/*
 * coot-utils/contacts-by-bricks.hh
 *
 * Copyright 2019 by Medical Research Council
 * Author: Paul Emsley
 *
 * This file is part of Coot
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser 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
 * Lesser General Public License for more details.
 *
 * You should have received a copies of the GNU General Public License and
 * the GNU Lesser 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.
 * See http://www.gnu.org/licenses/
 *
 */

#ifndef CONTACTS_BY_BRICK_HH
#define CONTACTS_BY_BRICK_HH

#include <vector>
#include <set>
#include <string>
#include <mmdb2/mmdb_manager.h>

namespace coot {

   // The returned vector is partially asymmetric: indices are added if the base/index atom is not fixed.
   // so contains M-M and M-F, - and *not* F-F or F-M.
   // For moving atoms, there is symmetry: M1-M2 exists so does M2-M1. Use the index values
   // to add them uniquely.

   // For good speed, this needs to exist for the lifetime of a restraints_container_t

   class contacts_by_bricks {
      float dist_nbc_max; // 8.0 say
      mmdb::PAtom *atoms;
      int n_atoms;
      bool only_between_different_residues_flag;
      std::vector<bool> fixed_flags; // a flag for every atom
      float lower_left[3]; // lowest coordinates (x,y,z) of bricking system
      float brick_size; // 6.0
      int range[3]; // how many bricks along x, y z, yes use int.
      unsigned int get_brick_index(mmdb::Atom *at) const;
      unsigned int idx_3d_to_idx_1d(int idx_3d[3]) const;
      void set_lower_left_and_range(mmdb::PAtom *atoms_in, int n_atoms);
      std::vector<std::set<unsigned int> > atoms_in_bricks;
      std::vector<std::vector<unsigned int> > thread_index_sets;
      void find_the_contacts_in_bricks(std::vector<std::set<unsigned int> > *vec,
                                       bool only_between_different_residues_flag) const; // fill vec
      void find_the_contacts_between_bricks(std::vector<std::set<unsigned int> > *vec,
                                            bool only_between_different_residues_flag) const; // fill vec
      void find_the_contacts_between_bricks_simple(std::vector<std::set<unsigned int> > *vec,
                                                   bool only_between_different_residues_flag) const; // fill vec
      void find_the_contacts_between_bricks_multi_thread(std::vector<std::set<unsigned int> > *vec,
                                                         bool only_between_different_residues_flag) const; // fill vec
      // the function for the thread:
      static void find_the_contacts_between_bricks_multi_thread_workpackage(std::vector<std::set<unsigned int> > *vec,
                                                                            const std::vector<unsigned int> &index_set,
                                                                            const std::vector<std::set<unsigned int> > &atoms_in_bricks,
                                                                            const std::vector<bool> &fixed_flags,
                                                                            const int brick_range[3],
                                                                            mmdb::PAtom *atoms,
                                                                            int brick_index_max,
                                                                            float dist_max,
                                                                            bool only_between_different_residues_flag);
      void fill_the_bricks();

   public:
      // Fill (or edit) contacts vec - which may or may not be filled already.
      // The fixed atom indices should also be passed, so that
      // fixed to fixed atom indices don't get added to the contact vector
      contacts_by_bricks(mmdb::PAtom *, int n_atoms, const std::set<unsigned int> &fixed_atom_indices);
      void set_dist_max(float dist_max_in);
      void find_the_contacts(std::vector<std::set<unsigned int> > *vec,
                             bool only_between_different_residues_flag=false);
   };

}

#endif // CONTACTS_BY_BRICK_HH
