An individual helix. This class stores start and end positions, plus helical parameters. More...
#include <HBPHelixAssignments.hh>
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.
Constructor & Destructor Documentation
◆ HBPHelix() [1/2]
| protocols::helical_bundle_predict::HBPHelix::HBPHelix | ( | ) |
Default constructor.
◆ HBPHelix() [2/2]
| protocols::helical_bundle_predict::HBPHelix::HBPHelix | ( | HBPHelix const & | src | ) |
Copy constructor.
Deep-copies paramters.
◆ ~HBPHelix()
|
override |
Destructor.
Member Function Documentation
◆ clone()
| HBPHelixOP protocols::helical_bundle_predict::HBPHelix::clone | ( | ) | const |
Create a copy of this object and return an owning pointer to the copy.
◆ crick_params_filename()
|
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().
◆ determine_repeating_unit_offset()
| 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().
◆ end_position()
|
inline |
◆ extension_prob()
|
inline |
Get the probability of extending an existing helix.
References extension_prob_.
◆ get_torsions_for_helix()
| 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().
◆ is_in_helix()
| 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().
◆ nucleation_prob()
|
inline |
Get the probability of nucleating a helix.
References nucleation_prob_.
◆ parameters() [1/2]
| HBPHelixParametersOP protocols::helical_bundle_predict::HBPHelix::parameters | ( | ) |
Get the parameters (nonconst access).
References parameters_.
◆ parameters() [2/2]
|
inline |
◆ residues_per_turn()
| core::Size protocols::helical_bundle_predict::HBPHelix::residues_per_turn | ( | ) | const |
Get the number of residues per turn of this helix type.
References parameters_.
◆ retraction_prob()
|
inline |
Get the probability of shrinking an existing helix.
References retraction_prob_.
◆ set_crick_params_filename()
| 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_.
◆ set_end_position()
| void protocols::helical_bundle_predict::HBPHelix::set_end_position | ( | core::Size const | position_in | ) |
Set the end position.
References end_position_, start_position_, and core::id::to_string().
◆ set_extension_prob()
| void protocols::helical_bundle_predict::HBPHelix::set_extension_prob | ( | core::Real const & | setting | ) |
Set the probability of extending an existing helix.
References extension_prob_.
◆ set_nucleation_prob()
| void protocols::helical_bundle_predict::HBPHelix::set_nucleation_prob | ( | core::Real const & | setting | ) |
Set the probability of nucleating a helix.
References nucleation_prob_.
◆ set_retraction_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_.
◆ set_start_position()
| void protocols::helical_bundle_predict::HBPHelix::set_start_position | ( | core::Size const | position_in | ) |
Set the start position.
References end_position_, and start_position_.
◆ start_position()
|
inline |
Friends And Related Function Documentation
◆ ::HBPHelixAssignmentsTests
|
friend |
Member Data Documentation
◆ 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().
◆ end_position_
|
private |
The end of the helix.
Referenced by end_position(), get_torsions_for_helix(), set_end_position(), and set_start_position().
◆ extension_prob_
|
private |
The probability of extending a nucleated helix.
Referenced by extension_prob(), and set_extension_prob().
◆ nucleation_prob_
|
private |
The probability of nucleating.
Referenced by nucleation_prob(), and set_nucleation_prob().
◆ 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().
◆ retraction_prob_
|
private |
The probability of retracting a nucleated helix.
Referenced by retraction_prob(), and set_retraction_prob().
◆ 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
