OBResidue Class Reference

Residue information. More...

#include <openbabel/residue.h>

Inheritance diagram for OBResidue:
OBBase

List of all members.

Public Member Functions

 OBResidue (void)
 OBResidue (const OBResidue &)
virtual ~OBResidue (void)
OBResidueoperator= (const OBResidue &)
void AddAtom (OBAtom *atom)
void InsertAtom (OBAtom *atom)
void RemoveAtom (OBAtom *atom)
bool Clear ()
void SetName (const std::string &resname)
void SetNum (const unsigned int resnum)
void SetNum (const std::string resnum)
void SetChain (const char chain)
void SetChainNum (const unsigned int chainnum)
void SetIdx (const unsigned int idx)
void SetAtomID (OBAtom *atom, const std::string &id)
void SetHetAtom (OBAtom *atom, bool hetatm)
void SetSerialNum (OBAtom *atom, unsigned int sernum)
std::string GetName (void) const
unsigned int GetNum (void)
std::string GetNumString (void)
unsigned int GetNumAtoms () const
char GetChain (void) const
unsigned int GetChainNum (void) const
unsigned int GetIdx (void) const
unsigned int GetResKey (void) const
std::vector< OBAtom * > GetAtoms (void) const
std::vector< OBBond * > GetBonds (bool exterior=true) const
std::string GetAtomID (OBAtom *atom) const
unsigned GetSerialNum (OBAtom *atom) const
bool GetAminoAcidProperty (int) const
bool GetAtomProperty (OBAtom *a, int) const
bool GetResidueProperty (int) const
bool IsHetAtom (OBAtom *atom) const
bool IsResidueType (int) const
virtual OBBaseDoTransformations (const std::map< std::string, std::string > *, OBConversion *)
template<class T >
T * CastAndClear (bool clear=true)
virtual const char * GetTitle (bool replaceNewlines=true) const
virtual void SetTitle (const char *)
Iterator methods
OBAtomIterator BeginAtoms ()
OBAtomIterator EndAtoms ()
OBAtomBeginAtom (std::vector< OBAtom * >::iterator &i)
OBAtomNextAtom (std::vector< OBAtom * >::iterator &i)
Generic data handling methods (via OBGenericData)
bool HasData (const std::string &)
bool HasData (const char *)
bool HasData (const unsigned int type)
void DeleteData (unsigned int type)
void DeleteData (OBGenericData *)
void DeleteData (std::vector< OBGenericData * > &)
bool DeleteData (const std::string &s)
void SetData (OBGenericData *d)
void CloneData (OBGenericData *d)
size_t DataSize () const
OBGenericDataGetData (const unsigned int type)
OBGenericDataGetData (const std::string &)
OBGenericDataGetData (const char *)
std::vector< OBGenericData * > & GetData ()
std::vector< OBGenericData * > GetData (DataOrigin source)
std::vector< OBGenericData * > GetAllData (const unsigned int type)
OBDataIterator BeginData ()
OBDataIterator EndData ()

Static Public Member Functions

static const char * ClassDescription ()

Protected Attributes

unsigned int _idx
char _chain
unsigned int _aakey
unsigned int _reskey
std::string _resnum
std::string _resname
std::vector< bool > _hetatm
std::vector< std::string > _atomid
std::vector< OBAtom * > _atoms
std::vector< unsigned int > _sernum
std::vector< OBGenericData * > _vdata

Detailed Description

Residue information.

The residue information is drawn from PDB or MOL2 files (or similar), which track biomolecule information, and are stored in the OBResidue class. OBResidues are stored inside the OBAtom class and OBMol classes. The residue information for an atom can be requested in the following way:

      OBAtom *atom;
      OBResidue *r;
      atom = mol.GetAtom(1);
      r = atom->GetResidue();

The residue information for a molecule can be manipulated too:

      cout << "This molecule has " << mol.NumResidues() << " residues." << endl;
      OBResidue *r;
      r = mol.GetResidue(1);

Constructor & Destructor Documentation

OBResidue ( void   )

Constructor.

OBResidue ( const OBResidue src )

Copy constructor.

~OBResidue ( void   ) [virtual]

Destructor.


Member Function Documentation

OBResidue & operator= ( const OBResidue src )
void AddAtom ( OBAtom atom )

Add atom to this residue. Updates the atom via OBAtom::SetResidue()

Referenced by OBMol::AddHydrogens(), OBResidue::InsertAtom(), and OBMol::operator=().

void InsertAtom ( OBAtom atom )

Add atom to this residue. Updates the atom via OBAtom::SetResidue()

void RemoveAtom ( OBAtom atom )

Remove atom from this residue and update the atom.

bool Clear ( void   ) [virtual]

Clear any and all data associated with this residue. Updates all atoms included in the residue, as well as calling OBBase::Clear() for any generic data.

Returns:
Whether the call was successful.

Reimplemented from OBBase.

void SetName ( const std::string &  resname )

Set the name of this residue (e.g., "ALA"). Use 3-char PDB standard names. http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_79.html MODRES records for modified residues: http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_36.html.

Referenced by OBMol::operator=().

void SetNum ( const unsigned int  resnum )

Set the residue number (in the sequence)

Referenced by OBMol::operator=().

void SetNum ( const std::string  resnum )
void SetChain ( const char  chain )

Set the chain ID for this residue.

Referenced by OBMol::operator=().

void SetChainNum ( const unsigned int  chainnum )

Set the chain number for this residue.

Referenced by OBMol::operator=().

void SetIdx ( const unsigned int  idx )

Set the internal index of this residue in the parent OBMol. Intended mostly for internal use

Referenced by OBMol::AddResidue(), and OBMol::NewResidue().

void SetAtomID ( OBAtom atom,
const std::string &  id 
)

Set the character code ID for an ATOM record for the supplied atom This does nothing if the supplied atom is not found in the residue

Referenced by OBMol::AddHydrogens(), and OBMol::operator=().

void SetHetAtom ( OBAtom atom,
bool  hetatm 
)

Referenced by OBMol::operator=().

void SetSerialNum ( OBAtom atom,
unsigned int  sernum 
)

Set the atomic serial number for a given atom (see OBSerialNums)

Referenced by OBMol::operator=().

string GetName ( void   ) const
Returns:
The residue name

Referenced by OBResidueData::AssignBonds(), and OBMol::operator=().

unsigned int GetNum ( void   )
Returns:
The residue number (in the sequence)
std::string GetNumString ( void   )
unsigned int GetNumAtoms ( void   ) const
Returns:
The number of atoms in this residue
char GetChain ( void   ) const
Returns:
The ID of the chain which includes this residue

Referenced by OBResidueData::AssignBonds(), and OBMol::operator=().

unsigned int GetChainNum ( void   ) const
Returns:
The number of the chain which includes this residue

Referenced by OBMol::operator=().

unsigned int GetIdx ( void   ) const
Returns:
The internal index of this residue in the parent OBMol

Referenced by OBMol::DeleteResidue().

unsigned int GetResKey ( void   ) const
Returns:
The residue key (i.e., an entry in the OBResidueIndex namespace)
vector< OBAtom * > GetAtoms ( void   ) const
Returns:
a vector of all atoms in this residue
vector< OBBond * > GetBonds ( bool  exterior = true ) const
Returns:
all bonds in this residue. exterior includes bonds to atoms outside this residue (default is true)
string GetAtomID ( OBAtom atom ) const
Returns:
the atom ID (character code) for the supplied atom or "" if the atom is not found in this residue

Referenced by OBResidueData::AssignBonds(), OBResidue::GetAtomProperty(), and OBMol::operator=().

unsigned int GetSerialNum ( OBAtom atom ) const
Returns:
the serial number of the supplied atom (uses OBSerialNums)

Referenced by OBMol::operator=().

bool GetAminoAcidProperty ( int  property ) const
Returns:
Whether this residue has the supplied amino acid property defined from the OBAminoAcidProperty namespace
bool GetAtomProperty ( OBAtom a,
int  property 
) const
Returns:
Whether atom a has the supplied residue atom property defined from the OBResidueAtomProperty namespace
bool GetResidueProperty ( int  property ) const
Returns:
Whether this residue has the supplied property defined from the OBResidueProperty namespace

Referenced by OBResidue::GetAtomProperty().

bool IsHetAtom ( OBAtom atom ) const
Returns:
If the given atom is a HETATM record

Referenced by OBResidue::GetAtomProperty(), and OBMol::operator=().

bool IsResidueType ( int  restype ) const
Returns:
If this residue matches the supplied restype Set by SetResidueKeys()
OBAtomIterator BeginAtoms (  ) [inline]
Returns:
An iterator to the beginning of the atom list in this residue
OBAtomIterator EndAtoms (  ) [inline]
Returns:
An iterator to the end of the atom list in this residue
OBAtom * BeginAtom ( std::vector< OBAtom * >::iterator &  i )

Set the iterator i to the beginning of the atom list in this residue

Returns:
The first atom (or NULL if none exist)

Referenced by OBMol::operator=().

OBAtom * NextAtom ( std::vector< OBAtom * >::iterator &  i )

Increment the iterator i

Returns:
The next atom (or NULL if none exist)

Referenced by OBResidueAtomIter::operator++(), and OBMol::operator=().

virtual OBBase* DoTransformations ( const std::map< std::string, std::string > *  ,
OBConversion  
) [inline, virtual, inherited]

Perform a set of transformations specified by the user

Typically these are program options to filter or modify an object For example, see OBMol::DoTransformations() and OBMol::ClassDescription() Base type does nothing

Reimplemented in OBMol.

static const char* ClassDescription (  ) [inline, static, inherited]
Returns:
A list of descriptions of command-line options for DoTransformations()

Reimplemented in OBMol, and OBReaction.

T* CastAndClear ( bool  clear = true ) [inline, inherited]

By default clears the object. Called from ReadMolecule of most format classes.

virtual const char* GetTitle ( bool  replaceNewlines = true ) const [inline, virtual, inherited]

Base type does nothing Made virtual around r3535 to simplify code which passes around OBBase*.

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

virtual void SetTitle ( const char *   ) [inline, virtual, inherited]

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

bool HasData ( const char *  s ) [inherited]
Returns:
whether the generic attribute/value pair exists
bool HasData ( const unsigned int  type ) [inherited]
Returns:
whether the generic attribute/value pair exists, for a given OBGenericDataType
void DeleteData ( unsigned int  type ) [inherited]
void DeleteData ( OBGenericData gd ) [inherited]

Delete the given generic data from this object.

void DeleteData ( std::vector< OBGenericData * > &  vg ) [inherited]

Delete all of the given generic data from this object.

bool DeleteData ( const std::string &  s ) [inherited]

Deletes the generic data with the specified attribute, returning false if not found.

void CloneData ( OBGenericData d ) [inherited]

Adds a copy of a data object; does nothing if d == NULL

Since:
version 2.2
size_t DataSize (  ) const [inline, inherited]
Returns:
the number of OBGenericData items attached to this molecule.
OBGenericData * GetData ( const std::string &  s ) [inherited]
Returns:
any data matching the given attribute name or NULL if nothing matches
the value given an attribute name
OBGenericData * GetData ( const char *  s ) [inherited]
Returns:
any data matching the given attribute name or NULL if nothing matches
the value given an attribute name
std::vector<OBGenericData*>& GetData (  ) [inline, inherited]
Returns:
all data, suitable for iterating

Referenced by OBMol::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().

std::vector< OBGenericData * > GetData ( DataOrigin  source ) [inherited]
Returns:
all data with a specific origin, suitable for iterating
std::vector< OBGenericData * > GetAllData ( const unsigned int  type ) [inherited]
Returns:
the all matching data for a given type from OBGenericDataType or an empty vector if nothing matches
Since:
version 2.2

Referenced by OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().

OBDataIterator BeginData (  ) [inline, inherited]
Returns:
An iterator pointing to the beginning of the data

Referenced by OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

OBDataIterator EndData (  ) [inline, inherited]
Returns:
An iterator pointing to the end of the data

Referenced by OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().


Member Data Documentation

unsigned int _idx [protected]

Residue index (i.e., internal index in an OBMol)

Referenced by OBResidue::Clear(), OBResidue::GetIdx(), and OBResidue::SetIdx().

std::string _resnum [protected]
std::vector<OBGenericData*> _vdata [protected, inherited]

Custom data.

Referenced by OBMol::OBMol().


The documentation for this class was generated from the following files:
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