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tim |
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/********************************************************************** |
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ring.h - Deal with rings, find smallest set of smallest rings (SSSR). |
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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#ifndef OB_RING_H |
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#define OB_RING_H |
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#include <deque> |
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#include <algorithm> |
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namespace OpenBabel |
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{ |
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class OBMol; |
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class OBAtom; |
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class OBBond; |
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//! Internal class for OBRing search algorithms to create a search tree of OBAtom objects |
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class OBAPI OBRTree |
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{ |
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OBAtom *_atom; //!< Atom represented by this node in the tree |
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OBRTree *_prv; //!< Previous (parent) entry in an OBRing tree |
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public: |
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OBRTree(OBAtom*,OBRTree*); |
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~OBRTree() {} |
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//! \return the OBAtom::GetIdx() index of the atom in this node |
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int GetAtomIdx(); |
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//! Recursively find the root of this tree, building up a vector of OBAtom nodes. |
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void PathToRoot(std::vector<OBNodeBase*>&); |
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}; |
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// class introduction in ring.cpp |
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class OBAPI OBRing |
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{ |
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OBMol *_parent; |
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public: |
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//public data members |
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std::vector<int> _path; |
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OBBitVec _pathset; |
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bool findCenterAndNormal(vector3 & center, vector3 &norm1, vector3 &norm2); |
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//constructors |
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OBRing() {} |
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OBRing(std::vector<int>&,int); |
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OBRing(const OBRing &src); |
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OBRing& operator=(const OBRing &src); |
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//member functions |
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int Size() const |
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{ |
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return(_path.size()); |
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} |
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int PathSize() const |
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{ |
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return(_path.size()); |
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} |
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bool IsMember(OBAtom *a); |
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bool IsMember(OBBond *b); |
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bool IsAromatic(); |
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bool IsInRing(int i) |
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{ |
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return(_pathset.BitIsOn(i)); |
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} |
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void SetParent(OBMol *m) |
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{ |
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_parent = m; |
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} |
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OBMol *GetParent() |
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{ |
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return(_parent); |
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} |
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}; |
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bool CompareRingSize(const OBRing *,const OBRing *); |
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//! Internal class to facilitate OBMol::FindSSSR() |
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class OBAPI OBRingSearch |
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{ |
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std::vector<OBBond*> _bonds; |
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std::vector<OBRing*> _rlist; |
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public: |
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OBRingSearch() {} |
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~OBRingSearch(); |
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//! Sort ring sizes from smallest to largest |
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void SortRings() |
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{ |
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std::sort(_rlist.begin(),_rlist.end(),CompareRingSize); |
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} |
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//! Starting with a full ring set - reduce to SSSR set |
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void RemoveRedundant(int); |
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void AddRingFromClosure(OBMol &,OBBond *); |
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//! For debugging only, write the rings to std::cout |
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void WriteRings(); |
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bool SaveUniqueRing(std::deque<int>&,std::deque<int>&); |
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std::vector<OBRing*>::iterator BeginRings() |
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{ |
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return(_rlist.begin()); |
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} |
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std::vector<OBRing*>::iterator EndRings() |
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{ |
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return(_rlist.end()); |
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} |
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}; |
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} // end namespace OpenBabel |
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#endif // OB_RING_H |
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//! \file ring.h |
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//! \brief Deal with rings, find smallest set of smallest rings (SSSR). |
