//

//  Copyright (C) 2002-2021 Greg Landrum and other RDKit contributors

//

//   @@ 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 <RDGeneral/export.h>

#ifndef RD_SMILESWRITE_H_012020

#define RD_SMILESWRITE_H_012020

#include <string>

#include <vector>

#include <memory>

#include <cstdint>

#include <limits>

#include <RDGeneral/BetterEnums.h>

#include <boost/shared_ptr.hpp>

namespace RDKit {

class Atom;

class Bond;

class ROMol;

typedef std::vector<boost::shared_ptr<ROMol>> MOL_SPTR_VECT;

struct RDKIT_SMILESPARSE_EXPORT SmilesWriteParams {

  bool doIsomericSmiles =

      true;              /**< include stereochemistry and isotope information */

  bool doKekule = false; /**< kekulize the molecule before generating the SMILES

                            and output single/double bonds. NOTE that the output

                            is not canonical and that this will thrown an

                            exception if the molecule cannot be kekulized. */

  bool canonical = true; /**< generate canonical SMILES */

  bool cleanStereo = true;       /**< clean up stereo */

  bool allBondsExplicit = false; /**< include symbols for all bonds */

  bool allHsExplicit = false;    /**< provide hydrogen counts for every atom */

  bool doRandom = false; /**< randomize the output order. The resulting SMILES

                              is not canonical and the value of the canonical

                              parameter will be ignored. */

  int rootedAtAtom = -1; /**< make sure the SMILES starts at the specified

                             atom. The resulting SMILES is not canonical and

                             the value of the canonical parameter will be

                             ignored. */

  bool includeDativeBonds =

      true; /**< include the RDKit extension for dative bonds. Otherwise dative

               bonds will be written as single bonds*/

  bool ignoreAtomMapNumbers = false; /**< If true, ignores any atom map numbers

                                        when canonicalizing the molecule */

};

namespace SmilesWrite {

BETTER_ENUM(CXSmilesFields, uint32_t,  // clang-format off

  CX_NONE = 0,

  CX_ATOM_LABELS = 1 << 0,

  CX_MOLFILE_VALUES = 1 << 1,

  CX_COORDS = 1 << 2,

  CX_RADICALS = 1 << 3,

  CX_ATOM_PROPS = 1 << 4,

  CX_LINKNODES = 1 << 5,

  CX_ENHANCEDSTEREO = 1 << 6,

  CX_SGROUPS = 1 << 7,

  CX_POLYMER = 1 << 8,

  CX_BOND_CFG = 1 << 9,

  CX_BOND_ATROPISOMER = 1 << 10,

  CX_COORDINATE_BONDS = 1 << 11,

  CX_HYDROGEN_BONDS = 1 << 12,

  CX_ZERO_BONDS = 1 << 13,

  CX_ALL = 0x7fffffff,

  CX_ALL_BUT_COORDS = CX_ALL ^ CX_COORDS

);

//! \brief returns the cxsmiles data for a molecule

RDKIT_SMILESPARSE_EXPORT std::string getCXExtensions(

    const ROMol &mol, std::uint32_t flags = CXSmilesFields::CX_ALL);

//! \brief returns the cxsmiles data for a vector of molecules

RDKIT_SMILESPARSE_EXPORT std::string getCXExtensions(

  const std::vector<ROMol *> &mols, std::uint32_t flags);

//! \brief returns true if the atom number is in the SMILES organic subset

RDKIT_SMILESPARSE_EXPORT bool inOrganicSubset(int atomicNumber);

//! \brief returns the SMILES for an atom

/*!

  \param atom : the atom to work with

  \param ps : the parameters controlling the SMILES generation

*/

RDKIT_SMILESPARSE_EXPORT std::string GetAtomSmiles(const Atom *atom,

                                                   const SmilesWriteParams &ps);

//! \brief returns the SMILES for an atom

/*!

  \param atom : the atom to work with

  \param doKekule : we're doing kekulized smiles (e.g. don't use

    lower case for the atom label)

  \param bondIn : the bond we came into the atom on (unused)

  \param allHsExplicit : if true, hydrogen counts will be provided for every

  atom.

  \param isomericSmiles : if true, isomeric SMILES will be generated

*/

inline std::string GetAtomSmiles(const Atom *atom, bool doKekule = false,

                                 const Bond * = nullptr,

                                 bool allHsExplicit = false,

                                 bool isomericSmiles = true) {

  // RDUNUSED_PARAM(bondIn);

  SmilesWriteParams ps;

  ps.doIsomericSmiles = isomericSmiles;

  ps.doKekule = doKekule;

  ps.allHsExplicit = allHsExplicit;

  return GetAtomSmiles(atom, ps);

};

//! \brief returns the SMILES for a bond

/*!

  \param bond : the bond to work with

  \param ps : the parameters controlling the SMILES generation

  \param atomToLeftIdx : the index of the atom preceding \c bond

    in the SMILES

*/

RDKIT_SMILESPARSE_EXPORT std::string GetBondSmiles(const Bond *bond,

                                                   const SmilesWriteParams &ps,

                                                   int atomToLeftIdx = -1);

//! \brief returns the SMILES for a bond

/*!

  \param bond : the bond to work with

  \param atomToLeftIdx : the index of the atom preceding \c bond

    in the SMILES

  \param doKekule : we're doing kekulized smiles (e.g. write out

    bond orders for aromatic bonds)

  \param allBondsExplicit : if true, symbols will be included for all bonds.

*/

inline std::string GetBondSmiles(const Bond *bond, int atomToLeftIdx = -1,

                                 bool doKekule = false,

                                 bool allBondsExplicit = false) {

  SmilesWriteParams ps;

  ps.doKekule = doKekule;

  ps.allBondsExplicit = allBondsExplicit;

  ps.doIsomericSmiles = false;

  return GetBondSmiles(bond, ps, atomToLeftIdx);

};

namespace detail {

RDKIT_SMILESPARSE_EXPORT std::string MolToSmiles(

    const ROMol &mol, const SmilesWriteParams &params, bool doingCXSmiles, bool includeStereoGroups=true);

}

}  // namespace SmilesWrite

//! \brief returns canonical SMILES for a molecule

RDKIT_SMILESPARSE_EXPORT std::string MolToSmiles(

    const ROMol &mol, const SmilesWriteParams &params);

//! \brief returns SMILES for a molecule, canonical by default

/*!

  \param mol : the molecule in question.

  \param doIsomericSmiles : include stereochemistry and isotope information

      in the SMILES

  \param doKekule : do Kekule smiles (i.e. don't use aromatic bonds) NOTE that

      this will throw an exception if the molecule cannot be kekulized.

  \param rootedAtAtom : make sure the SMILES starts at the specified atom.

      The resulting SMILES is not, of course, canonical.

  \param canonical : if false, no attempt will be made to canonicalize the

  SMILES

  \param allBondsExplicit : if true, symbols will be included for all bonds.

  \param allHsExplicit : if true, hydrogen counts will be provided for every

  atom.

  \param doRandom : if true, the first atom in the SMILES string will be

  selected at random and the SMILES string will not be canonical

  \param ignoreAtomMapNumbers : if true, ignores any atom map numbers when

  canonicalizing the molecule

 */

inline std::string MolToSmiles(const ROMol &mol, bool doIsomericSmiles = true,

                               bool doKekule = false, int rootedAtAtom = -1,

                               bool canonical = true,

                               bool allBondsExplicit = false,

                               bool allHsExplicit = false,

                               bool doRandom = false,

                               bool ignoreAtomMapNumbers = false) {

  SmilesWriteParams ps;

  ps.doIsomericSmiles = doIsomericSmiles;

  ps.doKekule = doKekule;

  ps.rootedAtAtom = rootedAtAtom;

  ps.canonical = canonical;

  ps.allBondsExplicit = allBondsExplicit;

  ps.allHsExplicit = allHsExplicit;

  ps.doRandom = doRandom;

  ps.ignoreAtomMapNumbers = ignoreAtomMapNumbers;

  return MolToSmiles(mol, ps);

};

//! \brief returns a vector of random SMILES for a molecule (may contain

//! duplicates)

/*!

  \param mol : the molecule in question.

  \param numSmiles : the number of SMILES to return

  \param randomSeed : if >0, will be used to seed the random number generator

  \param doIsomericSmiles : include stereochemistry and isotope information

      in the SMILES

  \param doKekule : do Kekule smiles (i.e. don't use aromatic bonds)

  \param allBondsExplicit : if true, symbols will be included for all bonds.

  \param allHsExplicit : if true, hydrogen counts will be provided for every

  atom.

 */

RDKIT_SMILESPARSE_EXPORT std::vector<std::string> MolToRandomSmilesVect(

    const ROMol &mol, unsigned int numSmiles, unsigned int randomSeed = 0,

    bool doIsomericSmiles = true, bool doKekule = false,

    bool allBondsExplicit = false, bool allHsExplicit = false);

//! \brief returns canonical SMILES for part of a molecule

RDKIT_SMILESPARSE_EXPORT std::string MolFragmentToSmiles(

    const ROMol &mol, const SmilesWriteParams &params,

    const std::vector<int> &atomsToUse,

    const std::vector<int> *bondsToUse = nullptr,

    const std::vector<std::string> *atomSymbols = nullptr,

    const std::vector<std::string> *bondSymbols = nullptr);

//! \brief returns canonical SMILES for part of a molecule

/*!

  \param mol : the molecule in question.

  \param atomsToUse : indices of the atoms in the fragment

  \param bondsToUse : indices of the bonds in the fragment. If this is not

  provided,

                      all bonds between the atoms in atomsToUse will be included

  \param atomSymbols : symbols to use for the atoms in the output SMILES

  \param bondSymbols : symbols to use for the bonds in the output SMILES

  \param doIsomericSmiles : include stereochemistry and isotope information

      in the SMILES

  \param doKekule : do Kekule smiles (i.e. don't use aromatic bonds)

  \param rootedAtAtom : make sure the SMILES starts at the specified atom.

      The resulting SMILES is not, of course, canonical.

  \param canonical : if false, no attempt will be made to canonicalize the

  SMILES

  \param allBondsExplicit : if true, symbols will be included for all bonds.

  \param allHsExplicit : if true, hydrogen counts will be provided for every

  atom.

  \param doRandom : generate a randomized smiles string by randomly choosing

                    the priority to follow in the DFS traversal. [default false]

  \b NOTE: the bondSymbols are *not* currently used in the canonicalization.

 */

inline std::string MolFragmentToSmiles(

    const ROMol &mol, const std::vector<int> &atomsToUse,

    const std::vector<int> *bondsToUse = nullptr,

    const std::vector<std::string> *atomSymbols = nullptr,

    const std::vector<std::string> *bondSymbols = nullptr,

    bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1,

    bool canonical = true, bool allBondsExplicit = false,

    bool allHsExplicit = false) {

  SmilesWriteParams ps;

  ps.doIsomericSmiles = doIsomericSmiles;

  ps.doKekule = doKekule;

  ps.rootedAtAtom = rootedAtAtom;

  ps.canonical = canonical;

  ps.allBondsExplicit = allBondsExplicit;

  ps.allHsExplicit = allHsExplicit;

  return MolFragmentToSmiles(mol, ps, atomsToUse, bondsToUse, atomSymbols,

                             bondSymbols);

}

BETTER_ENUM(RestoreBondDirOption, unsigned int,

  RestoreBondDirOptionTrue = 0,  //<!DO restore bond dirs

  RestoreBondDirOptionClear = 1  //<!clear all bond dir information

);

//! \brief returns canonical CXSMILES for a molecule

RDKIT_SMILESPARSE_EXPORT std::string MolToCXSmiles(

    const ROMol &mol, const SmilesWriteParams &ps,

    std::uint32_t flags = SmilesWrite::CXSmilesFields::CX_ALL,

    RestoreBondDirOption restoreBondDirs =

        RestoreBondDirOption::RestoreBondDirOptionClear);

//! \brief returns canonical CXSMILES for a molecule

/*!

  \param mol : the molecule in question.

  \param doIsomericSmiles : include stereochemistry and isotope information

      in the SMILES

  \param doKekule : do Kekule smiles (i.e. don't use aromatic bonds)

  \param rootedAtAtom : make sure the SMILES starts at the specified atom.

      The resulting SMILES is not, of course, canonical.

  \param canonical : if false, no attempt will be made to canonicalize the

  SMILES

  \param allBondsExplicit : if true, symbols will be included for all bonds.

  \param allHsExplicit : if true, hydrogen counts will be provided for every

  \param doRandom : generate a randomized smiles string by randomly choosing

                    the priority to follow in the DFS traversal. [default false]

  atom.

 */

inline std::string MolToCXSmiles(const ROMol &mol, bool doIsomericSmiles = true,

                                 bool doKekule = false, int rootedAtAtom = -1,

                                 bool canonical = true,

                                 bool allBondsExplicit = false,

                                 bool allHsExplicit = false,

                                 bool doRandom = false) {

  SmilesWriteParams ps;

  ps.doIsomericSmiles = doIsomericSmiles;

  ps.doKekule = doKekule;

  ps.rootedAtAtom = rootedAtAtom;

  ps.canonical = canonical;

  ps.allBondsExplicit = allBondsExplicit;

  ps.allHsExplicit = allHsExplicit;

  ps.doRandom = doRandom;

  return MolToCXSmiles(mol, ps, SmilesWrite::CXSmilesFields::CX_ALL);

};

//! \brief returns canonical CXSMILES for part of a molecule

RDKIT_SMILESPARSE_EXPORT std::string MolFragmentToCXSmiles(

    const ROMol &mol, const SmilesWriteParams &params,

    const std::vector<int> &atomsToUse,

    const std::vector<int> *bondsToUse = nullptr,

    const std::vector<std::string> *atomSymbols = nullptr,

    const std::vector<std::string> *bondSymbols = nullptr);

//! \brief returns canonical CXSMILES for part of a molecule

/*!

  \param mol : the molecule in question.

  \param atomsToUse : indices of the atoms in the fragment

  \param bondsToUse : indices of the bonds in the fragment. If this is not

  provided,

                      all bonds between the atoms in atomsToUse will be included

  \param atomSymbols : symbols to use for the atoms in the output SMILES

  \param bondSymbols : symbols to use for the bonds in the output SMILES

  \param doIsomericSmiles : include stereochemistry and isotope information

      in the SMILES

  \param doKekule : do Kekule smiles (i.e. don't use aromatic bonds)

  \param rootedAtAtom : make sure the SMILES starts at the specified atom.

      The resulting SMILES is not, of course, canonical.

  \param canonical : if false, no attempt will be made to canonicalize the

  SMILES

  \param allBondsExplicit : if true, symbols will be included for all bonds.

  \param allHsExplicit : if true, hydrogen counts will be provided for every

  atom.

  \b NOTE: the bondSymbols are *not* currently used in the canonicalization.

 */

inline std::string MolFragmentToCXSmiles(

    const ROMol &mol, const std::vector<int> &atomsToUse,

    const std::vector<int> *bondsToUse = nullptr,

    const std::vector<std::string> *atomSymbols = nullptr,

    const std::vector<std::string> *bondSymbols = nullptr,

    bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1,

    bool canonical = true, bool allBondsExplicit = false,

    bool allHsExplicit = false) {

  SmilesWriteParams ps;

  ps.doIsomericSmiles = doIsomericSmiles;

  ps.doKekule = doKekule;

  ps.rootedAtAtom = rootedAtAtom;

  ps.canonical = canonical;

  ps.allBondsExplicit = allBondsExplicit;

  ps.allHsExplicit = allHsExplicit;

  return MolFragmentToCXSmiles(mol, ps, atomsToUse, bondsToUse, atomSymbols,

                               bondSymbols);

}

}  // namespace RDKit

#endif