BundleParametersSet class, used to store sets of parameters for parametric helical bundle generation. More...

#include <BundleParametersSet.hh>

Inheritance diagram for protocols::helical_bundle::parameters::BundleParametersSet:

Public Types
typedef core::conformation::parametric::Parameters	Parameters

typedef core::conformation::parametric::ParametersOP	ParametersOP

typedef core::conformation::parametric::ParametersSet	ParametersSet

typedef core::conformation::parametric::ParametersSetOP	ParametersSetOP

Public Member Functions
	BundleParametersSet ()
	constructors More...

	BundleParametersSet (BundleParametersSet const &src)

	~BundleParametersSet () override

ParametersSetOP	clone () const override
	Copy this residue( allocate actual memory for it ) More...

core::Size	bundle_symmetry () const
	Returns the symmetry of the bundle created. More...

core::Size	bundle_symmetry_copies () const
	Returns the number of symmetry copies to generate. More...

core::Size	n_helices () const
	Get the number of helices defined in each symmetry copy of this bundle. More...

void	set_bundle_symmetry (core::Size const val)
	Sets the symmetry of the bundle created. More...

void	set_bundle_symmetry_copies (core::Size const val)
	Sets the number of symmetry copies to generate. More...

void	set_n_helices (core::Size const val)
	Set the number of helices defined in each symmetry copy of this bundle. More...

void	get_pdb_remark (std::stringstream &remark) const override
	Get a summary of this ParametersSet object, for output to remark lines of a PDB file. More...

Public Member Functions inherited from core::conformation::parametric::ParametersSet
	ParametersSet ()
	constructors More...

	ParametersSet (ParametersSet const &src)
	Copy constructor. More...

	~ParametersSet () override

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...

Private Attributes
core::Size	bundle_symmetry_
	The symmetry of the bundle created. More...

core::Size	bundle_symmetry_copies_
	The symmetry copies to generate. More...

core::Size	n_helices_
	The number of helices defined in each symmetry copy of this bundle. More...

Detailed Description

BundleParametersSet class, used to store sets of parameters for parametric helical bundle generation.

Member Typedef Documentation

typedef core::conformation::parametric::Parameters protocols::helical_bundle::parameters::BundleParametersSet::Parameters

typedef core::conformation::parametric::ParametersOP protocols::helical_bundle::parameters::BundleParametersSet::ParametersOP

typedef core::conformation::parametric::ParametersSet protocols::helical_bundle::parameters::BundleParametersSet::ParametersSet

typedef core::conformation::parametric::ParametersSetOP protocols::helical_bundle::parameters::BundleParametersSet::ParametersSetOP

Constructor & Destructor Documentation

protocols::helical_bundle::parameters::BundleParametersSet::BundleParametersSet ( )

constructors

Constructor.

protocols::helical_bundle::parameters::BundleParametersSet::BundleParametersSet ( BundleParametersSet const & src )

default

protocols::helical_bundle::parameters::BundleParametersSet::~BundleParametersSet ( )

overridedefault

Member Function Documentation

core::Size protocols::helical_bundle::parameters::BundleParametersSet::bundle_symmetry ( ) const

inline

Returns the symmetry of the bundle created.

A value of 0 or 1 indicates no symmetry. Larger values indicate n-fold radial symmetry (for example, 3 means threefold radial symmetry about the bundle axis, and each helix defined will be replicated a total of three times).

References bundle_symmetry_.

Referenced by get_pdb_remark().

core::Size protocols::helical_bundle::parameters::BundleParametersSet::bundle_symmetry_copies ( ) const

inline

Returns the number of symmetry copies to generate.

A value of 0 means to generate all copies. Higher values mean to generate only the first N copies. For example, if the symmetry were 16 but bundle_symmetry_copies_ were set to 4, only the first 4 symmetry repeats would be generated.

References bundle_symmetry_copies_.

Referenced by get_pdb_remark().

core::conformation::parametric::ParametersSetOP protocols::helical_bundle::parameters::BundleParametersSet::clone ( ) const

overridevirtual

Copy this residue( allocate actual memory for it )

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

Reimplemented from core::conformation::parametric::ParametersSet.

void protocols::helical_bundle::parameters::BundleParametersSet::get_pdb_remark ( std::stringstream & remark ) const

overridevirtual

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

Default function can be overridden by derived classes. This version actually outputs Crick parameter information.

Reimplemented from core::conformation::parametric::ParametersSet.

References bundle_symmetry(), bundle_symmetry_copies(), n_helices(), and core::conformation::parametric::ParametersSet::parameters().

core::Size protocols::helical_bundle::parameters::BundleParametersSet::n_helices ( ) const

inline

Get the number of helices defined in each symmetry copy of this bundle.

References n_helices_.

Referenced by get_pdb_remark().

void protocols::helical_bundle::parameters::BundleParametersSet::set_bundle_symmetry ( core::Size const val )

inline

Sets the symmetry of the bundle created.

A value of 0 or 1 indicates no symmetry. Larger values indicate n-fold radial symmetry (for example, 3 means threefold radial symmetry about the bundle axis, and each helix defined will be replicated a total of three times).

References bundle_symmetry_, and protocols::hybridization::val.

void protocols::helical_bundle::parameters::BundleParametersSet::set_bundle_symmetry_copies ( core::Size const val )

inline

Sets the number of symmetry copies to generate.

A value of 0 means to generate all copies. Higher values mean to generate only the first N copies. For example, if the symmetry were 16 but bundle_symmetry_copies_ were set to 4, only the first 4 symmetry repeats would be generated.

References bundle_symmetry_copies_, and protocols::hybridization::val.

void protocols::helical_bundle::parameters::BundleParametersSet::set_n_helices ( core::Size const val )

inline

Set the number of helices defined in each symmetry copy of this bundle.

References n_helices_, and protocols::hybridization::val.

Member Data Documentation

core::Size protocols::helical_bundle::parameters::BundleParametersSet::bundle_symmetry_

private

The symmetry of the bundle created.

A value of 0 or 1 indicates no symmetry. Larger values indicate n-fold radial symmetry (for example, 3 means threefold radial symmetry about the bundle axis, and each helix defined will be replicated a total of three times).

Referenced by bundle_symmetry(), and set_bundle_symmetry().

core::Size protocols::helical_bundle::parameters::BundleParametersSet::bundle_symmetry_copies_

private

The symmetry copies to generate.

A value of 0 means to generate all copies. Higher values mean to generate only the first N copies. For example, if the symmetry were 16 but bundle_symmetry_copies_ were set to 4, only the first 4 symmetry repeats would be generated.

Referenced by bundle_symmetry_copies(), and set_bundle_symmetry_copies().

core::Size protocols::helical_bundle::parameters::BundleParametersSet::n_helices_

private

The number of helices defined in each symmetry copy of this bundle.

Referenced by n_helices(), and set_n_helices().

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

src/protocols/helical_bundle/parameters/BundleParametersSet.hh
src/protocols/helical_bundle/parameters/BundleParametersSet.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation