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protocols::helical_bundle_predict::HBPHelix Class Reference

An individual helix. This class stores start and end positions, plus helical parameters. More...

#include <HBPHelixAssignments.hh>

Inheritance diagram for protocols::helical_bundle_predict::HBPHelix:
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Public Member Functions

 HBPHelix ()
 Default constructor. More...
 
 HBPHelix (HBPHelix const &src)
 Copy constructor. More...
 
 ~HBPHelix () override
 Destructor. More...
 
HBPHelixOP clone () const
 Create a copy of this object and return an owning pointer to the copy. More...
 
HBPHelixParametersOP parameters ()
 Get the parameters (nonconst access). More...
 
HBPHelixParametersCOP parameters () const
 Get the parameters (read-only). More...
 
bool is_in_helix (core::Size const seqpos) const
 Is a sequence position within a helix? More...
 
core::Size residues_per_turn () const
 Get the number of residues per turn of this helix type. More...
 
bool get_torsions_for_helix (std::map< core::id::TorsionID, core::Real > &torsion_map_out, core::pose::Pose const &pose_for_reference) const
 Generate a map of (TorsionID->torsion value) for all mainchain torsions in the current helix. More...
 
core::Size determine_repeating_unit_offset (core::pose::Pose const &pose, core::Size const start_position, core::Size const end_position) const
 Given the start and end position of a helix, determine from the residue composition what the repeating unit offset should be. More...
 
void set_start_position (core::Size const position_in)
 Set the start position. More...
 
void set_end_position (core::Size const position_in)
 Set the end position. More...
 
void set_nucleation_prob (core::Real const &setting)
 Set the probability of nucleating a helix. More...
 
void set_extension_prob (core::Real const &setting)
 Set the probability of extending an existing helix. More...
 
void set_retraction_prob (core::Real const &setting)
 Set the probability of shrinking an existing helix. More...
 
void set_crick_params_filename (std::string const &name_in)
 Set the filename for the Crick params for this helix. More...
 
core::Size start_position () const
 Get the start position. More...
 
core::Size end_position () const
 Get the end position. More...
 
core::Real const & nucleation_prob () const
 Get the probability of nucleating a helix. More...
 
core::Real const & extension_prob () const
 Get the probability of extending an existing helix. More...
 
core::Real const & retraction_prob () const
 Get the probability of shrinking an existing helix. More...
 
std::string const & crick_params_filename () const
 Get the filename for the Crick params for this helix. More...
 

Private Attributes

HBPStartPosition start_position_
 The start of the helix. More...
 
HBPEndPosition end_position_
 The end of the helix. More...
 
core::Real nucleation_prob_
 The probability of nucleating. More...
 
core::Real extension_prob_
 The probability of extending a nucleated helix. More...
 
core::Real retraction_prob_
 The probability of retracting a nucleated helix. More...
 
HBPHelixParametersOP parameters_
 The helical parameters. Will be nullptr if parameters not stored. More...
 
std::string crick_params_filename_
 The name of the Crick params file. Used to determine whether two helices are of a matching type. More...
 

Friends

class ::HBPHelixAssignmentsTests
 

Detailed Description

An individual helix. This class stores start and end positions, plus helical parameters.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Constructor & Destructor Documentation

protocols::helical_bundle_predict::HBPHelix::HBPHelix ( )

Default constructor.

protocols::helical_bundle_predict::HBPHelix::HBPHelix ( HBPHelix const &  src)

Copy constructor.

Deep-copies paramters.

protocols::helical_bundle_predict::HBPHelix::~HBPHelix ( )
override

Destructor.

Member Function Documentation

HBPHelixOP protocols::helical_bundle_predict::HBPHelix::clone ( ) const

Create a copy of this object and return an owning pointer to the copy.

std::string const& protocols::helical_bundle_predict::HBPHelix::crick_params_filename ( ) const
inline

Get the filename for the Crick params for this helix.

Used to determine whether two helices are of a matching type.

References crick_params_filename_.

Referenced by protocols::helical_bundle_predict::HBPHelixAssignments::helix_types_match().

core::Size protocols::helical_bundle_predict::HBPHelix::determine_repeating_unit_offset ( core::pose::Pose const &  pose,
core::Size const  start_position,
core::Size const  end_position 
) const

Given the start and end position of a helix, determine from the residue composition what the repeating unit offset should be.

For example, if the stretch had pattern alpha-alpha-beta-alpha, and the Crick params file expected alpha-alpha-alpha-beta, the offset would be 3.

References parameters_.

Referenced by get_torsions_for_helix().

core::Size protocols::helical_bundle_predict::HBPHelix::end_position ( ) const
inline

Get the end position.

References end_position_.

Referenced by is_in_helix().

core::Real const& protocols::helical_bundle_predict::HBPHelix::extension_prob ( ) const
inline

Get the probability of extending an existing helix.

References extension_prob_.

bool protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix ( std::map< core::id::TorsionID, core::Real > &  torsion_map_out,
core::pose::Pose const &  pose_for_reference 
) const
bool protocols::helical_bundle_predict::HBPHelix::is_in_helix ( core::Size const  seqpos) const

Is a sequence position within a helix?

Returns false if either of startpos or endpos is zero.

References end_position(), and start_position().

core::Real const& protocols::helical_bundle_predict::HBPHelix::nucleation_prob ( ) const
inline

Get the probability of nucleating a helix.

References nucleation_prob_.

HBPHelixParametersOP protocols::helical_bundle_predict::HBPHelix::parameters ( )

Get the parameters (nonconst access).

References parameters_.

HBPHelixParametersCOP protocols::helical_bundle_predict::HBPHelix::parameters ( ) const
inline

Get the parameters (read-only).

Returns nullptr if no object exists.

References parameters_.

core::Size protocols::helical_bundle_predict::HBPHelix::residues_per_turn ( ) const

Get the number of residues per turn of this helix type.

References parameters_.

core::Real const& protocols::helical_bundle_predict::HBPHelix::retraction_prob ( ) const
inline

Get the probability of shrinking an existing helix.

References retraction_prob_.

void protocols::helical_bundle_predict::HBPHelix::set_crick_params_filename ( std::string const &  name_in)

Set the filename for the Crick params for this helix.

Used to determine whether two helices are of a matching type.

References crick_params_filename_.

void protocols::helical_bundle_predict::HBPHelix::set_end_position ( core::Size const  position_in)

Set the end position.

References end_position_, and start_position_.

void protocols::helical_bundle_predict::HBPHelix::set_extension_prob ( core::Real const &  setting)

Set the probability of extending an existing helix.

References extension_prob_.

void protocols::helical_bundle_predict::HBPHelix::set_nucleation_prob ( core::Real const &  setting)

Set the probability of nucleating a helix.

References nucleation_prob_.

void protocols::helical_bundle_predict::HBPHelix::set_retraction_prob ( core::Real const &  setting)

Set the probability of shrinking an existing helix.

References retraction_prob_.

void protocols::helical_bundle_predict::HBPHelix::set_start_position ( core::Size const  position_in)

Set the start position.

References end_position_, and start_position_.

core::Size protocols::helical_bundle_predict::HBPHelix::start_position ( ) const
inline

Get the start position.

References start_position_.

Referenced by is_in_helix().

Friends And Related Function Documentation

friend class ::HBPHelixAssignmentsTests
friend

Member Data Documentation

std::string protocols::helical_bundle_predict::HBPHelix::crick_params_filename_
private

The name of the Crick params file. Used to determine whether two helices are of a matching type.

Referenced by crick_params_filename(), and set_crick_params_filename().

HBPEndPosition protocols::helical_bundle_predict::HBPHelix::end_position_
private
core::Real protocols::helical_bundle_predict::HBPHelix::extension_prob_
private

The probability of extending a nucleated helix.

Referenced by extension_prob(), and set_extension_prob().

core::Real protocols::helical_bundle_predict::HBPHelix::nucleation_prob_
private

The probability of nucleating.

Referenced by nucleation_prob(), and set_nucleation_prob().

HBPHelixParametersOP protocols::helical_bundle_predict::HBPHelix::parameters_
private

The helical parameters. Will be nullptr if parameters not stored.

Referenced by determine_repeating_unit_offset(), get_torsions_for_helix(), parameters(), and residues_per_turn().

core::Real protocols::helical_bundle_predict::HBPHelix::retraction_prob_
private

The probability of retracting a nucleated helix.

Referenced by retraction_prob(), and set_retraction_prob().

HBPStartPosition protocols::helical_bundle_predict::HBPHelix::start_position_
private

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