// $Id$
//
//  Copyright (C) 2003-2009 Greg Landrum and Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include "MolOps.h"
#include "RDKitBase.h"
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>

#include <boost/dynamic_bitset.hpp>
#include <iomanip>

namespace RDKit {
namespace MolOps {
double computeBalabanJ(double *distMat, int nb, int nAts) {
  // NOTE that the distance matrix is modified here for the sake of
  // efficiency
  PRECONDITION(distMat, "bogus distance matrix")
  double sum = 0.0;
  int nActive = nAts;
  int mu = nb - nActive + 1;

  if (mu == -1) return 0.0;

  for (int i = 0; i < nAts; i++) {
    int iTab = i * nAts;
    sum = 0.0;
    for (int j = 0; j < nAts; j++) {
      if (j != i) {
        sum += distMat[iTab + j];
      }
    }
    distMat[iTab + i] *= sum;
  }
  double accum = 0.0;
  for (int i = 0; i < nAts; i++) {
    int iTab = i * nAts + i;
    for (int j = i + 1; j < nAts; j++) {
      // NOTE: this isn't strictly the Balaban J value, because we
      // aren't only adding in adjacent atoms.  Since we're doing a
      // discriminator, that shouldn't be a problem.
      if (j != i) {
        accum += (1.0 / sqrt(distMat[iTab] * distMat[j * nAts + j]));
      }
    }
  }
  return nActive / ((mu + 1) * accum);
}

double computeBalabanJ(const ROMol &mol, bool useBO, bool force,
                       const std::vector<int> *bondPath, bool cacheIt) {
  RDUNUSED_PARAM(useBO);
  double res = 0.0;
  if (!force && mol.hasProp(common_properties::BalabanJ)) {
    mol.getProp(common_properties::BalabanJ, res);
  } else {
    double *dMat;
    int nb = 0, nAts = 0;
    if (bondPath) {
      boost::dynamic_bitset<> atomsUsed(mol.getNumAtoms());
      boost::dynamic_bitset<> bondsUsed(mol.getNumBonds());
      for (int ci : *bondPath) {
        bondsUsed[ci] = 1;
      }
      std::vector<const Bond *> bonds;
      bonds.reserve(bondPath->size());
      std::vector<int> atomsInPath;
      atomsInPath.reserve(bondPath->size() + 1);

      ROMol::EDGE_ITER beg, end;
      boost::tie(beg, end) = mol.getEdges();
      while (beg != end) {
        const Bond *bond = mol[*beg];
        if (bondsUsed[bond->getIdx()]) {
          int begIdx = bond->getBeginAtomIdx();
          int endIdx = bond->getEndAtomIdx();
          bonds.push_back(bond);
          if (!atomsUsed[begIdx]) {
            atomsInPath.push_back(begIdx);
            atomsUsed[begIdx] = 1;
          }
          if (!atomsUsed[endIdx]) {
            atomsInPath.push_back(endIdx);
            atomsUsed[endIdx] = 1;
          }
        }
        beg++;
      }
      nb = rdcast<int>(bondPath->size());
      nAts = rdcast<int>(atomsInPath.size());
      dMat = MolOps::getDistanceMat(mol, atomsInPath, bonds, true, true);
      res = computeBalabanJ(dMat, nb, nAts);
      delete[] dMat;
    } else {
      nb = mol.getNumBonds();
      nAts = mol.getNumAtoms();
      dMat = MolOps::getDistanceMat(mol, true, true, true, nullptr);
      res = computeBalabanJ(dMat, nb, nAts);
      delete[] dMat;
    }

    if (cacheIt) mol.setProp(common_properties::BalabanJ, res, true);
  }
  return res;
}
}  // end of namespace MolOps
}  // end of namespace RDKit
