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

#include <Parameters.hh>

Inheritance diagram for core::conformation::parametric::Parameters:

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< ParameterOP >	parameter_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

A list of the parameters that describe these residues.

Referenced by add_parameter(), num_parameters(), parameter_cop(), parameter_op(), Parameters(), replace_parameter_via_clone(), and reset_sampling_and_perturbing_info().

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:

src/core/conformation/parametric/Parameters.hh
src/core/conformation/parametric/Parameters.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation