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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/chemical__graph_8cpp_source.html below:

NCBI C++ ToolKit: src/app/cn3d/chemical_graph.cpp Source File

81 FATALMSG

(

"Error reading standard residue dictionary: "

<< err);

86 standardDictionary

GetId

().front().GetObject().GetOther_database().GetDb() !=

"Standard residue dictionary"

89 FATALMSG

(

"file '"

<< filename <<

"' does not contain expected dictionary data"

);

106 FATALMSG

(

"need to load standard dictionary first"

);

117

CBiostruc_graph::TDescr::const_iterator d, de = graph.

GetDescr

().end();

118 for

(d=graph.

GetDescr

().begin(); d!=de; ++d) {

119 if

((*d)->IsName()) {

120 name

= (*d)->GetName();

131

object->

coordSets

.front()->atomSet->ensembles.size() > 1) {

133 AtomSet

*atomSet =

object

->coordSets.front()->atomSet;

134

AtomSet::EnsembleList::iterator e, ee=atomSet->

ensembles

.end();

135 for

(e=atomSet->

ensembles

.begin(); e!=ee; ++e) {

143

StructureObject::CoordSetList::const_iterator c, ce=

object

->coordSets.end();

144 for

(c=object->

coordSets

.begin(); c!=ce; ++c) {

146 reinterpret_cast<const string

>

(

NULL

)));

153 WARNINGMSG

(

"ChemicalGraph has zero AtomSets!"

);

161

CBiostruc_graph::TMolecule_graphs::const_iterator

, ie=graph.

GetMolecule_graphs

().end();

169 ERRORMSG

(

"confused by repeated Molecule-graph ID's"

);

176 for

(

int n

=0;

<nAlts; ++

) {

199 int

order = j->GetObject().IsSetBond_order() ?

202

j->GetObject().GetAtom_id_1(),

203

j->GetObject().GetAtom_id_2(),

208

j->GetObject().GetAtom_id_1(), j->GetObject().GetAtom_id_2(),

222 for

(

int n

=0;

<nAlts; ++

) {

229

FeatureList::const_iterator

= features.end();

230 for

(

=features.begin();

; ++

) {

231 if

(

->GetObject().IsSetDescr()) {

234

CBiostruc_feature_set::TDescr::const_iterator d, de =

->GetObject().GetDescr().end();

235 for

(d=

->GetObject().GetDescr().begin(); d!=de; ++d) {

236 if

(d->GetObject().IsName()) {

237 if

(d->GetObject().GetName() ==

"NCBI assigned secondary structure"

)

239 else if

(d->GetObject().GetName() ==

"NCBI Domains"

)

250

list < int > moleculeIDs;

251

MoleculeMap::iterator m, me =

molecules

.end();

252 for

(m=

molecules

.begin(); m!=me; ++m) {

253 if

(m->second->IsProtein() || m->second->IsNucleotide())

254

moleculeIDs.push_back(m->first);

257

list < int >::const_iterator id, ide = moleculeIDs.end();

258 for

(

id

=moleculeIDs.begin();

id

!=ide; ++id) {

266

(

const_cast<StructureObject

>

(object))->domainMap[domainID] = molecule;

267

(

const_cast<StructureObject

>

(object))->domainID2MMDB[domainID] = -1;

276 TRACEMSG

(

"unpacking NCBI domain features"

);

277

CBiostruc_feature_set::TFeatures::const_iterator

, fe = featureSet.

GetFeatures

().end();

280 f

->GetObject().IsSetLocation() &&

281 f

->GetObject().GetLocation().IsSubgraph() &&

282 f

->GetObject().GetLocation().GetSubgraph().IsResidues() &&

283 f

->GetObject().GetLocation().GetSubgraph().GetResidues().IsInterval()) {

290

CResidue_pntrs::TInterval::const_iterator

291

ie =

->GetObject().GetLocation().GetSubgraph().GetResidues().GetInterval().end();

292 for

(

->GetObject().GetLocation().GetSubgraph().GetResidues().GetInterval().begin();

!=ie; ++

) {

293

MoleculeMap::const_iterator m =

molecules

.find(

->GetObject().GetMolecule_id().Get());

296 f

->GetObject().GetLocation().GetSubgraph().GetResidues().GetInterval().

297 front

().GetObject().GetMolecule_id().Get()) {

298 WARNINGMSG

(

"Bad moleculeID in domain interval"

);

301

molecule =

const_cast<Molecule

>

(m->second);

302 for

(

int r

->GetObject().GetFrom().Get()-1;

->GetObject().GetTo().Get()-1; ++

) {

303 if

(r < 0 || r >= (

int

)molecule->

residues

.size()) {

304 ERRORMSG

(

"Bad residue range in domain feature for moleculeID " 305

<< molecule->

" residueID "

+1);

308 WARNINGMSG

(

"Overlapping domain feature for moleculeID " 309

<< molecule->

" residueID "

+1);

322 f

->GetObject().GetId().Get();

331 TRACEMSG

(

"unpacking NCBI sec. struc. features"

);

332

CBiostruc_feature_set::TFeatures::const_iterator

, fe = featureSet.

GetFeatures

().end();

336 f

->GetObject().IsSetLocation() &&

337 f

->GetObject().GetLocation().IsSubgraph() &&

338 f

->GetObject().GetLocation().GetSubgraph().IsResidues() &&

339 f

->GetObject().GetLocation().GetSubgraph().GetResidues().IsInterval()) {

342 if

(

->GetObject().GetLocation().GetSubgraph().GetResidues().GetInterval().size() > 1) {

343 WARNINGMSG

(

"Can't deal with multi-interval sec. struc. regions"

);

347 f

->GetObject().GetLocation().GetSubgraph().GetResidues().GetInterval().front().GetObject();

350 WARNINGMSG

(

"Bad moleculeID in sec. struc. interval"

);

355 if

(r < 0 || r >= (

int

)molecule->

residues

.size()) {

356 ERRORMSG

(

"Bad residue range in sec. struc. feature for moleculeID " 357

<< molecule->

" residueID "

+1);

360 WARNINGMSG

(

"Overlapping sec. struc. feature at moleculeID " 361

<< molecule->

" residueID "

+1);

389

" of ChemicalGraph of object "

<< object->

GetPDBID

());

394 bool

continueDraw =

false

;

396

MoleculeMap::const_iterator m, me=

molecules

.end();

397 for

(m=

molecules

.begin(); m!=me; ++m) {

398 if

(!m->second->IsProtein() && !m->second->IsNucleotide())

continue

;

401

Molecule::DisplayListList::const_iterator md=m->second->displayLists.begin();

410 a

->first->SetActiveEnsemble(

->second);

411

continueDraw = m->second->DrawAllWithTerminiLabels(

->first);

416 if

(

->first->GetParentOfType(&coordSet)) {

417

CoordSet::Object3DMap::const_iterator objList = coordSet->

objectMap

.find(m->second->id);

418 if

(objList != coordSet->

objectMap

.end()) {

419

CoordSet::Object3DList::const_iterator o, oe=objList->second.end();

420 for

(o=objList->second.begin(); o!=oe; ++o) {

421 if

(!(continueDraw = (*o)->Draw(

->first)))

break

;

430 if

(!continueDraw)

return false

;

447 a

->first->SetActiveEnsemble(

->second);

450

continueDraw =

true

;

451 for

(m=

molecules

.begin(); m!=me; ++m) {

452 if

(m->second->IsProtein() || m->second->IsNucleotide())

continue

;

453 if

(!(continueDraw = m->second->DrawAll(

->first)))

break

;

459 if

(!(continueDraw = (*b)->Draw(

->first)))

break

;

465 if

(!continueDraw)

return false

;

480

mol1 = mol2 = molecule;

482

MoleculeMap::const_iterator

486 ERRORMSG

(

"ChemicalGraph::CheckForDisulfide() - bad molecule ID"

);

493

Molecule::ResidueMap::const_iterator

497 ERRORMSG

(

"ChemicalGraph::CheckForDisulfide() - bad residue ID"

);

506

*atom1 = res1->second->GetAtomInfo(atomPtr1.

GetAtom_id

().

Get

()),

507

*atom2 = res2->second->GetAtomInfo(atomPtr2.

GetAtom_id

().

Get

());

508 if

(!atom1 || !atom2) {

509 ERRORMSG

(

"ChemicalGraph::CheckForDisulfide() - bad atom ID"

);

530 if

(!virtualDisulfide)

return false

;

532

bondList->push_back(virtualDisulfide);

User-defined methods of the data storage class.

const Bond * MakeBond(StructureBase *parent, int mID1, int rID1, int aID1, int mID2, int rID2, int aID2, int bondOrder)

void LoadStandardDictionary(const char *filename)

static const CBiostruc_residue_graph_set * standardDictionary

void DeleteStandardDictionary(void)

static int moleculeToRedraw

std::list< ncbi::CRef< ncbi::objects::CBiostruc_feature_set > > FeatureList

CBiostruc_feature_set â.

CBiostruc_residue_graph_set â.

CResidue_interval_pntr â.

bool CheckForDisulfide(const Molecule *molecule, const ncbi::objects::CAtom_pntr &atomPtr1, const ncbi::objects::CAtom_pntr &atomPtr2, std::list< const Bond * > *bondList, Bond *bond, StructureBase *parent)

unsigned int displayListOtherStart

BondList interMoleculeBonds

void RedrawMolecule(int moleculeID) const

void UnpackSecondaryStructureFeatures(const ncbi::objects::CBiostruc_feature_set &featureSet)

bool DrawAll(const AtomSet *atomSet=NULL) const

void UnpackDomainFeatures(const ncbi::objects::CBiostruc_feature_set &featureSet)

ChemicalGraph(StructureBase *parent, const ncbi::objects::CBiostruc_graph &graph, const FeatureList &features)

std::vector< int > residueDomains

bool IsNucleotide(void) const

DisplayListList displayLists

std::vector< eSecStruc > residueSecondaryStructures

static const int NO_DOMAIN_SET

bool IsProtein(void) const

void StartDisplayList(unsigned int list)

void EndDisplayList(void)

static const unsigned int NO_LIST

static const int NO_ALPHA_ID

bool GetParentOfType(const T **ptr, bool warnIfNotFound=true) const

std::string GetPDBID(char separator='_') const

unsigned int lastDisplayList

TransformMap transformMap

bool IsMultiStructure(void) const

OpenGLRenderer * renderer

Include a standard set of the NCBI C++ Toolkit most basic headers.

static bool ReadASNFromFile(const char *filename, ASNClass *ASNobject, bool isBinary, std::string *err)

const TPrim & Get(void) const

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

const TMolecule_id & GetMolecule_id(void) const

Get the Molecule_id member data.

const TResidue_graphs & GetResidue_graphs(void) const

Get the Residue_graphs member data.

bool IsSetDescr(void) const

Check if a value has been assigned to Descr data member.

const TInter_molecule_bonds & GetInter_molecule_bonds(void) const

Get the Inter_molecule_bonds member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TResidue_id & GetResidue_id(void) const

Get the Residue_id member data.

const TAtom_id & GetAtom_id(void) const

Get the Atom_id member data.

const TMolecule_graphs & GetMolecule_graphs(void) const

Get the Molecule_graphs member data.

bool IsSetInter_molecule_bonds(void) const

Check if a value has been assigned to Inter_molecule_bonds data member.

const TFeatures & GetFeatures(void) const

Get the Features member data.

const TTo & GetTo(void) const

Get the To member data.

const TFrom & GetFrom(void) const

Get the From member data.

const TMolecule_id & GetMolecule_id(void) const

Get the Molecule_id member data.

@ eType_subgraph

NCBI domain reserved.

const TResidue_graphs & GetResidue_graphs(void) const

Get the Residue_graphs member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetId(void) const

Check if a value has been assigned to Id data member.

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

bool le(T x_, T y_, T round_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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