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protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator Class Reference

A class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose. This version uses helix-coil transition theory to nucleate and extend helices. More...

#include <HBP_HelixCoilMoveGenerator.hh>

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

 HBP_HelixCoilMoveGenerator ()
 Constructor. More...
 
 HBP_HelixCoilMoveGenerator (HBP_HelixCoilMoveGenerator const &src)
 Copy constructor. More...
 
 ~HBP_HelixCoilMoveGenerator () override
 Destructor. More...
 
HBP_MoveGeneratorOP clone () const override
 Clone this object: that is, make a copy and return an owning pointer to the copy. More...
 
protocols::rosetta_scripts::ParsedProtocolOP generate_monte_carlo_move (core::Size const current_step, core::Size const num_steps, core::pose::Pose const &pose) const override
 Given the current step index, the total number of steps in the trajectory, and the pose for analysis, construct a ParsedProtocol of things to do to this pose for this move in the Monte Carlo trajectory. More...
 
void mark_move_accepted () const override
 When a move is accepted, set the current helix assignments to the candidate helix assignments. More...
 
void set_up_user_helix_assignments (std::string const &file_contents)
 Given a helix assignment file's contents, set up the helix assignments. More...
 
- Public Member Functions inherited from protocols::helical_bundle_predict::HBP_MoveGenerator
 HBP_MoveGenerator ()
 Constructor. More...
 
 HBP_MoveGenerator (HBP_MoveGenerator const &src)
 Copy constructor. More...
 
 ~HBP_MoveGenerator () override
 Destructor. More...
 
virtual void mark_move_rejected () const
 Does nothing in base class. Can be overridden in derived classes to do something more useful when a move is rejected. More...
 
void set_current_round (core::Size const setting)
 Set the current round. More...
 
void set_max_rounds (core::Size const setting)
 Set the total nunmber of rounds. More...
 
core::Size current_round () const
 Get the current round. More...
 
core::Size max_rounds () const
 Get the maximum number of rounds. More...
 

Private Member Functions

void add_helix_nucleation_moves (core::pose::Pose const &pose) const
 Update the helix assignments to nucleate helices. More...
 
void add_helix_elongation_moves (core::pose::Pose const &pose) const
 Update the helix assignments to elongate helices. More...
 
void add_helix_retraction_moves (core::pose::Pose const &pose) const
 Update the helix assignments to shrink helices. More...
 
void add_global_parameter_perturbations (core::pose::Pose const &pose) const
 Add global parameter perturbations. More...
 
void add_local_parameter_perturbations (core::pose::Pose const &pose) const
 Add local parameter perturbations. More...
 
bool add_helix_update_moves (core::pose::Pose const &pose, protocols::rosetta_scripts::ParsedProtocol &protocol) const
 Add movers to the move list to update the helices based on the helix assignments. More...
 
void add_nonhelix_small_moves (core::pose::Pose const &pose, protocols::rosetta_scripts::ParsedProtocol &protocol) const
 Add the SmallMover moves to the protocol, at non-helix positions. More...
 

Private Attributes

HBPHelixAssignments user_helix_assignments_
 Stores information about what parts of a pose might be helical, as provided by the user. More...
 
HBPHelixAssignments current_helix_assignments_
 Stores information about what parts of a pose are currently believed to be helical, at a given step in a trajectory. More...
 
HBPHelixAssignments candidate_helix_assignments_
 Tentatively-considered helix assignments. More...
 
core::scoring::ScoreFunctionOP ramaprepro_sfxn_
 A RamaPrePro scorefunction for general use of SmallMover. More...
 

Detailed Description

A class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose. This version uses helix-coil transition theory to nucleate and extend helices.

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::HBP_HelixCoilMoveGenerator::HBP_HelixCoilMoveGenerator ( )

Constructor.

References core::scoring::rama_prepro, and ramaprepro_sfxn_.

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

Copy constructor.

protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::~HBP_HelixCoilMoveGenerator ( )
override

Destructor.

Member Function Documentation

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_global_parameter_perturbations ( core::pose::Pose const &  pose) const
private
void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_elongation_moves ( core::pose::Pose const &  pose) const
private
void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_nucleation_moves ( core::pose::Pose const &  pose) const
private
void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_retraction_moves ( core::pose::Pose const &  pose) const
private
bool protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves ( core::pose::Pose const &  pose,
protocols::rosetta_scripts::ParsedProtocol protocol 
) const
private
void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_local_parameter_perturbations ( core::pose::Pose const &  pose) const
private
void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_nonhelix_small_moves ( core::pose::Pose const &  pose,
protocols::rosetta_scripts::ParsedProtocol protocol 
) const
private
HBP_MoveGeneratorOP protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::clone ( ) const
overridevirtual

Clone this object: that is, make a copy and return an owning pointer to the copy.

Implements protocols::helical_bundle_predict::HBP_MoveGenerator.

protocols::rosetta_scripts::ParsedProtocolOP protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::generate_monte_carlo_move ( core::Size const  current_step,
core::Size const  num_steps,
core::pose::Pose const &  pose 
) const
overridevirtual

Given the current step index, the total number of steps in the trajectory, and the pose for analysis, construct a ParsedProtocol of things to do to this pose for this move in the Monte Carlo trajectory.

This override uses helix-coil transition theory to nucleate, extend, or remove helix segments. Non-helix segments are simply subjected to small moves.

Returns
A ParsedProtocolOP with the new protocol for success, or nullptr for failure.

Implements protocols::helical_bundle_predict::HBP_MoveGenerator.

References add_global_parameter_perturbations(), add_helix_elongation_moves(), add_helix_nucleation_moves(), add_helix_retraction_moves(), add_helix_update_moves(), add_local_parameter_perturbations(), add_nonhelix_small_moves(), candidate_helix_assignments_, and current_helix_assignments_.

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::mark_move_accepted ( ) const
overridevirtual

When a move is accepted, set the current helix assignments to the candidate helix assignments.

Reimplemented from protocols::helical_bundle_predict::HBP_MoveGenerator.

References candidate_helix_assignments_, and current_helix_assignments_.

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::set_up_user_helix_assignments ( std::string const &  file_contents)

Given a helix assignment file's contents, set up the helix assignments.

Involves no read from disk.

References protocols::helical_bundle_predict::HBPHelixAssignments::clear(), protocols::helical_bundle_predict::HBPHelixAssignments::initialize_from_file_contents(), and user_helix_assignments_.

Member Data Documentation

HBPHelixAssignments protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::candidate_helix_assignments_
mutableprivate
HBPHelixAssignments protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::current_helix_assignments_
mutableprivate

Stores information about what parts of a pose are currently believed to be helical, at a given step in a trajectory.

Referenced by add_helix_update_moves(), generate_monte_carlo_move(), and mark_move_accepted().

core::scoring::ScoreFunctionOP protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::ramaprepro_sfxn_
private

A RamaPrePro scorefunction for general use of SmallMover.

Referenced by add_nonhelix_small_moves(), and HBP_HelixCoilMoveGenerator().

HBPHelixAssignments protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::user_helix_assignments_
private

Stores information about what parts of a pose might be helical, as provided by the user.

Referenced by add_helix_elongation_moves(), add_helix_nucleation_moves(), add_helix_retraction_moves(), and set_up_user_helix_assignments().


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