/*==============================================*/
/* Copyright (C)  2019       NextMove Software  */
/* All rights reserved.                         */
/*                                              */
/* This file is part of molhash.                */
/*                                              */
/* The contents are covered by the terms of the */
/* BSD license, which is included in the file   */
/* license.txt.                                 */
/*==============================================*/

#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include "nmmolhash.h"

namespace RDKit {
namespace MolHash {
void Strip(RWMol *mol, unsigned int striptype) {
  // The order of these operations is significant to some degree
  // - Hydrogens should be at the end as that is the common
  //   use case

  if (striptype & static_cast<unsigned>(StripType::AtomStereo)) {
    for (auto aptr : mol->atoms()) {
      aptr->setChiralTag(RDKit::Atom::CHI_UNSPECIFIED);
    }
  }
  if (striptype & static_cast<unsigned>(StripType::BondStereo)) {
    for (auto bptr : mol->bonds()) {
      if (bptr->getStereo() > RDKit::Bond::STEREOANY) {
        bptr->setStereo(RDKit::Bond::STEREOANY);
      }
    }
  }
  if (striptype & static_cast<unsigned>(StripType::Isotope)) {
    for (auto aptr : mol->atoms()) {
      aptr->setIsotope(0);
    }
  }
  if (striptype & static_cast<unsigned>(StripType::AtomMap)) {
    for (auto aptr : mol->atoms()) {
      aptr->setAtomMapNum(0);
    }
  }
  if (striptype & static_cast<unsigned>(StripType::Hydrogen)) {
    MolOps::removeHs(*mol);
  }
}

void SplitMolecule(RWMol *mol, std::vector<RWMol *> &molv) {
  RDKit::MOL_SPTR_VECT mfrags = RDKit::MolOps::getMolFrags(*mol);
  RDKit::MOL_SPTR_VECT::iterator vit;
  for (vit = mfrags.begin(); vit != mfrags.end(); ++vit) {
    RDKit::ROMol *wrappedmol =
        (*vit).get();  // reach inside the shared pointer...
    molv.push_back(new RWMol(*wrappedmol));  // ...and make a copy
  }
}
}  // namespace MolHash
}  // namespace RDKit