Detailed Description

A decorator for a residue.

As with the Atom, the names of residues may be expanded dynamically. This can be easily done in an analogous manner when we need it.

Inheritance diagram for IMP::atom::Residue:

Public Member Functions
	Residue (Model *m, ParticleIndex id)
	Residue (::IMP::Particle *p)
Int	get_index () const
	The residues index in the chain.
char	get_insertion_code () const
bool	get_is_dna () const
bool	get_is_protein () const
bool	get_is_rna () const
ResidueType	get_residue_type () const
void	set_index (Int t)
void	set_insertion_code (char insertion_code)
void	set_residue_type (ResidueType t)
	Update the stored ResidueType and the atom::Hierarchy::Name.
Static Public Member Functions
static Residue	decorate_particle (::IMP::Particle *p)
static IntKey	get_index_key ()
static IntKey	get_insertion_code_key ()
static IntKey	get_residue_type_key ()
static bool	particle_is_instance (Particle *p)
static Residue	setup_particle (Particle *p, ResidueType t=UNK, int index=-1, int insertion_code=32)
	Add the required attributes to the particle and create a Residue.
static Residue	setup_particle (Particle *p, Residue o)
	Copy data from the other Residue to the particle p.
Related Functions
(Note that these are not member functions.)
Chain	get_chain (Residue rd, bool nothrow=false)
Hierarchy	get_next_residue (Residue rd)
Atoms	get_phi_dihedral_atoms (Residue rd)
Hierarchy	get_previous_residue (Residue rd)
Atoms	get_psi_dihedral_atoms (Residue rd)

Member Function Documentation

Int IMP::atom::Residue::get_index ( ) const

The residues index in the chain.

static bool IMP::atom::Residue::particle_is_instance ( Particle * p ) [static]

Check if the particle has the needed attributes for a cast to succeed

void IMP::atom::Residue::set_residue_type ( ResidueType t )

Update the stored ResidueType and the atom::Hierarchy::Name.

static Residue IMP::atom::Residue::setup_particle	(	Particle *	p,
		ResidueType	t = `UNK`,
		int	index = `-1`,
		int	insertion_code = `32`
	)		`[static]`

Add the required attributes to the particle and create a Residue.

static Residue IMP::atom::Residue::setup_particle	(	Particle *	p,
		Residue	o
	)		`[static]`

Copy data from the other Residue to the particle p.

Return the chain containing the residue.

Exceptions:

ValueException if no residue is found, unless nothrow is true.

Hierarchy get_next_residue ( Residue rd ) [related]

Return the residue from the same chain with one higher index, or Hierarchy().

Note:: Currently, this function only works if the parent of rd is the chain. This should be fixed later. Ask if you need it.

The return type is Hierarchy since the particle representing the next residue might not be a Residue particle.

Atoms get_phi_dihedral_atoms ( Residue rd ) [related]

Return the atoms comprising the phi dihedral. If all atoms cannot be found, an empty list is returned.

Hierarchy get_previous_residue ( Residue rd ) [related]

Return the residue from the same chain with one lower index, or Hierarchy().

Atoms get_psi_dihedral_atoms ( Residue rd ) [related]

Return the atoms comprising the psi dihedral. If all atoms cannot be found, an empty list is returned.

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