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protocols::helical_bundle::parameters::BundleParametersSet Class Reference

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:
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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

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: