~ubuntu-branches/ubuntu/feisty/openbabel/feisty

Viewing changes to src/base.cpp

Committer: Bazaar Package Importer
Author(s): Michael Banck
Date: 2006-05-14 19:46:01 UTC
mfrom: (1.1.2 upstream)
Revision ID: james.westby@ubuntu.com-20060514194601-h3j1wovvc42cigxl

Tags: 2.0.1-1

http://bugs.debian.org/341628

* New upstream release. (Closes: #341628)
* debian/patches/04_zipstream_fix.diff: Removed, applied upstream.
* debian/rules (DEB_MAKE_CHECK_TARGET): Readded.

files added:
INSTALL.Windows

data

data/Makefile.am

data/Makefile.in

data/SMARTS_InteLigand.txt

data/aromatic.h

data/aromatic.txt

data/atomtyp.h

data/atomtyp.txt

data/bin2hex.pl

data/bondtyp.h

data/bondtyp.txt

data/element.h

data/element.txt

data/isotope-small.txt

data/isotope.h

data/isotope.txt

data/patterns.txt

data/phmodel.txt

data/phmodeldata.h

data/resdata.h

data/resdata.txt

data/torlib.h

data/torlib.txt

data/types.h

data/types.txt

debian/libopenbabel1.install

doc/Doxyfile-man

doc/OBTwoMigration.html

doc/babel.html

doc/obchiral.1

doc/obchiral.html

doc/obfit.1

doc/obfit.html

doc/obgrep.1

doc/obgrep.html

doc/obprop.1

doc/obprop.html

doc/obrotate.1

doc/obrotate.html

openbabel-2.0.pc.in

scripts

scripts/Makefile.am

scripts/Makefile.in

scripts/openbabel.i

scripts/perl

scripts/perl/COPYING

scripts/perl/Changes

scripts/perl/MANIFEST

scripts/perl/META.yml

scripts/perl/Makefile.PL

scripts/perl/OpenBabel.pm

scripts/perl/README

scripts/perl/examples

scripts/perl/examples/example.pl

scripts/perl/openbabel_perl.cpp

scripts/perl/t

scripts/perl/t/atom.t

scripts/perl/t/bond.t

scripts/perl/t/conversion.t

scripts/perl/t/data.t

scripts/perl/t/format.t

scripts/perl/t/internalcoord.t

scripts/perl/t/mol.t

scripts/perl/t/residue.t

scripts/python

scripts/python/Examples.html

scripts/python/MANIFEST

scripts/python/README

scripts/python/examples.py

scripts/python/openbabel.py

scripts/python/openbabel_python.cpp

scripts/python/setup.py

scripts/python/temp.mdl

src/bondtyper.cpp

src/config.h.in

src/dlhandler.h

src/dlhandler_unix.cpp

src/dlhandler_win32.cpp

src/fingerprint.cpp

src/fingerprint.h

src/fingerprints

src/fingerprints/Makefile.am

src/fingerprints/Makefile.in

src/fingerprints/finger2.cpp

src/fingerprints/finger3.cpp

src/formats

src/formats/APIInterface.cpp

src/formats/CSRformat.cpp

src/formats/Makefile.am

src/formats/Makefile.in

src/formats/PQSformat.cpp

src/formats/alchemyformat.cpp

src/formats/amberformat.cpp

src/formats/balstformat.cpp

src/formats/bgfformat.cpp

src/formats/boxformat.cpp

src/formats/cacaoformat.cpp

src/formats/cacheformat.cpp

src/formats/carformat.cpp

src/formats/cccformat.cpp

src/formats/chem3dformat.cpp

src/formats/chemdrawformat.cpp

src/formats/chemtoolformat.cpp

src/formats/copyformat.cpp

src/formats/crkformat.cpp

src/formats/cssrformat.cpp

src/formats/dmolformat.cpp

src/formats/exampleformat.cpp

src/formats/fastsearchformat.cpp

src/formats/featformat.cpp

src/formats/fhformat.cpp

src/formats/fingerprintformat.cpp

src/formats/freefracformat.cpp

src/formats/gamessformat.cpp

src/formats/gaussformat.cpp

src/formats/ghemicalformat.cpp

src/formats/gromos96format.cpp

src/formats/hinformat.cpp

src/formats/inchi

src/formats/inchi/COPYING.LIB

src/formats/inchi/IChICan2.c

src/formats/inchi/IChICano.c

src/formats/inchi/IChIPrt1.c

src/formats/inchi/IChIPrt2.c

src/formats/inchi/IChIPrt3.c

src/formats/inchi/IchiMak2.c

src/formats/inchi/IchiMake.c

src/formats/inchi/IchiNorm.c

src/formats/inchi/IchiParm.c

src/formats/inchi/IchiTaut.c

src/formats/inchi/Makefile.am

src/formats/inchi/Makefile.in

src/formats/inchi/README.html

src/formats/inchi/RunICHI.c

src/formats/inchi/aux2atom.h

src/formats/inchi/comdef.h

src/formats/inchi/extr_ct.h

src/formats/inchi/ichi.h

src/formats/inchi/ichi_bns.c

src/formats/inchi/ichi_bns.h

src/formats/inchi/ichicano.h

src/formats/inchi/ichicans.c

src/formats/inchi/ichicant.h

src/formats/inchi/ichicomn.h

src/formats/inchi/ichicomp.h

src/formats/inchi/ichidrp.h

src/formats/inchi/ichierr.h

src/formats/inchi/ichiisot.c

src/formats/inchi/ichilnct.c

src/formats/inchi/ichimain.h

src/formats/inchi/ichimake.h

src/formats/inchi/ichimap1.c

src/formats/inchi/ichimap2.c

src/formats/inchi/ichimap4.c

src/formats/inchi/ichinorm.h

src/formats/inchi/ichiparm.h

src/formats/inchi/ichiqueu.c

src/formats/inchi/ichiring.c

src/formats/inchi/ichiring.h

src/formats/inchi/ichisize.h

src/formats/inchi/ichisort.c

src/formats/inchi/ichister.c

src/formats/inchi/ichister.h

src/formats/inchi/ichitaut.h

src/formats/inchi/ichitime.h

src/formats/inchi/inchi_api.h

src/formats/inchi/inchi_dll.c

src/formats/inchi/inchi_dll.h

src/formats/inchi/inchi_dll_main.c

src/formats/inchi/inchi_dll_main.h

src/formats/inchi/inpdef.h

src/formats/inchi/lreadmol.h

src/formats/inchi/mode.h

src/formats/inchi/strutil.c

src/formats/inchi/strutil.h

src/formats/inchi/util.c

src/formats/inchi/util.h

src/formats/inchi_api.h

src/formats/inchiformat.cpp

src/formats/jaguarformat.cpp

src/formats/mdlformat.cpp

src/formats/mmodformat.cpp

src/formats/mol2format.cpp

src/formats/mopacformat.cpp

src/formats/mpdformat.cpp

src/formats/mpqcformat.cpp

src/formats/nwchemformat.cpp

src/formats/pcmodelformat.cpp

src/formats/pdbformat.cpp

src/formats/povrayformat.cpp

src/formats/qchemformat.cpp

src/formats/reportformat.cpp

src/formats/rxnformat.cpp

src/formats/shelxformat.cpp

src/formats/smilesformat.cpp

src/formats/tinkerformat.cpp

src/formats/turbomoleformat.cpp

src/formats/unichemformat.cpp

src/formats/viewmolformat.cpp

src/formats/xedformat.cpp

src/formats/xml

src/formats/xml/Makefile.am

src/formats/xml/Makefile.in

src/formats/xml/cmlreactlformat.cpp

src/formats/xml/pubchem.cpp

src/formats/xml/xcmlformat.cpp

src/formats/xml/xml.cpp

src/formats/xml/xml.h

src/formats/xml/xmlformat.cpp

src/formats/xyzformat.cpp

src/formats/yasaraformat.cpp

src/formats/zindoformat.cpp

src/kekulize.cpp

src/obconversion.cpp

src/obconversion.h

src/obiter.cpp

src/obiter.h

src/obmolecformat.h

src/reaction.h

src/rotamer.cpp

src/rotamer.h

src/transform.cpp

src/zipstream.h

src/zipstreamimpl.h

test/ringtest.sh

test/smartstest.sh

tools/obchiral.cpp

tools/obprop.cpp

windows

windows/ReadMe.txt

windows/VC6

windows/VC6/OBabel

windows/VC6/OBabel/OBabel.dsp

windows/VC6/OpenBabel.dsw

windows/VC6/babelconfig.h

windows/VC8

windows/VC8/OBabel

windows/VC8/OBabel/OBabel.vcproj

windows/VC8/OpenBabel.sln

windows/VC8/OpenBabelGUI

windows/VC8/OpenBabelGUI/OBGUI.cpp

windows/VC8/OpenBabelGUI/OBGUI.h

windows/VC8/OpenBabelGUI/OBGUI.rc

windows/VC8/OpenBabelGUI/OpenBabelGUI.html

windows/VC8/OpenBabelGUI/OpenBabelGUI.sln

windows/VC8/OpenBabelGUI/OpenBabelGUI.vcproj

windows/VC8/OpenBabelGUI/babel.xpm

windows/VC8/OpenBabelGUI/babel2.ico

windows/VC8/OpenBabelGUI/optswx.cpp

windows/VC8/OpenBabelGUI/optswx.h

windows/VC8/OpenBabelGUI/selformats.h

windows/VC8/OpenBabelGUI/stdwx.cpp

windows/VC8/OpenBabelGUI/stdwx.h

windows/VC8/babelconfig.h

windows/iconv.h

windows/libinchi.dll

windows/libinchi.lib

windows/libxml

windows/libxml/DOCBparser.h

windows/libxml/HTMLparser.h

windows/libxml/HTMLtree.h

windows/libxml/OpenBabel.suo

windows/libxml/SAX.h

windows/libxml/SAX2.h

windows/libxml/c14n.h

windows/libxml/catalog.h

windows/libxml/chvalid.h

windows/libxml/debugXML.h

windows/libxml/dict.h

windows/libxml/encoding.h

windows/libxml/entities.h

windows/libxml/globals.h

windows/libxml/hash.h

windows/libxml/list.h

windows/libxml/nanoftp.h

windows/libxml/nanohttp.h

windows/libxml/parser.h

windows/libxml/parserInternals.h

windows/libxml/pattern.h

windows/libxml/relaxng.h

windows/libxml/schemasInternals.h

windows/libxml/threads.h

windows/libxml/tree.h

windows/libxml/uri.h

windows/libxml/valid.h

windows/libxml/xinclude.h

windows/libxml/xlink.h

windows/libxml/xmlIO.h

windows/libxml/xmlautomata.h

windows/libxml/xmlerror.h

windows/libxml/xmlexports.h

windows/libxml/xmlmemory.h

windows/libxml/xmlmodule.h

windows/libxml/xmlreader.h

windows/libxml/xmlregexp.h

windows/libxml/xmlsave.h

windows/libxml/xmlschemas.h

windows/libxml/xmlschemastypes.h

windows/libxml/xmlstring.h

windows/libxml/xmlunicode.h

windows/libxml/xmlversion.h

windows/libxml/xmlwin32version.h

windows/libxml/xmlwriter.h

windows/libxml/xpath.h

windows/libxml/xpathInternals.h

windows/libxml/xpointer.h

windows/libxml2.lib

windows/zconf.h

windows/zdll.lib

windows/zlib.h

windows/zlib1.dll

files removed:
bc32.mak

debian/libopenbabel0c2a.install

debian/patches

debian/patches-old

debian/patches-old/01_strstream_h_fix.patch

debian/patches-old/02_math_headers.patch

debian/patches/03_unitcell_test.patch

doc/Migration.html

openbabel.pc.in

src/README

src/alchemy.cpp

src/amber.cpp

src/aromatic.h

src/aromatic.txt

src/atomtyp.h

src/atomtyp.txt

src/babelconfig.h

src/babelconfig.h.in

src/balst.cpp

src/bc32.mak

src/bgf.cpp

src/bin2hex.pl

src/binary.cpp

src/binary.h

src/bondtyp.h

src/bondtyp.txt

src/borland.bat

src/box.cpp

src/c3d.cpp

src/cacao.cpp

src/cache.cpp

src/car.cpp

src/ccc.cpp

src/chdrw.cpp

src/chemtool.cpp

src/cml.cpp

src/crk.cpp

src/crk.h

src/csr.cpp

src/cssr.cpp

src/dmol.cpp

src/element.h

src/element.txt

src/extable.h

src/extable.txt

src/feat.cpp

src/fh.cpp

src/fileformat.cpp

src/fileformat.h

src/gamess.cpp

src/gaussian.cpp

src/ghemical.cpp

src/gromos96.cpp

src/hin.cpp

src/isotope-small.txt

src/isotope.h

src/isotope.txt

src/jaguar.cpp

src/mdl.cpp

src/mm3.cpp

src/mmod.cpp

src/mol2.cpp

src/molvector.cpp

src/molvector.h

src/mopac.cpp

src/mpqc.cpp

src/nwchem.cpp

src/obifstream.h

src/oblib.dsp

src/oblib.dsw

src/parsmi.cpp

src/pdb.cpp

src/phmodel.txt

src/phmodeldata.h

src/povray.cpp

src/pqs.cpp

src/qchem.cpp

src/report.cpp

src/resdata.h

src/resdata.txt

src/shelx.cpp

src/smi.cpp

src/smi.h

src/tinker.cpp

src/types.h

src/types.txt

src/unichem.cpp

src/viewmol.cpp

src/windows

src/windows/Makefile.am

src/windows/Makefile.in

src/windows/winbabeldialog.aps

src/windows/winbabeldialog.clw

src/windows/winbabeldialog.cpp

src/windows/winbabeldialog.dsp

src/windows/winbabeldialog.dsw

src/windows/winbabeldialog.h

src/windows/winbabeldialog.ncb

src/windows/winbabeldialog.opt

src/windows/winbabeldialog.rc

src/windows/winbabeldialogDlg.cpp

src/windows/winbabeldialogDlg.h

src/xed.cpp

src/xyz.cpp

src/zindo.cpp

files modified:
AUTHORS

COPYING

ChangeLog

Doxyfile

Makefile.am

Makefile.in

NEWS

README

THANKS

acinclude.m4

aclocal.m4

config.guess

config.sub

configure

configure.in

debian/changelog

debian/control

debian/libopenbabel-dev.install

debian/openbabel.docs

debian/rules

depcomp

doc/FAQ.html

doc/Makefile.am

doc/Makefile.in

doc/babel.1

install-sh

ltmain.sh

missing

mkinstalldirs

src/Makefile.am

src/Makefile.in

src/atom.cpp

src/base.cpp

src/base.h

src/bitvec.cpp

src/bitvec.h

src/bond.cpp

src/bondtyper.h

src/chains.cpp

src/chains.h

src/chiral.cpp

src/chiral.h

src/data.cpp

src/data.h

src/generic.cpp

src/generic.h

src/grid.cpp

src/grid.h

src/main.cpp

src/math/Makefile.am

src/math/Makefile.in

src/math/matrix3x3.cpp

src/math/matrix3x3.h

src/math/vector3.cpp

src/math/vector3.h

src/matrix.cpp

src/matrix.h

src/mol.cpp

src/mol.h

src/molchrg.cpp

src/molchrg.h

src/oberror.cpp

src/oberror.h

src/obutil.cpp

src/obutil.h

src/parsmart.cpp

src/parsmart.h

src/patty.cpp

src/patty.h

src/phmodel.cpp

src/phmodel.h

src/rand.cpp

src/residue.cpp

src/ring.cpp

src/ring.h

src/rotor.cpp

src/rotor.h

src/snprintf.c

src/snprintf.h

src/strncasecmp.c

src/tokenst.cpp

src/typer.cpp

src/typer.h

test/Makefile.am

test/Makefile.in

test/attype.00.smi

test/cmltest/Makefile.in

test/cmltest/nsc2dcml.xml *

test/cmltest/nsc2dmol.mol *

test/cmltest/nsc3dcml.xml *

test/cmltest/nsc3dmol.mol *

test/cmltest/readme.txt *

test/cmltest/test.sh *

test/main.cpp

test/matrixtest.cpp

test/ringtest.cpp

test/roundtrip.cpp

test/smartsresults.txt

test/smartstest.cpp

test/unitcell.cpp

test/unitcell.txt

tools/Makefile.am

tools/Makefile.in

tools/README

tools/obfit.cpp

tools/obgrep.cpp

tools/obrotate.cpp

Show diffs side-by-side

added added

removed removed

src/base.cpp

/**********************************************************************

base.cpp - Base classes to build a graph

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

***********************************************************************/

#include "babelconfig.h"

#include "base.h"

#if HAVE_IOSTREAM

using namespace std;

namespace OpenBabel {

//! 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());

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)

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;

100

seed->SetMatch(node);

101

Match(g,i,i->second.begin());

102

seed->SetMatch((OBNodeBase*)NULL);

103

node->Visit = false;

104

if (SingleMatch() && FinishedMatch()) break;

105

}

106

return(true);

107

}

108

109

OBEdgeBase *edge = *j++;

110

if (edge->IsClosure()) //check to see if matched atoms are bonded

111

{

112

if (edge->GetBgn()->GetMatch()->IsConnected(edge->GetEnd()->GetMatch()))

113

Match(g,i,j);

114

}

115

else //bond hasn't been covered yet

116

{

117

OBNodeBase *nbr;

118

OBNodeBase *curr = edge->GetBgn();

119

OBNodeBase *next = edge->GetEnd();

120

OBNodeBase *match = curr->GetMatch();

121

vector<OBEdgeBase*>::iterator k;

122

123

for (nbr = match->BeginNbr(k);nbr;nbr = match->NextNbr(k))

124

if (!nbr->Visit && next->Eval(nbr) && edge->Eval(*k))

125

{

126

nbr->Visit = true;

127

next->SetMatch(nbr);

128

Match(g,i,j);

129

next->SetMatch(NULL);

130

nbr->Visit = false;

131

}

132

}

133

134

return(false);

//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))

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);

135

139

}

136

140

137

141

OBNodeBase *OBGraphBase::Begin(vector<OBNodeBase*>::iterator &i)

138

142

{

139

i = _vatom.begin();

140

return((i != _vatom.end()) ? *i : NULL);

143

i = _vatom.begin();

144

return((i != _vatom.end()) ? *i : NULL);

141

145

}

142

146

143

147

OBNodeBase *OBGraphBase::Next(vector<OBNodeBase*>::iterator &i)

144

148

{

145

i++;

146

return((i != _vatom.end()) ? *i : NULL);

149

i++;

150

return((i != _vatom.end()) ? *i : NULL);

147

151

}

148

152

149

OBEdgeBase *OBGraphBase::Begin(vector<OBEdgeBase*>::iterator &i)

153

OBEdgeBase *OBGraphBase::Begin(vector<OBEdgeBase*>::iterator &i)

150

154

{

151

i = _vbond.begin();

152

return((i != _vbond.end()) ? *i : NULL);

155

i = _vbond.begin();

156

return((i != _vbond.end()) ? *i : NULL);

153

157

}

154

158

155

159

OBEdgeBase *OBGraphBase::Next(vector<OBEdgeBase*>::iterator &i)

156

160

{

157

i++;

158

return((i != _vbond.end()) ? *i : NULL);

161

i++;

162

return((i != _vbond.end()) ? *i : NULL);

159

163

}

160

164

161

165

OBNodeBase *OBNodeBase::BeginNbr(vector<OBEdgeBase*>::iterator &i)

162

166

{

163

i = _vbond.begin();

167

i = _vbond.begin();

164

168

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if (i == _vbond.end()) return(NULL);

166

return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());

169

if (i == _vbond.end())

170

return(NULL);

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return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());

167

172

}

168

173

169

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OBNodeBase *OBNodeBase::NextNbr(vector<OBEdgeBase*>::iterator &i)

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{

171

i++;

172

if (i == _vbond.end()) return(NULL);

173

return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());

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i++;

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if (i == _vbond.end())

178

return(NULL);

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return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());

174

180

}

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181

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void OBNodeBase::SetParent(OBGraphBase *p)

177

183

{

178

_parent = p;

184

_parent = p;

179

185

}

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void OBEdgeBase::SetParent(OBGraphBase *p)

182

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{

183

_parent = p;

189

_parent = p;

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190

}

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bool OBNodeBase::IsConnected(OBNodeBase *nb)

187

193

{

188

vector<OBEdgeBase*>::iterator i;

189

for (i = _vbond.begin();i != _vbond.end();i++)

190

if (nb == (*i)->GetBgn() || nb == (*i)->GetEnd())

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return(true);

194

vector<OBEdgeBase*>::iterator i;

195

for (i = _vbond.begin();i != _vbond.end();i++)

196

if (nb == (*i)->GetBgn() || nb == (*i)->GetEnd())

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return(true);

192

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return(false);

199

return(false);

194

200

}

195

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void OBGraphBase::ResetVisitFlags()

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{

198

OBNodeBase *nb;

199

vector<OBNodeBase*>::iterator i;

200

for (nb = Begin(i);nb;nb = Next(i)) nb->Visit = false;

204

OBNodeBase *nb;

205

vector<OBNodeBase*>::iterator i;

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for (nb = Begin(i);nb;nb = Next(i))

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nb->Visit = false;

201

208

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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)) eb->Visit = false;

209

OBEdgeBase *eb;

210

vector<OBEdgeBase*>::iterator j;

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for (eb = Begin(j);eb;eb = Next(j))

212

eb->Visit = false;

205

213

}

206

214

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bool OBGraphBase::SetVisitLock(bool v)

208

216

{

209

if (v && _vlock) return(false);

210

_vlock = v;

211

return(true);

217

if (v && _vlock)

218

return(false);

219

_vlock = v;

220

return(true);

212

221

}

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/*! \mainpage

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\section intro Introduction

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(portions adapted from the OELib primer, written by Matt Stahl, Open

218

Eye Scientific Software, Inc.)

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220

It is fair to say that Open Babel (and before it, OELib) is a direct

221

result of the original Babel. Programmers have long known that

222

application development is facilitated by building software on top of

223

libraries rich in functionality. Babel was the first experience for

224

Matt Stahl in designing a molecule library. In addition to developing

225

Babel, Pat Walters and Matt developed `OBabel' at Vertex

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Pharmaceuticals. OBabel was the first attempt at developing an

227

object oriented molecule library. Although OBabel was a successful

228

project, Matt's departure from Vertex Pharmaceuticals provided a great

229

opportunity to include much of what I had learned in previous projects

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into a new molecule class library. OELib was then designed to be flexible,

231

extensible, portable, and efficient class library for processing small

232

molecules.

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224

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\section intro Introduction and History

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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

234

237

OELib was released under the GNU General Public License (GPL) by Matt Stahl

235

238

and Open Eye Scientific Software, Inc. to take advantage of many of

236

the "great minds writing chemical software." Eventually Open Eye

237

decided to write a next-generation class library as proprietary

238

software. The result was that Open Babel took up where OELib left off,

239

using the existing GPL version of OELib, and has continued to evolve

240

and improve.

241

242

There are several advantages to having the source code to Open Babel

243

available. First, development time can be shortened by basing projects

244

on Open Babel. Many chemical and molecular concepts and code are

245

already implemented. The fewer people who have to reinvent the wheel

246

(or the function), the better. Second, as free software, hopefully

247

other programmers will contribute to the project.

248

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

249

245

Thanks to all who have helped with Babel, OBabel, OELib and Open Babel.

250

246

The list is long and growing.

251

247

252

248

\section pointers Key Modules

253

249

254

250

The heart of Open Babel lies in the \link OpenBabel::OBMol OBMol\endlink,

255

251

\link OpenBabel::OBAtom OBAtom\endlink, and

256

252

\link OpenBabel::OBBond OBBond\endlink classes,

259

255

designed to store the basic information

260

256

in a molecule and to perceive information about a molecule.

261

257

262

263

transformations and automatic perception of properties is performed in a

264

"lazy" manner. That is, until you call for partial atomic charges, no

265

charges are calculated. This ensures faster transformations of chemical data

266

calculated.

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.

267

281

268

282

269

283

270

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} // namespace OpenBabel

271

285

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//! \file base.cpp

287

//! \brief Implementation of base classes.

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