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core::conformation::parametric::ParametersSet Class Reference

ParametersSet class, used to store sets of parameters for parametric backbone generation. More...

#include <ParametersSet.hh>

Inheritance diagram for core::conformation::parametric::ParametersSet:
Inheritance graph
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Public Member Functions

 ParametersSet ()
 constructors More...
 
 ParametersSet (ParametersSet const &src)
 Copy constructor. More...
 
 ~ParametersSet () override
 
virtual ParametersSetOP clone () const
 Copy this residue( allocate actual memory for it ) More...
 
ParametersSetCOP get_self_ptr () const
 self pointers More...
 
ParametersSetOP get_self_ptr ()
 
ParametersSetCAP get_self_weak_ptr () const
 
ParametersSetAP get_self_weak_ptr ()
 
virtual void clear_parameters_list ()
 Delete all owning pointers in the parameters_ list and reset the list. More...
 
virtual void add_parameters (ParametersOP new_parameters)
 Add a Parameters object to the set included in this ParametersSet object. More...
 
void update_residue_links (core::conformation::Conformation &new_conf)
 Only for copying Conformation objects, this ensures that the new ParametersSet object's Parameters objects have lists of ResidueOPs that point to residues in the new Conformation object, rather than to residues that only exist in the Parameters objects. More...
 
core::Size n_parameters () const
 Get the number of Parameters objects associated with this ParametersSet. More...
 
ParametersOP parameters (core::Size const index)
 Get a Parameters object by index. More...
 
ParametersCOP parameters (core::Size const index) const
 Get a Parameters object by index (const-access). More...
 
virtual void get_pdb_remark (std::stringstream &remark) const
 Get a summary of this ParametersSet object, for output to remark lines of a PDB file. More...
 

Private Attributes

utility::vector1< ParametersOPparameters_
 List of pointers to parameters objects associated with this ParametersSet. More...
 

Detailed Description

ParametersSet class, used to store sets of parameters for parametric backbone generation.

Constructor & Destructor Documentation

core::conformation::parametric::ParametersSet::ParametersSet ( )

constructors

Constructor.

core::conformation::parametric::ParametersSet::ParametersSet ( ParametersSet const &  src)

Copy constructor.

References n_parameters(), parameters(), and parameters_.

core::conformation::parametric::ParametersSet::~ParametersSet ( )
overridedefault

Member Function Documentation

void core::conformation::parametric::ParametersSet::add_parameters ( ParametersOP  new_parameters)
virtual

Add a Parameters object to the set included in this ParametersSet object.

References parameters_.

void core::conformation::parametric::ParametersSet::clear_parameters_list ( )
virtual

Delete all owning pointers in the parameters_ list and reset the list.

References parameters_.

ParametersSetOP core::conformation::parametric::ParametersSet::clone ( ) const
virtual

Copy this residue( allocate actual memory for it )

make a copy of this residue( allocate actual memory for it )

Reimplemented in protocols::helical_bundle::parameters::BundleParametersSet.

void core::conformation::parametric::ParametersSet::get_pdb_remark ( std::stringstream &  remark) const
virtual

Get a summary of this ParametersSet object, for output to remark lines of a PDB file.

Default function can be overridden by derived classes. The default message just says that the parameterization does not support output to PDB remark lines. Note that messages must have lines less than about fifty characters, or they get truncated in REMARK output.

Reimplemented in protocols::helical_bundle::parameters::BundleParametersSet.

ParametersSetCOP core::conformation::parametric::ParametersSet::get_self_ptr ( ) const
inline

self pointers

ParametersSetOP core::conformation::parametric::ParametersSet::get_self_ptr ( )
inline
ParametersSetCAP core::conformation::parametric::ParametersSet::get_self_weak_ptr ( ) const
inline
ParametersSetAP core::conformation::parametric::ParametersSet::get_self_weak_ptr ( )
inline
core::Size core::conformation::parametric::ParametersSet::n_parameters ( ) const

Get the number of Parameters objects associated with this ParametersSet.

References parameters_.

Referenced by ParametersSet().

ParametersOP core::conformation::parametric::ParametersSet::parameters ( core::Size const  index)
ParametersCOP core::conformation::parametric::ParametersSet::parameters ( core::Size const  index) const

Get a Parameters object by index (const-access).

References parameters_.

void core::conformation::parametric::ParametersSet::update_residue_links ( core::conformation::Conformation new_conf)

Only for copying Conformation objects, this ensures that the new ParametersSet object's Parameters objects have lists of ResidueOPs that point to residues in the new Conformation object, rather than to residues that only exist in the Parameters objects.

References parameters_, core::conformation::Conformation::residue_cop(), and core::conformation::Conformation::size().

Member Data Documentation

utility::vector1< ParametersOP > core::conformation::parametric::ParametersSet::parameters_
private

List of pointers to parameters objects associated with this ParametersSet.

Each Parameters object has parameters describing, for example, one piece of secondary structure (e.g. one helix in a helical bundle). Each ParametersSet object is a collection of Parameters objects, and can describe an assemblage of secondary structure elements (e.g. a helical bundle). A Conformation can link to many ParametersSet objects.

Referenced by add_parameters(), clear_parameters_list(), n_parameters(), parameters(), ParametersSet(), and update_residue_links().


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