builder.h

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/**********************************************************************
builder.h - OBBuilder class.

Copyright (C) 2007-2008 by Tim Vandermeersch
                           <tim.vandermeersch@gmail.com>

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

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.
***********************************************************************/

#ifndef OB_BUILDER_H
#define OB_BUILDER_H

#include <vector>
#include <string>
#include <map>

#include <list>
#include <set>
#include <openbabel/base.h>
#include <openbabel/mol.h>
#include <openbabel/stereo/stereo.h>

namespace OpenBabel
{
  class OBAPI OBBuilder {
    public:

      OBBuilder(): _keeprings(false) {}



      bool Build(OBMol &mol);



      void SetKeepRings() { _keeprings = true; }
      void UnsetKeepRings() { _keeprings = false; }


      void LoadFragments();

      static vector3 GetNewBondVector(OBAtom *atom);
      static vector3 GetNewBondVector(OBAtom *atom, double length);

      static bool Connect(OBMol &mol, int a, int b, vector3 &newpos, int bondOrder = 1);
      static bool Connect(OBMol &mol, int a, int b, int bondOrder = 1);
      static bool Swap(OBMol &mol, int a, int b, int c, int d);
      //bool Insert(OBMol &mol, int a, int b, std::string smiles, int c, int d);
      static void CorrectStereoBonds(OBMol &mol);
      static void CorrectStereoAtoms(OBMol &mol);
      static bool IsSpiroAtom(unsigned long atomId, OBMol &mol);
      static OBBitVec GetFragment(OBAtom *atom);
      static void AddNbrs(OBBitVec &fragment, OBAtom *atom);

    private:
      static std::vector<std::pair<OBSmartsPattern*, std::vector<vector3> > > _fragments;
      //  supports the case where the fragments overlap at a spiro atom only.
      static void ConnectFrags(OBMol &mol, OBMol &workmol, std::vector<int> match, std::vector<vector3> coords,
                               std::vector<int> pivot);
      static void FlipSpiro(OBMol &mol, int idx);
      static bool FixRingStereo(std::vector<std::pair<OBStereo::Ref, bool> > atomIds,
                                OBMol &mol, OBStereo::Refs &unfixedcenters);
      static void AddRingNbrs(OBBitVec &fragment, OBAtom *atom, OBMol &mol);
      static bool SwapWithVector(OBMol &mol, int a, int b, int c, const vector3 &newlocation);
      bool _keeprings;
  }; // class OBBuilder

}// namespace OpenBabel

#endif   // OB_BUILDER_H