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Public Member Functions
ResidueImpl Class Reference

#include <residue_impl.hh>

Inherits GenericPropContainerImpl, and enable_shared_from_this< ResidueImpl >.

Public Member Functions

 ResidueImpl (const EntityImplPtr &ent, const ChainImplPtr &ch, const ResNum &num, const ResidueKey &key)
 
AtomImplPtr InsertAtom (const String &name, const geom::Vec3 &pos, const String &ele)
 
AtomImplPtr InsertAtom (const AtomImplPtr &atom)
 
AtomImplPtr InsertAltAtom (const String &name, const String &alt_group, const geom::Vec3 &pos, const String &ele, Real occ, Real b_factor)
 
const ResNumGetNumber () const
 
void SetNumber (const ResNum &num)
 
const ResidueKeyGetKey () const
 
void SetKey (const ResidueKey &key)
 
ChainImplPtr GetChain () const
 
AtomImplPtr GetCentralAtom () const
 
void SetCentralAtom (const AtomImplPtr &a)
 
geom::Vec3 GetCentralNormal () const
 
char GetOneLetterCode () const
 
void SetOneLetterCode (const char olc)
 
AtomImplPtr FindAtom (const String &aname) const
 
void Apply (EntityVisitor &v)
 
int GetAtomCount () const
 
int GetBondCount () const
 
EntityImplPtr GetEntity () const
 
TorsionImplP GetPhiTorsion () const
 
TorsionImplP GetOmegaTorsion () const
 
TorsionImplP GetPsiTorsion () const
 
SecStructure GetSecStructure () const
 
void SetSecStructure (SecStructure ss)
 
const AtomImplListGetAtomList () const
 
AtomImplListGetAtomList ()
 
Real GetMass () const
 
geom::Vec3 GetCenterOfMass () const
 
geom::Vec3 GetCenterOfAtoms () const
 
geom::AlignedCuboid GetBounds () const
 
void DeleteAtom (const AtomImplPtr &atom)
 
void DeleteAtoms (const String &atom_name)
 
void DeleteAllAtoms ()
 
void AddTorsion (const TorsionImplP &torsion)
 
const TorsionImplListGetTorsionList () const
 
bool HasAltAtomGroup (const String &group) const
 
std::vector< StringGetAltAtomGroupNames () const
 
std::vector< StringGetAltAtomGroupNames (const AtomImplPtr &atom) const
 
bool HasAltAtoms () const
 
Real GetAverageBFactor () const
 
bool SwitchAtomPos (const String &group)
 
void AddAltAtomPos (const String &group, const AtomImplPtr &atom, const geom::Vec3 &position, Real occ, Real b_factor)
 
geom::Vec3 GetAltAtomPos (const AtomImplPtr &atom, const String &group) const
 
Real GetAltAtomOcc (const AtomImplPtr &atom, const String &group) const
 
Real GetAltAtomBFactor (const AtomImplPtr &atom, const String &group) const
 
const StringGetCurrentAltGroupName () const
 
int GetIndex () const
 
String GetQualifiedName () const
 
const StringGetName () const
 
TorsionImplListGetTorsionList ()
 
void SetChemClass (ChemClass cc)
 
ChemClass GetChemClass () const
 
ChemType GetChemType () const
 
void SetChemType (ChemType ct)
 
TorsionImplP FindTorsion (const String &torsion_name) const
 
String GetStringProperty (Prop::ID prop_id) const
 
Real GetFloatProperty (Prop::ID prop_id) const
 
int GetIntProperty (Prop::ID prop_id) const
 
void SetProtein (bool protein)
 
bool IsProtein () const
 
bool IsLigand () const
 
void SetIsLigand (bool flag)
 
void UpdateTransformedPos ()
 
- Public Member Functions inherited from GenericPropContainerImpl
 GenericPropContainerImpl ()
 
 ~GenericPropContainerImpl ()
 
 GenericPropContainerImpl (const GenericPropContainerImpl &rhs)
 
GenericPropContainerImploperator= (const GenericPropContainerImpl &r)
 
GenericPropValueGenericProp (const String &key)
 
const GenericPropValueGenericProp (const String &key) const
 
bool HasProp (const String &key) const
 
void ClearProps ()
 
void RemoveProp (const String &key)
 
void Assign (const GenericPropContainerImpl &impl)
 
PropertyMap GetPropMap () const
 
std::vector< StringGetPropList () const
 

Detailed Description

Definition at line 47 of file residue_impl.hh.

Constructor & Destructor Documentation

ResidueImpl ( const EntityImplPtr ent,
const ChainImplPtr ch,
const ResNum num,
const ResidueKey key 
)

Member Function Documentation

void AddAltAtomPos ( const String group,
const AtomImplPtr atom,
const geom::Vec3 position,
Real  occ,
Real  b_factor 
)
void AddTorsion ( const TorsionImplP torsion)
void Apply ( EntityVisitor v)
void DeleteAllAtoms ( )
void DeleteAtom ( const AtomImplPtr atom)
void DeleteAtoms ( const String atom_name)
AtomImplPtr FindAtom ( const String aname) const

Find atom by name.

Todo:
make the return type a AtomImplList, since there may be several atoms with the given name.
Returns
The first atom matchin the name, or an invalid AtomImplPtr if there is no such atom.
TorsionImplP FindTorsion ( const String torsion_name) const
Real GetAltAtomBFactor ( const AtomImplPtr atom,
const String group 
) const
std::vector<String> GetAltAtomGroupNames ( ) const
std::vector<String> GetAltAtomGroupNames ( const AtomImplPtr atom) const
Real GetAltAtomOcc ( const AtomImplPtr atom,
const String group 
) const
geom::Vec3 GetAltAtomPos ( const AtomImplPtr atom,
const String group 
) const
int GetAtomCount ( ) const

Get number of atoms of this residue.

const AtomImplList& GetAtomList ( ) const
AtomImplList& GetAtomList ( )
inline

Definition at line 136 of file residue_impl.hh.

Real GetAverageBFactor ( ) const

retrieve average temperature factor of residue.

int GetBondCount ( ) const

Get number of bonds of this residue.

geom::AlignedCuboid GetBounds ( ) const
geom::Vec3 GetCenterOfAtoms ( ) const
geom::Vec3 GetCenterOfMass ( ) const
AtomImplPtr GetCentralAtom ( ) const
geom::Vec3 GetCentralNormal ( ) const
ChainImplPtr GetChain ( ) const
ChemClass GetChemClass ( ) const
inline

Definition at line 201 of file residue_impl.hh.

ChemType GetChemType ( ) const
inline

Definition at line 204 of file residue_impl.hh.

const String& GetCurrentAltGroupName ( ) const
inline

Definition at line 178 of file residue_impl.hh.

EntityImplPtr GetEntity ( ) const
Real GetFloatProperty ( Prop::ID  prop_id) const
int GetIndex ( ) const
int GetIntProperty ( Prop::ID  prop_id) const
const ResidueKey& GetKey ( ) const
inline

Definition at line 66 of file residue_impl.hh.

Real GetMass ( ) const
const String& GetName ( ) const
inline

Get name of residue. At the moment an alias for GetKey.

Definition at line 189 of file residue_impl.hh.

const ResNum& GetNumber ( ) const
inline

Definition at line 63 of file residue_impl.hh.

TorsionImplP GetOmegaTorsion ( ) const

Retrieve omega torsion between this and the previous residue.

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

char GetOneLetterCode ( ) const
TorsionImplP GetPhiTorsion ( ) const

Get phi torsion.

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

TorsionImplP GetPsiTorsion ( ) const

Get psi torsion.

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

String GetQualifiedName ( ) const

Get fully qualified name of the residue, including chain name, residue name and number.

See Also
AtomHandle::GetQualifiedName()
SecStructure GetSecStructure ( ) const

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

String GetStringProperty ( Prop::ID  prop_id) const
const TorsionImplList& GetTorsionList ( ) const
inline

Definition at line 153 of file residue_impl.hh.

TorsionImplList& GetTorsionList ( )
inline

Get all torsions this residue is involved in.

Definition at line 194 of file residue_impl.hh.

bool HasAltAtomGroup ( const String group) const

Test if residue has alternative atoms with a certain name.

bool HasAltAtoms ( ) const
AtomImplPtr InsertAltAtom ( const String name,
const String alt_group,
const geom::Vec3 pos,
const String ele,
Real  occ,
Real  b_factor 
)
AtomImplPtr InsertAtom ( const String name,
const geom::Vec3 pos,
const String ele 
)
AtomImplPtr InsertAtom ( const AtomImplPtr atom)

insert new residue with exactly the same parameters as atom, but no bonds

bool IsLigand ( ) const
inline

Definition at line 224 of file residue_impl.hh.

bool IsProtein ( ) const
inline

Definition at line 222 of file residue_impl.hh.

void SetCentralAtom ( const AtomImplPtr a)

explicitely set central atom

if this is set, it will override the heuristic encoded in GetCentralAtom; pass an invalid ptr to deactivate again

void SetChemClass ( ChemClass  cc)
inline

Definition at line 198 of file residue_impl.hh.

void SetChemType ( ChemType  ct)
inline

Definition at line 207 of file residue_impl.hh.

void SetIsLigand ( bool  flag)
inline

Definition at line 225 of file residue_impl.hh.

void SetKey ( const ResidueKey key)
inline

Definition at line 70 of file residue_impl.hh.

void SetNumber ( const ResNum num)
inline

Definition at line 64 of file residue_impl.hh.

void SetOneLetterCode ( const char  olc)
void SetProtein ( bool  protein)
inline

Definition at line 220 of file residue_impl.hh.

void SetSecStructure ( SecStructure  ss)

Set secondary structure type.

bool SwitchAtomPos ( const String group)
void UpdateTransformedPos ( )

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