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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/molecule_8cpp_source.html below:

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

77

CMolecule_graph::TDescr::const_iterator k, ke=graph.

GetDescr

().end();

78 for

(k=graph.

GetDescr

().begin(); k!=ke; ++k) {

79 if

(k->GetObject().IsMolecule_type()) {

80 type

static_cast<eType>

(k->GetObject().GetMolecule_type());

82 if

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

83 name

= k->GetObject().GetName();

93 ERRORMSG

(

"Molecule::Molecule() - biopolymer molecule, but can't get Seq-id"

);

102

CMolecule_graph::TInter_residue_bonds::const_iterator j, je, jOrig;

114 const Residue

*residue =

new Residue

(

this

, (*i).GetObject(),

id

121 if

(residue->

!= nResidues)

122 ERRORMSG

(

"Residue ID's must be ordered consecutively starting with one"

);

128 bool

foundReal =

false

;

134 if

((j->GetObject().GetAtom_id_1().GetResidue_id().Get() == prevResidue->

135

j->GetObject().GetAtom_id_2().GetResidue_id().Get() == residue->

) ||

136

(j->GetObject().GetAtom_id_2().GetResidue_id().Get() == prevResidue->

137

j->GetObject().GetAtom_id_1().GetResidue_id().Get() == residue->

))

140

}

while

(!foundReal && j != jOrig);

151 const AtomCoord

* atom1 =

object

->coordSets.front()->atomSet->GetAtom(ap1,

true

);

153 const AtomCoord

* atom2 =

object

->coordSets.front()->atomSet->GetAtom(ap2,

true

);

156 if

(atom1 && atom2 &&

157

(atom1->

site

- atom2->

site

).length() <=

164 id

, prevResidue->

alphaID

170

(

const_cast<Bond

>

(prevBond))->nextVirtual = bond;

180

prevResidue = residue;

193 int

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

196

j->GetObject().GetAtom_id_1(),

197

j->GetObject().GetAtom_id_2(),

203

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

206 disulfideMap

[j->GetObject().GetAtom_id_1().GetResidue_id().Get()] =

207

j->GetObject().GetAtom_id_2().GetResidue_id().Get();

208 disulfideMap

[j->GetObject().GetAtom_id_2().GetResidue_id().Get()] =

209

j->GetObject().GetAtom_id_1().GetResidue_id().Get();

220 static const Vector

gray(.5,.5,.5);

225

ResidueMap::const_iterator

residues

.find(sequenceIndex + 1);

228 const Residue

*residue =

->second;

237 const AtomCoord

*atomCoord =

object

->coordSets.front()->atomSet->

239 if

(!atomCoord)

return

gray;

243 return

style.

color

;

251 ERRORMSG

(

"Can't align structures with multiple CoordSets"

);

256 for

(

int i

=0;

<nResidues; ++

) {

260 if

(seqIndexes[

] < 0)

262 int

rID = seqIndexes[

] + 1;

264

ResidueMap::const_iterator

residues

.find(rID);

266 ERRORMSG

(

"Can't find residueID "

<< rID

273 int

aID = (

->second->alphaID);

275 WARNINGMSG

(

"No alpha atom in residueID "

<< rID

283 const AtomCoord

* atomCoord =

object

->coordSets.front()->atomSet->GetAtom(atom);

286

id

",r"

<< rID <<

",a"

<< aID <<

")"

);

290

coords[

] = &(atomCoord->

site

);

300 if

DrawAll

(atomSet))

return false

;

310 static const Vector

white(1,1,1), black(0,0,0);

311 const Vector

& labelColor =

315 for

(

int

startTerminus=1; startTerminus>=0; --startTerminus) {

319 int

res = startTerminus ? 1 :

residues

.size(),

320

resEnd = startTerminus ?

residues

.size() : 1,

321

resInc = startTerminus ? 1 : -1;

325 for

(; res!=resEnd; res+=resInc) {

333

alphaPos = &(atom->

site

);

335

}

else if

(!prevPos) {

336

prevPos = &(atom->

site

);

342 if

(!(alphaPos && prevPos)) {

343 WARNINGMSG

(

"Molecule::DrawAllWithTerminiLabels() - " 344

"can't get two terminal alpha coords"

);

348 Vector

labelPosition = *alphaPos + 0.5 * (*alphaPos - *prevPos);

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)

static const CBiostruc_residue_graph_set * standardDictionary

const AtomCoord * GetAtom(const AtomPntr &atom, bool getAny=false, bool suppressWarning=false) const

const Bond * previousVirtual

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

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)

static bool IsLightColor(const Vector &color)

std::list< ncbi::CRef< ncbi::objects::CSeq_id > > SeqIdList

static const MoleculeIdentifier * GetIdentifier(const Molecule *molecule, const SeqIdList &ids)

std::vector< int > residueDomains

int GetAlphaCoords(int nResidues, const int *seqIndexes, const Vector **coords) const

DisulfideMap disulfideMap

bool IsNucleotide(void) const

Vector GetResidueColor(int sequenceIndex) const

std::vector< eSecStruc > residueSecondaryStructures

static const int NO_DOMAIN_SET

const MoleculeIdentifier * identifier

bool DrawAllWithTerminiLabels(const AtomSet *atomSet=NULL) const

BondList interResidueBonds

Molecule(ChemicalGraph *parentGraph, const ncbi::objects::CMolecule_graph &graph, const ResidueGraphList &standardDictionary, const ResidueGraphList &localDictionary)

bool IsProtein(void) const

unsigned int NResidues(void) const

void DrawLabel(const std::string &text, const Vector &center, const Vector &color)

int NAtomsWithAnyCoords(void) const

static const int NO_ALPHA_ID

bool OverlayConfEnsembles(void) const

bool IsVisible(const StructureBase *entity) const

virtual bool DrawAll(const AtomSet *atomSet=NULL) const

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

ShowHideManager * showHideManager

OpenGLRenderer * renderer

StyleManager * styleManager

const StyleSettings & GetGlobalStyle(void) const

bool GetAtomStyle(const Residue *residue, const AtomPntr &atom, const AtomCoord *coord, AtomStyle *atomStyle, const StyleSettings::BackboneStyle **saveBackboneStyle=NULL, const StyleSettings::GeneralStyle **saveGeneralStyle=NULL) const

LabelStyle nucleotideLabels

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

const TPrim & Get(void) const

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

bool IsSetInter_residue_bonds(void) const

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

const TDescr & GetDescr(void) const

Get the Descr member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

const TInter_residue_bonds & GetInter_residue_bonds(void) const

Get the Inter_residue_bonds member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetSeq_id(void) const

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

const TResidue_sequence & GetResidue_sequence(void) const

Get the Residue_sequence member data.

std::list< ncbi::CRef< ncbi::objects::CResidue_graph > > ResidueGraphList

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

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