//
//  Copyright (C) 2001-2012 Greg Landrum and Rational Discovery LLC
//  Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
//
//   @@ 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.
//
#ifndef _RD_MOL_OPS_H_
#define _RD_MOL_OPS_H_

#include <vector>
#include <map>
#include <list>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/smart_ptr.hpp>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <RDGeneral/types.h>

extern const int ci_LOCAL_INF;
namespace RDKit {
class ROMol;
class RWMol;
class Atom;
class Bond;
typedef std::vector<double> INVAR_VECT;
typedef INVAR_VECT::iterator INVAR_VECT_I;
typedef INVAR_VECT::const_iterator INVAR_VECT_CI;

//! \brief Groups a variety of molecular query and transformation operations.
namespace MolOps {

//! return the number of electrons available on an atom to donate for
// aromaticity
/*!
   The result is determined using the default valency, number of lone pairs,
   number of bonds and the formal charge. Note that the atom may not donate
   all of these electrons to a ring for aromaticity (also used in Conjugation
   and hybridization code).

   \param at the atom of interest

   \return the number of electrons
*/
int countAtomElec(const Atom *at);

//! sums up all atomic formal charges and returns the result
int getFormalCharge(const ROMol &mol);

//! returns whether or not the given Atom is involved in a conjugated bond
bool atomHasConjugatedBond(const Atom *at);

//! find fragments (disconnected components of the molecular graph)
/*!

  \param mol     the molecule of interest
  \param mapping used to return the mapping of Atoms->fragments.
     On return \c mapping will be <tt>mol->getNumAtoms()</tt> long
     and will contain the fragment assignment for each Atom

  \return the number of fragments found.

*/
unsigned int getMolFrags(const ROMol &mol, std::vector<int> &mapping);
//! find fragments (disconnected components of the molecular graph)
/*!

  \param mol    the molecule of interest
  \param frags  used to return the Atoms in each fragment
     On return \c mapping will be \c numFrags long, and each entry
     will contain the indices of the Atoms in that fragment.

  \return the number of fragments found.

*/
unsigned int getMolFrags(const ROMol &mol,
                         std::vector<std::vector<int> > &frags);

//! splits a molecule into its component fragments
//  (disconnected components of the molecular graph)
/*!

  \param mol     the molecule of interest
  \param sanitizeFrags  toggles sanitization of the fragments after
                        they are built
  \param frags used to return the mapping of Atoms->fragments.
     if provided, \c frags will be <tt>mol->getNumAtoms()</tt> long
         on return and will contain the fragment assignment for each Atom
  \param fragsMolAtomMapping  used to return the Atoms in each fragment
     On return \c mapping will be \c numFrags long, and each entry
     will contain the indices of the Atoms in that fragment.
   \param copyConformers  toggles copying conformers of the fragments after
                        they are built
  \return a vector of the fragments as smart pointers to ROMols

*/
std::vector<boost::shared_ptr<ROMol> > getMolFrags(
    const ROMol &mol, bool sanitizeFrags = true, std::vector<int> *frags = 0,
    std::vector<std::vector<int> > *fragsMolAtomMapping = 0,
    bool copyConformers = true);

//! splits a molecule into pieces based on labels assigned using a query
/*!

  \param mol     the molecule of interest
  \param query   the query used to "label" the molecule for fragmentation
  \param sanitizeFrags  toggles sanitization of the fragments after
                        they are built
  \param whiteList  if provided, only labels in the list will be kept
  \param negateList if true, the white list logic will be inverted: only labels
                    not in the list will be kept

  \return a map of the fragments and their labels

*/
template <typename T>
std::map<T, boost::shared_ptr<ROMol> > getMolFragsWithQuery(
    const ROMol &mol, T (*query)(const ROMol &, const Atom *),
    bool sanitizeFrags = true, const std::vector<T> *whiteList = 0,
    bool negateList = false);

#if 0
    //! finds a molecule's minimium spanning tree (MST)
    /*!
      \param mol  the molecule of interest
      \param mst  used to return the MST as a vector of bond indices
    */
    void findSpanningTree(const ROMol &mol,std::vector<int> &mst);
#endif

//! calculates Balaban's J index for the molecule
/*!
  \param mol      the molecule of interest
  \param useBO    toggles inclusion of the bond order in the calculation
                  (when false, we're not really calculating the J value)
  \param force    forces the calculation (instead of using cached results)
  \param bondPath when included, only paths using bonds whose indices occur
                  in this vector will be included in the calculation
  \param cacheIt  If this is true, the calculated value will be cached
                  as a property on the molecule
  \return the J index

*/
double computeBalabanJ(const ROMol &mol, bool useBO = true, bool force = false,
                       const std::vector<int> *bondPath = 0,
                       bool cacheIt = true);
//! \overload
double computeBalabanJ(double *distMat, int nb, int nAts);

//! \name Dealing with hydrogens
//{@

//! returns a copy of a molecule with hydrogens added in as explicit Atoms
/*!
    \param mol          the molecule to add Hs to
    \param explicitOnly (optional) if this \c true, only explicit Hs will be
   added
    \param addCoords    (optional) If this is true, estimates for the atomic
   coordinates
                of the added Hs will be used.
    \param onlyOnAtoms   (optional) if provided, this should be a vector of
                IDs of the atoms that will be considered for H addition.

    \return the new molecule

    <b>Notes:</b>
       - it makes no sense to use the \c addCoords option if the molecule's
   heavy
         atoms don't already have coordinates.
       - the caller is responsible for <tt>delete</tt>ing the pointer this
   returns.
 */
ROMol *addHs(const ROMol &mol, bool explicitOnly = false,
             bool addCoords = false, const UINT_VECT *onlyOnAtoms = NULL);
//! \overload
// modifies the molecule in place
void addHs(RWMol &mol, bool explicitOnly = false, bool addCoords = false,
           const UINT_VECT *onlyOnAtoms = NULL);

//! returns a copy of a molecule with hydrogens removed
/*!
    \param mol          the molecule to remove Hs from
    \param implicitOnly (optional) if this \c true, only implicit Hs will be
   removed
    \param updateExplicitCount  (optional) If this is \c true, when explicit Hs
   are removed
         from the graph, the heavy atom to which they are bound will have its
   counter of
         explicit Hs increased.
    \param sanitize:  (optional) If this is \c true, the final molecule will be
   sanitized

    \return the new molecule

    <b>Notes:</b>
       - Hydrogens which aren't connected to a heavy atom will not be
         removed.  This prevents molecules like <tt>"[H][H]"</tt> from having
         all atoms removed.
       - Labelled hydrogen (e.g. atoms with atomic number=1, but mass > 1),
         will not be removed.
       - two coordinate Hs, like the central H in C[H-]C, will not be removed
       - Hs connected to dummy atoms will not be removed

       - the caller is responsible for <tt>delete</tt>ing the pointer this
   returns.
*/
ROMol *removeHs(const ROMol &mol, bool implicitOnly = false,
                bool updateExplicitCount = false, bool sanitize = true);
//! \overload
// modifies the molecule in place
void removeHs(RWMol &mol, bool implicitOnly = false,
              bool updateExplicitCount = false, bool sanitize = true);

//! returns a copy of a molecule with hydrogens removed and added as queries
//!  to the heavy atoms to which they are bound.
/*!
  This is really intended to be used with molecules that contain QueryAtoms

  \param mol the molecule to remove Hs from

  \return the new molecule

  <b>Notes:</b>
    - Atoms that do not already have hydrogen count queries will have one
            added, other H-related queries will not be touched. Examples:
          - C[H] -> [C;!H0]
          - [C;H1][H] -> [C;H1]
          - [C;H2][H] -> [C;H2]
    - Hydrogens which aren't connected to a heavy atom will not be
      removed.  This prevents molecules like <tt>"[H][H]"</tt> from having
      all atoms removed.
    - the caller is responsible for <tt>delete</tt>ing the pointer this returns.
    - By default all hydrogens are removed, however if
      mergeUnmappedOnly is true, any hydrogen participating
      in an atom map will be retained

*/
ROMol *mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly = false);
//! \overload
// modifies the molecule in place
void mergeQueryHs(RWMol &mol, bool mergeUnmappedOnly = false);

typedef enum {
  ADJUST_IGNORENONE = 0x0,
  ADJUST_IGNORECHAINS = 0x1,
  ADJUST_IGNORERINGS = 0x4,
  ADJUST_IGNOREDUMMIES = 0x2,
  ADJUST_IGNORENONDUMMIES = 0x8,
  ADJUST_IGNOREMAPPED = 0x10,
  ADJUST_IGNOREALL = 0xFFFFFFF
} AdjustQueryWhichFlags;

struct AdjustQueryParameters {
  bool adjustDegree; /**< add degree queries */
  boost::uint32_t adjustDegreeFlags;
  bool adjustRingCount; /**< add ring-count queries */
  boost::uint32_t adjustRingCountFlags;

  bool makeDummiesQueries; /**< convert dummy atoms without isotope labels to
                              any-atom queries */
  bool aromatizeIfPossible;
  bool makeBondsGeneric; /**< convert bonds to generic queries (any bonds) */
  boost::uint32_t makeBondsGenericFlags;
  bool makeAtomsGeneric; /**< convert atoms to generic queries (any atoms) */
  boost::uint32_t makeAtomsGenericFlags;
  bool adjustHeavyDegree; /**< adjust the heavy-atom degree instead of overall
                             degree */
  boost::uint32_t adjustHeavyDegreeFlags;

  AdjustQueryParameters()
      : adjustDegree(true),
        adjustDegreeFlags(ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS),
        adjustRingCount(false),
        adjustRingCountFlags(ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS),
        makeDummiesQueries(true),
        aromatizeIfPossible(true),
        makeBondsGeneric(false),
        makeBondsGenericFlags(ADJUST_IGNORENONE),
        makeAtomsGeneric(false),
        makeAtomsGenericFlags(ADJUST_IGNORENONE),
        adjustHeavyDegree(false),
        adjustHeavyDegreeFlags(ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS) {}
};
//! returns a copy of a molecule with query properties adjusted
/*!
  \param mol the molecule to adjust
  \param params controls the adjustments made

  \return the new molecule
*/
ROMol *adjustQueryProperties(const ROMol &mol,
                             const AdjustQueryParameters *params = NULL);
//! \overload
// modifies the molecule in place
void adjustQueryProperties(RWMol &mol,
                           const AdjustQueryParameters *params = NULL);

//! returns a copy of a molecule with the atoms renumbered
/*!

  \param mol the molecule to work with
  \param newOrder the new ordering of the atoms (should be numAtoms long)
     for example: if newOrder is [3,2,0,1], then atom 3 in the original
     molecule will be atom 0 in the new one

  \return the new molecule

  <b>Notes:</b>
    - the caller is responsible for <tt>delete</tt>ing the pointer this returns.

*/
ROMol *renumberAtoms(const ROMol &mol,
                     const std::vector<unsigned int> &newOrder);

//@}

//! \name Sanitization
//@{

typedef enum {
  SANITIZE_NONE = 0x0,
  SANITIZE_CLEANUP = 0x1,
  SANITIZE_PROPERTIES = 0x2,
  SANITIZE_SYMMRINGS = 0x4,
  SANITIZE_KEKULIZE = 0x8,
  SANITIZE_FINDRADICALS = 0x10,
  SANITIZE_SETAROMATICITY = 0x20,
  SANITIZE_SETCONJUGATION = 0x40,
  SANITIZE_SETHYBRIDIZATION = 0x80,
  SANITIZE_CLEANUPCHIRALITY = 0x100,
  SANITIZE_ADJUSTHS = 0x200,
  SANITIZE_ALL = 0xFFFFFFF
} SanitizeFlags;

//! \brief carries out a collection of tasks for cleaning up a molecule and
// ensuring
//! that it makes "chemical sense"
/*!
   This functions calls the following in sequence
     -# MolOps::cleanUp()
     -# mol.updatePropertyCache()
     -# MolOps::symmetrizeSSSR()
     -# MolOps::Kekulize()
     -# MolOps::assignRadicals()
     -# MolOps::setAromaticity()
     -# MolOps::setConjugation()
     -# MolOps::setHybridization()
     -# MolOps::cleanupChirality()
     -# MolOps::adjustHs()

   \param mol : the RWMol to be cleaned

   \param operationThatFailed : the first (if any) sanitization operation that
   fails is set here.
                                The values are taken from the \c SanitizeFlags
   enum.
                                On success, the value is  \c
   SanitizeFlags::SANITIZE_NONE

   \param sanitizeOps : the bits here are used to set which sanitization
   operations are carried
                        out. The elements of the \c SanitizeFlags enum define
   the operations.

   <b>Notes:</b>
    - If there is a failure in the sanitization, a \c SanitException
      will be thrown.
    - in general the user of this function should cast the molecule following
   this
      function to a ROMol, so that new atoms and bonds cannot be added to the
      molecule and screw up the sanitizing that has been done here
*/
void sanitizeMol(RWMol &mol, unsigned int &operationThatFailed,
                 unsigned int sanitizeOps = SANITIZE_ALL);
//! \overload
void sanitizeMol(RWMol &mol);

//! Possible aromaticity models
/*!
- \c AROMATICITY_DEFAULT at the moment always uses \c AROMATICITY_RDKIT
- \c AROMATICITY_RDKIT is the standard RDKit model (as documented in the RDKit
Book)
- \c AROMATICITY_SIMPLE only considers 5- and 6-membered simple rings (it
does not consider the outer envelope of fused rings)
- \c AROMATICITY_CUSTOM uses a caller-provided function
*/
typedef enum {
  AROMATICITY_DEFAULT = 0x0,  ///< future proofing
  AROMATICITY_RDKIT = 0x1,
  AROMATICITY_SIMPLE = 0x2,
  AROMATICITY_CUSTOM = 0xFFFFFFF  ///< use a function
} AromaticityModel;

//! Sets up the aromaticity for a molecule
/*!

  This is what happens here:
     -# find all the simple rings by calling the findSSSR function
     -# loop over all the Atoms in each ring and mark them if they are
  candidates
        for aromaticity. A ring atom is a candidate if it can spare electrons
        to the ring and if it's from the first two rows of the periodic table.
     -# based on the candidate atoms, mark the rings to be either candidates
        or non-candidates. A ring is a candidate only if all its atoms are
  candidates
     -# apply Hueckel rule to each of the candidate rings to check if the ring
  can be
        aromatic

  \param mol the RWMol of interest
  \param model the aromaticity model to use
  \param func a custom function for assigning aromaticity (only used when
  model=\c AROMATICITY_CUSTOM)

  \return >0 on success, <= 0 otherwise

  <b>Assumptions:</b>
    - Kekulization has been done (i.e. \c MolOps::Kekulize() has already
      been called)

*/
int setAromaticity(RWMol &mol, AromaticityModel model = AROMATICITY_DEFAULT,
                   int (*func)(RWMol &) = NULL);

//! Designed to be called by the sanitizer to handle special cases before
// anything is done.
/*!

    Currently this:
     - modifies nitro groups, so that the nitrogen does not have an unreasonable
       valence of 5, as follows:
         - the nitrogen gets a positive charge
         - one of the oxygens gets a negative chage and the double bond to this
           oxygen is changed to a single bond
       The net result is that nitro groups can be counted on to be:
         \c "[N+](=O)[O-]"
     - modifies halogen-oxygen containing species as follows:
        \c [Cl,Br,I](=O)(=O)(=O)O -> [X+3]([O-])([O-])([O-])O
        \c [Cl,Br,I](=O)(=O)O -> [X+3]([O-])([O-])O
        \c [Cl,Br,I](=O)O -> [X+]([O-])O
     - converts the substructure [N,C]=P(=O)-* to [N,C]=[P+](-[O-])-*

   \param mol    the molecule of interest

*/
void cleanUp(RWMol &mol);

//! Called by the sanitizer to assign radical counts to atoms
void assignRadicals(RWMol &mol);

//! adjust the number of implicit and explicit Hs for special cases
/*!

    Currently this:
     - modifies aromatic nitrogens so that, when appropriate, they have an
       explicit H marked (e.g. so that we get things like \c "c1cc[nH]cc1"

    \param mol    the molecule of interest

    <b>Assumptions</b>
       - this is called after the molecule has been sanitized,
         aromaticity has been perceived, and the implicit valence of
         everything has been calculated.

*/
void adjustHs(RWMol &mol);

//! Kekulizes the molecule
/*!

   \param mol             the molecule of interest
   \param markAtomsBonds  if this is set to true, \c isAromatic boolean settings
                          on both the Bonds and Atoms are turned to false
   following
                          the Kekulization, otherwise they are left alone in
   their
                          original state.
   \param maxBackTracks   the maximum number of attempts at back-tracking. The
   algorithm
                          uses a back-tracking procedure to revist a previous
   setting of
                          double bond if we hit a wall in the kekulization
   process

   <b>Notes:</b>
     - even if \c markAtomsBonds is \c false the \c BondType for all aromatic
       bonds will be changed from \c RDKit::Bond::AROMATIC to \c
   RDKit::Bond::SINGLE
       or RDKit::Bond::DOUBLE during Kekulization.

*/
void Kekulize(RWMol &mol, bool markAtomsBonds = true,
              unsigned int maxBackTracks = 100);

//! flags the molecule's conjugated bonds
void setConjugation(ROMol &mol);

//! calculates and sets the hybridization of all a molecule's Stoms
void setHybridization(ROMol &mol);

// @}

//! \name Ring finding and SSSR
//@{

//! finds a molecule's Smallest Set of Smallest Rings
/*!
  Currently this implements a modified form of Figueras algorithm
    (JCICS - Vol. 36, No. 5, 1996, 986-991)

  \param mol the molecule of interest
  \param res used to return the vector of rings. Each entry is a vector with
      atom indices.  This information is also stored in the molecule's
      RingInfo structure, so this argument is optional (see overload)

  \return number of smallest rings found

  Base algorithm:
    - The original algorithm starts by finding representative degree 2
      nodes.
    - Representative because if a series of deg 2 nodes are found only
      one of them is picked.
    - The smallest ring around each of them is found.
    - The bonds that connect to this degree 2 node are them chopped off,
  yielding
      new deg two nodes
    - The process is repeated on the new deg 2 nodes.
    - If no deg 2 nodes are found, a deg 3 node is picked. The smallest ring
      with it is found. A bond from this is "carefully" (look in the paper)
      selected and chopped, yielding deg 2 nodes. The process is same as
      above once this is done.

  Our Modifications:
    - If available, more than one smallest ring around a representative deg 2
      node will be computed and stored
    - Typically 3 rings are found around a degree 3 node (when no deg 2s are
  available)
      and all the bond to that node are chopped.
    - The extra rings that were found in this process are removed after all the
  nodes
      have been covered.

  These changes were motivated by several factors:
    - We believe the original algorithm fails to find the correct SSSR
      (finds the correct number of them but the wrong ones) on some sample mols
    - Since SSSR may not be unique, a post-SSSR step to symmetrize may be done.
      The extra rings this process adds can be quite useful.
*/
int findSSSR(const ROMol &mol, std::vector<std::vector<int> > &res);
//! \overload
int findSSSR(const ROMol &mol, std::vector<std::vector<int> > *res = 0);

//! use a DFS algorithm to identify ring bonds and atoms in a molecule
/*!
  \b NOTE: though the RingInfo structure is populated by this function,
  the only really reliable calls that can be made are to check if
  mol.getRingInfo().numAtomRings(idx) or mol.getRingInfo().numBondRings(idx)
  return values >0
*/
void fastFindRings(const ROMol &mol);

//! symmetrize the molecule's Smallest Set of Smallest Rings
/*!
   SSSR rings obatined from "findSSSR" can be non-unique in some case.
   For example, cubane has five SSSR rings, not six as one would hope.

   This function adds additional rings to the SSSR list if necessary
   to make the list symmetric, e.g. all atoms in cubane will be part of the same
  number
   of SSSRs. This function choses these extra rings from the extra rings
  computed
   and discarded during findSSSR. The new ring are chosen such that:
    - replacing a same sized ring in the SSSR list with an extra ring yields
      the same union of bond IDs as the orignal SSSR list

  \param mol - the molecule of interest
  \param res used to return the vector of rings. Each entry is a vector with
      atom indices.  This information is also stored in the molecule's
      RingInfo structure, so this argument is optional (see overload)

  \return the total number of rings = (new rings + old SSSRs)

  <b>Notes:</b>
   - if no SSSR rings are found on the molecule - MolOps::findSSSR() is called
  first
*/
int symmetrizeSSSR(ROMol &mol, std::vector<std::vector<int> > &res);
//! \overload
int symmetrizeSSSR(ROMol &mol);

//@}

//! \name Shortest paths and other matrices
//@{

//! returns a molecule's adjacency matrix
/*!
  \param mol             the molecule of interest
  \param useBO           toggles use of bond orders in the matrix
  \param emptyVal        sets the empty value (for non-adjacent atoms)
  \param force           forces calculation of the matrix, even if already
  computed
  \param propNamePrefix  used to set the cached property name

  \return the adjacency matrix.

  <b>Notes</b>
    - The result of this is cached in the molecule's local property dictionary,
      which will handle deallocation. The caller should <b>not</b> \c delete
      this pointer.

*/
double *getAdjacencyMatrix(const ROMol &mol, bool useBO = false,
                           int emptyVal = 0, bool force = false,
                           const char *propNamePrefix = 0,
                           const boost::dynamic_bitset<> *bondsToUse = 0);

//! Computes the molecule's topological distance matrix
/*!
   Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.

  \param mol             the molecule of interest
  \param useBO           toggles use of bond orders in the matrix
  \param useAtomWts      sets the diagonal elements of the result to
           6.0/(atomic number) so that the matrix can be used to calculate
           Balaban J values.  This does not affect the bond weights.
  \param force           forces calculation of the matrix, even if already
  computed
  \param propNamePrefix  used to set the cached property name

  \return the distance matrix.

  <b>Notes</b>
    - The result of this is cached in the molecule's local property dictionary,
      which will handle deallocation. The caller should <b>not</b> \c delete
      this pointer.


*/
double *getDistanceMat(const ROMol &mol, bool useBO = false,
                       bool useAtomWts = false, bool force = false,
                       const char *propNamePrefix = 0);

//! Computes the molecule's topological distance matrix
/*!
   Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.

  \param mol             the molecule of interest
  \param activeAtoms     only elements corresponding to these atom indices
                         will be included in the calculation
  \param bonds           only bonds found in this list will be included in the
                         calculation
  \param useBO           toggles use of bond orders in the matrix
  \param useAtomWts      sets the diagonal elements of the result to
           6.0/(atomic number) so that the matrix can be used to calculate
           Balaban J values.  This does not affect the bond weights.

  \return the distance matrix.

  <b>Notes</b>
    - The results of this call are not cached, the caller <b>should</b> \c
  delete
      this pointer.


*/
double *getDistanceMat(const ROMol &mol, const std::vector<int> &activeAtoms,
                       const std::vector<const Bond *> &bonds,
                       bool useBO = false, bool useAtomWts = false);

//! Computes the molecule's 3D distance matrix
/*!

  \param mol             the molecule of interest
  \param confId          the conformer to use
  \param useAtomWts      sets the diagonal elements of the result to
           6.0/(atomic number)
  \param force           forces calculation of the matrix, even if already
  computed
  \param propNamePrefix  used to set the cached property name
                         (if set to an empty string, the matrix will not be
  cached)

  \return the distance matrix.

  <b>Notes</b>
    - The result of this is cached in the molecule's local property dictionary,
      which will handle deallocation. Do the caller should <b>not</b> \c delete
      this pointer.

*/
double *get3DDistanceMat(const ROMol &mol, int confId = -1,
                         bool useAtomWts = false, bool force = false,
                         const char *propNamePrefix = 0);
//! Find the shortest path between two atoms
/*!
  Uses the Bellman-Ford algorithm

 \param mol  molecule of interest
 \param aid1 index of the first atom
 \param aid2 index of the second atom

 \return an std::list with the indices of the atoms along the shortest
    path

 <b>Notes:</b>
   - the starting and end atoms are included in the path
   - if no path is found, an empty path is returned

*/
std::list<int> getShortestPath(const ROMol &mol, int aid1, int aid2);

//@}

#if 0
    //! \name Canonicalization
    //@{

    //! assign a canonical ordering to a molecule's atoms
    /*!
      The algorithm used here is a modification of the published Daylight canonical
      smiles algorithm (i.e. it uses atom invariants and products of primes).

      \param mol               the molecule of interest
      \param ranks             used to return the ranks
      \param breakTies         toggles breaking of ties (see below)
      \param includeChirality  toggles inclusion of chirality in the invariants
      \param includeIsotopes   toggles inclusion of isotopes in the invariants
      \param rankHistory       used to return the rank history (see below)

      <b>Notes:</b>
        - Tie breaking should be done when it's important to have a full ordering
          of the atoms (e.g. when generating canonical traversal trees). If it's
	        acceptable to have ties between symmetry-equivalent atoms (e.g. when
	        generating CIP codes), tie breaking can/should be skipped.
	      - if the \c rankHistory argument is provided, the evolution of the ranks of
	        individual atoms will be tracked.  The \c rankHistory pointer should be
	        to a VECT_INT_VECT that has at least \c mol.getNumAtoms() elements.
    */
    void rankAtoms(const ROMol &mol,std::vector<int> &ranks,
                   bool breakTies=true,
                   bool includeChirality=true,
                   bool includeIsotopes=true,
                   std::vector<std::vector<int> > *rankHistory=0);
    //! assign a canonical ordering to a sub-molecule's atoms
    /*!
      The algorithm used here is a modification of the published Daylight canonical
      smiles algorithm (i.e. it uses atom invariants and products of primes).

      \param mol               the molecule of interest
      \param atomsToUse        atoms to be included
      \param bondsToUse        bonds to be included
      \param atomSymbols       symbols to use for the atoms in the output (these are
                               used in place of atomic number and isotope information)
      \param ranks             used to return the ranks
      \param breakTies         toggles breaking of ties (see below)
      \param rankHistory       used to return the rank history (see below)

      <b>Notes:</b>
        - Tie breaking should be done when it's important to have a full ordering
          of the atoms (e.g. when generating canonical traversal trees). If it's
	        acceptable to have ties between symmetry-equivalent atoms (e.g. when
	        generating CIP codes), tie breaking can/should be skipped.
	      - if the \c rankHistory argument is provided, the evolution of the ranks of
	        individual atoms will be tracked.  The \c rankHistory pointer should be
	        to a VECT_INT_VECT that has at least \c mol.getNumAtoms() elements.
    */
    void rankAtomsInFragment(const ROMol &mol,std::vector<int> &ranks,
                             const boost::dynamic_bitset<> &atomsToUse,
                             const boost::dynamic_bitset<> &bondsToUse,
                             const std::vector<std::string> *atomSymbols=0,
                             const std::vector<std::string> *bondSymbols=0,
                             bool breakTies=true,
                             std::vector<std::vector<int> > *rankHistory=0);

    // @}
#endif
//! \name Stereochemistry
//@{

//! removes bogus chirality markers (those on non-sp3 centers):
void cleanupChirality(RWMol &mol);

//! \brief Uses a conformer to assign ChiralType to a molecule's atoms
/*!
  \param mol                  the molecule of interest
  \param confId               the conformer to use
  \param replaceExistingTags  if this flag is true, any existing atomic chiral
                              tags will be replaced

  If the conformer provided is not a 3D conformer, nothing will be done.
*/
void assignChiralTypesFrom3D(ROMol &mol, int confId = -1,
                             bool replaceExistingTags = true);

//! \brief Uses a conformer to assign ChiralTypes to a molecule's atoms and
//! stereo flags to its bonds
/*!

  \param mol                  the molecule of interest
  \param confId               the conformer to use
  \param replaceExistingTags  if this flag is true, any existing info about
                              stereochemistry will be replaced

*/
void assignStereochemistryFrom3D(ROMol &mol, int confId = -1,
                                 bool replaceExistingTags = true);

//! \brief Uses a conformer to assign directionality to the single bonds
//!   around double bonds
/*!

  \param mol                  the molecule of interest
  \param confId               the conformer to use
*/
void detectBondStereochemistry(ROMol &mol, int confId = -1);

//! Assign stereochemistry tags to atoms (i.e. R/S) and bonds (i.e. Z/E)
/*!

  \param mol     the molecule of interest
  \param cleanIt toggles removal of stereo flags from double bonds that can
                 not have stereochemistry
  \param force   forces the calculation to be repeated even if it has
                 already been done
  \param flagPossibleStereoCenters   set the _ChiralityPossible property on
                                     atoms that are possible stereocenters

  <b>Notes:M</b>
    - Throughout we assume that we're working with a hydrogen-suppressed
      graph.

*/
void assignStereochemistry(ROMol &mol, bool cleanIt = false, bool force = false,
                           bool flagPossibleStereoCenters = false);
//! Removes all stereochemistry information from atoms (i.e. R/S) and bonds
//(i.e. Z/E)
/*!

  \param mol     the molecule of interest
*/
void removeStereochemistry(ROMol &mol);

//! \brief finds bonds that could be cis/trans in a molecule and mark them as
//!  Bond::STEREOANY.
/*!
  \param mol     the molecule of interest
  \param cleanIt toggles removal of stereo flags from double bonds that can
                 not have stereochemistry

  This function finds any double bonds that can potentially be part of
  a cis/trans system. No attempt is made here to mark them cis or
  trans. No attempt is made to detect double bond stereo in ring systems.

  This function is useful in the following situations:
    - when parsing a mol file; for the bonds marked here, coordinate
      information on the neighbors can be used to indentify cis or trans states
    - when writing a mol file; bonds that can be cis/trans but not marked as
      either need to be specially marked in the mol file
    - finding double bonds with unspecified stereochemistry so they
      can be enumerated for downstream 3D tools

  The CIPranks on the neighboring atoms are checked in this function. The
  _CIPCode property if set to any on the double bond.
*/
void findPotentialStereoBonds(ROMol &mol, bool cleanIt = false);
//@}

//! returns the number of atoms which have a particular property set
unsigned getNumAtomsWithDistinctProperty(const ROMol &mol, std::string prop);

};  // end of namespace MolOps
};  // end of namespace RDKit

#endif
