src/openbabel/base.cpp

/**********************************************************************
base.cpp - Base classes to build a graph
 
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
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.
***********************************************************************/

#include "babelconfig.hpp"
#include "base.hpp"

#if HAVE_IOSTREAM
#include <iostream>
#elif HAVE_IOSTREAM_H
#include <iostream.h>
#endif

#if HAVE_FSTREAM
#include <fstream>
#elif HAVE_FSTREAM_H
#include <fstream.h>
#endif

using namespace std;

//! Global namespace for all Open Babel code
namespace OpenBabel
{
/*
bool OBGraphBase::Match(OBGraphBase &g,bool singleMatch)
{
    SetFinishedMatch(false);
    SetSingleMatch(singleMatch);
    ClearMatches();
    g.SetVisitLock(true);
    g.ResetVisitFlags();

    OBNodeBase *node;
    OBNodeBase *seed = GetFirstSeed();
    vector<OBNodeBase*>::iterator i;

    for (node = g.Begin(i);node;node = g.Next(i))
        if (!node->Visit && seed->Eval(node))
        {
            node->Visit = true;
            seed->SetMatch(node);
            Match(g,BgnMatch(),BgnMatch()->second.begin());
            seed->SetMatch((OBNodeBase*)NULL);
            node->Visit = false;
            if (SingleMatch() && FinishedMatch())
                break;
        }

    g.SetVisitLock(false);

    return(FinishedMatch());
}

bool OBGraphBase::Match(OBGraphBase &g,
                        vector<pair<OBNodeBase*,vector<OBEdgeBase*> > >::iterator i,
                        vector<OBEdgeBase*>::iterator j)
{
    //bail if only one match has been requested
    if (SingleMatch() && FinishedMatch())
        return(true);

    //full match completed
    if (i == EndMatch() || (j == i->second.end() && (i+1) == EndMatch()))
    {
        SetFinishedMatch(true);
        OBNodeBase *node;
        vector<OBNodeBase*> vn;
        vector<OBNodeBase*>::iterator i;
        for (node = Begin(i);node;node = Next(i))
            vn.push_back(node->GetMatch());
        PushBack(vn);

        return(true);
    }

    //handle next seed of disconnected pattern
    if (j == i->second.end())
    {
        i++;
        OBNodeBase *node;
        OBNodeBase *seed = i->first;
        vector<OBNodeBase*>::iterator k;
        for (node = g.Begin(k);node;node = g.Next(k))
            if (!node->Visit && seed->Eval(node))
            {
                node->Visit = true;
                seed->SetMatch(node);
                Match(g,i,i->second.begin());
                seed->SetMatch((OBNodeBase*)NULL);
                node->Visit = false;
                if (SingleMatch() && FinishedMatch())
                    break;
            }
        return(true);
    }

    OBEdgeBase *edge = *j++;
    if (edge->IsClosure()) //check to see if matched atoms are bonded
    {
        if (edge->GetBgn()->GetMatch()->IsConnected(edge->GetEnd()->GetMatch()))
            Match(g,i,j);
    }
    else //bond hasn't been covered yet
    {
        OBNodeBase *nbr;
        OBNodeBase *curr = edge->GetBgn();
        OBNodeBase *next = edge->GetEnd();
        OBNodeBase *match = curr->GetMatch();
        vector<OBEdgeBase*>::iterator k;

        for (nbr = match->BeginNbr(k);nbr;nbr = match->NextNbr(k))
            if (!nbr->Visit && next->Eval(nbr) && edge->Eval(*k))
            {
                nbr->Visit = true;
                next->SetMatch(nbr);
                Match(g,i,j);
                next->SetMatch(NULL);
                nbr->Visit = false;
            }
    }

    return(false);
}
*/
OBNodeBase *OBGraphBase::Begin(vector<OBNodeBase*>::iterator &i)
{
    i = _vatom.begin();
    return((i != _vatom.end()) ? *i : NULL);
}

OBNodeBase *OBGraphBase::Next(vector<OBNodeBase*>::iterator &i)
{
    i++;
    return((i != _vatom.end()) ? *i : NULL);
}

OBEdgeBase *OBGraphBase::Begin(vector<OBEdgeBase*>::iterator &i)
{
    i = _vbond.begin();
    return((i != _vbond.end()) ? *i : NULL);
}

OBEdgeBase *OBGraphBase::Next(vector<OBEdgeBase*>::iterator &i)
{
    i++;
    return((i != _vbond.end()) ? *i : NULL);
}

OBNodeBase *OBNodeBase::BeginNbr(vector<OBEdgeBase*>::iterator &i)
{
    i = _vbond.begin();

    if (i == _vbond.end())
        return(NULL);
    return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());
}

OBNodeBase *OBNodeBase::NextNbr(vector<OBEdgeBase*>::iterator &i)
{
    i++;
    if (i == _vbond.end())
        return(NULL);
    return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());
}

void OBNodeBase::SetParent(OBGraphBase *p)
{
    _parent = p;
}

void OBEdgeBase::SetParent(OBGraphBase *p)
{
    _parent = p;
}

bool OBNodeBase::IsConnected(OBNodeBase *nb)
{
    vector<OBEdgeBase*>::iterator i;
    for (i = _vbond.begin();i != _vbond.end();i++)
        if (nb == (*i)->GetBgn() || nb == (*i)->GetEnd())
            return(true);

    return(false);
}

void OBGraphBase::ResetVisitFlags()
{
    OBNodeBase *nb;
    vector<OBNodeBase*>::iterator i;
    for (nb = Begin(i);nb;nb = Next(i))
        nb->Visit = false;

    OBEdgeBase *eb;
    vector<OBEdgeBase*>::iterator j;
    for (eb = Begin(j);eb;eb = Next(j))
        eb->Visit = false;
}

bool OBGraphBase::SetVisitLock(bool v)
{
    if (v && _vlock)
        return(false);
    _vlock = v;
    return(true);
}

/*! \mainpage

  \section intro Introduction and History
 
It is fair to say that Open Babel is a direct result of the original Babel.
Application development is facilitated
by building software on top of libraries rich in functionality. Babel
was the first experience for Matt Stahl in designing a molecule
library. In addition to developing Babel, Pat Walters and Matt
developed `OBabel' at Vertex Pharmaceuticals, a first
attempt at developing an object oriented molecule library.
Matt later designed a new molecule class library, OELib -- designed
to be flexible, extensible, portable, and efficient.
 
OELib was released under the GNU General Public License (GPL) by Matt Stahl
and Open Eye Scientific Software, Inc. to take advantage of many of
the "great minds writing chemical software." Open Babel took up where
OELib and Babel left off, starting from the existing GPL version of
OELib, and has continued to evolve and improve into a separate
high-quality chemistry class library and tool. Open Babel is now a
separate project and library and has changed considerably from the OELib days.
 
Thanks to all who have helped with Babel, OBabel, OELib and Open Babel.
The list is long and growing.
 
  \section pointers Key Modules
 
The heart of Open Babel lies in the \link OpenBabel::OBMol OBMol\endlink, 
\link OpenBabel::OBAtom OBAtom\endlink, and 
\link OpenBabel::OBBond OBBond\endlink classes,
which handle operations on atoms, bonds and molecules. Newcomers should 
start with looking at the \link OpenBabel::OBMol OBMol\endlink class, 
designed to store the basic information
in a molecule and to perceive information about a molecule.

One of the key philosophies in the code is that transformations and
automatic perception of properties are performed in a <a href="http://en.wikipedia.org/wiki/Lazy_evaluation">"lazy"</a>
manner. That is, until you call for partial atomic charges, no
charges are calculated. This ensures faster transformations of
chemical data -- properties that are not needed for your code will
typically not be calculated. When such data is needed, appropriate
routines are called, and a "flag" is set (e.g., via OBMol::SetFlag
or OBAtom::SetFlag etc.) so that the code is only run once.

Arbitrary custom data and text descriptors can be stored in any atom,
bond, molecule, or residue using the \link OpenBabel::OBGenericData
OBGenericData\endlink or \link OpenBabel::OBPairData
OBPairData\endlink classes.

Conversion between various chemical file formats is accomplished through
the \link OpenBabel::OBConversion OBConversion\endlink and \link 
OpenBabel::OBFormat OBFormat\endlink classes, often through use of the \link 
OpenBabel::OBMoleculeFormat OBMoleculeFormat\endlink subclass which is designed
for easy read/write access to one or more \link OpenBabel::OBMol OBMol\endlink
objects. The philosophy of the file format codes is to parse as much
chemical information from a given file as possible (no data left
behind) and ideally any perception or transformations will occur when
writing to some other format later.

*/

} // namespace OpenBabel

//! \file base.cpp
//! \brief Implementation of base classes.
Revision:	741
Committed:	Wed Nov 16 19:42:11 2005 UTC (19 years, 5 months ago) by tim
File size:	8962 byte(s)
Log Message:	adding openbabel
#	User	Rev	Content
1	tim	741	/**********************************************************************
2			base.cpp - Base classes to build a graph
3
4			Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
5			Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
6
7			This file is part of the Open Babel project.
8			For more information, see <http://openbabel.sourceforge.net/>
9
10			This program is free software; you can redistribute it and/or modify
11			it under the terms of the GNU General Public License as published by
12			the Free Software Foundation version 2 of the License.
13
14			This program is distributed in the hope that it will be useful,
15			but WITHOUT ANY WARRANTY; without even the implied warranty of
16			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17			GNU General Public License for more details.
18			***********************************************************************/
19
20			#include "babelconfig.hpp"
21			#include "base.hpp"
22
23			#if HAVE_IOSTREAM
24			#include <iostream>
25			#elif HAVE_IOSTREAM_H
26			#include <iostream.h>
27			#endif
28
29			#if HAVE_FSTREAM
30			#include <fstream>
31			#elif HAVE_FSTREAM_H
32			#include <fstream.h>
33			#endif
34
35			using namespace std;
36
37			//! Global namespace for all Open Babel code
38			namespace OpenBabel
39			{
40			/*
41			bool OBGraphBase::Match(OBGraphBase &g,bool singleMatch)
42			{
43			SetFinishedMatch(false);
44			SetSingleMatch(singleMatch);
45			ClearMatches();
46			g.SetVisitLock(true);
47			g.ResetVisitFlags();
48
49			OBNodeBase *node;
50			OBNodeBase *seed = GetFirstSeed();
51			vector<OBNodeBase*>::iterator i;
52
53			for (node = g.Begin(i);node;node = g.Next(i))
54			if (!node->Visit && seed->Eval(node))
55			{
56			node->Visit = true;
57			seed->SetMatch(node);
58			Match(g,BgnMatch(),BgnMatch()->second.begin());
59			seed->SetMatch((OBNodeBase*)NULL);
60			node->Visit = false;
61			if (SingleMatch() && FinishedMatch())
62			break;
63			}
64
65			g.SetVisitLock(false);
66
67			return(FinishedMatch());
68			}
69
70			bool OBGraphBase::Match(OBGraphBase &g,
71			vector<pair<OBNodeBase,vector<OBEdgeBase> > >::iterator i,
72			vector<OBEdgeBase*>::iterator j)
73			{
74			//bail if only one match has been requested
75			if (SingleMatch() && FinishedMatch())
76			return(true);
77
78			//full match completed
79			if (i == EndMatch() \|\| (j == i->second.end() && (i+1) == EndMatch()))
80			{
81			SetFinishedMatch(true);
82			OBNodeBase *node;
83			vector<OBNodeBase*> vn;
84			vector<OBNodeBase*>::iterator i;
85			for (node = Begin(i);node;node = Next(i))
86			vn.push_back(node->GetMatch());
87			PushBack(vn);
88
89			return(true);
90			}
91
92			//handle next seed of disconnected pattern
93			if (j == i->second.end())
94			{
95			i++;
96			OBNodeBase *node;
97			OBNodeBase *seed = i->first;
98			vector<OBNodeBase*>::iterator k;
99			for (node = g.Begin(k);node;node = g.Next(k))
100			if (!node->Visit && seed->Eval(node))
101			{
102			node->Visit = true;
103			seed->SetMatch(node);
104			Match(g,i,i->second.begin());
105			seed->SetMatch((OBNodeBase*)NULL);
106			node->Visit = false;
107			if (SingleMatch() && FinishedMatch())
108			break;
109			}
110			return(true);
111			}
112
113			OBEdgeBase edge = j++;
114			if (edge->IsClosure()) //check to see if matched atoms are bonded
115			{
116			if (edge->GetBgn()->GetMatch()->IsConnected(edge->GetEnd()->GetMatch()))
117			Match(g,i,j);
118			}
119			else //bond hasn't been covered yet
120			{
121			OBNodeBase *nbr;
122			OBNodeBase *curr = edge->GetBgn();
123			OBNodeBase *next = edge->GetEnd();
124			OBNodeBase *match = curr->GetMatch();
125			vector<OBEdgeBase*>::iterator k;
126
127			for (nbr = match->BeginNbr(k);nbr;nbr = match->NextNbr(k))
128			if (!nbr->Visit && next->Eval(nbr) && edge->Eval(*k))
129			{
130			nbr->Visit = true;
131			next->SetMatch(nbr);
132			Match(g,i,j);
133			next->SetMatch(NULL);
134			nbr->Visit = false;
135			}
136			}
137
138			return(false);
139			}
140			*/
141			OBNodeBase OBGraphBase::Begin(vector<OBNodeBase>::iterator &i)
142			{
143			i = _vatom.begin();
144			return((i != _vatom.end()) ? *i : NULL);
145			}
146
147			OBNodeBase OBGraphBase::Next(vector<OBNodeBase>::iterator &i)
148			{
149			i++;
150			return((i != _vatom.end()) ? *i : NULL);
151			}
152
153			OBEdgeBase OBGraphBase::Begin(vector<OBEdgeBase>::iterator &i)
154			{
155			i = _vbond.begin();
156			return((i != _vbond.end()) ? *i : NULL);
157			}
158
159			OBEdgeBase OBGraphBase::Next(vector<OBEdgeBase>::iterator &i)
160			{
161			i++;
162			return((i != _vbond.end()) ? *i : NULL);
163			}
164
165			OBNodeBase OBNodeBase::BeginNbr(vector<OBEdgeBase>::iterator &i)
166			{
167			i = _vbond.begin();
168
169			if (i == _vbond.end())
170			return(NULL);
171			return((this == (i)->GetBgn()) ? (i)->GetEnd() : (*i)->GetBgn());
172			}
173
174			OBNodeBase OBNodeBase::NextNbr(vector<OBEdgeBase>::iterator &i)
175			{
176			i++;
177			if (i == _vbond.end())
178			return(NULL);
179			return((this == (i)->GetBgn()) ? (i)->GetEnd() : (*i)->GetBgn());
180			}
181
182			void OBNodeBase::SetParent(OBGraphBase *p)
183			{
184			_parent = p;
185			}
186
187			void OBEdgeBase::SetParent(OBGraphBase *p)
188			{
189			_parent = p;
190			}
191
192			bool OBNodeBase::IsConnected(OBNodeBase *nb)
193			{
194			vector<OBEdgeBase*>::iterator i;
195			for (i = _vbond.begin();i != _vbond.end();i++)
196			if (nb == (i)->GetBgn() \|\| nb == (i)->GetEnd())
197			return(true);
198
199			return(false);
200			}
201
202			void OBGraphBase::ResetVisitFlags()
203			{
204			OBNodeBase *nb;
205			vector<OBNodeBase*>::iterator i;
206			for (nb = Begin(i);nb;nb = Next(i))
207			nb->Visit = false;
208
209			OBEdgeBase *eb;
210			vector<OBEdgeBase*>::iterator j;
211			for (eb = Begin(j);eb;eb = Next(j))
212			eb->Visit = false;
213			}
214
215			bool OBGraphBase::SetVisitLock(bool v)
216			{
217			if (v && _vlock)
218			return(false);
219			_vlock = v;
220			return(true);
221			}
222
223			/*! \mainpage
224
225			\section intro Introduction and History
226
227			It is fair to say that Open Babel is a direct result of the original Babel.
228			Application development is facilitated
229			by building software on top of libraries rich in functionality. Babel
230			was the first experience for Matt Stahl in designing a molecule
231			library. In addition to developing Babel, Pat Walters and Matt
232			developed `OBabel' at Vertex Pharmaceuticals, a first
233			attempt at developing an object oriented molecule library.
234			Matt later designed a new molecule class library, OELib -- designed
235			to be flexible, extensible, portable, and efficient.
236
237			OELib was released under the GNU General Public License (GPL) by Matt Stahl
238			and Open Eye Scientific Software, Inc. to take advantage of many of
239			the "great minds writing chemical software." Open Babel took up where
240			OELib and Babel left off, starting from the existing GPL version of
241			OELib, and has continued to evolve and improve into a separate
242			high-quality chemistry class library and tool. Open Babel is now a
243			separate project and library and has changed considerably from the OELib days.
244
245			Thanks to all who have helped with Babel, OBabel, OELib and Open Babel.
246			The list is long and growing.
247
248			\section pointers Key Modules
249
250			The heart of Open Babel lies in the \link OpenBabel::OBMol OBMol\endlink,
251			\link OpenBabel::OBAtom OBAtom\endlink, and
252			\link OpenBabel::OBBond OBBond\endlink classes,
253			which handle operations on atoms, bonds and molecules. Newcomers should
254			start with looking at the \link OpenBabel::OBMol OBMol\endlink class,
255			designed to store the basic information
256			in a molecule and to perceive information about a molecule.
257
258			One of the key philosophies in the code is that transformations and
259			automatic perception of properties are performed in a <a href="http://en.wikipedia.org/wiki/Lazy_evaluation">"lazy"</a>
260			manner. That is, until you call for partial atomic charges, no
261			charges are calculated. This ensures faster transformations of
262			chemical data -- properties that are not needed for your code will
263			typically not be calculated. When such data is needed, appropriate
264			routines are called, and a "flag" is set (e.g., via OBMol::SetFlag
265			or OBAtom::SetFlag etc.) so that the code is only run once.
266
267			Arbitrary custom data and text descriptors can be stored in any atom,
268			bond, molecule, or residue using the \link OpenBabel::OBGenericData
269			OBGenericData\endlink or \link OpenBabel::OBPairData
270			OBPairData\endlink classes.
271
272			Conversion between various chemical file formats is accomplished through
273			the \link OpenBabel::OBConversion OBConversion\endlink and \link
274			OpenBabel::OBFormat OBFormat\endlink classes, often through use of the \link
275			OpenBabel::OBMoleculeFormat OBMoleculeFormat\endlink subclass which is designed
276			for easy read/write access to one or more \link OpenBabel::OBMol OBMol\endlink
277			objects. The philosophy of the file format codes is to parse as much
278			chemical information from a given file as possible (no data left
279			behind) and ideally any perception or transformations will occur when
280			writing to some other format later.
281
282			*/
283
284			} // namespace OpenBabel
285
286			//! \file base.cpp
287			//! \brief Implementation of base classes.