoms_moved[iw].second.x();
                  water_atoms_moved[iw].first->y = water_atoms_moved[iw].second.y();
                  water_atoms_moved[iw].first->z = water_atoms_moved[iw].second.z();
                  n_moved++;
               }
            }
         }
      }
   }
   catch (const std::runtime_error &rte) {
      std::cout << rte.what() << std::endl;
   }

   return n_moved;
}

// move hetgroups round protein.  Find the centres of each
// hetgroup and move it to the protein.  Waters are handled individually.
// Fiddle with mol.
//
void
coot::util::move_hetgroups_around_protein(mmdb::Manager *mol) {

   if (mol) {
      // do the waters first
      coot::util::move_waters_around_protein(mol);

      // now other stuff
      // 
      try { 
         // Now clipperize the variables.
         std::pair<clipper::Cell,clipper::Spacegroup> csp = get_cell_symm(mol);
         clipper::Cell cell = csp.first;
         clipper::Spacegroup spacegroup = csp.second;

         if (cell.is_null()) {
            std::cout << "WARNING:: null cell in move_waters_around_protein" << std::endl;
         } else {
            if (spacegroup.is_null()) { 
               std::cout << "WARNING:: null spgr in move_waters_around_protein" << std::endl;
            } else {

               for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
                  // first find the protein coords
                  std::vector<clipper::Coord_orth> protein_coords;
                  mmdb::Model *model_p = mol->GetModel(imod);
                  if (! model_p) continue;
                  mmdb::Chain *chain_p;
                  // run over chains of the existing mol
                  int nchains = model_p->GetNumberOfChains();
                  for (int ichain=0; ichain<nchains; ichain++) {
                     chain_p = model_p->GetChain(ichain);
                     int nres = chain_p->GetNumberOfResidues();
                     mmdb::Residue *residue_p;
                     mmdb::Atom *at = 0;
                     for (int ires=0; ires<nres; ires++) {
                        residue_p = chain_p->GetResidue(ires);
                        int n_atoms = residue_p->GetNumberOfAtoms();
                        for (int iat=0; iat<n_atoms; iat++) {
                           at = residue_p->GetAtom(iat);
                           if (! at->Het) { 
                              std::string element(at->element);
                              if (element != "C" && element != " C") {
                                 clipper::Coord_orth pt(at->x, at->y, at->z);
                                 protein_coords.push_back(pt);
                              }
                           }
                        }
                     }
                  }
                  // OK, protein_coords is set.

                  // run over chains of the existing mol
                  for (int ichain=0; ichain<nchains; ichain++) {
                     chain_p = model_p->GetChain(ichain);
                     int nres = chain_p->GetNumberOfResidues();
                     mmdb::Residue *residue_p;
                     mmdb::Atom *at = 0;
                     for (int ires=0; ires<nres; ires++) {
                        residue_p = chain_p->GetResidue(ires);
                        std::string residue_name(residue_p->name);
                        if (residue_name == "WAT" ||
                            residue_name == "HOH") {
                           // Waters are handled above.
                        } else {
                           if (coot::util::residue_has_hetatms(residue_p)) {
                              std::pair<bool, clipper::Coord_orth> centre =
                                 coot::util::get_residue_centre(residue_p);
                              if (centre.first) {

                                 // fill hetgroup_atoms:
                                 std::vector<std::pair<mmdb::Atom*, clipper::Coord_orth> > hetgroup_atoms;
                                 mmdb::PPAtom residue_atoms = 0;
                                 int n_residue_atoms;
                                 residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
                                 for (int iat=0; iat<n_residue_atoms; iat++) {
                                    clipper::Coord_orth co(residue_atoms[iat]->x,
                                                           residue_atoms[iat]->y,
                                                           residue_atoms[iat]->z);
                                    std::pair<mmdb::Atom*, clipper::Coord_orth> p(residue_atoms[iat], co);
                                    hetgroup_atoms.push_back(p);
                                 }
                                 
                                 std::vector<std::pair<mmdb::Atom*, clipper::Coord_orth> > atoms_moved =
                                    symmetry_move_atoms(protein_coords, hetgroup_atoms, cell, spacegroup);

                                 for (unsigned int iw=0; iw<atoms_moved.size(); iw++) {
                                    if (atoms_moved[iw].first) {
                                       atoms_moved[iw].first->x = atoms_moved[iw].second.x();
                                       atoms_moved[iw].first->y = atoms_moved[iw].second.y();
                                       atoms_moved[iw].first->z = atoms_moved[iw].second.z();
                                    }
                                 }
                              }
                           }
                        }
                     }
                  }
               }
            }
         }
      }
      catch (const std::runtime_error &rte) {
         std::cout << rte.what() << std::endl;
      }
   }
} 


// Return waters atoms of the same size as the input, except if the
// first is NULL, then the atom need not move, if it is not null, then
// the water atom (first) should be moved to the second position.
// 
std::vector<std::pair<mmdb::Atom *, clipper::Coord_orth> >
coot::util::symmetry_move_atoms(const std::vector<clipper::Coord_orth> &protein_coords,
                                const std::vector<std::pair<mmdb::Atom*, clipper::Coord_orth> > &water_atoms_in,
                                clipper::Cell cell,
                                clipper::Spacegroup spacegroup) {

   std::vector<double> current_best_dist(water_atoms_in.size(), -1);

   clipper::Coord_frac pre_shift_frac = coot::util::shift_to_origin(protein_coords, cell, spacegroup);
   clipper::Coord_orth pre_shift_orth = pre_shift_frac.coord_orth(cell);

   // Let's not move atoms if the best distance is not better than the current best distance
   // so let's make a note of those now.
   std::vector<std::pair<mmdb::Atom*, clipper::Coord_orth> > water_atoms = water_atoms_in;
   for (unsigned int iat=0; iat<water_atoms_in.size(); iat++) { 
      for (unsigned int iprot=0; iprot<protein_coords.size(); iprot++) { 
         double d = clipper::Coord_orth::length(water_atoms_in[iat].second, protein_coords[iprot]);
         if (current_best_dist[iat] < 0) { 
            current_best_dist[iat] = d;
         } else {
            if (d < current_best_dist[iat])
               current_best_dist[iat] = d;
         }
      }
   }

   if (0)
      std::cout << "DEBUG:: pre_shift_frac " << pre_shift_frac.format()
                << " pre_shift_orth " << pre_shift_orth.format()
                << std::endl;

   // create shifted protein coords
   std::vector<clipper::Coord_orth> protein_coords_origin_shifted(protein_coords.size());
   for (unsigned int ip=0; ip<protein_coords.size(); ip++) { 
      protein_coords_origin_shifted[ip] =
         protein_coords[ip] + pre_shift_orth;
      //          if (ip < 20)
      //             std::cout << "  shifting "
      //                       << protein_coords[ip].format() << " by "
      //                       << pre_shift_orth.format() << " gives "
      //                       << protein_coords_origin_shifted[ip].format()
      //                       << std::endl;
   }

   // Do the cell shift search
   int n = spacegroup.num_symops();
   clipper::Coord_frac cell_shift; 
   for (unsigned int iw=0; iw<water_atoms.size(); iw++) {
      clipper::Coord_orth water_pos_pre(water_atoms[iw].second);
      clipper::Coord_orth water_pos = translate_close_to_origin(water_pos_pre, cell);

      // std::cout << " water_pos " << water_pos.format() << std::endl;
      double d_best = 99999999.9;
      // The compiler doesn't like rtop_best being used below
      // without being initialized properly here.
      // clipper::RTop_orth rtop_best; // old
      clipper::RTop_orth rtop_best(clipper::Mat33<double>(1,0,0,0,1,0,0,0,1), clipper::Coord_orth(0,0,0));
      bool improved = 0;
      // 
      for (int isym=0; isym<n; isym++) {
         for (int x_shift = -1; x_shift<2; x_shift++) { 
            for (int y_shift = -1; y_shift<2; y_shift++) { 
               for (int z_shift = -1; z_shift<2; z_shift++) {
                  cell_shift = clipper::Coord_frac(x_shift, y_shift, z_shift); 
                  clipper::RTop_orth orthop =
                     clipper::RTop_frac(spacegroup.symop(isym).rot(),
                                        spacegroup.symop(isym).trn() + cell_shift).rtop_orth(cell);
                  clipper::Coord_orth t_point = water_pos.transform(orthop);
                  double t_dist = coot::util::min_dist_to_points(t_point, protein_coords_origin_shifted);
                  if (t_dist < d_best) {
//                      std::cout << " better dist " << t_dist << "  "  << t_point.format() << " "
//                                << current_best_dist[iw] << std::endl;
                     if (t_dist < current_best_dist[iw]) {
                        d_best = t_dist;
                        rtop_best = orthop;
                        improved = 1;
                     }
                  }
               }
            }
         }
      }

      if (improved) { 
         // Apply the transformation then.
         clipper::Coord_orth t_point = water_pos.transform(rtop_best);
         water_atoms[iw].second = t_point - pre_shift_orth;
      } else {
         // std::cout << "debug:: no improvement NULLING the atom " << iw << std::endl;
         water_atoms[iw].first = 0; // NULL, don't move it.
      }
   }
   return water_atoms;
}



// Throw an std::runtime_error exception on
// not-able-to-extract-cell/symm-info.  (In such a case, we convert a
// clipper::Message_base to a std::runtime_error).
// 
std::pair<clipper::Cell, clipper::Spacegroup>
coot::util::get_cell_symm(mmdb::Manager *mol) {

   // Now clipperize the variables.

   mmdb::mat44 my_matt;
   int err = mol->GetTMatrix(my_matt, 0, 0, 0, 0);
   if (err != 0) {
      std::string mess = "No symmetry available";
      throw std::runtime_error(mess);
   } else { 
      try { 
         const clipper::MMDBManager* pcmmdb =
            static_cast<const clipper::MMDBManager*>( mol );

         clipper::Spacegroup spacegroup(pcmmdb->spacegroup());
         clipper::Cell cell(pcmmdb->cell());
         if (spacegroup.is_null())
            std::cout << "Null clipper spacegroup from " << mol->GetSpaceGroup()
                      << std::endl;
         if (cell.is_null())
            std::cout << "Null clipper cell  " << std::endl;
         return std::pair<clipper::Cell, clipper::Spacegroup> (cell, spacegroup);
      }
      catch (const clipper::Message_generic &except) {
         std::string message = "Fail to make clipper::Spacegroup from ";
         message += mol->GetSpaceGroup();
         throw std::runtime_error(message);
      }
   }
   std::cout << "got to here - bad! in get_cell_symm()"
             << std::endl;
}


// shove a cell from a clipper cell into the passed mol.
bool
coot::util::set_mol_cell(mmdb::Manager *mol, clipper::Cell cell_local) {

   bool status = 0; 
   mol->SetCell(cell_local.a(), cell_local.b(), cell_local.c(),
                clipper::Util::rad2d(cell_local.alpha()),
                clipper::Util::rad2d(cell_local.beta()),
                clipper::Util::rad2d(cell_local.gamma()));

   mmdb::realtype cell[6], vol;
   int orthog;
   
   mol->GetCell(cell[0], cell[1], cell[2], cell[3], cell[4], cell[5], vol, orthog);
   if (fabs(cell[0] - cell_local.a()) < 0.1)
      if (fabs(cell[1] - cell_local.b()) < 0.1)
         if (fabs(cell[2] - cell_local.c()) < 0.1)
            if (fabs(clipper::Util::d2rad(cell[3]) - cell_local.alpha()) < 0.1)
               if (fabs(clipper::Util::d2rad(cell[4]) - cell_local.beta()) < 0.1)
                  if (fabs(clipper::Util::d2rad(cell[5]) - cell_local.gamma()) < 0.1)
                     status = 1;

   return status;
}

// c.f. get_ori_to_this_res().
//
clipper::Mat33<double>
coot::util::residue_orientation(mmdb::Residue *residue_p, const clipper::Mat33<double> &orientation_in) {

   std::vector<clipper::Coord_orth> pts;
   mmdb::PPAtom residue_atoms = 0;
   int n_residue_atoms;
   clipper::Mat33<double> r = orientation_in;
   clipper::Coord_orth n_vec(0,0,1);
   mmdb::Atom *ca = 0;
   mmdb::Atom *n = 0;
   
   if (residue_p) { 
      residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int i=0; i<n_residue_atoms; i++) {
         if (!is_main_chain_p(residue_atoms[i])) {
            pts.push_back(clipper::Coord_orth(residue_atoms[i]->x,
                                              residue_atoms[i]->y,
                                              residue_atoms[i]->z));
         } else {
            std::string atom_name(residue_atoms[i]->name);
            if (atom_name == " CA ")
               ca = residue_atoms[i];
            if (atom_name == " N  ")
               n = residue_atoms[i];
         } 
      }
      
      if (pts.size() > 0) {

         if (ca) { 
            clipper::Coord_orth ca_pos(ca->x, ca->y, ca->z);
            clipper::Coord_orth average_pos = coot::util::average_position(pts);
            clipper::Coord_orth u((average_pos-ca_pos).unit());

            // reset n_vect to something sensible, if we have the CA and N.
            if (ca && n) {
               clipper::Coord_orth  n_pos( n->x,  n->y,  n->z);
               n_vec = n_pos - ca_pos;
            }
         
            // now make a mat...
            //
            clipper::Coord_orth n_vec_unit(n_vec.unit());
            
            clipper::Coord_orth p1(clipper::Coord_orth::cross(n_vec_unit, u).unit());
            clipper::Coord_orth p2(clipper::Coord_orth::cross( p1, u).unit());
            clipper::Coord_orth p3 = u;

            std::cout << "primary sidechain direction: " << u.format() << std::endl;
            r = clipper::Mat33<double> (p1.x(), p1.y(), p1.z(),
                                        p2.x(), p2.y(), p2.z(),
                                        p3.x(), p3.y(), p3.z());
            std::cout << r.format() << std::endl;
            std::cout << "determinant: " << r.det() << std::endl;
            
         }
      }
   }
   return r;
} 


// 
clipper::Coord_orth
coot::util::average_position(std::vector<clipper::Coord_orth> &pts) {
   
   if (pts.size() > 0) {
      double xsum = 0.0;
      double ysum = 0.0;
      double zsum = 0.0;
      for (unsigned int i=0; i<pts.size(); i++) { 
         xsum += pts[i].x();
         ysum += pts[i].y();
         zsum += pts[i].z();
      }
      double denom=1.0/double(pts.size());
      return clipper::Coord_orth(denom*xsum, denom*ysum, denom*zsum);
   } else {
      return clipper::Coord_orth(0,0,0);
   }
}

clipper::Coord_orth
coot::util::average_position(mmdb::Residue *residue_p) {

   mmdb::Atom **residue_atoms = 0;
   int n_residue_atoms;
   clipper::Coord_orth sum(0,0,0);
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int i=0; i<n_residue_atoms; i++) {
      mmdb::Atom *at = residue_atoms[i];
      clipper::Coord_orth atom_pos = co(at);
      sum += atom_pos;
   }
   if (n_residue_atoms > 0) {
      double r = 1.0/double(n_residue_atoms);
      clipper::Coord_orth pt(sum.x() * r, sum.y() * r, sum.z() * r);
      return pt;
   } else {
      return sum;
   }
}




// caller must check that others has some points in it.
// 
double
coot::util::min_dist_to_points(const clipper::Coord_orth &pt,
                               const std::vector<clipper::Coord_orth> &others) {

   double best_dist = 9999999.9;
   for (unsigned int i=0; i<others.size(); i++) {
      double d = (pt - others[i]).lengthsq();
      if (d<best_dist) {
         best_dist = d;
      }
   }
   return sqrt(best_dist);
}


// Return the fractional shift needed to translate the protein
// as close as possible to the origin (do not apply the shift).
// 
//
// Throw a clipper::Message_base exception (e.g. no cell or symmetry).
//
// Can throw a std::runtime_error other times.
// 
clipper::Coord_frac
coot::util::shift_to_origin(mmdb::Manager *mol) {

   // Throw a clipper::Message_base exception on no cell or symmetry.
   std::pair<clipper::Cell, clipper::Spacegroup> csp = get_cell_symm(mol);
   clipper::Cell cell = csp.first;
   clipper::Spacegroup spacegroup = csp.second;

   // Throws an exception
   clipper::Coord_orth median_pos = median_position(mol);

   clipper::Coord_frac mpf = median_pos.coord_frac(cell);
   clipper::Coord_frac rf (round(-mpf.u()), round(-mpf.v()), round(-mpf.w()));
   return rf;
}

clipper::Coord_frac
coot::util::shift_to_origin(const std::vector<clipper::Coord_orth> &protein_coords,
                            clipper::Cell cell,
                            clipper::Spacegroup spacegroup) {

   clipper::Coord_orth median_pos = median_position(protein_coords);
   clipper::Coord_frac mpf = median_pos.coord_frac(cell);
   clipper::Coord_frac rf (round(-mpf.u()), round(-mpf.v()), round(-mpf.w()));
   return rf;
}

bool
coot::util::is_000_shift(const clipper::Coord_frac &cf_shift) {

   // This is for testing the results of the above function

   if (std::abs(cf_shift.u()) > 0.1) {
      return false;
   } else {
      if (std::abs(cf_shift.v()) > 0.1) {
         return false;
      } else {
         if (std::abs(cf_shift.w()) > 0.1) {
            return false;
         }
      }
   }
   return true;
}



// Can throw a std::runtime_error
// 
clipper::Coord_orth
coot::util::median_position(const std::vector<clipper::Coord_orth> &pts) {

   if (pts.size() == 0 ) {
      std::string message = "No atoms in molecule - no mediain position";
      throw std::runtime_error(message);
   }
   
   std::vector<float> pts_x;
   std::vector<float> pts_y;
   std::vector<float> pts_z;
   for (unsigned int i=0; i<pts.size(); i++) {
      pts_x.push_back(pts[i].x());
      pts_y.push_back(pts[i].y());
      pts_z.push_back(pts[i].z());
   }
   std::sort(pts_x.begin(), pts_x.end());
   std::sort(pts_y.begin(), pts_y.end());
   std::sort(pts_z.begin(), pts_z.end());
   unsigned int mid_index = pts_x.size()/2;
   return clipper::Coord_orth(pts_x[mid_index], pts_y[mid_index], pts_z[mid_index]);
}



// Can throw a std::runtime_error
// 
clipper::Coord_orth
coot::util::median_position(mmdb::Manager *mol) {

   std::vector<float> pts_x;
   std::vector<float> pts_y;
   std::vector<float> pts_z;

   // for(int imod = 1; imod<=asc.mol->GetNumberOfModels(); imod++) {
   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (! model_p) {
      std::string message = "No Model 1";
      throw std::runtime_error(message);
   }
   mmdb::Chain *chain_p;
   // run over chains of the existing mol
   int nchains = model_p->GetNumberOfChains();
   for (int ichain=0; ichain<nchains; ichain++) {
      chain_p = model_p->GetChain(ichain);
      int nres = chain_p->GetNumberOfResidues();
      mmdb::Residue *residue_p;
      mmdb::Atom *at;
      for (int ires=0; ires<nres; ires++) { 
         residue_p = chain_p->GetResidue(ires);
         int n_atoms = residue_p->GetNumberOfAtoms();
         
         for (int iat=0; iat<n_atoms; iat++) {
            at = residue_p->GetAtom(iat);
            if (! at->isTer()) {
               pts_x.push_back(at->x);
               pts_y.push_back(at->y);
               pts_z.push_back(at->z);
            }
         }
      }
   }

   if (pts_x.size() == 0) {
      std::string message = "No atoms in molecule - no mediain position";
      throw std::runtime_error(message);
   }

   std::sort(pts_x.begin(), pts_x.end());
   std::sort(pts_y.begin(), pts_y.end());
   std::sort(pts_z.begin(), pts_z.end());
   unsigned int mid_index = pts_x.size()/2;

   return clipper::Coord_orth(pts_x[mid_index], pts_y[mid_index], pts_z[mid_index]);
} 



//
clipper::Coord_orth
coot::util::translate_close_to_origin(const clipper::Coord_orth pos,
                                      const clipper::Cell &cell) {

   clipper::Coord_frac cf = pos.coord_frac(cell);
   clipper::Coord_frac cfi(round(-cf.u()), round(-cf.v()), round(-cf.w()));
   return pos + cfi.coord_orth(cell);
} 

void
coot::util::print_secondary_structure_info(mmdb::Model *model_p) {

   // secondary structure information
   //
   int nhelix = model_p->GetNumberOfHelices();
   int nsheet = model_p->GetNumberOfSheets();
   std::cout << "INFO:: There are " << nhelix << " helices and "
             << nsheet << " sheets\n";
   mmdb::PHelix helix_p;
   mmdb::PSheet sheet_p;
   mmdb::PStrand strand_p;

   if (nhelix > 0) {
      std::cout << "               Helix info: " << std::endl;
      std::cout << "------------------------------------------------\n";
      for (int ih=1; ih<=nhelix; ih++) {
         helix_p = model_p->GetHelix(ih);
         if (helix_p) {
            std::cout << helix_p->serNum << " " << helix_p->helixID << " "
                      << helix_p->initChainID << " " << helix_p->initSeqNum
                      << " " << helix_p->endChainID << " " << helix_p->endSeqNum << " "
                      << helix_p->length << " " << helix_p->comment << std::endl;
         } else {
            std::cout << "ERROR: null helix!?" << std::endl;
         }
      }
   }

   if (nsheet > 0) {
      std::cout << "               Sheet info: " << std::endl;
      std::cout << "------------------------------------------------\n";
      for (int is=1; is<=nsheet; is++) {
         sheet_p = model_p->GetSheet(is);

         int nstrand = sheet_p->nStrands;
         for (int istrand=0; istrand<nstrand; istrand++) {
            strand_p = sheet_p->strand[istrand];
            if (strand_p) {
               std::cout << strand_p->sheetID << " " << strand_p->strandNo << " "
                         << strand_p->initChainID << " " << strand_p->initSeqNum
                         << " " << strand_p->endChainID << " " << strand_p->endSeqNum
                         << std::endl;
            }
         }
      }
      std::cout << "------------------------------------------------\n";
   }
}

// return a string description of MMDB SSE values
std::string
coot::util::sse_to_string(int sse) {

   std::string r;
   switch (sse)  {
   case mmdb::SSE_None:
      r = "None";
      break;
   case mmdb::SSE_Strand:
      r = "Strand";
      break;
   case mmdb::SSE_Bulge:  
      r = "Bulge";
      break;
   case mmdb::SSE_3Turn:  
      r = "Turn";
      break;
   case mmdb::SSE_4Turn:  
      r = "4Turn";
      break;
   case mmdb::SSE_5Turn:  
      r = "5Turn";
      break;
   case mmdb::SSE_Helix:  
      r = "Helix";
      break;
   default:
      r = "None";
   }
   return r;
} 

   

// return success status as first element
// 
std::pair<bool, clipper::Coord_orth>
coot::centre_of_molecule(mmdb::Manager *mol) {

   bool status = 0;
   clipper::Coord_orth centre(0,0,0);

   if (mol) {

      int n_atoms = 0;
      double xs=0, ys=0, zs=0;

      for(int imod=1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
         int nchains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<nchains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            mmdb::Atom *at;
            for (int ires=0; ires<nres; ires++) { 
               residue_p = chain_p->GetResidue(ires);
               int n_residue_atoms = residue_p->GetNumberOfAtoms();
         
               for (int iat=0; iat<n_residue_atoms; iat++) {
                  at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     xs += at->x;
                     ys += at->y;
                     zs += at->z;
                     n_atoms++;
                  }
               }
            }
         }
      }
      
      if (n_atoms > 0) {
         status = true;
         double dna = static_cast<double> (n_atoms);
         centre = clipper::Coord_orth(xs/dna, ys/dna, zs/dna);
      }
   }

   return std::pair<bool, clipper::Coord_orth> (status, centre);
}

std::pair<bool, clipper::Coord_orth>
coot::centre_of_molecule_using_masses(mmdb::Manager *mol) {

   std::map<std::string, double> pdb_element_weights = {
      {" H", 1.008},   {"HE", 4.0026}, {"LI", 6.94},   {"BE", 9.0122}, {" B", 10.81},  {" C", 12.011},
      {" N", 14.007},  {" O", 15.999}, {" F", 18.998}, {"NE", 20.180}, {"NA", 22.990}, {"MG", 24.305},
      {"AL", 26.982},  {"SI", 28.085}, {" P", 30.974}, {" S", 32.06},  {"CL", 35.45},  {"AR", 39.948},
      {" K", 39.098},  {"CA", 40.078}, {"SC", 44.956}, {"TI", 47.867}, {" V", 50.942}, {"CR", 51.996},
      {"MN", 54.938},  {"FE", 55.845}, {"CO", 58.933}, {"NI", 58.693}, {"CU", 63.546}, {"ZN", 65.38},
      {"GA", 69.723},  {"GE", 72.630}, {"AS", 74.922}, {"SE", 78.971}, {"BR", 79.904}, {"KR", 83.798},
      {"RB", 85.468},  {"SR", 87.62},  {" Y", 88.906}, {"ZR", 91.224}, {"NB", 92.906}, {"MO", 95.95},
      {"TC", 98.0},    {"RU", 101.07}, {"RH", 102.91}, {"PD", 106.42}, {"AG", 107.87}, {"CD", 112.41},
      {"IN", 114.82},  {"SN", 118.71}, {"SB", 121.76}, {"TE", 127.60}, {" I", 126.90}, {"XE", 131.29},
      {"CS", 132.91},  {"BA", 137.33}, {"LA", 138.91}, {"CE", 140.12}, {"PR", 140.91}, {"ND", 144.24},
      {"PM", 145.0},   {"SM", 150.36}, {"EU", 151.96}, {"GD", 157.25}, {"TB", 158.93}, {"DY", 162.50},
      {"HO", 164.93},  {"ER", 167.26}, {"TM", 168.93}, {"YB", 173.05}, {"LU", 174.97}, {"HF", 178.49},
      {"TA", 180.95},  {" W", 183.84}, {"RE", 186.21}, {"OS", 190.23}, {"IR", 192.22}, {"PT", 195.08},
      {"AU", 196.97},  {"HG", 200.59}, {"TL", 204.38}, {"PB", 207.2},  {"BI", 208.98}, {"PO", 209.0},
      {"AT", 210.0},   {"RN", 222.0},  {"FR", 223.0},  {"RA", 226.0},  {"AC", 227.0},  {"TH", 232.04},
      {"PA", 231.04},  {" U", 238.03}, {"NP", 237.0},  {"PU", 244.0},  {"AM", 243.0},  {"CM", 247.0},
      {"BK", 247.0},   {"CF", 251.0},  {"ES", 252.0},  {"FM", 257.0},  {"MD", 258.0},  {"NO", 259.0},
      {"LR", 262.0},   {"RF", 267.0},  {"DB", 270.0},  {"SG", 271.0},  {"BH", 270.0},  {"HS", 277.0},
      {"MT", 278.0},   {"DS", 281.0},  {"RG", 282.0},  {"CN", 285.0},  {"FL", 289.0},  {"LV", 293.0},
      {"TS", 294.0},   {"OG", 294.0}
   };

   int n_atoms = 0;
   double xs=0, ys=0, zs=0;
   double sum_weight = 0.0;
   for(int imod=1; imod<=mol->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol->GetModel(imod);
      if (! model_p) continue;
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         int nres = chain_p->GetNumberOfResidues();
         for (int ires=0; ires<nres; ires++) { 
         mmdb::Residue *residue_p = chain_p->GetResidue(ires);
            int n_residue_atoms = residue_p->GetNumberOfAtoms();
            for (int iat=0; iat<n_residue_atoms; iat++) {
               mmdb::Atom *at = residue_p->GetAtom(iat);
               if (! at->isTer()) {
                  std::string ele = at->element;
                  double w = 6.0;
                  std::map<std::string, double>::const_iterator it;
                  it = pdb_element_weights.find(ele);
                  if (it != pdb_element_weights.end()) w = it->second;
                  xs += w * at->x; ys += w * at->y; zs += w * at->z;
                  sum_weight += w;
                  n_atoms++;
               }
            }
         }
      }
   }
   if (n_atoms > 0) {
      double x = xs / static_cast<double>(sum_weight);
      double y = ys / static_cast<double>(sum_weight);
      double z = zs / static_cast<double>(sum_weight);
      return std::make_pair(true, clipper::Coord_orth(x,y,z));
   } else {
      return std::make_pair(false, clipper::Coord_orth(0,0,0));
   }
}

//! get the radius of gyration - using the centre from above
std::pair<bool, double>
coot::radius_of_gyration(mmdb::Manager *mol) {

   std::map<std::string, double> pdb_element_weights = {
      {" H", 1.008},   {"HE", 4.0026}, {"LI", 6.94},   {"BE", 9.0122}, {" B", 10.81},  {" C", 12.011},
      {" N", 14.007},  {" O", 15.999}, {" F", 18.998}, {"NE", 20.180}, {"NA", 22.990}, {"MG", 24.305},
      {"AL", 26.982},  {"SI", 28.085}, {" P", 30.974}, {" S", 32.06},  {"CL", 35.45},  {"AR", 39.948},
      {" K", 39.098},  {"CA", 40.078}, {"SC", 44.956}, {"TI", 47.867}, {" V", 50.942}, {"CR", 51.996},
      {"MN", 54.938},  {"FE", 55.845}, {"CO", 58.933}, {"NI", 58.693}, {"CU", 63.546}, {"ZN", 65.38},
      {"GA", 69.723},  {"GE", 72.630}, {"AS", 74.922}, {"SE", 78.971}, {"BR", 79.904}, {"KR", 83.798},
      {"RB", 85.468},  {"SR", 87.62},  {" Y", 88.906}, {"ZR", 91.224}, {"NB", 92.906}, {"MO", 95.95},
      {"TC", 98.0},    {"RU", 101.07}, {"RH", 102.91}, {"PD", 106.42}, {"AG", 107.87}, {"CD", 112.41},
      {"IN", 114.82},  {"SN", 118.71}, {"SB", 121.76}, {"TE", 127.60}, {" I", 126.90}, {"XE", 131.29},
      {"CS", 132.91},  {"BA", 137.33}, {"LA", 138.91}, {"CE", 140.12}, {"PR", 140.91}, {"ND", 144.24},
      {"PM", 145.0},   {"SM", 150.36}, {"EU", 151.96}, {"GD", 157.25}, {"TB", 158.93}, {"DY", 162.50},
      {"HO", 164.93},  {"ER", 167.26}, {"TM", 168.93}, {"YB", 173.05}, {"LU", 174.97}, {"HF", 178.49},
      {"TA", 180.95},  {" W", 183.84}, {"RE", 186.21}, {"OS", 190.23}, {"IR", 192.22}, {"PT", 195.08},
      {"AU", 196.97},  {"HG", 200.59}, {"TL", 204.38}, {"PB", 207.2},  {"BI", 208.98}, {"PO", 209.0},
      {"AT", 210.0},   {"RN", 222.0},  {"FR", 223.0},  {"RA", 226.0},  {"AC", 227.0},  {"TH", 232.04},
      {"PA", 231.04},  {" U", 238.03}, {"NP", 237.0},  {"PU", 244.0},  {"AM", 243.0},  {"CM", 247.0},
      {"BK", 247.0},   {"CF", 251.0},  {"ES", 252.0},  {"FM", 257.0},  {"MD", 258.0},  {"NO", 259.0},
      {"LR", 262.0},   {"RF", 267.0},  {"DB", 270.0},  {"SG", 271.0},  {"BH", 270.0},  {"HS", 277.0},
      {"MT", 278.0},   {"DS", 281.0},  {"RG", 282.0},  {"CN", 285.0},  {"FL", 289.0},  {"LV", 293.0},
      {"TS", 294.0},   {"OG", 294.0}
   };

   double xs=0, ys=0, zs=0;
   double sum_weight = 0.0;
   double sum_dd = 0.0;
   auto centre_pair = centre_of_molecule_using_masses(mol);
   if (centre_pair.first) {
      clipper::Coord_orth centre = centre_pair.second;
      for(int imod=1; imod<=mol->GetNumberOfModels(); imod++) {
         mmdb::Model *model_p = mol->GetModel(imod);
         if (! model_p) continue;
         int nchains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<nchains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int nres = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<nres; ires++) { 
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               int n_residue_atoms = residue_p->GetNumberOfAtoms();
               for (int iat=0; iat<n_residue_atoms; iat++) {
                  mmdb::Atom *at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     std::string ele = at->element;
                     double w = 14.0;
                     std::map<std::string, double>::const_iterator it;
                     it = pdb_element_weights.find(ele);
                     if (it != pdb_element_weights.end()) w = it->second;
                     clipper::Coord_orth pt(at->x, at->y, at->z);
                     clipper::Coord_orth delta = pt - centre;
                     double dd = delta.lengthsq();
                     sum_dd += dd * w;
                     sum_weight += w;
                  }
               }
            }
         }
      }
      double rr = sum_dd / sum_weight;
      double radius_of_gyration = std::sqrt(rr);
      return std::make_pair(true, radius_of_gyration);
   } else {
      return std::make_pair(false, 0);
   }

}

      

std::pair<bool, clipper::Coord_orth>
coot::centre_of_residues(const std::vector<mmdb::Residue *> &residues) {

   bool status = false;
   clipper::Coord_orth centre(0,0,0);
   int n_atoms = 0;
   double xs=0, ys=0, zs=0;

   for (unsigned int ires=0; ires<residues.size(); ires++) {
      mmdb::PPAtom residue_atoms = 0;
      int n_residue_atoms;
      residues[ires]->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) { 
         xs += residue_atoms[iat]->x;
         ys += residue_atoms[iat]->y;
         zs += residue_atoms[iat]->z;
         n_atoms++;
      }
   }

   if (n_atoms) {
      status = true;
      double dna = static_cast<double> (n_atoms);
      centre = clipper::Coord_orth(xs/dna, ys/dna, zs/dna);
   } 
   return std::pair<bool, clipper::Coord_orth> (status, centre);
}


mmdb::Residue *
coot::nearest_residue_by_sequence(mmdb::Manager *mol,
                                  const residue_spec_t &spec) {

   mmdb::Residue *r = NULL;
   int resno_closest_high = -9999;
      
   if (mol) {
      int imod = 1;
      mmdb::Model *model_p = mol->GetModel(imod);
      if (! model_p) return nullptr;
      int nchains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<nchains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         std::string chain_id = chain_p->GetChainID();
         if (chain_id == spec.chain_id) { 
            int nres = chain_p->GetNumberOfResidues();
            mmdb::Residue *residue_p;
            for (int ires=0; ires<nres; ires++) { 
               residue_p = chain_p->GetResidue(ires);
               int this_resno = residue_p->GetSeqNum();
               if (labs(spec.res_no - this_resno)
                   < (labs(spec.res_no - resno_closest_high))) {
                  resno_closest_high = this_resno;
                  r = residue_p;
               }
            }
         }
      }
   }
   return r;
}




// copy cell, symm, origin and scale cards from m1 to m2 (if possible)
bool
coot::util::copy_cell_and_symm_headers(mmdb::Manager *m1, mmdb::Manager *m2) {

   bool r = 0;

   if (m1 && m2) {

      //       mmdb::realtype a[6];
      //       mmdb::realtype vol;
      //       int orthcode;
      
      //       m1->GetCell(a[0], a[1], a[2], a[3], a[4], a[5], vol, orthcode);
      //       char *sg = m1->GetSpaceGroup();
      //       m2->SetSpaceGroup(sg);
      //       m2->SetCell(a[0], a[1], a[2], a[3], a[4], a[5]);

      m2->Copy(m1, mmdb::MMDBFCM_Cryst);
      r = 1;
   }
   return r;
}

// copy all except, optionally, cell, symm, origin and scale cards from m1 to m2 (if possible)
bool
coot::util::copy_headers(mmdb::Manager *m1, mmdb::Manager *m2, bool include_cryst) {

   bool r = 0;

   if (m1 && m2) {

      mmdb::COPY_MASK cm = mmdb::MMDBFCM_All;
      if (! include_cryst) {

         // What about Footnotes? CONECT records?

         // Yuck, yuck. This works because mmdb enums are ints.
         cm = static_cast<mmdb::COPY_MASK> (mmdb::MMDBFCM_All & ~mmdb::MMDBFCM_Cryst & ~mmdb::MMDBFCM_Coord);
      }
      m2->Copy(m1, cm);
      r = 1;
   }
   return r;
}

// The plan for positioning NAGs on ASN (N-link):
//
// Scenario Simple Beam-in:
//    User has an ASN onto which they want to beam in a NAG.
// 
//    setup:
//    Make mmdb::Residue *s and/or molecule for the N-linked NAG reference residues.
// 
///   Get the mmdb::Residue * for the user residue ASN 
//    Get the mmdb::Atoms *s for the OD1, ND2, GC and CB in user residue [1]
//    Get the mmdb::Atoms *s for the OD1, ND2, GC and CB in N-linked ASN molecule [2]
//
//    LSQ fit the NAG residue from the reference ASN+NAG pair using
//    matrix that rotates [2] onto [1].  (We don't need the ASN from
//    that pair).  Now we can add that rotated NAG mmdb::Residue * to user
//    molecule.  we have N-linked-NAG template - consider renaming to
//    ASN-NAG-via-NAG-ASN i.e. the general case
//    {ResType1}-{ResType2}-via-{LinkName} where ResType1 and ResType2
//    are comp-ids, of course.  Actually, NAG-ASN is a pyronose-ASN
//    link (group to comp_id). Hmm...
//
//
//  Scenario Torsion-angle Density Search:
//    User has an ASN and a density map and want to add a NAG.
//    or:
//    User has a NAG and want to 1-4 (or other link) add another.
//    This is harder.
//
//    OK, for the general case of ResType - link_type - ResType we need
//    a template for that.
// 
// 
// 
coot::position_residue_by_internal_coordinates::position_residue_by_internal_coordinates(mmdb::Residue *residue_ref,
                                                                                         mmdb::Residue *residue_moving,
                                                                                         const atom_name_quad &quad,
                                                                                         const double &bond_length,
                                                                                         const double &bond_angle,
                                                                                         const double &bond_torsion) {  // degrees

   bool status = 0;

   // first, can we find the atoms in the residues?
   if (residue_ref) {
      if (residue_moving) {

         mmdb::Atom *at_0 = get_atom(residue_ref, residue_moving, quad, 0);
         mmdb::Atom *at_1 = get_atom(residue_ref, residue_moving, quad, 1);
         mmdb::Atom *at_2 = get_atom(residue_ref, residue_moving, quad, 2);
         mmdb::Atom *at_3 = get_atom(residue_ref, residue_moving, quad, 3);

         if (at_0 && at_1 && at_2 && at_3) {

            // OK, we have found the atoms of the residue
            
         } 
      }
   } 
}


// return success status (0 = fail)
//
// 
bool 
coot::position_residue_by_internal_coordinates::move_moving_residue() {

   bool status = 0;

   return status;
} 

// return NULL on atom not found (res_1 and res_2 are guarenteed to be non-null)
mmdb::Atom *
coot::position_residue_by_internal_coordinates::get_atom(mmdb::Residue *res_1,
                                                         mmdb::Residue *res_2,
                                                         const atom_name_quad &quad,
                                                         int atom_index) {

   mmdb::Atom *at = NULL;

   std::string atom_name;

   if (atom_name.length() > 0) {

      mmdb::Residue *residue_p = res_1;
      std::string torsion_atom_name = quad.atom_name(atom_index);
      if (quad.atom_residue_index[atom_index] == 2)
         residue_p = res_2;
      mmdb::PPAtom residue_atoms = 0;
      int n_residue_atoms;
      residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
      for (int iat=0; iat<n_residue_atoms; iat++) {
         mmdb::Atom *atom = residue_atoms[iat];
         std::string atom_name(atom->name);
         if (atom_name == torsion_atom_name) {
            at = atom;
            break;
         }
      }
   }
   return at;
}

// can throw a std::runtime_error exception
// 
coot::arc_info_type::arc_info_type(mmdb::Atom *at_1, mmdb::Atom *at_2, mmdb::Atom *at_3) {

   if (! at_1) throw("null at_1");
   if (! at_2) throw("null at_2");
   if (! at_3) throw("null at_3");

   clipper::Coord_orth p1(at_1->x, at_1->y, at_1->z);
   clipper::Coord_orth p2(at_2->x, at_2->y, at_2->z);
   clipper::Coord_orth p3(at_3->x, at_3->y, at_3->z);

   clipper::Coord_orth v1(clipper::Coord_orth(p3 - p2).unit());
   clipper::Coord_orth v2(clipper::Coord_orth(p1 - p2).unit()); // vectors away from central atom

   clipper::Coord_orth v3 = clipper::Coord_orth(clipper::Coord_orth::cross(v1, v2).unit());
   clipper::Coord_orth v4 = clipper::Coord_orth(clipper::Coord_orth::cross(v3, v1).unit());

   normal = v3;
   start_point = p2;
   start_dir = clipper::Coord_orth(v2.unit());

   delta  = clipper::Util::rad2d(clipper::Coord_orth::angle(p1,p2,p3));

   orientation_matrix = clipper::Mat33<double>(v1.x(), v1.y(), v1.z(),
                                               v4.x(), v4.y(), v4.z(),
                                               v3.x(), v3.y(), v3.z());
}


clipper::Coord_orth
coot::co(mmdb::Atom *at) {
   return clipper::Coord_orth(at->x, at->y, at->z);
}

void
coot::update_position(mmdb::Atom *at, const clipper::Coord_orth &pos) {
   at->x = pos.x();
   at->y = pos.y();
   at->z = pos.z();
}



// 
mmdb::Atom *
coot::chiral_4th_atom(mmdb::Residue *residue_p, mmdb::Atom *at_centre,
                      mmdb::Atom *at_1, mmdb::Atom *at_2, mmdb::Atom *at_3) {

   mmdb::Atom *rat = NULL;
   double d_crit = sqrt(1.7);
   double d_sqrd = d_crit * d_crit; // tracks "best/closest"

   mmdb::PPAtom residue_atoms = 0;
   int n_residue_atoms;
   clipper::Coord_orth p_c = co(at_centre);
   std::string alt_conf = at_centre->altLoc;
   residue_p->GetAtomTable(residue_atoms, n_residue_atoms);
   for (int iat=0; iat<n_residue_atoms; iat++) { 
      mmdb::Atom *at = residue_atoms[iat];
      if (at != at_centre && at != at_1 && at != at_2 && at != at_3) { 
         clipper::Coord_orth pt = co(at);
         double d2 = (p_c - pt).clipper::Coord_orth::lengthsq();
         if (d2 < d_sqrd) {
            rat = at;
            d_sqrd = d2;
         }
      }
   }

   return rat;
} 





#include <fstream>

std::vector<clipper::RTop_orth>
coot::mtrix_info(const std::string &file_name) {

   // This is a placeholder for std::vector<clipper::RTop_orth mtrix_inf(mmdb::Manager *mol)
   
   std::vector<clipper::RTop_orth> r;

   if (file_exists(file_name)) {
      std::ifstream f(file_name.c_str());
      if (f) {
         std::vector<std::string> lines;
         std::string line_in;
         while (std::getline(f, line_in)) {
            if (line_in.length() > 10) {
               if (line_in.substr(0,5) == "MTRIX") {
                  // std::cout << "found " << line << std::endl;
                  lines.push_back(line_in);
               }
            }
         }
         if (lines.size() > 0) {
            clipper::Mat33<double> rot_running;
            clipper::Coord_orth trn_running;
            for (unsigned int i=0; i<lines.size(); i++) {
               const std::string &line = lines[i];
               char line_char = line[5];
               int line_n = line_char - 48;
               if ((line_n > 0) && (line_n < 4)) {
                  std::vector<std::string> bits = util::split_string_no_blanks(line);
                  if (bits.size() > 5) {
                     try {
                        int rtop_index = util::string_to_int(bits[1]);
                        float f0 = util::string_to_float(bits[2]);
                        float f1 = util::string_to_float(bits[3]);
                        float f2 = util::string_to_float(bits[4]);
                        float ft = util::string_to_float(bits[5]);
                        rot_running(line_n-1, 0) = f0;
                        rot_running(line_n-1, 1) = f1;
                        rot_running(line_n-1, 2) = f2;
                        trn_running[line_n-1] = ft;
                        if (line_n == 3) {
                           clipper::RTop_orth rt(rot_running, trn_running);
                           // std::cout << "adding\n" << rt.format() << std::endl;
                           r.push_back(rt);
                        } 
                     }
                     catch (const std::runtime_error &rte) {
                        std::cout << "failed to parse " << line<< std::endl;
                     } 
                  }
               }
            }
         } 
      }
   }
   std::cout << "INFO:: Founds " << r.size() << " MTRIX matrices" << std::endl;
   return r;

} 

double
coot::util::refmac_atom_radius(mmdb::Atom *at) {

   double u = at->tempFactor / (8 * M_PI * M_PI);
   double v = 2 * u;
   v = std::max(v, 0.38); // don't have tiny atoms

   // I want small atoms than refmac has.
   //             v += 0.7;
   //             v *= 5;
   v += 0.6;
   v *= 4;
   return sqrt(v);
}

// get the number of residue in chain, protein first.
std::pair<unsigned int, unsigned int>
coot::util::get_number_of_protein_or_nucleotides(mmdb::Chain *chain_p) {

   std::pair<unsigned int, unsigned int> n(0,0);
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      for (int ires=0; ires<nres; ires++) {
         mmdb::Residue *residue_p = chain_p->GetResidue(ires);
         std::string res_name(residue_p->GetResName());
         if (is_standard_amino_acid_name(res_name))
            n.first++;
         if (is_standard_nucleotide_name(res_name))
            n.second++;
      }
   }

   return n;
}


// CBs in GLY etc - using ProteinDBSearch
void
coot::util::delete_anomalous_atoms(mmdb::Manager *mol) {

   bool changed = false;
   for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol->GetModel(imod);
      if (model_p) {
         int n_chains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<n_chains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int nres = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<nres; ires++) {
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               int n_atoms = residue_p->GetNumberOfAtoms();
               std::string res_name(residue_p->GetResName());
               std::set<int> delete_these_atoms;
               for (int iat=0; iat<n_atoms; iat++) {
                  mmdb::Atom *at = residue_p->GetAtom(iat);
                  std::string atom_name(at->GetAtomName());
                  if (atom_name == " CB ") { // PDBv3 FIXME
                     if (res_name == "GLY") {
                        delete_these_atoms.insert(iat);
                     }
                  }
               }
               if (! delete_these_atoms.empty()) {
                  std::set<int>::reverse_iterator it;
                  for (it=delete_these_atoms.rbegin(); it!=delete_these_atoms.rend(); it++) {
                     int idx = *it;
                     if (idx >= 0) {
                        // std::cout << "------------ delete! " << idx << std::endl;
                        residue_p->DeleteAtom(idx);
                        changed = true;
                     }
                  }
                  residue_p->TrimAtomTable();
               }
            }
         }
      }
   }

   if (changed) {
      mol->PDBCleanup(mmdb::PDBCLEAN_SERIAL|mmdb::PDBCLEAN_INDEX);
      mol->FinishStructEdit();
   }
}

std::vector<mmdb::Residue *>
coot::util::residues_in_chain(mmdb::Manager *mol, const std::string &chain_id_in) {

   std::vector<mmdb::Residue *> v;

   if (! mol) return v;

   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (model_p) {
      int n_chains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<n_chains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         if (std::string(chain_p->GetChainID()) == chain_id_in) {
            v = residues_in_chain(chain_p);
         }
      }
   }
   return v;
}

std::vector<mmdb::Residue *>
coot::util::residues_in_chain(mmdb::Chain *chain_p) {

   std::vector<mmdb::Residue *> v;
   if (chain_p) {
      int nres = chain_p->GetNumberOfResidues();
      for (int ires=0; ires<nres; ires++) {
         mmdb::Residue *residue_p = chain_p->GetResidue(ires);
         v.push_back(residue_p);
      }
   }
   return v;
}

std::vector<mmdb::Residue *>
coot::util::residues_in_molecule(mmdb::Manager *mol) {

   std::vector<mmdb::Residue *> v;
   for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol->GetModel(imod);
      if (model_p) {
         int n_chains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<n_chains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int n_res = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<n_res; ires++) {
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               if (residue_p) {
                  v.push_back(residue_p);
               }
            }
         }
      }
   }
   return v;
}

std::pair<std::set<mmdb::Residue *>, std::set<mmdb::Residue *> >
coot::interface_residues(mmdb::Manager *mol,
                         const std::string &chain_A,
                         const std::string &chain_B,
                         float min_dist) {

   std::pair<std::set<mmdb::Residue *>, std::set<mmdb::Residue *> > p; // return this
   std::map<mmdb::Residue *, std::set<mmdb::Residue *> > all_molecule_map;

   // fill all_molecule_map using seekcontacts
   if (mol) {

      int SelectionHandle = mol->NewSelection(); // d
      mol->SelectAtoms (SelectionHandle, 0, "*",
                        mmdb::ANY_RES, // starting resno, an int
                        "*", // any insertion code
                        mmdb::ANY_RES, // ending resno
                        "*", // ending insertion code
                        "*", // any residue name
                        "*", // atom name
                        "*", // elements
                        "*"  // alt loc.
                        );

      mmdb::Atom **atom_selection = 0;
      int n_selected_atoms = 0;
      mol->GetSelIndex(SelectionHandle, atom_selection, n_selected_atoms);
      if (n_selected_atoms > 0) {

         mmdb::Contact *pscontact = NULL;
         int n_contacts;
         long i_contact_group = 1;
         mmdb::mat44 my_matt;
         mmdb::SymOps symm;
         for (int i=0; i<4; i++) 
            for (int j=0; j<4; j++) 
               my_matt[i][j] = 0.0;      
         for (int i=0; i<4; i++) my_matt[i][i] = 1.0;

         mol->SeekContacts(atom_selection, n_selected_atoms, 
                           atom_selection, n_selected_atoms,
                           0.01, min_dist,
                           0,        // seqDist 0 -> in same res also
                           pscontact, n_contacts,
                           0, &my_matt, i_contact_group);

         if (n_contacts > 0) {
            if (pscontact) { 
               for (int i=0; i<n_contacts; i++) {
                  mmdb::Atom *at_1 = atom_selection[pscontact[i].id1];
                  mmdb::Atom *at_2 = atom_selection[pscontact[i].id2];
                  mmdb::Residue *r_1 = at_1->residue;
                  mmdb::Residue *r_2 = at_2->residue;
                  mmdb::Chain *ch_1 = r_1->chain;
                  mmdb::Chain *ch_2 = r_2->chain;
                  if (r_1 != r_2) {
                     if (ch_1 != ch_2) {
                        all_molecule_map[r_1].insert(r_2);
                     }
                  }
               }
            }
         }
      }
      mol->DeleteSelection(SelectionHandle);

      std::vector<mmdb::Residue *> r1 = util::residues_in_chain(mol, chain_A);
      std::vector<mmdb::Residue *> r2 = util::residues_in_chain(mol, chain_B);
      // the limits are in the "contactors" - i.e. residues of the map, not the set
      std::set<mmdb::Residue *> limit_to_these_residues_vec_chain_A;
      std::set<mmdb::Residue *> limit_to_these_residues_vec_chain_B;

      for (unsigned int i=0; i<r1.size(); i++) limit_to_these_residues_vec_chain_A.insert(r1[i]);
      for (unsigned int i=0; i<r2.size(); i++) limit_to_these_residues_vec_chain_B.insert(r2[i]);

      std::map<mmdb::Residue *, std::set<mmdb::Residue *> > mA = residues_near_residues_for_residues(all_molecule_map,
                                                                                                     limit_to_these_residues_vec_chain_A);
      std::map<mmdb::Residue *, std::set<mmdb::Residue *> > mB = residues_near_residues_for_residues(all_molecule_map,
                                                                                                     limit_to_these_residues_vec_chain_B);
      std::set<mmdb::Residue *> r_1_residues;
      std::set<mmdb::Residue *> r_2_residues;

      std::map<mmdb::Residue *, std::set<mmdb::Residue *> >::const_iterator it_map;
      for(it_map=mA.begin(); it_map!=mA.end(); ++it_map) r_1_residues.insert(it_map->first);
      for(it_map=mB.begin(); it_map!=mB.end(); ++it_map) r_2_residues.insert(it_map->first);
      p = std::pair<std::set<mmdb::Residue *>, std::set<mmdb::Residue *> >(r_1_residues, r_2_residues);
   }
   return p;
}


// copy the chain and add it to a new molecule hierarchy
std::pair<mmdb::Chain *, mmdb::Manager *>
coot::util::copy_chain(mmdb::Chain *chain_p) {

   mmdb::Chain *new_chain = new mmdb::Chain;
   new_chain->Copy(chain_p);
   mmdb::Manager *mol = new mmdb::Manager;
   mmdb::Model *model_p = new mmdb::Model;
   model_p->AddChain(new_chain);
   mol->AddModel(model_p);
   mol->FinishStructEdit();
   coot::util::pdbcleanup_serial_residue_numbers(mol);
   return std::make_pair(new_chain, mol);
}


// to be used with

void
coot::util::copy_atoms_from_chain_to_chain(mmdb::Chain *from_chain, mmdb::Chain *to_chain) {

   // This will scramble atoms if the are not in exactly the same order

   int n_residues_1 = from_chain->GetNumberOfResidues();
   int n_residues_2 =   to_chain->GetNumberOfResidues();
   if (n_residues_2 == n_residues_1) {
      for (int ires=0; ires<n_residues_1; ires++) {
         mmdb::Residue *residue_from_p = from_chain->GetResidue(ires);
         mmdb::Residue *residue_to_p   =   to_chain->GetResidue(ires);
         int n_atoms_1 = residue_from_p->GetNumberOfAtoms();
         int n_atoms_2 =   residue_to_p->GetNumberOfAtoms();
         if (n_atoms_2 == n_atoms_1) {
            for (int iat=0; iat<n_atoms_1; iat++) {
               mmdb::Atom *at_from = residue_from_p->GetAtom(iat);
               mmdb::Atom *at_to   =   residue_to_p->GetAtom(iat);
               at_to->x = at_from->x;
               at_to->y = at_from->y;
               at_to->z = at_from->z;
            }
         } else {
            std::cout << "ERROR:: mismatching atom count in copy_atoms_from_chain_to_chain() " << std::endl;
         }
      }
   } else {
      std::cout << "ERROR:: mismatching residue count in copy_atoms_from_chain_to_chain() " << std::endl;
   }
}


// add or delete residues and atoms as needed.
void
coot::util::replace_chain_contents_with_atoms_from_chain(mmdb::Chain *orig_from_chain,
                                                         mmdb::Manager *orig_mol,
                                                         mmdb::Chain *modified_chain,
                                                         bool do_finishstructedit) {

   // say I have copied a chain and then changed it by trimming or addition of residues, I want
   // to now update orig_to_chain with the contents of modified_chain

   orig_from_chain->Copy(modified_chain);
   if (orig_mol)
      if (do_finishstructedit)
         orig_mol->FinishStructEdit();

}



float
coot::get_position_hash(mmdb::Manager *mol) {

   // terrible but fast and tells me what I want.

   float h = 0.0;
   if (! mol) {
      std::cout << "WARNING:: get_position_hash() called with null mol " << std::endl;
      return h;
   }

   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (model_p) {
      int n_chains = model_p->GetNumberOfChains();
      unsigned int atom_count = 0;
      for (int ichain=0; ichain<n_chains; ichain++) {
         float x_prev = 0.0;
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         int n_res = chain_p->GetNumberOfResidues();
         for (int ires=0; ires<n_res; ires++) {
            mmdb::Residue *residue_p = chain_p->GetResidue(ires);
            if (residue_p) {
               int n_atoms = residue_p->GetNumberOfAtoms();
               for (int iat=0; iat<n_atoms; iat++) {
                  mmdb::Atom *at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     if (atom_count > 0) {
                        h += at->x - x_prev;
                     }
                     atom_count++;
                     x_prev = at->x;
                  }
               }
            }
         }
      }
   }

   return h;
}

std::vector<mmdb::Atom *>
coot::atoms_with_zero_occupancy(mmdb::Manager *mol) {

   std::vector<mmdb::Atom *> v;
   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (model_p) {
      int n_chains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<n_chains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         int n_res = chain_p->GetNumberOfResidues();
         for (int ires=0; ires<n_res; ires++) {
            mmdb::Residue *residue_p = chain_p->GetResidue(ires);
            if (residue_p) {
               int n_atoms = residue_p->GetNumberOfAtoms();
               for (int iat=0; iat<n_atoms; iat++) {
                  mmdb::Atom *at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     if (at->occupancy < 0.01) {
                        v.push_back(at);
                     }
                  }
               }
            }
         }
      }
   }
   return v;
}


std::vector<mmdb::Residue *>
coot::residues_with_alt_confs(mmdb::Manager *mol) {

   std::vector<mmdb::Residue *> v;
   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (model_p) {
      int n_chains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<n_chains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         int n_res = chain_p->GetNumberOfResidues();
         for (int ires=0; ires<n_res; ires++) {
            mmdb::Residue *residue_p = chain_p->GetResidue(ires);
            if (residue_p) {
               int n_atoms = residue_p->GetNumberOfAtoms();
               bool found = false;
               for (int iat=0; iat<n_atoms; iat++) {
                  mmdb::Atom *at = residue_p->GetAtom(iat);
                  if (! at->isTer()) {
                     std::string a(at->altLoc);
                     if (a.length() > 0) {
                        found = true;
                        break;
                     }
                  }
               }
               if (found) {
                  v.push_back(residue_p);
               }
            }
         }
      }
   }
   return v;
}


std::vector<std::vector<mmdb::Chain *> >
coot::ncs_related_chains(mmdb::Manager *mol, int imod) {

   std::vector<std::vector<mmdb::Chain *> > v;

   if (!mol) return v;

   auto chains_match = [] (mmdb::Chain *c1, mmdb::Chain *c2) {
      int n_res_1 = c1->GetNumberOfResidues();
      int n_res_2 = c2->GetNumberOfResidues();
      if (false)
         std::cout << "chains_match() start "
                   << c1->GetChainID() << " has " << n_res_1 << " residues "
                   << c2->GetChainID() << " has " << n_res_2 << " residues " << std::endl;
      std::map<int, std::string> m1;
      std::map<int, std::string> m2;
      for (int ires=0; ires<n_res_1; ires++) {
         mmdb::Residue *residue_p = c1->GetResidue(ires);
         if (residue_p) {
            std::string res_name = residue_p->GetResName();
            int res_no = residue_p->GetSeqNum();
            if (res_name != "HOH")
               m1[res_no] = res_name;
         }
      }
      for (int ires=0; ires<n_res_2; ires++) {
         mmdb::Residue *residue_p = c2->GetResidue(ires);
         if (residue_p) {
            std::string res_name = residue_p->GetResName();
            int res_no = residue_p->GetSeqNum();
            if (res_name != "HOH")
               m2[res_no] = res_name;
         }
      }

      std::map<int, std::string>::const_iterator it_1;
      unsigned int n_count =  0;
      unsigned int n_match = 0;
      for (it_1=m1.begin(); it_1!=m1.end(); ++it_1) {
         n_count++;
         std::map<int, std::string>::const_iterator it_2 = m2.find(it_1->first);
         if (it_2 != m2.end()) {
            if (it_2->second == it_1->second)
               n_match++;
         }
      }
      if (n_count > 0) {
         float f1 = static_cast<float>(n_count);
         float f2 = static_cast<float>(n_match);
         if (false)
            std::cout << "debug:: chain-id " << c1->GetChainID() << " vs " << c2->GetChainID() << " n-match: " << n_match << " n-count " << n_count
                      << " r " << f2/f1 << std::endl;
         if (f2/f1 > 0.7)
            return true;
      } else {
         // std::cout << "debug:: chain-id " << c1->GetChainID() << " vs " << c2->GetChainID() << " n-count " << n_count << std::endl;
      }
      return false;
   };

   mmdb::Model *model_p = mol->GetModel(imod);
   if (model_p) {
      int n_chains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<n_chains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);

         // std::cout << "------------- checking chain ich " << ichain << ": " << chain_p->GetChainID() << std::endl;
         if (chain_p->GetNumberOfResidues() > 0) {

            // now check if this is like anything else we've seen
            bool found_a_match = false;
            for (unsigned int iv1=0; iv1<v.size(); ++iv1) {
               std::vector<mmdb::Chain *> &vv = v[iv1];
               mmdb::Chain *vv_chain_p = vv[0];
               bool cm = chains_match(vv_chain_p, chain_p);
               if (cm) {
                  vv.push_back(chain_p);
                  found_a_match = true;
                  break;
               }
            }
            if (! found_a_match) {
               // std::cout << "   starting a new group with chain-id " << chain_p->GetChainID() << std::endl;
               v.push_back({chain_p});
            }
         } else {
            // std::cout << "debug:: no residues in chain " << chain_p->GetChainID() << std::endl;
         }
      }
   }

   if (false) {
      std::cout << "------------------------------------ debug in coot::ncs_related_chains()  --------------------------" << std::endl;
      unsigned int n_chains = 0;
      for (unsigned int iv1=0; iv1<v.size(); ++iv1) {
         std::cout << "New Set .... " << std::endl;
         std::vector<mmdb::Chain *> &vv = v[iv1];
         for (unsigned int iv2=0; iv2<vv.size(); ++iv2) {
            mmdb::Chain *c = vv[iv2];
            std::string chain_id(c->GetChainID());
            std::cout << " " << chain_id;
            n_chains++;
         }
         std::cout << std::endl;
      }
      std::cout << "Found " << n_chains << " total chains" << std::endl;
   }

   return v;

}


// split an NMR model into multiple models all with MODEL 1.
std::vector<mmdb::Manager *>
coot::util::split_multi_model_molecule(mmdb::Manager *mol) {

   std::vector<mmdb::Manager *> v;

   for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol->GetModel(imod);
      if (model_p) {
         mmdb::Model *new_model = new mmdb::Model;
         mmdb::Manager *new_mol = new mmdb::Manager;
         new_model->Copy(model_p);
         new_mol->AddModel(new_model);
         v.push_back(new_mol);
      }
   }

   return v;
}




std::vector<std::string>
coot::util::alt_confs_in_molecule(mmdb::Manager *mol) {

   std::vector<std::string> v;
   std::set<std::string> s;
   int imod = 1;
   mmdb::Model *model_p = mol->GetModel(imod);
   if (model_p) {
      int n_chains = model_p->GetNumberOfChains();
      for (int ichain=0; ichain<n_chains; ichain++) {
         mmdb::Chain *chain_p = model_p->GetChain(ichain);
         int n_res = chain_p->GetNumberOfResidues();
         for (int ires=0; ires<n_res; ires++) {
            mmdb::Residue *residue_p = chain_p->GetResidue(ires);
            if (residue_p) {
               int n_atoms = residue_p->GetNumberOfAtoms();
               for (int iat=0; iat<n_atoms; iat++) {
                  mmdb::Atom *at = residue_p->GetAtom(iat);
                  std::string alt_conf(at->altLoc);
                  if (! at->isTer()) {
                     s.insert(alt_conf);
                  }
               }
            }
         }
      }
   }
   // now convert s to v;
   std::set<std::string>::const_iterator it;
   for (it=s.begin(); it!=s.end(); ++it)
      v.push_back(*it);
   return v;
}

//! delete all carbohydrate
bool
coot::util::delete_all_carbohydrate(mmdb::Manager *mol) {

   bool deleted = false;

   std::set<std::string> cho_set;
   cho_set.insert("NAG"); cho_set.insert("MAN"); cho_set.insert("BMA"); cho_set.insert("FUL");
   cho_set.insert("FUC"); cho_set.insert("XYP"); cho_set.insert("SIA"); cho_set.insert("GAL");
   cho_set.insert("NDG"); cho_set.insert("BGC"); cho_set.insert("A2G");

   std::vector<mmdb::Residue *> residues_to_be_removed;

   if (! mol) return false;

   for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
      mmdb::Model *model_p = mol->GetModel(imod);
      if (model_p) {
         int n_chains = model_p->GetNumberOfChains();
         for (int ichain=0; ichain<n_chains; ichain++) {
            mmdb::Chain *chain_p = model_p->GetChain(ichain);
            int n_res = chain_p->GetNumberOfResidues();
            for (int ires=0; ires<n_res; ires++) {
               mmdb::Residue *residue_p = chain_p->GetResidue(ires);
               if (residue_p) {
                  std::string rn = residue_p->GetResName();
                  if (cho_set.find(rn) != cho_set.end()) {
                     residues_to_be_removed.push_back(residue_p);
                  }
               }
            }
         }
      }
   }

   if (! residues_to_be_removed.empty()) {
      for (mmdb::Residue *r : residues_to_be_removed) {
         delete r;
      }
      deleted = true;
   }
   return deleted;
}
