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

Viewing changes to src/bond.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/bond.cpp

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

bond.cpp - Handle OBBond class

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

using namespace std;

namespace OpenBabel {

namespace OpenBabel

{

extern OBAromaticTyper aromtyper;

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

OBBond::OBBond()

{

_idx=0;

_order=0;

_flags=0;

_bgn=NULL;

_end=NULL;

_vdata.clear();

}

{

_idx=0;

_order=0;

_flags=0;

_bgn=NULL;

_end=NULL;

_vdata.clear();

}

OBBond::~OBBond()

{

if (!_vdata.empty())

{

vector<OBGenericData*>::iterator m;

for (m = _vdata.begin();m != _vdata.end();m++) delete *m;

_vdata.clear();

vector<OBGenericData*>::iterator m;

for (m = _vdata.begin();m != _vdata.end();m++)

delete *m;

_vdata.clear();

}

void OBBond::Set(int idx,OBAtom *begin,OBAtom *end,int order,int flags)

{

SetIdx(idx);

SetBegin(begin);

SetEnd(end);

SetBO(order);

SetFlag(flags);

SetIdx(idx);

SetBegin(begin);

SetEnd(end);

SetBO(order);

SetFlag(flags);

}

void OBBond::SetBO(int order)

{

_order = (char)order;

if (order == 5)

_order = (char)order;

if (order == 5)

{

SetAromatic();

if (_bgn) _bgn->SetAromatic();

if (_end) _end->SetAromatic();

SetAromatic();

if (_bgn)

_bgn->SetAromatic();

if (_end)

_end->SetAromatic();

}

else UnsetAromatic();

else

{

if (order == 1)

SetKSingle();

else if (order == 2)

SetKDouble();

else if (order == 3)

SetKTriple();

UnsetAromatic();

}

void OBBond::SetLength(OBAtom *fixed, double length)

{

unsigned int i;

OBMol *mol = (OBMol*)fixed->GetParent();

vector3 v1,v2,v3,v4,v5;

vector<int> children;

int a = fixed->GetIdx();

int b = GetNbrAtom(fixed)->GetIdx();

mol->FindChildren(children,a,b);

children.push_back(b);

v1 = GetNbrAtom(fixed)->GetVector();

v2 = fixed->GetVector();

v3 = v1 - v2;

100

v3.normalize();

101

v3 *= length;

102

v3 += v2;

103

v4 = v3 - v1;

104

105

for ( i = 0 ; i < children.size() ; i++ )

100

unsigned int i;

101

OBMol *mol = (OBMol*)fixed->GetParent();

102

vector3 v1,v2,v3,v4,v5;

103

vector<int> children;

104

105

obErrorLog.ThrowError(__FUNCTION__,

106

"Ran OpenBabel::SetBondLength", obAuditMsg);

107

108

int a = fixed->GetIdx();

109

int b = GetNbrAtom(fixed)->GetIdx();

110

111

mol->FindChildren(children,a,b);

112

children.push_back(b);

113

114

v1 = GetNbrAtom(fixed)->GetVector();

115

v2 = fixed->GetVector();

116

v3 = v1 - v2;

117

v3.normalize();

118

v3 *= length;

119

v3 += v2;

120

v4 = v3 - v1;

121

122

for ( i = 0 ; i < children.size() ; i++ )

106

123

{

107

v1 = mol->GetAtom(children[i])->GetVector();

108

v1 += v4;

109

mol->GetAtom(children[i])->SetVector(v1);

110

111

idx = (children[i]-1) * 3;

112

c[idx] += x;

113

c[idx+1] += y;

114

c[idx+2] += z;

115

124

v1 = mol->GetAtom(children[i])->GetVector();

125

v1 += v4;

126

mol->GetAtom(children[i])->SetVector(v1);

127

128

idx = (children[i]-1) * 3;

129

c[idx] += x;

130

c[idx+1] += y;

131

c[idx+2] += z;

132

116

133

}

117

134

}

118

135

119

136

bool OBBond::IsRotor()

120

137

{

121

return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 &&

122

_order == 1 && !IsInRing() && _bgn->GetHyb() != 1 &&

123

_end->GetHyb() != 1);

138

return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 &&

139

_order == 1 && !IsInRing() && _bgn->GetHyb() != 1 &&

140

_end->GetHyb() != 1);

124

141

}

125

142

126

143

bool OBBond::IsAmide()

127

144

{

128

OBAtom *a1,*a2;

129

a1 = a2 = NULL;

130

131

if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)

132

{a1 = (OBAtom*)_bgn; a2 = (OBAtom*)_end;}

133

134

if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)

135

{a1 = (OBAtom*)_end; a2 = (OBAtom*)_bgn;}

136

137

if (!a1 || !a2) return(false);

138

if (GetBO() != 1) return(false);

139

140

OBBond *bond;

141

vector<OBEdgeBase*>::iterator i;

142

for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

143

if (bond->IsCarbonyl())

144

return(true);

145

146

return(false);

145

OBAtom *a1,*a2;

146

a1 = a2 = NULL;

147

148

if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)

149

{

150

a1 = (OBAtom*)_bgn;

151

a2 = (OBAtom*)_end;

152

}

153

154

if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)

155

{

156

a1 = (OBAtom*)_end;

157

a2 = (OBAtom*)_bgn;

158

}

159

160

if (!a1 || !a2)

161

return(false);

162

if (GetBO() != 1)

163

return(false);

164

165

OBBond *bond;

166

vector<OBEdgeBase*>::iterator i;

167

for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

168

if (bond->IsCarbonyl())

169

return(true);

170

171

return(false);

147

172

}

148

173

149

174

bool OBBond::IsPrimaryAmide()

150

175

{

151

OBAtom *a1,*a2;

152

a1 = a2 = NULL;

153

154

if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)

155

{a1 = (OBAtom*)_bgn; a2 = (OBAtom*)_end;}

156

157

if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)

158

{a1 = (OBAtom*)_end; a2 = (OBAtom*)_bgn;}

159

160

if (!a1 || !a2) return(false);

161

if (GetBO() != 1) return(false);

162

163

OBBond *bond;

164

vector<OBEdgeBase*>::iterator i;

165

for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

166

if (bond->IsCarbonyl())

167

if (a2->GetHvyValence() == 2)

168

return(true);

169

170

171

return(false);

176

OBAtom *a1,*a2;

177

a1 = a2 = NULL;

178

179

if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)

180

{

181

a1 = (OBAtom*)_bgn;

182

a2 = (OBAtom*)_end;

183

}

184

185

if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)

186

{

187

a1 = (OBAtom*)_end;

188

a2 = (OBAtom*)_bgn;

189

}

190

191

if (!a1 || !a2)

192

return(false);

193

if (GetBO() != 1)

194

return(false);

195

196

OBBond *bond;

197

vector<OBEdgeBase*>::iterator i;

198

for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

199

if (bond->IsCarbonyl())

200

if (a2->GetHvyValence() == 2)

201

return(true);

202

203

return(false);

172

204

}

173

205

206

//! \todo Implement this properly -- currently always returns false

174

207

bool OBBond::IsSecondaryAmide()

175

208

{

176

177

178

return(false);

209

return(false);

179

210

}

180

211

181

212

bool OBBond::IsEster()

182

213

{

183

OBAtom *a1,*a2;

184

a1 = a2 = NULL;

185

186

if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8)

187

{a1 = (OBAtom*)_bgn; a2 = (OBAtom*)_end;}

188

189

if (_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6)

190

{a1 = (OBAtom*)_end; a2 = (OBAtom*)_bgn;}

191

192

if (!a1 || !a2) return(false);

193

if (GetBO() != 1) return(false);

194

195

OBBond *bond;

196

vector<OBEdgeBase*>::iterator i;

197

for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

198

if (bond->IsCarbonyl())

199

return(true);

200

201

202

return(false);

214

OBAtom *a1,*a2;

215

a1 = a2 = NULL;

216

217

if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8)

218

{

219

a1 = (OBAtom*)_bgn;

220

a2 = (OBAtom*)_end;

221

}

222

223

if (_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6)

224

{

225

a1 = (OBAtom*)_end;

226

a2 = (OBAtom*)_bgn;

227

}

228

229

if (!a1 || !a2)

230

return(false);

231

if (GetBO() != 1)

232

return(false);

233

234

OBBond *bond;

235

vector<OBEdgeBase*>::iterator i;

236

for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

237

if (bond->IsCarbonyl())

238

return(true);

239

240

return(false);

203

241

}

204

242

205

243

bool OBBond::IsCarbonyl()

206

244

{

207

if (GetBO() != 2) return(false);

208

209

if ((_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8) ||

210

(_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6))

211

return(true);

212

213

return(false);

245

if (GetBO() != 2)

246

return(false);

247

248

if ((_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8) ||

249

(_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6))

250

return(true);

251

252

return(false);

214

253

}

215

254

216

255

bool OBBond::IsSingle()

217

256

{

218

if (HasFlag(OB_AROMATIC_BOND)) return(false);

219

220

if (!((OBMol*)GetParent())->HasAromaticPerceived())

221

{

222

aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));

223

}

224

225

if ((this->GetBondOrder()==1) && !(HasFlag(OB_AROMATIC_BOND)))

226

return(true);

227

228

return(false);

257

if (HasFlag(OB_AROMATIC_BOND))

258

return(false);

259

260

if (!((OBMol*)GetParent())->HasAromaticPerceived())

261

{

262

aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));

263

}

264

265

if ((this->GetBondOrder()==1) && !(HasFlag(OB_AROMATIC_BOND)))

266

return(true);

267

268

return(false);

229

269

}

230

270

231

271

bool OBBond::IsDouble()

232

272

{

233

if (HasFlag(OB_AROMATIC_BOND)) return(false);

234

235

if (!((OBMol*)GetParent())->HasAromaticPerceived())

236

{

237

aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));

238

}

239

240

if ((this->GetBondOrder()==2) && !(HasFlag(OB_AROMATIC_BOND)))

241

return(true);

242

243

return(false);

273

if (HasFlag(OB_AROMATIC_BOND))

274

return(false);

275

276

if (!((OBMol*)GetParent())->HasAromaticPerceived())

277

{

278

aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));

279

}

280

281

if ((this->GetBondOrder()==2) && !(HasFlag(OB_AROMATIC_BOND)))

282

return(true);

283

284

return(false);

244

285

}

245

286

246

287

bool OBBond::IsTriple()

247

288

{

248

if (HasFlag(OB_AROMATIC_BOND)) return(false);

249

250

if (!((OBMol*)GetParent())->HasAromaticPerceived())

251

{

252

aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));

253

}

254

255

if ((this->GetBondOrder()==3) && !(HasFlag(OB_AROMATIC_BOND)))

256

return(true);

257

258

return(false);

289

if (HasFlag(OB_AROMATIC_BOND))

290

return(false);

291

292

if (!((OBMol*)GetParent())->HasAromaticPerceived())

293

{

294

aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));

295

}

296

297

if ((this->GetBondOrder()==3) && !(HasFlag(OB_AROMATIC_BOND)))

298

return(true);

299

300

return(false);

259

301

}

260

302

261

303

bool OBBond::IsAromatic() const

262

304

{

263

if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND)) return(true);

305

if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND))

306

return(true);

264

307

265

OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();

266

if (!mol->HasAromaticPerceived())

308

OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();

309

if (!mol->HasAromaticPerceived())

267

310

{

268

aromtyper.AssignAromaticFlags(*mol);

269

if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND)) return(true);

311

aromtyper.AssignAromaticFlags(*mol);

312

if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND))

313

return(true);

270

314

}

271

315

272

return(false);

316

return(false);

317

}

318

319

/*! This method checks if the geometry around this bond looks unsaturated

320

by measuring the torsion angles formed by all connected atoms X-start=end-Y

321

and checking that they are close to 0 or 180 degrees */

322

bool OBBond::IsDoubleBondGeometry()

323

{

324

double torsion;

325

OBAtom *nbrStart,*nbrEnd;

326

vector<OBEdgeBase*>::iterator i,j;

327

// We concentrate on sp2 atoms with valence up to 3 and ignore the rest (like sp1 or S,P)

328

// As this is called from PerceiveBondOrders, GetHyb() may still be undefined.

329

if (_bgn->GetHyb()==1 || _bgn->GetValence()>3||

330

_end->GetHyb()==1 || _end->GetValence()>3)

331

return(true);

332

333

for (nbrStart = static_cast<OBAtom*>(_bgn)->BeginNbrAtom(i); nbrStart;

334

nbrStart = static_cast<OBAtom*>(_bgn)->NextNbrAtom(i))

335

{

336

if (nbrStart != _end)

337

{

338

for (nbrEnd = static_cast<OBAtom*>(_end)->BeginNbrAtom(j);

339

nbrEnd; nbrEnd = static_cast<OBAtom*>(_end)->NextNbrAtom(j))

340

{

341

if (nbrEnd != _bgn)

342

{

343

torsion=fabs(CalcTorsionAngle(nbrStart->GetVector(),

344

static_cast<OBAtom*>(_bgn)->GetVector(),

345

static_cast<OBAtom*>(_end)->GetVector(),

346

nbrEnd->GetVector()));

347

348

// >12&&<168 not enough

349

if (torsion > 15.0f && torsion < 165.0f)

350

{

351

// Geometry does not match a double bond

352

return(false);

353

}

354

355

}

356

} // end loop for neighbors of end

357

}

358

} // end loop for neighbors of start

359

return(true);

273

360

}

274

361

275

362

void OBBond::SetKSingle()

276

363

{

277

_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));

278

_flags |= OB_KSINGLE_BOND;

364

_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));

365

_flags |= OB_KSINGLE_BOND;

279

366

}

280

367

281

368

void OBBond::SetKDouble()

282

369

{

283

_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));

284

_flags |= OB_KDOUBLE_BOND;

370

_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));

371

_flags |= OB_KDOUBLE_BOND;

285

372

}

286

373

287

374

void OBBond::SetKTriple()

288

375

{

289

_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));

290

_flags |= OB_KTRIPLE_BOND;

376

_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));

377

_flags |= OB_KTRIPLE_BOND;

291

378

}

292

379

293

380

bool OBBond::IsKSingle()

294

381

{

295

if (_flags & OB_KSINGLE_BOND) return(true);

296

if (!((OBMol*)GetParent())->HasKekulePerceived())

297

((OBMol*)GetParent())->PerceiveKekuleBonds();

382

if (_flags & OB_KSINGLE_BOND)

383

return(true);

384

if (!((OBMol*)GetParent())->HasKekulePerceived())

385

((OBMol*)GetParent())->NewPerceiveKekuleBonds();

298

386

299

return((_flags & OB_KSINGLE_BOND) != 0) ? true : false;

387

return((_flags & OB_KSINGLE_BOND) != 0) ? true : false;

300

388

}

301

389

302

390

bool OBBond::IsKDouble()

303

391

{

304

if (_flags & OB_KDOUBLE_BOND) return(true);

305

if (!((OBMol*)GetParent())->HasKekulePerceived())

306

((OBMol*)GetParent())->PerceiveKekuleBonds();

392

if (_flags & OB_KDOUBLE_BOND)

393

return(true);

394

if (!((OBMol*)GetParent())->HasKekulePerceived())

395

((OBMol*)GetParent())->NewPerceiveKekuleBonds();

307

396

308

return((_flags & OB_KDOUBLE_BOND) != 0) ? true : false;

397

return((_flags & OB_KDOUBLE_BOND) != 0) ? true : false;

309

398

}

310

399

311

400

bool OBBond::IsKTriple()

312

401

{

313

if (_flags & OB_KTRIPLE_BOND) return(true);

314

if (!((OBMol*)GetParent())->HasKekulePerceived())

315

((OBMol*)GetParent())->PerceiveKekuleBonds();

402

if (_flags & OB_KTRIPLE_BOND)

403

return(true);

404

if (!((OBMol*)GetParent())->HasKekulePerceived())

405

((OBMol*)GetParent())->NewPerceiveKekuleBonds();

316

406

317

return((_flags & OB_KTRIPLE_BOND) != 0) ? true : false;

407

return((_flags & OB_KTRIPLE_BOND) != 0) ? true : false;

318

408

}

319

409

320

410

bool OBBond::IsInRing() const

321

411

{

322

if (((OBBond*)this)->HasFlag(OB_RING_BOND)) return(true);

323

324

OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();

325

if (!mol->HasRingAtomsAndBondsPerceived())

412

if (((OBBond*)this)->HasFlag(OB_RING_BOND))

413

return(true);

414

415

OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();

416

if (!mol->HasRingAtomsAndBondsPerceived())

326

417

{

327

mol->FindRingAtomsAndBonds();

328

if (((OBBond*)this)->HasFlag(OB_RING_BOND)) return(true);

418

mol->FindRingAtomsAndBonds();

419

if (((OBBond*)this)->HasFlag(OB_RING_BOND))

420

return(true);

329

421

}

330

422

331

return(false);

423

return(false);

332

424

}

333

425

334

426

bool OBBond::IsClosure()

335

427

{

336

OBMol *mol = (OBMol*)GetParent();

337

if (!mol) return(false);

338

if (mol->HasClosureBondsPerceived()) return(HasFlag(OB_CLOSURE_BOND));

339

340

mol->SetClosureBondsPerceived();

341

342

OBBond *bond;

343

OBAtom *atom,*nbr;

344

OBBitVec uatoms,ubonds;

345

vector<OBNodeBase*> curr,next;

346

vector<OBNodeBase*>::iterator i;

347

vector<OBEdgeBase*>::iterator j;

348

349

uatoms.Resize(mol->NumAtoms()+1);

350

ubonds.Resize(mol->NumAtoms()+1);

351

352

for (;uatoms.CountBits() < (signed)mol->NumAtoms();)

428

OBMol *mol = (OBMol*)GetParent();

429

if (!mol)

430

return(false);

431

if (mol->HasClosureBondsPerceived())

432

return(HasFlag(OB_CLOSURE_BOND));

433

434

mol->SetClosureBondsPerceived();

435

436

obErrorLog.ThrowError(__FUNCTION__,

437

"Ran OpenBabel::PerceiveClosureBonds", obAuditMsg);

438

439

OBBond *bond;

440

OBAtom *atom,*nbr;

441

OBBitVec uatoms,ubonds;

442

vector<OBNodeBase*> curr,next;

443

vector<OBNodeBase*>::iterator i;

444

vector<OBEdgeBase*>::iterator j;

445

446

uatoms.Resize(mol->NumAtoms()+1);

447

ubonds.Resize(mol->NumAtoms()+1);

448

449

for (;uatoms.CountBits() < (signed)mol->NumAtoms();)

353

450

{

354

if (curr.empty())

355

for (atom = mol->BeginAtom(i);atom;atom = mol->NextAtom(i))

356

if (!uatoms[atom->GetIdx()])

357

{

358

uatoms |= atom->GetIdx();

359

curr.push_back(atom);

360

break;

361

}

362

363

for (;!curr.empty();)

364

{

365

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

366

for (nbr = ((OBAtom*)*i)->BeginNbrAtom(j);nbr;nbr = ((OBAtom*)*i)->NextNbrAtom(j))

367

if (!uatoms[nbr->GetIdx()])

368

{

369

uatoms |= nbr->GetIdx();

370

ubonds |= (*j)->GetIdx();

371

next.push_back(nbr);

372

}

373

374

curr = next;

375

next.clear();

376

}

451

if (curr.empty())

452

for (atom = mol->BeginAtom(i);atom;atom = mol->NextAtom(i))

453

if (!uatoms[atom->GetIdx()])

454

{

455

uatoms |= atom->GetIdx();

456

curr.push_back(atom);

457

break;

458

}

459

460

for (;!curr.empty();)

461

{

462

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

463

for (nbr = ((OBAtom*)*i)->BeginNbrAtom(j);nbr;nbr = ((OBAtom*)*i)->NextNbrAtom(j))

464

if (!uatoms[nbr->GetIdx()])

465

{

466

uatoms |= nbr->GetIdx();

467

ubonds |= (*j)->GetIdx();

468

next.push_back(nbr);

469

}

470

471

curr = next;

472

next.clear();

473

}

377

474

}

378

475

379

for (bond = mol->BeginBond(j);bond;bond = mol->NextBond(j))

380

if (!ubonds[bond->GetIdx()])

381

bond->SetClosure();

382

383

return(HasFlag(OB_CLOSURE_BOND));

476

for (bond = mol->BeginBond(j);bond;bond = mol->NextBond(j))

477

if (!ubonds[bond->GetIdx()])

478

bond->SetClosure();

479

480

return(HasFlag(OB_CLOSURE_BOND));

384

481

}

385

482

386

483

double OBBond::GetEquibLength()

387

484

{

388

double length;

389

OBAtom *begin, *end;

390

// CorrectedBondRad will always return a # now

391

// if (!CorrectedBondRad(GetBeginAtom(),rad1)) return(0.0);

392

// if (!CorrectedBondRad(GetEndAtom(),rad2)) return(0.0);

393

394

begin = GetBeginAtom();

395

end = GetEndAtom();

396

length = etab.CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())

397

+ etab.CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());

398

399

if (IsAromatic()) length *= 0.93;

400

else if (GetBO() == 2) length *= 0.91;

401

else if (GetBO() == 3) length *= 0.87;

402

return(length);

485

double length;

486

OBAtom *begin, *end;

487

// CorrectedBondRad will always return a # now

488

// if (!CorrectedBondRad(GetBeginAtom(),rad1)) return(0.0);

489

// if (!CorrectedBondRad(GetEndAtom(),rad2)) return(0.0);

490

491

begin = GetBeginAtom();

492

end = GetEndAtom();

493

length = etab.CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())

494

+ etab.CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());

495

496

if (IsAromatic())

497

length *= 0.93;

498

else if (GetBO() == 2)

499

length *= 0.91;

500

else if (GetBO() == 3)

501

length *= 0.87;

502

return(length);

403

503

}

404

504

405

505

double OBBond::GetLength()

406

506

{

407

double d2;

408

OBAtom *begin, *end;

409

begin = GetBeginAtom();

410

end = GetEndAtom();

411

412

d2 = SQUARE(begin->GetX() - end->GetX());

413

d2 += SQUARE(begin->GetY() - end->GetY());

414

d2 += SQUARE(begin->GetZ() - end->GetZ());

415

416

return(sqrt(d2));

507

double d2;

508

OBAtom *begin, *end;

509

begin = GetBeginAtom();

510

end = GetEndAtom();

511

512

d2 = SQUARE(begin->GetX() - end->GetX());

513

d2 += SQUARE(begin->GetY() - end->GetY());

514

d2 += SQUARE(begin->GetZ() - end->GetZ());

515

516

return(sqrt(d2));

417

517

}

418

518

419

519

// OBGenericData methods

420

520

bool OBBond::HasData(string &s)

421

//returns true if the generic attribute/value pair exists

521

//returns true if the generic attribute/value pair exists

422

522

{

423

if (_vdata.empty()) return(false);

523

if (_vdata.empty())

524

return(false);

424

525

425

526

vector<OBGenericData*>::iterator i;

426

527

427

528

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

428

529

if ((*i)->GetAttribute() == s)

429

530

return(true);

430

531

431

532

return(false);

432

533

}

433

534

434

535

bool OBBond::HasData(const char *s)

435

//returns true if the generic attribute/value pair exists

536

//returns true if the generic attribute/value pair exists

436

537

{

437

if (_vdata.empty()) return(false);

538

if (_vdata.empty())

539

return(false);

438

540

439

541

vector<OBGenericData*>::iterator i;

440

542

441

543

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

442

544

if ((*i)->GetAttribute() == s)

443

545

return(true);

444

546

445

547

return(false);

446

548

}

447

549

448

bool OBBond::HasData(obDataType dt)

449

//returns true if the generic attribute/value pair exists

550

bool OBBond::HasData(unsigned int dt)

551

//returns true if the generic attribute/value pair exists

450

552

{

451

if (_vdata.empty()) return(false);

553

if (_vdata.empty())

554

return(false);

452

555

453

556

vector<OBGenericData*>::iterator i;

454

557

455

558

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

456

559

if ((*i)->GetDataType() == dt)

457

560

return(true);

458

561

459

562

return(false);

460

563

}

461

564

462

565

OBGenericData *OBBond::GetData(string &s)

463

//returns the value given an attribute

566

//returns the value given an attribute

464

567

{

465

568

vector<OBGenericData*>::iterator i;

466

569

467

570

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

468

if ((*i)->GetAttribute() == s)

571

if ((*i)->GetAttribute() == s)

469

572

return(*i);

470

573

471

574

return(NULL);

472

575

}

473

576

474

577

OBGenericData *OBBond::GetData(const char *s)

475

//returns the value given an attribute

476

{

477

vector<OBGenericData*>::iterator i;

478

479

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

480

if ((*i)->GetAttribute() == s)

481

return(*i);

482

483

return(NULL);

484

}

485

486

OBGenericData *OBBond::GetData(obDataType dt)

487

{

488

vector<OBGenericData*>::iterator i;

489

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

490

if ((*i)->GetDataType() == dt)

491

return(*i);

492

return(NULL);

493

}

494

495

void OBBond::DeleteData(obDataType dt)

496

{

497

vector<OBGenericData*> vdata;

498

vector<OBGenericData*>::iterator i;

499

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

500

if ((*i)->GetDataType() == dt) delete *i;

501

else vdata.push_back(*i);

502

_vdata = vdata;

578

//returns the value given an attribute

579

{

580

vector<OBGenericData*>::iterator i;

581

582

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

583

if ((*i)->GetAttribute() == s)

584

return(*i);

585

586

return(NULL);

587

}

588

589

OBGenericData *OBBond::GetData(unsigned int dt)

590

{

591

vector<OBGenericData*>::iterator i;

592

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

593

if ((*i)->GetDataType() == dt)

594

return(*i);

595

return(NULL);

596

}

597

598

void OBBond::DeleteData(unsigned int dt)

599

{

600

vector<OBGenericData*> vdata;

601

vector<OBGenericData*>::iterator i;

602

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

603

if ((*i)->GetDataType() == dt)

604

delete *i;

605

else

606

vdata.push_back(*i);

607

_vdata = vdata;

503

608

}

504

609

505

610

void OBBond::DeleteData(vector<OBGenericData*> &vg)

506

611

{

507

vector<OBGenericData*> vdata;

508

vector<OBGenericData*>::iterator i,j;

612

vector<OBGenericData*> vdata;

613

vector<OBGenericData*>::iterator i,j;

509

614

510

bool del;

511

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

512

{

513

del = false;

514

for (j = vg.begin();j != vg.end();j++)

515

if (*i == *j)

516

{

517

del = true;

518

break;

519

}

520

if (del) delete *i;

521

else vdata.push_back(*i);

522

}

523

_vdata = vdata;

615

bool del;

616

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

617

{

618

del = false;

619

for (j = vg.begin();j != vg.end();j++)

620

if (*i == *j)

621

{

622

del = true;

623

break;

624

}

625

if (del)

626

delete *i;

627

else

628

vdata.push_back(*i);

629

}

630

_vdata = vdata;

524

631

}

525

632

526

633

void OBBond::DeleteData(OBGenericData *gd)

527

634

{

528

vector<OBGenericData*>::iterator i;

529

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

530

if (*i == gd)

531

{

532

delete *i;

533

_vdata.erase(i);

534

}

535

536

}

537

538

}

635

vector<OBGenericData*>::iterator i;

636

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

637

if (*i == gd)

638

{

639

delete *i;

640

_vdata.erase(i);

641

}

642

643

}

644

645

} // end namespace OpenBabel

646

647

//! \file bond.cpp

648

//! \brief Handle OBBond class

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