ResidueBase Class Reference

base class for ResidueHandle and ResidueView More...

#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)

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

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 (  ) 
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.

const GenericPropContainerImpl* GpImpl (  )  const [protected]
GenericPropContainerImpl* GpImpl (  )  [protected]
const impl::ResidueImplPtr& Impl (  )  const
impl::ResidueImplPtr& Impl (  ) 
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 [inline]

check validity of handle

See also:
operator bool()

Reimplemented in ResidueView.

Definition at line 84 of file residue_base.hh.

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.

Reimplemented in ResidueView.

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:
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