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Viewing changes to src/smi.cpp

Committer: Bazaar Package Importer
Author(s): Michael Banck
Date: 2002-02-01 01:19:44 UTC
Revision ID: james.westby@ubuntu.com-20020201011944-4a9guzcsnpezzawx

Tags: upstream-1.99

Import upstream version 1.99

files added:

AUTHORS

COPYING

ChangeLog

INSTALL

Makefile.in

README

THANKS

config.guess

config.sub

configure

configure.in

doc/FAQ

doc/Migration

doc/Primer.html

doc/babel.1

install-sh

ltconfig

ltmain.sh

missing

mkinstalldirs

src/Makefile

src/Makefile.in

src/StdAfx.cpp

src/StdAfx.h

src/Vector.cpp

src/Vector.h

src/alchemy.cpp

src/amber.cpp

src/aromatic.h

src/aromatic.txt

src/atom.cpp

src/atomtyp.h

src/atomtyp.txt

src/balst.cpp

src/base.cpp

src/base.h

src/bgf.cpp

src/bin2hex.pl

src/binary.cpp

src/binary.h

src/binary_io.cpp

src/binary_io.h

src/bitgrid.cpp

src/bitgrid.h

src/bitvec.cpp

src/bitvec.h

src/bond.cpp

src/box.cpp

src/c3d.cpp

src/cacao.cpp

src/cache.cpp

src/car.cpp

src/ccc.cpp

src/chains.cpp

src/chains.h

src/chdrw.cpp

src/chiral.cpp

src/chiral.h

src/commandline.cpp

src/commandline.h

src/csr.cpp

src/cssr.cpp

src/ctransform.cpp

src/ctransform.h

src/cwrap.cpp

src/cwrap.h

src/data.cpp

src/data.h

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/generic.cpp

src/generic.h

src/ghemical.cpp

src/grid.cpp

src/grid.h

src/gromos96.cpp

src/hin.cpp

src/jaguar.cpp

src/main.cpp

src/matrix.cpp

src/matrix.h

src/mdl.cpp

src/mmod.cpp

src/mol.cpp

src/mol.h

src/mol2.cpp

src/molchrg.cpp

src/molchrg.h

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/obutil.cpp

src/obutil.h

src/parsmart.cpp

src/parsmart.h

src/parsmi.cpp

src/patty.cpp

src/patty.h

src/pdb.cpp

src/phmodel.cpp

src/phmodel.h

src/phmodel.txt

src/phmodeldata.h

src/qchem.cpp

src/quat.c

src/rand.cpp

src/report.cpp

src/resdata.h

src/resdata.txt

src/ring.cpp

src/ring.h

src/rotor.cpp

src/rotor.h

src/smarts.cpp

src/smarts.h

src/smi.cpp

src/smi.h

src/tinker.cpp

src/tokenst.cpp

src/typer.cpp

src/typer.h

src/types.h

src/types.txt

src/unichem.cpp

src/version.h.in

src/xed.cpp

src/xyz.cpp

stamp-h.in

stamp.h

test

test/Makefile

test/Makefile.in

test/attype.00.smi

test/main.cpp

test/ringresults.txt

test/ringtest.cpp

test/smartsresults.txt

test/smartstest.cpp

test/smartstest.txt

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added added

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src/smi.cpp

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

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 "mol.h"

#include "typer.h"

#include "smi.h"

//#define KEKULE

namespace OpenBabel {

bool WriteSmiles(ostream &ofs,OBMol &mol,char *title)

{

char buffer[BUFF_SIZE],tmp[BUFF_SIZE];

OBMol2Smi m2s;

m2s.Init();

m2s.CorrectAromaticAmineCharge(mol);

m2s.CreateSmiString(mol,buffer);

strcpy(tmp,(title) ? title:mol.GetTitle());

ofs << buffer << ' ' << tmp << endl;

return(true);

}

void OBMol2Smi::CreateSmiString(OBMol &mol,char *buffer)

{

OBAtom *atom;

OBSmiNode *root;

buffer[0] = '\0';

vector<OBNodeBase*>::iterator i;

for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))

// if ((!atom->IsHydrogen() || atom->GetValence() == 0) && !_uatoms[atom->GetIdx()])

if (!atom->IsHydrogen() && !_uatoms[atom->GetIdx()])

if (!atom->IsChiral()) //don't use chiral atoms as root node

{

//clear out closures in case structure is dot disconnected

_vclose.clear();

_atmorder.clear();

_storder.clear();

_vopen.clear();

//dot disconnected structure

if (strlen(buffer) > 0) strcat(buffer,".");

root = new OBSmiNode (atom);

BuildTree(root);

FindClosureBonds(mol);

if (mol.Has2D()) AssignCisTrans(root);

ToSmilesString(root,buffer);

delete root;

}

bool OBMol2Smi::BuildTree(OBSmiNode *node)

{

vector<OBEdgeBase*>::iterator i;

OBAtom *nbr,*atom = node->GetAtom();

_uatoms.SetBitOn(atom->GetIdx()); //mark the atom as visited

_atmorder.push_back(atom->GetIdx()); //store the atom ordering

_storder.push_back(atom->GetIdx()); //store the atom ordering for stereo

for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))

if (!nbr->IsHydrogen() && !_uatoms[nbr->GetIdx()])

{

_ubonds.SetBitOn((*i)->GetIdx());

OBSmiNode *next = new OBSmiNode (nbr);

next->SetParent(atom);

node->SetNextNode(next,(OBBond*)*i);

BuildTree(next);

}

return(true);

}

void OBMol2Smi::ToSmilesString(OBSmiNode *node,char *buffer)

{

char tmpbuf[10];

OBAtom *atom = node->GetAtom();

//write the current atom to the string

GetSmilesElement(node,tmpbuf);

strcat(buffer,tmpbuf);

//handle ring closures here

vector<pair<int,OBBond*> > vc = GetClosureDigits(atom);

if (!vc.empty())

{

100

vector<pair<int,OBBond*> >::iterator i;

101

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

102

{

103

if (i->second)

104

{

105

if (i->second->IsUp()) strcat(buffer,"\\");

106

if (i->second->IsDown()) strcat(buffer,"/");

107

#ifndef KEKULE

108

if (i->second->GetBO() == 2 && !i->second->IsAromatic()) strcat(buffer,"=");

109

#else

110

if (i->second->GetBO() == 2) strcat(buffer,"=");

111

#endif

112

if (i->second->GetBO() == 3) strcat(buffer,"#");

113

}

114

115

if (i->first > 9) strcat(buffer,"%");

116

sprintf(tmpbuf,"%d",i->first);

117

strcat(buffer,tmpbuf);

118

}

119

}

120

121

//follow path to child atoms

122

OBBond *bond;

123

for (int i = 0;i < node->Size();i++)

124

{

125

bond = node->GetNextBond(i);

126

if (i+1 < node->Size()) strcat(buffer,"(");

127

if (bond->IsUp()) strcat(buffer,"\\");

128

if (bond->IsDown()) strcat(buffer,"/");

129

#ifndef KEKULE

130

if (bond->GetBO() == 2 && !bond->IsAromatic()) strcat(buffer,"=");

131

#else

132

if (bond->GetBO() == 2) strcat(buffer,"=");

133

#endif

134

if (bond->GetBO() == 3) strcat(buffer,"#");

135

136

ToSmilesString(node->GetNextNode(i),buffer);

137

if (i+1 < node->Size()) strcat(buffer,")");

138

}

139

}

140

141

void OBMol2Smi::GetClosureAtoms(OBAtom *atom,vector<OBNodeBase*> &va)

142

{

143

144

//look through closure list for start atom

145

vector<OBEdgeBase*>::iterator i;

146

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

147

if (*i)

148

{

149

if (((OBBond*)*i)->GetBeginAtom() == atom)

150

va.push_back(((OBBond*)*i)->GetEndAtom());

151

if (((OBBond*)*i)->GetEndAtom() == atom)

152

va.push_back(((OBBond*)*i)->GetBeginAtom());

153

}

154

155

OBAtom *nbr;

156

vector<pair<OBAtom*,pair<int,int> > >::iterator j;

157

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

158

for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))

159

if (nbr == j->first)

160

va.push_back(nbr);

161

}

162

163

vector<pair<int,OBBond*> > OBMol2Smi::GetClosureDigits(OBAtom *atom)

164

{

165

vector<pair<int,OBBond*> > vc; vc.clear();

166

167

//look through closure list for start atom

168

int idx,bo;

169

OBBond *bond;

170

vector<OBEdgeBase*>::iterator i;

171

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

172

if ((bond=(OBBond*)*i))

173

if (bond->GetBeginAtom() == atom || bond->GetEndAtom() == atom)

174

{

175

idx = GetUnusedIndex();

176

vc.push_back(pair<int,OBBond*> (idx,bond));

177

bo = (bond->IsAromatic())? 1 : bond->GetBO();

178

_vopen.push_back(pair<OBAtom*,pair<int,int> >

179

(bond->GetNbrAtom(atom),pair<int,int>(idx,bo)));

180

*i = NULL;//remove bond from closure list

181

}

182

183

//try to complete closures

184

if (!_vopen.empty())

185

{

186

vector<pair<OBAtom*,pair<int,int> > >::iterator j;

187

for (j = _vopen.begin();j != _vopen.end();)

188

if (j->first == atom)

189

{

190

vc.push_back(pair<int,OBBond*> (j->second.first,(OBBond*)NULL));

191

_vopen.erase(j);

192

j = _vopen.begin();

193

}

194

else j++;

195

}

196

197

return(vc);

198

}

199

200

void OBMol2Smi::FindClosureBonds(OBMol &mol)

201

{

202

//find closure bonds

203

OBAtom *a1,*a2;

204

OBBond *bond;

205

vector<OBEdgeBase*>::iterator i;

206

OBBitVec bv;

207

bv.FromVecInt(_storder);

208

209

for (bond = mol.BeginBond(i);bond;bond = mol.NextBond(i))

210

if (!_ubonds[bond->GetIdx()] && bv[bond->GetBeginAtomIdx()])

211

{

212

a1 = bond->GetBeginAtom();

213

a2 = bond->GetEndAtom();

214

if (!a1->IsHydrogen() && !a2->IsHydrogen())

215

_vclose.push_back(bond);

216

}

217

218

vector<OBEdgeBase*>::reverse_iterator j;

219

vector<int>::iterator k;

220

221

//modify _order to reflect ring closures

222

for (j = _vclose.rbegin();j != _vclose.rend();j++)

223

{

224

bond = (OBBond*)*j;

225

a1 = a2 = NULL;

226

227

for (k = _storder.begin();k != _storder.end();k++)

228

if (bond->GetBeginAtomIdx() == *k ||

229

bond->GetEndAtomIdx() == *k)

230

if (!a1) a1 = mol.GetAtom(*k);

231

else if (!a2)

232

{

233

a2 = mol.GetAtom(*k);

234

_storder.erase(k);

235

break;

236

}

237

238

for (k = _storder.begin();k != _storder.end();k++)

239

if (a1->GetIdx() == *k)

240

{

241

k++;

242

if (k != _storder.end()) _storder.insert(k,a2->GetIdx());

243

else _storder.push_back(a2->GetIdx());

244

break;

245

}

246

}

247

}

248

249

int OBMol2Smi::GetUnusedIndex()

250

{

251

int idx=1;

252

253

vector<pair<OBAtom*,pair<int,int> > >::iterator j;

254

for (j = _vopen.begin();j != _vopen.end();)

255

if (j->second.first == idx)

256

{

257

idx++; //increment idx and start over if digit is already used

258

j = _vopen.begin();

259

}

260

else j++;

261

262

return(idx);

263

}

264

265

void OBMol2Smi::CorrectAromaticAmineCharge(OBMol &mol)

266

{

267

OBAtom *atom;

268

vector<OBNodeBase*>::iterator i;

269

270

_aromNH.clear();

271

_aromNH.resize(mol.NumAtoms()+1);

272

273

for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))

274

if (atom->IsNitrogen() && atom->IsAromatic())

275

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

276

{

277

if (atom->GetValence() == 3 || atom->GetImplicitValence() == 3)

278

_aromNH[atom->GetIdx()] = true;

279

}

280

}

281

282

void OBMol2Smi::AssignCisTrans(OBSmiNode *node)

283

{

284

//traverse the tree searching for acyclic olefins - if it

285

//has at least one heavy atom attachment on each end assign stereochem

286

287

OBBond *bond;

288

for (int i = 0;i < node->Size();i++)

289

{

290

bond = node->GetNextBond(i);

291

if (bond->GetBO() == 2 && !bond->IsInRing())

292

{

293

OBAtom *b = node->GetAtom();

294

OBAtom *c = bond->GetNbrAtom(b);

295

296

//skip allenes

297

if (b->GetHyb() == 1 || c->GetHyb() == 1) continue;

298

299

if (b->GetHvyValence() > 1 && c->GetHvyValence() > 1)

300

{

301

OBAtom *a,*d;

302

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

303

304

//look for bond with assigned stereo as in poly-ene

305

for (a = b->BeginNbrAtom(j);a;a = b->NextNbrAtom(j))

306

if (((OBBond*)*j)->IsUp() ||((OBBond*)*j)->IsDown())

307

break;

308

309

if (!a)

310

for (a = b->BeginNbrAtom(j);a;a = b->NextNbrAtom(j))

311

if (a != c && !a->IsHydrogen())

312

break;

313

for (d = c->BeginNbrAtom(k);d;d = c->NextNbrAtom(k))

314

if (d != b && !d->IsHydrogen())

315

break;

316

obAssert(a); obAssert(d);

317

318

if (((OBBond*)*j)->IsUp() || ((OBBond*)*j)->IsDown()) //stereo already assigned

319

{

320

if (fabs(CalcTorsionAngle(a->GetVector(),b->GetVector(),

321

c->GetVector(),d->GetVector())) > 10.0)

322

if (((OBBond*)*j)->IsUp()) ((OBBond*)*k)->SetUp();

323

else ((OBBond*)*k)->SetDown();

324

else

325

if (((OBBond*)*j)->IsUp()) ((OBBond*)*k)->SetDown();

326

else ((OBBond*)*k)->SetUp();

327

}

328

else //assign stereo to both ends

329

{

330

((OBBond*)*j)->SetUp();

331

if (fabs(CalcTorsionAngle(a->GetVector(),b->GetVector(),

332

c->GetVector(),d->GetVector())) > 10.0)

333

((OBBond*)*k)->SetUp();

334

else

335

((OBBond*)*k)->SetDown();

336

}

337

}

338

}

339

AssignCisTrans(node->GetNextNode(i));

340

}

341

}

342

343

void OBMol2Smi::Init()

344

{

345

_vclose.clear();

346

_atmorder.clear();

347

_storder.clear();

348

_aromNH.clear();

349

_uatoms.Clear();

350

_ubonds.Clear();

351

_vopen.clear();

352

}

353

354

bool OBMol2Smi::GetSmilesElement(OBSmiNode *node,char *element)

355

{

356

//***handle reference atom stuff here and return***

357

char symbol[10];

358

bool bracketElement = false;

359

bool normalValence = true;

360

361

OBAtom *atom = node->GetAtom();

362

363

int bosum = atom->KBOSum();

364

365

switch (atom->GetAtomicNum())

366

{

367

case 0: break;

368

case 5: /*bracketElement = !(normalValence = (bosum == 3)); break;*/ break;

369

case 6: break;

370

case 7:

371

if (atom->IsAromatic() && atom->GetHvyValence() == 2 && atom->GetImplicitValence() == 3)

372

{

373

bracketElement = !(normalValence = false); break;

374

}

375

else

376

bracketElement = !(normalValence = (bosum == 3 || bosum == 5)); break;

377

case 8: break;

378

case 9: break;

379

case 15: break;

380

case 16:

381

bracketElement = !(normalValence = (bosum == 2 || bosum == 4 || bosum == 6)); break;

382

case 17: break;

383

case 35: break;

384

case 53: break;

385

386

default:

387

bracketElement = true;

388

}

389

390

if (atom->GetHvyValence() > 2 && atom->IsChiral())

391

if (((OBMol*)atom->GetParent())->HasNonZeroCoords() || atom->HasChiralitySpecified())

392

bracketElement = true;

393

394

if (atom->GetFormalCharge() != 0) //bracket charged elements

395

bracketElement = true;

396

397

if (!bracketElement)

398

{

399

if (!atom->GetAtomicNum())

400

{

401

bool external = false;

402

vector<pair<int,pair<OBAtom *,OBBond *> > > *externalBonds =

403

(vector<pair<int,pair<OBAtom *,OBBond *> > > *)((OBMol*)atom->GetParent())->GetData("extBonds");

404

vector<pair<int,pair<OBAtom *,OBBond *> > >::iterator externalBond;

405

406

if (externalBonds)

407

for(externalBond = externalBonds->begin();externalBond != externalBonds->end();externalBond++)

408

{

409

if (externalBond->second.first == atom)

410

{

411

external = true;

412

strcpy(symbol,"&");

413

OBBond *bond = externalBond->second.second;

414

if (bond->IsUp()) strcat(symbol,"\\");

415

if (bond->IsDown()) strcat(symbol,"/");

416

#ifndef KEKULE

417

if (bond->GetBO() == 2 && !bond->IsAromatic()) strcat(symbol,"=");

418

if (bond->GetBO() == 2 && bond->IsAromatic()) strcat(symbol,";");

419

#else

420

if (bond->GetBO() == 2) strcat(symbol,"=");

421

#endif

422

if (bond->GetBO() == 3) strcat(symbol,"#");

423

sprintf(symbol,"%s%d",symbol,externalBond->first);

424

break;

425

}

426

}

427

428

if(!external) strcpy(symbol,"*");

429

}

430

else

431

{

432

strcpy(symbol,etab.GetSymbol(atom->GetAtomicNum()));

433

#ifndef KEKULE

434

if (atom->IsAromatic()) symbol[0] = tolower(symbol[0]);

435

#endif

436

}

437

strcpy(element,symbol);

438

439

return(true);

440

}

441

442

strcpy(element,"[");

443

if (!atom->GetAtomicNum()) strcpy(symbol,"*");

444

else

445

{

446

strcpy(symbol,etab.GetSymbol(atom->GetAtomicNum()));

447

#ifndef KEKULE

448

if (atom->IsAromatic()) symbol[0] = tolower(symbol[0]);

449

#endif

450

}

451

strcat(element,symbol);

452

453

//if (atom->IsCarbon() && atom->GetHvyValence() > 2 && atom->IsChiral())

454

if (atom->GetHvyValence() > 2 && atom->IsChiral())

455

{

456

char stereo[5];

457

if (GetChiralStereo(node,stereo))

458

strcat(element,stereo);

459

}

460

461

//add extra hydrogens

462

// if (!normalValence && atom->ImplicitHydrogenCount())

463

if (atom->ImplicitHydrogenCount())

464

{

465

strcat(element,"H");

466

if (atom->ImplicitHydrogenCount() > 1)

467

{

468

char tcount[10];

469

sprintf(tcount,"%d",atom->ImplicitHydrogenCount());

470

strcat(element,tcount);

471

}

472

}

473

474

//cat charge on the end

475

if (atom->GetFormalCharge() != 0)

476

{

477

478

479

if (atom->ImplicitHydrogenCount())

480

{

481

cerr << "imp = " << atom->GetAtomicNum() << ' ' << atom->GetImplicitValence() << endl;

482

strcat(element,"H");

483

if (atom->ImplicitHydrogenCount() > 1)

484

{

485

char tcount[10];

486

sprintf(tcount,"%d",atom->ImplicitHydrogenCount());

487

strcat(element,tcount);

488

}

489

}

490

491

if (atom->GetFormalCharge() > 0) strcat(element,"+");

492

else strcat(element,"-");

493

494

if (abs(atom->GetFormalCharge()) > 1)

495

{

496

char tcharge[10];

497

sprintf(tcharge,"%d",abs(atom->GetFormalCharge()));

498

strcat(element,tcharge);

499

}

500

}

501

502

strcat(element,"]");

503

504

return(true);

505

}

506

507

bool OBMol2Smi::GetChiralStereo(OBSmiNode *node,char *stereo)

508

{

509

bool is2D=false;

510

float torsion;

511

OBAtom *a,*b,*c,*d,hydrogen;

512

513

b = node->GetAtom();

514

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

515

516

if (!mol->HasNonZeroCoords()) //must have come in from smiles string

517

{

518

if (!b->HasChiralitySpecified()) return(false);

519

if (b->IsClockwise()) strcpy(stereo,"@@");

520

else if (b->IsAntiClockwise()) strcpy(stereo,"@");

521

else return(false);

522

//if (b->GetHvyValence() == 3) strcat(stereo,"H");

523

return(true);

524

}

525

526

//give peudo Z coords if mol is 2D

527

if (!mol->Has3D())

528

{

529

Vector v,vz(0.0,0.0,1.0);

530

is2D = true;

531

OBAtom *nbr;

532

OBBond *bond;

533

vector<OBEdgeBase*>::iterator i;

534

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

535

{

536

nbr = bond->GetEndAtom();

537

if (nbr != b)

538

{

539

v = nbr->GetVector();

540

if (bond->IsWedge()) v += vz;

541

else

542

if (bond->IsHash()) v -= vz;

543

544

nbr->SetVector(v);

545

}

546

else

547

{

548

nbr = bond->GetBeginAtom();

549

v = nbr->GetVector();

550

if (bond->IsWedge()) v -= vz;

551

else

552

if (bond->IsHash()) v += vz;

553

554

nbr->SetVector(v);

555

}

556

}

557

}

558

559

c = d = NULL;

560

a = node->GetParent();

561

obAssert(a); //chiral atom can't be used as root node - must have parent

562

563

if (b->GetHvyValence() == 3) //must have attached hydrogen

564

{

565

if (b->GetValence() == 4)//has explicit hydrogen

566

{

567

vector<OBEdgeBase*>::iterator i;

568

for (c = b->BeginNbrAtom(i);c;c = b->NextNbrAtom(i))

569

if (c->IsHydrogen())

570

break;

571

obAssert(c);

572

}

573

else //implicit hydrogen

574

{

575

Vector v;

576

b->GetNewBondVector(v,1.0);

577

hydrogen.SetVector(v);

578

c = &hydrogen;

579

}

580

}

581

582

//get connected atoms in order

583

OBAtom *nbr;

584

vector<int>::iterator j;

585

586

//try to get neighbors that are closure atoms in the order they appear in the string

587

vector<OBNodeBase*> va;

588

GetClosureAtoms(b,va);

589

if (!va.empty())

590

{

591

vector<OBNodeBase*>::iterator k;

592

for (k = va.begin();k != va.end();k++)

593

if (*k != a)

594

{

595

if (!c) c = (OBAtom*)*k;

596

else if (!d) d = (OBAtom*)*k;

597

}

598

}

599

600

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

601

{

602

nbr = mol->GetAtom(*j);

603

if (!b->IsConnected(nbr)) continue;

604

if (nbr == a || nbr == b || nbr == c) continue;

605

if (!c) c = nbr;

606

else if (!d) d = nbr;

607

}

608

609

torsion = CalcTorsionAngle(a->GetVector(),b->GetVector(),

610

c->GetVector(),d->GetVector());

611

612

strcpy(stereo,(torsion<0.0)?"@":"@@");

613

//if (b->GetHvyValence() == 3) strcat(stereo,"H");

614

615

//re-zero psuedo-coords

616

if (is2D)

617

{

618

Vector v;

619

OBAtom *atom;

620

vector<OBNodeBase*>::iterator k;

621

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

622

{

623

v = atom->GetVector();

624

v.SetZ(0.0);

625

atom->SetVector(v);

626

}

627

}

628

629

return(true);

630

}

631

632

bool WriteFixFile(ostream &ofs,OBMol &mol)

633

{

634

char buffer[BUFF_SIZE];

635

OBMol2Smi m2s;

636

637

m2s.Init();

638

//m2s.AssignCisTrans(mol);

639

m2s.CorrectAromaticAmineCharge(mol);

640

m2s.CreateSmiString(mol,buffer);

641

642

OBAtom *atom;

643

vector<int>::iterator i;

644

vector<int> order = m2s.GetOutputOrder();

645

ofs << buffer << endl;

646

647

int j;

648

for (j = 0;j < mol.NumConformers();j++)

649

{

650

mol.SetConformer(j);

651

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

652

{

653

atom = mol.GetAtom(*i);

654

sprintf(buffer,"%9.3f %9.3f %9.3f",atom->GetX(),atom->GetY(),atom->GetZ());

655

ofs << buffer<< endl;

656

}

657

}

658

return(true);

659

}

660

661

OBSmiNode::OBSmiNode(OBAtom *atom)

662

{

663

_atom = atom;

664

_parent = NULL;

665

_nextnode.clear();

666

_nextbond.clear();

667

}

668

669

void OBSmiNode::SetNextNode(OBSmiNode *node,OBBond *bond)

670

{

671

_nextnode.push_back(node);

672

_nextbond.push_back(bond);

673

}

674

675

OBSmiNode::~OBSmiNode()

676

{

677

vector<OBSmiNode*>::iterator i;

678

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

679

delete (*i);

680

}

681

682

683

bool WriteTheSmiles(OBMol & mol,char *out)

684

{

685

char buffer[2*BUFF_SIZE];

686

687

OBMol2Smi m2s;

688

689

m2s.Init();

690

m2s.CorrectAromaticAmineCharge(mol);

691

m2s.CreateSmiString(mol,buffer);

692

693

strcpy(out,buffer);

694

return(true);

695

696

}

697

698

}

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