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/********************************************************************** |
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base.cpp - 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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#include "babelconfig.hpp" |
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#include "base.hpp" |
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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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#if HAVE_FSTREAM |
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#include <fstream> |
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#elif HAVE_FSTREAM_H |
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#include <fstream.h> |
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#endif |
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|
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using namespace std; |
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|
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//! Global namespace for all Open Babel code |
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namespace OpenBabel |
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{ |
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/* |
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bool OBGraphBase::Match(OBGraphBase &g,bool singleMatch) |
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{ |
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SetFinishedMatch(false); |
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SetSingleMatch(singleMatch); |
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ClearMatches(); |
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g.SetVisitLock(true); |
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g.ResetVisitFlags(); |
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|
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OBNodeBase *node; |
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OBNodeBase *seed = GetFirstSeed(); |
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vector<OBNodeBase*>::iterator i; |
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|
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for (node = g.Begin(i);node;node = g.Next(i)) |
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if (!node->Visit && seed->Eval(node)) |
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{ |
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node->Visit = true; |
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seed->SetMatch(node); |
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Match(g,BgnMatch(),BgnMatch()->second.begin()); |
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seed->SetMatch((OBNodeBase*)NULL); |
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node->Visit = false; |
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if (SingleMatch() && FinishedMatch()) |
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break; |
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} |
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|
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g.SetVisitLock(false); |
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|
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return(FinishedMatch()); |
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} |
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|
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bool OBGraphBase::Match(OBGraphBase &g, |
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vector<pair<OBNodeBase*,vector<OBEdgeBase*> > >::iterator i, |
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vector<OBEdgeBase*>::iterator j) |
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{ |
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//bail if only one match has been requested |
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if (SingleMatch() && FinishedMatch()) |
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return(true); |
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|
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//full match completed |
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if (i == EndMatch() || (j == i->second.end() && (i+1) == EndMatch())) |
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{ |
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SetFinishedMatch(true); |
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OBNodeBase *node; |
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vector<OBNodeBase*> vn; |
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vector<OBNodeBase*>::iterator i; |
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for (node = Begin(i);node;node = Next(i)) |
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vn.push_back(node->GetMatch()); |
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PushBack(vn); |
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|
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return(true); |
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} |
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|
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//handle next seed of disconnected pattern |
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if (j == i->second.end()) |
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{ |
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i++; |
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OBNodeBase *node; |
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OBNodeBase *seed = i->first; |
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vector<OBNodeBase*>::iterator k; |
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for (node = g.Begin(k);node;node = g.Next(k)) |
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if (!node->Visit && seed->Eval(node)) |
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{ |
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node->Visit = true; |
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seed->SetMatch(node); |
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Match(g,i,i->second.begin()); |
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seed->SetMatch((OBNodeBase*)NULL); |
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node->Visit = false; |
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if (SingleMatch() && FinishedMatch()) |
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break; |
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} |
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return(true); |
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} |
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|
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OBEdgeBase *edge = *j++; |
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if (edge->IsClosure()) //check to see if matched atoms are bonded |
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{ |
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if (edge->GetBgn()->GetMatch()->IsConnected(edge->GetEnd()->GetMatch())) |
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Match(g,i,j); |
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} |
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else //bond hasn't been covered yet |
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{ |
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OBNodeBase *nbr; |
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OBNodeBase *curr = edge->GetBgn(); |
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OBNodeBase *next = edge->GetEnd(); |
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OBNodeBase *match = curr->GetMatch(); |
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vector<OBEdgeBase*>::iterator k; |
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|
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for (nbr = match->BeginNbr(k);nbr;nbr = match->NextNbr(k)) |
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if (!nbr->Visit && next->Eval(nbr) && edge->Eval(*k)) |
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{ |
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nbr->Visit = true; |
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next->SetMatch(nbr); |
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Match(g,i,j); |
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next->SetMatch(NULL); |
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nbr->Visit = false; |
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} |
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} |
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|
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return(false); |
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} |
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*/ |
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OBNodeBase *OBGraphBase::Begin(vector<OBNodeBase*>::iterator &i) |
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{ |
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i = _vatom.begin(); |
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return((i != _vatom.end()) ? *i : NULL); |
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} |
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|
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OBNodeBase *OBGraphBase::Next(vector<OBNodeBase*>::iterator &i) |
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{ |
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i++; |
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return((i != _vatom.end()) ? *i : NULL); |
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} |
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|
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OBEdgeBase *OBGraphBase::Begin(vector<OBEdgeBase*>::iterator &i) |
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{ |
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i = _vbond.begin(); |
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return((i != _vbond.end()) ? *i : NULL); |
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} |
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|
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OBEdgeBase *OBGraphBase::Next(vector<OBEdgeBase*>::iterator &i) |
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{ |
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i++; |
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return((i != _vbond.end()) ? *i : NULL); |
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} |
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|
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OBNodeBase *OBNodeBase::BeginNbr(vector<OBEdgeBase*>::iterator &i) |
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{ |
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i = _vbond.begin(); |
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|
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if (i == _vbond.end()) |
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return(NULL); |
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return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn()); |
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} |
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|
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OBNodeBase *OBNodeBase::NextNbr(vector<OBEdgeBase*>::iterator &i) |
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{ |
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i++; |
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if (i == _vbond.end()) |
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return(NULL); |
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return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn()); |
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} |
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|
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void OBNodeBase::SetParent(OBGraphBase *p) |
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{ |
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_parent = p; |
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} |
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|
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void OBEdgeBase::SetParent(OBGraphBase *p) |
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{ |
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_parent = p; |
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} |
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|
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bool OBNodeBase::IsConnected(OBNodeBase *nb) |
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{ |
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vector<OBEdgeBase*>::iterator i; |
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for (i = _vbond.begin();i != _vbond.end();i++) |
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if (nb == (*i)->GetBgn() || nb == (*i)->GetEnd()) |
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return(true); |
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|
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return(false); |
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} |
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|
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void OBGraphBase::ResetVisitFlags() |
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{ |
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OBNodeBase *nb; |
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vector<OBNodeBase*>::iterator i; |
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for (nb = Begin(i);nb;nb = Next(i)) |
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nb->Visit = false; |
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|
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OBEdgeBase *eb; |
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vector<OBEdgeBase*>::iterator j; |
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for (eb = Begin(j);eb;eb = Next(j)) |
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eb->Visit = false; |
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} |
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|
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bool OBGraphBase::SetVisitLock(bool v) |
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{ |
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if (v && _vlock) |
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return(false); |
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_vlock = v; |
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return(true); |
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} |
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|
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/*! \mainpage |
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|
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\section intro Introduction and History |
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|
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It is fair to say that Open Babel is a direct result of the original Babel. |
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Application development is facilitated |
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by building software on top of libraries rich in functionality. Babel |
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was the first experience for Matt Stahl in designing a molecule |
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library. In addition to developing Babel, Pat Walters and Matt |
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developed `OBabel' at Vertex Pharmaceuticals, a first |
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attempt at developing an object oriented molecule library. |
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Matt later designed a new molecule class library, OELib -- designed |
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to be flexible, extensible, portable, and efficient. |
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|
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OELib was released under the GNU General Public License (GPL) by Matt Stahl |
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and Open Eye Scientific Software, Inc. to take advantage of many of |
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the "great minds writing chemical software." Open Babel took up where |
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OELib and Babel left off, starting from the existing GPL version of |
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OELib, and has continued to evolve and improve into a separate |
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high-quality chemistry class library and tool. Open Babel is now a |
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separate project and library and has changed considerably from the OELib days. |
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|
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Thanks to all who have helped with Babel, OBabel, OELib and Open Babel. |
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The list is long and growing. |
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|
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\section pointers Key Modules |
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|
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The heart of Open Babel lies in the \link OpenBabel::OBMol OBMol\endlink, |
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\link OpenBabel::OBAtom OBAtom\endlink, and |
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\link OpenBabel::OBBond OBBond\endlink classes, |
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which handle operations on atoms, bonds and molecules. Newcomers should |
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start with looking at the \link OpenBabel::OBMol OBMol\endlink class, |
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designed to store the basic information |
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in a molecule and to perceive information about a molecule. |
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|
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One of the key philosophies in the code is that transformations and |
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automatic perception of properties are performed in a <a href="http://en.wikipedia.org/wiki/Lazy_evaluation">"lazy"</a> |
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manner. That is, until you call for partial atomic charges, no |
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charges are calculated. This ensures faster transformations of |
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chemical data -- properties that are not needed for your code will |
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typically not be calculated. When such data is needed, appropriate |
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routines are called, and a "flag" is set (e.g., via OBMol::SetFlag |
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or OBAtom::SetFlag etc.) so that the code is only run once. |
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|
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Arbitrary custom data and text descriptors can be stored in any atom, |
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bond, molecule, or residue using the \link OpenBabel::OBGenericData |
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OBGenericData\endlink or \link OpenBabel::OBPairData |
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OBPairData\endlink classes. |
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|
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Conversion between various chemical file formats is accomplished through |
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the \link OpenBabel::OBConversion OBConversion\endlink and \link |
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OpenBabel::OBFormat OBFormat\endlink classes, often through use of the \link |
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OpenBabel::OBMoleculeFormat OBMoleculeFormat\endlink subclass which is designed |
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for easy read/write access to one or more \link OpenBabel::OBMol OBMol\endlink |
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objects. The philosophy of the file format codes is to parse as much |
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chemical information from a given file as possible (no data left |
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behind) and ideally any perception or transformations will occur when |
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writing to some other format later. |
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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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//! \file base.cpp |
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//! \brief Implementation of base classes. |