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