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NCBI C++ ToolKit: src/app/cn3d/structure_set.hpp Source File

std::list < const StructureObject * >

;

std::map < unsigned int, const Matrix * const * >

;

(

)

;

(

*filename,

doBinary,

*changeFlags);

std::list < ncbi::CRef < ncbi::objects::CReject_id > >

;

masterDomainID,

dependentDomainID);

(

structureLimit);

std::pair < const Residue*, int >

;

std::map < unsigned int, NamePair >

;

std::map < const Residue *, const Molecule * >

;

*

*masterCoords,

*

*dependentCoords,

*weights,

dependentRow);

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.

bool SetTransformToMaster(const ncbi::objects::CBiostruc_annot_set &annot, int masterMMDBID)

void RealignStructure(int nCoords, const Vector *const *masterCoords, const Vector *const *dependentCoords, const double *weights, int dependentRow)

void SelectByDistance(double cutoff, unsigned int options, ResidueMap *selectedResidues) const

std::map< int, const Molecule * > DomainMap

StructureObject(StructureBase *parent, const ncbi::objects::CBiostruc &biostruc, bool isMaster)

static const double NO_TEMPERATURE

std::vector< std::string > pdbIDs

std::list< const CoordSet * > CoordSetList

bool IsMaster(void) const

Matrix * transformToMaster

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

const ChemicalGraph * graph

DomainIDMap domainID2MMDB

std::map< int, int > DomainIDMap

std::map< const Residue *, const Molecule * > ResidueMap

bool IsDependent(void) const

static const int NO_MMDB_ID

bool IsCDDInMime(void) const

bool AddBiostrucToASN(ncbi::objects::CBiostruc *biostruc)

const AlignmentSet * alignmentSet

static const unsigned int eRowOrderData

std::vector< std::string > TextLines

const RejectList * GetRejects(void) const

void ShowRejects(void) const

std::map< const ncbi::objects::CBiostruc *, bool > usedStructures

bool Draw(const AtomSet *atomSet) const

void SetCenter(const Vector *setTo=NULL)

static const unsigned int eUserAnnotationData

void SelectByDistance(double cutoff, unsigned int options) const

void InitStructureAlignments(int masterMMDBID)

unsigned int lastDisplayList

const Sequence * FindOrCreateSequence(ncbi::objects::CBioseq &bioseq)

static const unsigned int eAnyAlignmentData

std::map< unsigned int, const Matrix *const * > TransformMap

unsigned int lastAtomName

ncbi::objects::CCdd_descr_set * GetCDDDescrSet(void)

TransformMap transformMap

const SequenceSet * sequenceSet

bool SetCDDDescription(const std::string &descr)

static const unsigned int eSelectProtein

void RemoveUnusedSequences(void)

static const unsigned int eSequenceData

bool havePrevPickedAtomCoord

StructureSet(ncbi::objects::CCdd *cdd, unsigned int structureLimit, OpenGLRenderer *r)

void ReplaceAlignmentSet(AlignmentSet *newAlignmentSet)

void LoadAlignmentsAndStructures(unsigned int structureLimit)

static const unsigned int eSelectNucleotide

void CenterViewOnStructure(void)

bool MatchSequenceToMoleculeInObject(const Sequence *seq, const StructureObject *obj, const Sequence **seqHandle=NULL)

static const unsigned int eSelectHeterogen

static const unsigned int eCDDData

bool IsMultiStructure(void) const

bool SaveASNData(const char *filename, bool doBinary, unsigned int *changeFlags)

bool LoadMaster(int masterMMDBID)

bool CenterViewOnAlignedResidues(void)

std::map< int, bool > usedFeatures

bool SetCDDName(const std::string &name)

void SelectedAtom(unsigned int name, bool setCenter)

void AddStructureAlignment(ncbi::objects::CBiostruc_feature *feature, int masterDomainID, int dependentDomainID)

bool SetCDDNotes(const TextLines &lines)

bool MonitorAlignments(void) const

void RemoveStructureAlignments(void)

Vector prevPickedAtomCoord

std::map< unsigned int, NamePair > NameMap

AlignmentManager * alignmentManager

std::pair< const Residue *, int > NamePair

void LoadSequencesForSingleStructure(void)

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

ShowHideManager * showHideManager

bool ConvertMimeDataToCDD(const std::string &cddName)

static const unsigned int eOtherData

std::list< unsigned int > DisplayLists

bool HasStructuredMaster(void) const

static const unsigned int eUpdateData

static const unsigned int eStructureAlignmentData

void ReplaceUpdates(ncbi::objects::CCdd::TPending &newUpdates)

static const unsigned int eStyleData

void VerifyFrameMap(void) const

const std::string & GetCDDName(void) const

std::vector< DisplayLists > FrameMap

OpenGLRenderer * renderer

void RejectAndPurgeSequence(const Sequence *reject, std::string reason, bool purge)

void SetDataChanged(unsigned int what) const

bool HasDataChanged(void) const

static const unsigned int eSelectSolvent

StructureSet(ncbi::objects::CNcbi_mime_asn1 *mime, unsigned int structureLimit, OpenGLRenderer *r)

void Load(unsigned int structureLimit)

StyleManager * styleManager

ASNDataManager * dataManager

std::list< const StructureObject * > ObjectList

static const unsigned int eSelectOtherMoleculesOnly

ncbi::objects::CAlign_annot_set * GetCDDAnnotSet(void)

const std::string & GetCDDDescription(void) const

bool GetAtomFromName(unsigned int name, const Residue **residue, int *atomID) const

static const unsigned int ePSSMData

std::list< ncbi::CRef< ncbi::objects::CReject_id > > RejectList

bool GetCDDNotes(TextLines *lines) const

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

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

The NCBI C++/STL use hints.

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

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