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:

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

Generate a map of (TorsionID->torsion value) for all mainchain torsions in the current helix.

Returns

True for FAILURE (Crick parameters don't generate a helix), false for success.

References core::id::AtomID::atomno(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::id::BB, protocols::helical_bundle::BPC_atoms_per_residue, protocols::helical_bundle::BPC_delta_omega1, protocols::helical_bundle::BPC_delta_omega1_peratom, protocols::helical_bundle::BPC_delta_z1_peratom, protocols::helical_bundle::BPC_omega0, protocols::helical_bundle::BPC_omega1, protocols::helical_bundle::BPC_r0, protocols::helical_bundle::BPC_r1_peratom, protocols::helical_bundle::BPC_z1, core::pose::Pose::conformation(), determine_repeating_unit_offset(), end_position_, protocols::helical_bundle::generate_atom_positions(), core::conformation::Residue::mainchain_torsions(), parameters_, core::pose::Pose::residue(), core::id::AtomID::rsd(), start_position_, and protocols::TR().

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

The end of the helix.

Referenced by end_position(), get_torsions_for_helix(), set_end_position(), and set_start_position().

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 start of the helix.

Referenced by get_torsions_for_helix(), set_end_position(), set_start_position(), and start_position().

---

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

• src/protocols/helical_bundle_predict/HBPHelixAssignments.hh
• src/protocols/helical_bundle_predict/HBPHelixAssignments.cc