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/********************************************************************** |
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base.h - Base classes to build a graph |
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|
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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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|
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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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|
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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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|
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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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|
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#ifndef OB_BASE_H |
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#define OB_BASE_H |
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|
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#include "config.h" |
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|
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#include <vector> |
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#include <map> |
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|
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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|
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namespace OpenBabel |
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{ |
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|
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class OBBase; |
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class OBNodeBase; |
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class OBEdgeBase; |
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class OBGraphBase; |
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|
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/** \brief Base Class |
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|
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The various classes (Atom, Bond, Molecule) inherit from base classes-- |
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OBBase is just a placeholder class |
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*/ |
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class OBAPI OBBase |
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{ |
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public: |
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virtual ~OBBase() |
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{} |
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; //NF |
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virtual OBBase* DoTransformations(const std::map<std::string,std::string>*pOptions) |
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{ |
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return this; |
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} //NF Base type does nothing |
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static const char* ClassDescription() |
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{ |
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return ""; |
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} //NF |
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|
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}; |
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|
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/** \brief Node Base Class |
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|
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The base class for nodes (e.g. atoms) in a graph-theoretical representation. |
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*/ |
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class OBAPI OBNodeBase : public OBBase |
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{ |
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protected: |
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//! What is my unique node index? GetIdx(), SetIdx(int idx). |
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unsigned short int _idx; |
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//! To which graph do I belong? GetParent(), SetParent(OBGraphBase*). |
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OBGraphBase *_parent; |
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/** \brief What edges or bonds do I have? \sa AddEdge(), GetValence(), |
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This node is assumed to be one of the edge endpoints. |
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*/ |
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std::vector<OBEdgeBase*> _vbond; |
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|
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public: |
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//! Used internally by graph traversal algorithms |
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bool Visit; |
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|
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//! Constructor |
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OBNodeBase() |
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{ |
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Visit = false; |
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} |
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//! Destructor |
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virtual ~OBNodeBase() |
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{} |
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virtual unsigned int GetIdx() const |
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{ |
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return(_idx); |
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} |
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//! Set my unique node number. |
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void SetIdx(int idx) |
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{ |
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_idx = idx; |
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} |
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virtual OBGraphBase *GetParent() |
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{ |
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return(_parent); |
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} |
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//! Set my parent graph. |
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void SetParent(OBGraphBase*); |
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//! Add an edge. Assumes this node is an endpoint of \a b. |
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void AddEdge(OBEdgeBase *b) |
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{ |
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_vbond.push_back(b); |
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} |
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//! How many edges? |
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virtual unsigned int GetValence() const |
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{ |
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return(_vbond.size()); |
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} |
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//! Iterate over my edges, returning my connected nodes. |
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OBNodeBase *BeginNbr(std::vector<OBEdgeBase*>::iterator&); |
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OBNodeBase *NextNbr(std::vector<OBEdgeBase*>::iterator&); |
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//! Iterate over my edges, returning the edges. |
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OBEdgeBase *Begin(std::vector<OBEdgeBase*>::iterator&); |
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OBEdgeBase *Next(std::vector<OBEdgeBase*>::iterator&); |
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//! Is \a OBNodeBase* a beginning or end of some edge of mine? |
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virtual bool IsConnected(OBNodeBase*); |
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|
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//! Used to signal erroneously calling some of the nonfunctional members |
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void Error(int f) |
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{ |
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std::cerr << "atom vf called = " << f << std::endl; |
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} |
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/** \name Nonfunctional members |
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Nonfunctional or unused members of OpenBabel::OBNodeBase |
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are to be added by a derived class (e.g., OpenBabel::OBAtom) |
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@{ |
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*/ |
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virtual int GetFormalCharge() const |
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{ |
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((OBNodeBase*)this)->Error(1); |
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return(0); |
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} |
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virtual unsigned int ExplicitHydrogenCount() const |
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{ |
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((OBNodeBase*)this)->Error(22); |
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return(0); |
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} |
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virtual unsigned int ImplicitHydrogenCount() const |
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{ |
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((OBNodeBase*)this)->Error(22); |
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return(0); |
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} |
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virtual unsigned int GetImplicitValence() const |
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{ |
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((OBNodeBase*)this)->Error(3); |
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return(0); |
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} |
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virtual unsigned int GetHvyValence() const |
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{ |
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((OBNodeBase*)this)->Error(4); |
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return(0); |
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} |
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virtual unsigned int KBOSum() const |
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{ |
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((OBNodeBase*)this)->Error(5); |
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return(0); |
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} |
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virtual unsigned int GetHyb() const |
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{ |
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((OBNodeBase*)this)->Error(6); |
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return(0); |
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} |
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virtual unsigned int MemberOfRingCount() const |
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{ |
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((OBNodeBase*)this)->Error(7); |
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return(0); |
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} |
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virtual unsigned int GetAtomicNum() const |
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{ |
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((OBNodeBase*)this)->Error(8); |
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return(0); |
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} |
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virtual void SetMatch(OBNodeBase*) |
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{} |
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virtual void SetAromatic() |
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{} |
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virtual bool IsInRingSize(int) const |
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{ |
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((OBNodeBase*)this)->Error(9); |
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return(false); |
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} |
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virtual bool IsAromatic() const |
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{ |
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((OBNodeBase*)this)->Error(10); |
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return(false); |
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} |
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virtual bool IsInRing() const |
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{ |
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((OBNodeBase*)this)->Error(11); |
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return(false); |
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} |
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virtual bool Eval(OBNodeBase*) const |
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{ |
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((OBNodeBase*)this)->Error(12); |
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return(false); |
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} |
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virtual OBNodeBase *GetMatch() |
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{ |
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((OBNodeBase*)this)->Error(13); |
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return(NULL); |
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} |
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//@} |
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}; |
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|
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/** \brief Edge Base Class |
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|
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The base class for edges (e.g. bonds) in a graph-theoretical representation. |
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*/ |
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class OBAPI OBEdgeBase : public OBBase |
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{ |
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protected: |
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/// What is my unique edge index? GetIdx(), SetIdx(int idx) |
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unsigned short int _idx; |
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OBNodeBase *_bgn; //!< I connect one node |
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OBNodeBase *_end; //!< to another node |
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//! To which graph do I belong? GetParent(), SetParent(OBGraphBase*). |
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OBGraphBase *_parent; |
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public: |
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bool Visit; |
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|
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//! Constructor |
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OBEdgeBase() |
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{ |
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Visit = false; |
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_bgn = _end = NULL; |
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} |
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//! Constructor (populate from two OBNodeBase objects) |
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OBEdgeBase(OBNodeBase *bgn,OBNodeBase *end) |
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{} |
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//! Destructor |
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virtual ~OBEdgeBase() |
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{} |
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|
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virtual OBGraphBase* GetParent() |
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{ |
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return(_parent); |
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} |
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void SetParent(OBGraphBase*); |
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unsigned int GetIdx() |
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{ |
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return(_idx); |
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} |
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void SetIdx(int idx) |
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{ |
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_idx = idx; |
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} |
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void SetBgn(OBNodeBase *n) |
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{ |
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_bgn = n; |
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} |
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void SetEnd(OBNodeBase *n) |
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{ |
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_end = n; |
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} |
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void SwapEnds() |
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{ |
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std::swap(_bgn,_end); |
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} |
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OBNodeBase *GetBgn() |
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{ |
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return(_bgn); |
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} |
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OBNodeBase *GetEnd() |
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{ |
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return(_end); |
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} |
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|
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void Error(int f) |
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{ |
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std::cerr << "bond vf err = " << f << std::endl; |
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} |
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/** \name Nonfunctional members |
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Nonfunctional or unused members of OpenBabel::OBEdgeBase |
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are to be added by a derived class (e.g., OpenBabel::OBBond) |
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@{ |
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*/ |
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virtual void SetClosure() |
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{} |
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virtual bool IsAromatic() const |
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{ |
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((OBEdgeBase*)this)->Error(1); |
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return(false); |
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} |
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virtual bool IsInRing() const |
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{ |
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((OBEdgeBase*)this)->Error(2); |
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return(false); |
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} |
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virtual bool IsClosure() |
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{ |
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((OBEdgeBase*)this)->Error(3); |
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return(false); |
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} |
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virtual bool Eval(OBEdgeBase*) |
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{ |
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((OBEdgeBase*)this)->Error(4); |
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return(false); |
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} |
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virtual unsigned int GetBO() const |
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{ |
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((OBEdgeBase*)this)->Error(5); |
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return(0); |
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} |
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//@} |
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}; |
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|
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/*! \brief Graph Base Class |
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|
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The base class for graphs (e.g. rings, molecules, etc.) in a |
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graph-theoretical representation. |
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*/ |
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class OBAPI OBGraphBase : public OBBase |
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{ |
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protected: |
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bool _vlock; |
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std::vector<OBNodeBase*> _vatom; |
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std::vector<OBEdgeBase*> _vbond; |
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public: |
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OBGraphBase() |
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{ |
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_vlock = false; |
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_vatom.clear(); |
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_vbond.clear(); |
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} |
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OBGraphBase(const OBGraphBase &src) : OBBase() { } |
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virtual ~OBGraphBase() { } |
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unsigned int NumNodes() |
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{ |
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return(_vatom.empty() ? 0 : _vatom.size()); |
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} |
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unsigned int NumEdges() |
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{ |
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return(_vbond.empty() ? 0 : _vbond.size()); |
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} |
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void ResetVisitFlags(); |
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bool SetVisitLock(bool); |
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bool GetVisitLock() |
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{ |
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return(_vlock); |
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} |
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OBNodeBase *Begin(std::vector<OBNodeBase*>::iterator&); |
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OBNodeBase *Next(std::vector<OBNodeBase*>::iterator&); |
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OBEdgeBase *Begin(std::vector<OBEdgeBase*>::iterator&); |
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OBEdgeBase *Next(std::vector<OBEdgeBase*>::iterator&); |
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|
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/*The following (placeholder) routines removed to avoid finding solution to |
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iterators being illegally returned as NULL |
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//substructure search functions |
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virtual bool SingleMatch() const |
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{ |
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return(false); |
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} |
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virtual void SetSingleMatch(bool) |
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{} |
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virtual bool FinishedMatch() const |
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{ |
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return(false); |
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} |
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virtual void SetFinishedMatch(bool) |
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{} |
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virtual void ClearMatches() |
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{} |
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virtual void PushBack(std::vector<OBNodeBase*>&) |
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{} |
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virtual void PrepForMatch() |
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{} |
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virtual std::vector<std::pair<OBNodeBase*,std::vector<OBEdgeBase*> > >::iterator BgnMatch() |
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{ |
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return((std::vector<std::pair<OBNodeBase*,std::vector<OBEdgeBase*> > >::iterator) NULL); |
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} |
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virtual std::vector<std::pair<OBNodeBase*,std::vector<OBEdgeBase*> > >::iterator EndMatch() |
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{ |
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return((std::vector<std::pair<OBNodeBase*,std::vector<OBEdgeBase*> > >::iterator) NULL); |
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} |
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virtual OBNodeBase *GetFirstSeed() |
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{ |
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return((OBNodeBase*)NULL); |
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} |
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bool Match(OBGraphBase &,bool singleMatch=false); |
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bool Match(OBGraphBase &, |
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std::vector<std::pair<OBNodeBase*,std::vector<OBEdgeBase*> > >::iterator, |
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std::vector<OBEdgeBase*>::iterator); |
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*/ |
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}; |
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|
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} //namespace OpenBabel |
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|
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#endif // OB_BASE_H |
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|
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//! \file base.h |
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//! \brief Base classes to build a graph |
