Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
core::conformation::parametric::Parameters Class Reference

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

#include <Parameters.hh>

Inheritance diagram for core::conformation::parametric::Parameters:
Inheritance graph
[legend]

Public Member Functions

 Parameters ()
 constructors More...
 
 Parameters (Parameters const &src)
 Copy constructor. More...
 
 ~Parameters () override
 
virtual ParametersOP clone () const
 Copy this residue( allocate actual memory for it ) More...
 
ParametersCOP get_self_ptr () const
 self pointers More...
 
ParametersOP get_self_ptr ()
 
ParametersCAP get_self_weak_ptr () const
 
ParametersAP get_self_weak_ptr ()
 
void add_residue (core::conformation::ResidueCOP residue)
 Add a residue to the list of residues that these parameters describe. More...
 
core::conformation::ResidueCOP residue (core::Size const index) const
 Get an owning pointer to a residue in the list of residues that these parameters describe. More...
 
core::conformation::ResidueCOP first_residue () const
 Get a const owning pointer to the first residue in the list of residues that these parameters describe. More...
 
core::conformation::ResidueCOP last_residue () const
 Get a const owning pointer to the last residue in the list of residues that these parameters describe. More...
 
core::Size first_residue_index () const
 Get the index of the first residue. More...
 
core::Size last_residue_index () const
 Get the index of the last residue. More...
 
core::Size n_residue () const
 Returns the number (count) of residues that these parameters describe. More...
 
void reset_residue_list ()
 Clears the list of residues that these parameters describe. More...
 
void reset_sampling_and_perturbing_info () const
 Clears the sampling and perturbing information in the individual parameters. More...
 
void set_residue (core::Size const index, core::conformation::ResidueCOP existing_residue)
 Assign an element in the residue list to be an owning pointer to an existing residue. More...
 
core::Size num_parameters () const
 Get the number of parameters stored in this Parameters object. More...
 
void add_parameter (ParameterOP parameter)
 Add a parameter. More...
 
ParameterOP parameter_op (core::Size const index) const
 Access a parameter, by index. More...
 
ParameterCOP parameter_cop (core::Size const index) const
 Access a parameter, by index. More...
 
void replace_parameter_via_clone (core::Size const param_index, ParameterCOP new_parameter, bool const reset_sampling_copying_perturbing=true)
 Replace one of the contained parameter objects with a copy of an input parameter object. More...
 

Private Attributes

utility::vector1
< core::conformation::ResidueCOP
residue_list_
 A list of the residues in this conformation that are described by the parameters in this Parameters object. More...
 
utility::vector1< ParameterOPparameter_list_
 A list of the parameters that describe these residues. More...
 

Detailed Description

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

Constructor & Destructor Documentation

core::conformation::parametric::Parameters::Parameters ( )

constructors

Constructor.

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

Copy constructor.

Deep-copies the residue list and the parameters list.

References parameter_list_, and residue_list_.

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

Member Function Documentation

void core::conformation::parametric::Parameters::add_parameter ( ParameterOP  parameter)

Add a parameter.

Does NOT clone the parameter, but stores the OP directly.

References parameter_list_.

void core::conformation::parametric::Parameters::add_residue ( core::conformation::ResidueCOP  residue)

Add a residue to the list of residues that these parameters describe.

References residue_list_.

ParametersOP core::conformation::parametric::Parameters::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::BundleParameters.

core::conformation::ResidueCOP core::conformation::parametric::Parameters::first_residue ( ) const

Get a const owning pointer to the first residue in the list of residues that these parameters describe.

Note that this might not be the first residue in linear sequence, if the residues were put in in non- sequential order or the residue numbering has changed.

References residue_list_.

core::Size core::conformation::parametric::Parameters::first_residue_index ( ) const

Get the index of the first residue.

MUST BE REWRITTEN when the OP issue is resolved.

References residue_list_.

ParametersCOP core::conformation::parametric::Parameters::get_self_ptr ( ) const
inline

self pointers

ParametersOP core::conformation::parametric::Parameters::get_self_ptr ( )
inline
ParametersCAP core::conformation::parametric::Parameters::get_self_weak_ptr ( ) const
inline
ParametersAP core::conformation::parametric::Parameters::get_self_weak_ptr ( )
inline
core::conformation::ResidueCOP core::conformation::parametric::Parameters::last_residue ( ) const

Get a const owning pointer to the last residue in the list of residues that these parameters describe.

Note that this might not be the last residue in linear sequence, if the residues were put in in non- sequential order or the residue numbering has changed.

References residue_list_.

core::Size core::conformation::parametric::Parameters::last_residue_index ( ) const

Get the index of the last residue.

MUST BE REWRITTEN when the OP issue is resolved.

References residue_list_.

core::Size core::conformation::parametric::Parameters::n_residue ( ) const

Returns the number (count) of residues that these parameters describe.

References residue_list_.

core::Size core::conformation::parametric::Parameters::num_parameters ( ) const

Get the number of parameters stored in this Parameters object.

References parameter_list_.

ParameterCOP core::conformation::parametric::Parameters::parameter_cop ( core::Size const  index) const

Access a parameter, by index.

Const access.

References parameter_list_.

Referenced by protocols::helical_bundle::parameters::BundleParameters::get_pdb_remark().

ParameterOP core::conformation::parametric::Parameters::parameter_op ( core::Size const  index) const

Access a parameter, by index.

Non-const access.

References parameter_list_.

void core::conformation::parametric::Parameters::replace_parameter_via_clone ( core::Size const  param_index,
ParameterCOP  new_parameter,
bool const  reset_sampling_copying_perturbing = true 
)

Replace one of the contained parameter objects with a copy of an input parameter object.

If reset_sampling_copying_perturbing is true, then the sampling, copying, and perturbing information of the copied parameter object are all reset. True by default.

References parameter_list_.

void core::conformation::parametric::Parameters::reset_residue_list ( )

Clears the list of residues that these parameters describe.

References residue_list_.

void core::conformation::parametric::Parameters::reset_sampling_and_perturbing_info ( ) const

Clears the sampling and perturbing information in the individual parameters.

References parameter_list_.

core::conformation::ResidueCOP core::conformation::parametric::Parameters::residue ( core::Size const  index) const

Get an owning pointer to a residue in the list of residues that these parameters describe.

References residue_list_.

void core::conformation::parametric::Parameters::set_residue ( core::Size const  index,
core::conformation::ResidueCOP  existing_residue 
)

Assign an element in the residue list to be an owning pointer to an existing residue.

References residue_list_.

Member Data Documentation

utility::vector1< ParameterOP > core::conformation::parametric::Parameters::parameter_list_
private
utility::vector1< core::conformation::ResidueCOP > core::conformation::parametric::Parameters::residue_list_
private

A list of the residues in this conformation that are described by the parameters in this Parameters object.

This is a list of owning pointers so that the residue indices don't mess things up. (That is, as residue indices change, these should still point to the proper residues).

Referenced by add_residue(), first_residue(), first_residue_index(), last_residue(), last_residue_index(), n_residue(), Parameters(), reset_residue_list(), residue(), and set_residue().


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