builder.h

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

Copyright (C) 2007-2008 by Tim Vandermeersch
                           <[email protected]>

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/stereo/stereo.h>

namespace OpenBabel
{
  class OBMol;
  class OBAtom;
  class OBSmartsPattern;
  class vector3;
  class OBBitVec;

  class OBAPI OBBuilder {
    public:

      OBBuilder(): _keeprings(false) {}



    bool Build(OBMol &mol, bool stereoWarnings = true);



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


      void LoadFragments();
      std::vector<vector3> GetFragmentCoord(std::string smiles);

      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 bool CorrectStereoBonds(OBMol &mol);
      static bool CorrectStereoAtoms(OBMol &mol, bool warn = true);
      static bool IsSpiroAtom(unsigned long atomId, OBMol &mol);
      static OBBitVec GetFragment(OBAtom *atom);
      static void AddNbrs(OBBitVec &fragment, OBAtom *atom);

    private:
      //static std::map<std::string, double> _torsion;
      static std::vector<std::string> _rigid_fragments;
      static std::vector<std::pair<OBSmartsPattern*, std::vector<vector3> > > _ring_fragments;
      static std::map<std::string, int> _rigid_fragments_index;
      static std::map<std::string, std::vector<vector3> > _rigid_fragments_cache;
      //  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