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Public Member Functions
ResidueBase Class Reference

#include <residue_base.hh>

Inherits GenericPropContainer< ResidueBase >.

Inherited by ResidueHandle, and ResidueView.

Public Member Functions

 ResidueBase ()
 
 ResidueBase (const impl::ResidueImplPtr &impl)
 
 ResidueBase (const ResidueBase &rhs)
 
- Public Member Functions inherited from GenericPropContainer< ResidueBase >
void ClearProps ()
 
void SetStringProp (const String &key, const String &value)
 
void SetFloatProp (const String &key, Real value)
 
void SetIntProp (const String &key, int value)
 
void SetBoolProp (const String &key, bool value)
 
void SetVec3Prop (const String &key, geom::Vec3 value)
 
void RemoveProp (const String &key)
 
- Public Member Functions inherited from ConstGenericPropContainer< ResidueBase >
bool HasProp (const String &key) const
 
String GetPropAsString (const String &key) const
 
String GetStringProp (const String &key) const
 
String GetStringProp (const String &key, const String &def) const
 
Real GetFloatProp (const String &key) const
 
Real GetFloatProp (const String &key, Real def) const
 
int GetIntProp (const String &key) const
 
int GetIntProp (const String &key, int def) const
 
bool GetBoolProp (const String &key) const
 
bool GetBoolProp (const String &key, bool def) const
 
geom::Vec3 GetVec3Prop (const String &key) const
 
std::map< String,
GenericPropValue
GetPropMap () const
 
std::vector< StringGetPropList () const
 

Handle validity

class ConstGenericPropContainer< ResidueBase >
 
 operator bool () const
 
bool IsValid () const
 
const ResNumGetNumber () const
 
const ResidueKeyGetKey () const
 
const StringGetName () const
 
String GetQualifiedName () const
 
AtomHandle GetCentralAtom () const
 
void SetCentralAtom (const AtomHandle &a)
 
geom::Vec3 GetCentralNormal () const
 
bool IsPeptideLinking () const
 
bool IsNucleotideLinking () const
 
ChemClass GetChemClass () const
 
void SetChemClass (ChemClass cc)
 
ChemType GetChemType () const
 
void SetChemType (ChemType ct)
 
SecStructure GetSecStructure () const
 
void SetSecStructure (SecStructure ss)
 
TorsionHandle GetPhiTorsion () const
 
TorsionHandle GetPsiTorsion () const
 
TorsionHandle GetOmegaTorsion () const
 
char GetOneLetterCode () const
 
void SetOneLetterCode (char olc)
 
String GetStringProperty (Prop::ID prop_id) const
 
Real GetFloatProperty (Prop::ID prop_id) const
 
int GetIntProperty (Prop::ID prop_id) const
 
bool IsProtein () const
 
void SetIsProtein (bool protein)
 
void SetIsLigand (bool ligand)
 
bool IsLigand () const
 
impl::ResidueImplPtrImpl ()
 
const impl::ResidueImplPtrImpl () const
 
GenericPropContainerImplGpImpl ()
 
const GenericPropContainerImplGpImpl () const
 
void CheckValidity () const
 

Additional Inherited Members

- Protected Member Functions inherited from ConstGenericPropContainer< ResidueBase >
gp_get (const String &key) const
 
gp_get (const String &key, const T &def) const
 
GenericPropContainerImplGetImpl ()
 
const GenericPropContainerImplGetImpl () const
 

Detailed Description

base class for ResidueHandle and ResidueView

This class implements the common functionality for both ResidueHandle and ResidueView.

Like atoms and chains, residues are generic property containers and as such can store user-defined properties.

Each residue has a residue number that uniquely identifies the residue in a chain. This number consists of a numeric part and an optional alphanumeric insertion code.

Residues have names that are usually 3 characters long. The most common residue types such as the 20 standard amino acids and nucleotides also have a defined one-letter code. For other residues, the one-letter code is set to ?.

Residues have a chemical class. For standard amino acids this class is ChemClass::L_PEPTIDE_LINKING, indicating that the residue is capable to participate in a peptide bond. For nucleotides, the chemical class is either ChemClass::RNA_LINKING or ChemClass::DNA_LINKING. For unknown compounds the chemical class is ChemClass::UNKNOWN.

In addition, residues have a ChemType. A classification of all components into nine categories (ions, non-canonical molecules, saccharised, nucleotides, amino acids, co-enzymes, water coordinated ions, drugs, solvents) as obtained from the PDB.

Definition at line 65 of file residue_base.hh.

Constructor & Destructor Documentation

ResidueBase ( const impl::ResidueImplPtr impl)
ResidueBase ( const ResidueBase rhs)

Member Function Documentation

void CheckValidity ( ) const
protected
AtomHandle GetCentralAtom ( ) const

returns main atom, ie CA for amino acids

geom::Vec3 GetCentralNormal ( ) const
Returns
return specific normal of residue, usually CA-CB dir for AA
ChemClass GetChemClass ( ) const
ChemType GetChemType ( ) const

PDB ligand classification from component dictionary.

Real GetFloatProperty ( Prop::ID  prop_id) const

Get float property by id.

int GetIntProperty ( Prop::ID  prop_id) const

Get int property by id.

const ResidueKey& GetKey ( ) const

return the residue key.

const String& GetName ( ) const

return the residue name, at the moment an alias for GetKey().

const ResNum& GetNumber ( ) const

return residue number

TorsionHandle GetOmegaTorsion ( ) const

Get omega torsion.

If no omega torsion has been assigned to this residue an invalid TorsionHandle will be returned.

char GetOneLetterCode ( ) const
TorsionHandle GetPhiTorsion ( ) const

Get phi torsion.

If no phi torsion has been assigned to this residue an invalid TorsionHandle will be returned.

TorsionHandle GetPsiTorsion ( ) const

Get psi torsion.

If no psi torsion has been assigned to this residue an invalid TorsionHandle will be returned.

String GetQualifiedName ( ) const

get fully qualified name of residue, including the chain name, residue name and residue number

SecStructure GetSecStructure ( ) const

Get secondary structure type. By default, the residue is in COIL conformation.

String GetStringProperty ( Prop::ID  prop_id) const

Get String property by id.

GenericPropContainerImpl* GpImpl ( )
protected
const GenericPropContainerImpl* GpImpl ( ) const
protected
const impl::ResidueImplPtr& Impl ( ) const
bool IsLigand ( ) const
bool IsNucleotideLinking ( ) const

whether the residue can be part of a polynucleotide

bool IsPeptideLinking ( ) const

whether the residue can form peptide bonds

bool IsProtein ( ) const

whether the residue is part of the protein.

bool IsValid ( ) const

check validity of handle

See Also
operator bool()
operator bool ( ) const
inline

check validity of handle

check, whether the residue handle points to a valid residue.

Note
It is an error to use any method other than IsValid, Impl and operator bool() when the handle is invalid. An InvalidHandle exception will be thrown.

Definition at line 81 of file residue_base.hh.

void SetCentralAtom ( const AtomHandle a)

set explicit central atom

overrides the heuristic of GetCentralAtom to explicitely use the given one as the central atom; passing in an invalid handle reverts back to the heurstic determination

void SetChemClass ( ChemClass  cc)
void SetChemType ( ChemType  ct)
void SetIsLigand ( bool  ligand)
void SetIsProtein ( bool  protein)
void SetOneLetterCode ( char  olc)
void SetSecStructure ( SecStructure  ss)

Set secondary structure type.

See Also
ResidueHandle::GetSecStructure

Friends And Related Function Documentation

friend class ConstGenericPropContainer< ResidueBase >
friend

Definition at line 85 of file residue_base.hh.


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