builder.h

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00001 /**********************************************************************
00002 builder.h - OBBuilder class.
00003  
00004 Copyright (C) 2007-2008 by Tim Vandermeersch 
00005                            <tim.vandermeersch@gmail.com>
00006  
00007 This file is part of the Open Babel project.
00008 For more information, see <http://openbabel.sourceforge.net/>
00009  
00010 This program is free software; you can redistribute it and/or modify
00011 it under the terms of the GNU General Public License as published by
00012 the Free Software Foundation version 2 of the License.
00013  
00014 This program is distributed in the hope that it will be useful,
00015 but WITHOUT ANY WARRANTY; without even the implied warranty of
00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00017 GNU General Public License for more details.
00018 ***********************************************************************/
00019 
00020 #ifndef OB_BUILDER_H
00021 #define OB_BUILDER_H
00022 
00023 #include <vector>
00024 #include <string>
00025 #include <map>
00026 
00027 #include <list>
00028 #include <set>
00029 #include <openbabel/base.h>
00030 #include <openbabel/mol.h>
00031 
00032 namespace OpenBabel
00033 {
00036   class OBAPI OBBuilder {
00037     public:
00038 
00040       void LoadFragments();
00041 
00046       static vector3 GetNewBondVector(OBAtom *atom);
00047       static vector3 GetNewBondVector(OBAtom *atom, double length);
00053       bool Build(OBMol &mol);
00065       static bool Connect(OBMol &mol, int a, int b, vector3 &newpos, int bondOrder = 1);
00076       static bool Connect(OBMol &mol, int a, int b, int bondOrder = 1);
00104       static bool Swap(OBMol &mol, int a, int b, int c, int d);
00111       //bool Insert(OBMol &mol, int a, int b, std::string smiles, int c, int d);
00114       static void CorrectStereoBonds(OBMol &mol);
00117       static void CorrectStereoAtoms(OBMol &mol);
00122       static OBBitVec GetFragment(OBAtom *atom);
00123       static void AddNbrs(OBBitVec &fragment, OBAtom *atom);
00124  
00125     private:
00127       static std::vector<std::pair<OBSmartsPattern*, std::vector<vector3> > > _fragments;
00128   }; // class OBBuilder
00129 
00130 }// namespace OpenBabel
00131 
00132 #endif   // OB_BUILDER_H
00133
builder.h

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