//
//  Copyright (C) 2016 Novartis Institutes for BioMedical Research
//
//   @@ 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.
//
#pragma once
#include "StructChecker.h"
#include "Utilites.h"

namespace RDKit {
namespace StructureCheck {

RDKit::Bond::BondType convertBondType(AABondType bt);
AABondType convertBondType(RDKit::Bond::BondType rdbt);

unsigned getAtomicNumber(const std::string symbol);
bool AtomSymbolMatch(const std::string symbol, const std::string pattern);
bool LigandMatches(const Atom &a, const Bond &b, const Ligand &l,
                   bool use_charge = false);
bool isBondTypeMatch(const RDKit::Bond &b, AABondType lbt);
bool RecMatch(const ROMol &mol, unsigned atomIdx, const AugmentedAtom &aa,
              const std::vector<Neighbourhood> &nbp, bool verbose);
bool AAMatch(const ROMol &mol, unsigned i, const AugmentedAtom &aa,
             const std::vector<unsigned> &atom_ring_status,
             const std::vector<Neighbourhood> &nbp, bool verbose);

bool TransformAugmentedAtoms(
    RWMol &mol,
    const std::vector<std::pair<AugmentedAtom, AugmentedAtom> > &aapair, bool verbose);
bool CheckAtoms(const ROMol &mol, const std::vector<AugmentedAtom> &good_atoms,
                bool verbose);
}
}