/**
 * \file SolventAccessibleSurface \brief
 *
 * Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#include <IMP/saxs/SolventAccessibleSurface.h>
#include <IMP/constants.h>
#include <IMP/algebra/standard_grids.h>

IMPSAXS_BEGIN_NAMESPACE

IMP::Floats SolventAccessibleSurface::get_solvent_accessibility(
                                          const core::XYZRs& ps,
                                          float probe_radius,
                                          float density)
{
  IMP::Floats res;
  algebra::Vector3Ds coordinates(ps.size());
  IMP::Floats radii(ps.size());
  for(unsigned int i=0; i<ps.size(); i++) {
    coordinates[i] = ps[i].get_coordinates();
    radii[i] = ps[i].get_radius();
  }

  // init grid
  typedef IMP::algebra::DenseGrid3D<IMP::Ints> Grid;
  IMP::algebra::BoundingBox3D bb(coordinates);
  Grid grid(2.0, bb);
  for(unsigned int i=0; i<coordinates.size(); i++) {
    Grid::Index grid_index = grid.get_nearest_index(coordinates[i]);
    grid[grid_index].push_back(i);
  }

  // compute surface
  static float max_radius = 3.0;
  for(unsigned int i=0; i<ps.size(); i++) {
    const float atom_radius = radii[i];
    float radius = atom_radius + 2*probe_radius + max_radius;
    // query
    IMP::algebra::BoundingBox3D bb(coordinates[i]);
    bb+=radius;
    Grid::ExtendedIndex lb = grid.get_extended_index(bb.get_corner(0)),
      ub = grid.get_extended_index(bb.get_corner(1));
    std::vector<int> neighbours1, neighbours2;
    for (Grid::IndexIterator it= grid.indexes_begin(lb, ub);
         it != grid.indexes_end(lb, ub); ++it) {
       for(unsigned int vIndex=0; vIndex<grid[*it].size(); vIndex++) {
        int mol_index = grid[*it][vIndex];
        float radius_sum1 = atom_radius + radii[mol_index];
        float radius_sum2 = radius_sum1 + 2*probe_radius;
        float dist2 =
          algebra::get_squared_distance(coordinates[i], coordinates[mol_index]);

        if(dist2 < radius_sum1*radius_sum1) neighbours1.push_back(mol_index);
        else
          if(dist2 < radius_sum2*radius_sum2) neighbours2.push_back(mol_index);
      }
    }

    float ratio = (atom_radius + probe_radius)/atom_radius;
    algebra::Vector3Ds spoints = create_sphere_dots(atom_radius, density);
    int dotNum = 0;
    for(unsigned int s_index = 0; s_index<spoints.size(); s_index++) {
      IMP::algebra::Vector3D probe_center =
        coordinates[i] + ratio * spoints[s_index];
      // check for intersection with neighbours1
      bool collides = false;
      for(unsigned int n_index=0; n_index<neighbours1.size(); n_index++) {
        if(is_intersecting(probe_center, coordinates[neighbours1[n_index]],
                          probe_radius, radii[neighbours1[n_index]])) {
          collides = true;
          break;
        }
      }
      if(!collides) { // check for intersection with neighbours2
        for(unsigned int n_index=0; n_index<neighbours2.size(); n_index++) {
          if(is_intersecting(probe_center, coordinates[neighbours2[n_index]],
                             probe_radius, radii[neighbours2[n_index]])) {
            collides = true;
            break;
          }
        }
      }
      if(!collides) dotNum++;
    }
    res.push_back((float)dotNum/spoints.size());
  }
  return res;
}

algebra::Vector3Ds SolventAccessibleSurface::create_sphere_dots(float radius,
                                                                float density)
{
  algebra::Vector3Ds res;
  float num_equat = 2*PI*radius*sqrt(density);
  float vert_count = 0.5*num_equat;

  for(int i=0; i<vert_count; i++) {
    float phi = (PI*i)/vert_count;
    float z = cos(phi);
    float xy = sin(phi);
    float horz_count = xy*num_equat;
    for(int j=0; j<horz_count-1; j++) {
      float teta = (2*PI*j)/horz_count;
      float x = xy*cos(teta);
      float y = xy*sin(teta);
      res.push_back(algebra::Vector3D(radius*x,radius*y,radius*z));
    }
  }
  return res;
}


IMPSAXS_END_NAMESPACE