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//
// Copyright (C) 2002-2020 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 <RDGeneral/export.h>
#ifndef RD_SMILESWRITE_H_012020
#define RD_SMILESWRITE_H_012020
#include <string>
#include <vector>
#include <memory>
namespace RDKit {
class Atom;
class Bond;
class ROMol;
namespace SmilesWrite {
//! \brief returns the cxsmiles data for a molecule
RDKIT_SMILESPARSE_EXPORT std::string getCXExtensions(const ROMol &mol);
//! \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 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
*/
RDKIT_SMILESPARSE_EXPORT std::string GetAtomSmiles(const Atom *atom,
bool doKekule = false,
const Bond *bondIn = nullptr,
bool allHsExplicit = false,
bool isomericSmiles = true);
//! \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.
*/
RDKIT_SMILESPARSE_EXPORT std::string GetBondSmiles(
const Bond *bond, int atomToLeftIdx = -1, bool doKekule = false,
bool allBondsExplicit = false);
} // namespace SmilesWrite
//! \brief returns canonical SMILES 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
atom.
*/
RDKIT_SMILESPARSE_EXPORT 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);
//! \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
/*!
\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.
*/
RDKIT_SMILESPARSE_EXPORT 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);
//! \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
atom.
*/
RDKIT_SMILESPARSE_EXPORT 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);
//! \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.
\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.
*/
RDKIT_SMILESPARSE_EXPORT 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);
} // namespace RDKit
#endif
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