/**********************************************************************

opisomorph.cpp - Enhanced -s option

Copyright (C) 2010 by Chris Morley

This program is free software; you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.

***********************************************************************/

#include <openbabel/babelconfig.h>

#include <openbabel/op.h>

#include <openbabel/mol.h>

#include <openbabel/obconversion.h>

#include <openbabel/query.h>

#include <vector>

#include <string>

namespace OpenBabel

{

/**

@since version 2.3

Adds an OBPairData object to each atom and bond in a substructure.

The substructure's atoms are specified in an input parameter, a

vector of atom indx; the bonds are those in the molecule that join

these atoms. The attribute and value of the OBPairObject (the same

for all the added objects) are specified as parameters.

**/

extern bool AddDataToSubstruct(OBMol* pmol, const std::vector<int>& atomIdxs,

        const std::string& attribute, const std::string& value);

/**

@since version 2.3

Deletes all atoms except those in @p atomIndxs

**/

extern bool ExtractSubstruct(OBMol* pmol, const std::vector<int>& atomIdxs);

extern bool MakeQueriesFromMolInFile(std::vector<OBQuery*>& queries

                         , const std::string& filename, int* pnAtoms, bool noH);

//*****************************************************

class OpNewS : public OBOp

{

public:

  OpNewS(const char* ID) : OBOp(ID, false){}

  const char* Description() override;

  bool WorksWith(OBBase* pOb) const override { return dynamic_cast<OBMol*>(pOb) != nullptr; }

  bool Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion*) override;

  std::vector<int> GetMatchAtoms(){ return firstmatch; }

  bool ProcessVec(std::vector<OBBase*>& vec) override; //Extra target mols

private:

  std::vector<std::string> vec; //parsed parameter text

  std::vector<OBBase*> ExtraMols; //extra OBMols passed in via ProcessVec() (FastSearchFormat)

  OBSmartsPattern sp;  //if SMARTS (and not a filename) supplied

  std::string xsmarts; //extra SMARTS provided externally via ProcessVec()

  bool addHydrogens;   //The SMARTS contained one or more #1 to explicitly find hydrogen

  bool inv;

  int nPatternAtoms;   //non-zero for exact matches

  std::vector<OBQuery*> queries; //populated if a filename was supplied

  OBQuery* query;

  std::vector<int> firstmatch; //Idxes of first match by SMARTS or OBIsomorphismMapper

  bool showAll;

  int nmatches;

  char comparechar;

};

} //namespace