#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 ResNum &	GetNumber () const

void	SetNumber (const ResNum &num)

const ResidueKey &	GetKey () 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 AtomImplList &	GetAtomList () const

AtomImplList &	GetAtomList ()

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 TorsionImplList &	GetTorsionList () const

bool	HasAltAtomGroup (const String &group) const

std::vector< String >	GetAltAtomGroupNames () const

std::vector< String >	GetAltAtomGroupNames (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 String &	GetCurrentAltGroupName () const

int	GetIndex () const

String	GetQualifiedName () const

const String &	GetName () const

TorsionImplList &	GetTorsionList ()

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)

GenericPropContainerImpl &	operator= (const GenericPropContainerImpl &r)

GenericPropValue &	GenericProp (const String &key)

const GenericPropValue &	GenericProp (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< String >	GetPropList () 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:

stage/include/ost/mol/impl/residue_impl.hh

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation