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

(

==

||

==

)) ||

(

==

||

==

||

==

||

==

)) ||

& residue,

moleculeID,

nResidues,

moleculeType) :

dictionary = &localDictionary;

(

<<

<<

);

ResidueGraphList::const_iterator

, ie=dictionary->end();

(

=dictionary->begin();

!=ie; ++

) {

(

->GetObject().GetId().Get() == graphID) {

residueGraph =

->GetPointer();

(

<<

<<

<< graphID);

CResidue_graph::TDescr::const_iterator j, je = residueGraph->

().end();

(j=residueGraph->

().begin(); j!=je; ++j) {

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

(

);

CResidue_graph::TAtoms::const_iterator

, ae = residueGraph->

().end();

(

=residueGraph->

().begin();

!=ae; ++

) {

& atom =

->GetObject();

atomID = atom.

().

();

ap(moleculeID,

, atomID);

StructureObject::CoordSetList::const_iterator c, ce=

->coordSets.end();

(c=object->

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

(((*c)->atomSet->GetAtom(ap,

,

))) {

->residue =

;

->atomicNumber =

(atomicNumber);

->isIonizableProton =

;

->isIonizableProton =

;

(

<<

<<

<< atom.

().

());

CResidue_graph::TBonds::const_iterator

, be = residueGraph->

().end();

(

=residueGraph->

().begin();

!=be; ++

) {

order =

->GetObject().IsSetBond_order() ?

moleculeID,

,

->GetObject().GetAtom_id_1().Get(),

moleculeID,

,

->GetObject().GetAtom_id_2().Get(),

(bond)

.push_back(bond);

AtomInfoMap::iterator

, ae =

.end();

(

=

.begin();

!=ae; ++

)

->second;

(

);

(

);

alphaVisible =

, alphaOnly =

;

AtomInfoMap::const_iterator

, ae =

.end();

atom = atomSet->

(ap, overlayEnsembles,

);

(!atom)

;

((proteinLabel || nucleotideLabel) &&

->second->classification !=

) {

(

->second->name ==

) {

labelColor = atomStyle.

;

(

->second->name ==

) l2 = atom;

(

->second->name ==

) l3 = atom;

(

->second->name ==

) {

labelColor = atomStyle.

;

(l1 && (!l2 || !l3)) {

Molecule::ResidueMap::const_iterator prevRes, nextRes;

((prevRes=molecule->

.find(

- 1)) != molecule->

.end() &&

(prevAlpha=atomSet->

(

(molecule->

,

- 1, prevRes->second->alphaID))) !=

&&

(nextRes=molecule->

.find(

+ 1)) != molecule->

.end() &&

(nextAlpha=atomSet->

(

(molecule->

,

+ 1, nextRes->second->alphaID))) !=

)

(alphaVisible && (proteinLabel|| nucleotideLabel)) {

forward = - ((l2->site - l1->

) + (l3->site - l1->

));

labelPosition = l1->

+ 1.5 * forward;

up = vector_cross(l2->site - l1->

, l3->site - l1->

);

forward = (-((l2->site - l1->

) + (l3->site - l1->

)) / 2);

labelPosition = l1->

+ 1.5 * forward + 1.5 * up;

(

=0;

<

.size() &&

<3; ++

)

forward = - ((l2->site - l1->

) + (l3->site - l1->

));

labelPosition = l1->

+ 3 * forward;

labelPosition = l3->site + 3 * (l3->site - l2->site);

(

=0;

<3; ++

)

(oss.str().size() > 0) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

StyleManager::eDisplayStyle style

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

static bool IsLightColor(const Vector &color)

const Vector & Get(eColor which) const

bool IsHighlighted(const Molecule *molecule, int residueID) const

void DrawAtom(const Vector &site, const AtomStyle &atomStyle)

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

bool IsNucleotide(void) const

static const char NO_CODE

bool Draw(const AtomSet *atomSet) const

Residue(StructureBase *parent, const ncbi::objects::CResidue &residue, int moleculeID, const ResidueGraphList &standardDictionary, const ResidueGraphList &localDictionary, int nResidues, int moleculeType)

static const int NO_ALPHA_ID

bool IsAminoAcid(void) const

bool OverlayConfEnsembles(void) const

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

unsigned int CreateName(const Residue *residue, int atomID)

ShowHideManager * showHideManager

OpenGLRenderer * renderer

StyleManager * styleManager

const StyleSettings & GetStyleForResidue(const StructureObject *object, int moleculeID, int residueID) 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

void Set(double xs, double ys, double zs)

const Colors * GlobalColors(void)

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.

TResidue_type GetResidue_type(void) const

Get the Residue_type member data.

bool IsSetIupac_code(void) const

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

const TDescr & GetDescr(void) const

Get the Descr member data.

const TName & GetName(void) const

Get the Name member data.

bool IsSetDescr(void) const

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

const TResidue_graph_id & GetResidue_graph_id(void) const

Get the Residue_graph_id member data.

const TIupac_code & GetIupac_code(void) const

Get the Iupac_code member data.

const TBiostruc_residue_graph_set_id & GetBiostruc_residue_graph_set_id(void) const

Get the Biostruc_residue_graph_set_id member data.

TIonizable_proton GetIonizable_proton(void) const

Get the Ionizable_proton member data.

bool IsStandard(void) const

Check if variant Standard is selected.

bool IsSetResidue_type(void) const

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

const TResidue_graph & GetResidue_graph(void) const

Get the Residue_graph member data.

bool IsSetName(void) const

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

bool IsLocal(void) const

Check if variant Local is selected.

const TLocal & GetLocal(void) const

Get the variant data.

const TName & GetName(void) const

Get the Name member data.

const TBonds & GetBonds(void) const

Get the Bonds member data.

const TIupac_code & GetIupac_code(void) const

Get the Iupac_code member data.

TElement GetElement(void) const

Get the Element member data.

bool IsSetIupac_code(void) const

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

const TId & GetId(void) const

Get the Id member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetName(void) const

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

bool IsSetIonizable_proton(void) const

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

const TStandard & GetStandard(void) const

Get the variant data.

const TAtoms & GetAtoms(void) const

Get the Atoms member data.

bool IsOther_database(void) const

Check if variant Other_database is selected.

const TOther_database & GetOther_database(void) const

Get the variant data.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TDb & GetDb(void) const

Get the Db member data.

TId GetId(void) const

Get the variant data.

Messenger * GlobalMessenger(void)

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

static Residue::eAtomClassification ClassifyAtom(const Residue *residue, const CAtom &atom)

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