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

Add global parameter perturbations.

References candidate_helix_assignments_, and protocols::helical_bundle_predict::HBPHelixAssignments::try_perturbing_global_helix_parameters().

Referenced by generate_monte_carlo_move().

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_elongation_moves ( core::pose::Pose const & pose ) const

private

Update the helix assignments to elongate helices.

References candidate_helix_assignments_, core::pose::Pose::total_residue(), protocols::helical_bundle_predict::HBPHelixAssignments::try_elongating_helix(), and user_helix_assignments_.

Referenced by generate_monte_carlo_move().

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_nucleation_moves ( core::pose::Pose const & pose ) const

private

Update the helix assignments to nucleate helices.

References candidate_helix_assignments_, core::pose::Pose::total_residue(), protocols::helical_bundle_predict::HBPHelixAssignments::try_nucleating_helix(), and user_helix_assignments_.

Referenced by generate_monte_carlo_move().

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_retraction_moves ( core::pose::Pose const & pose ) const

private

Update the helix assignments to shrink helices.

References candidate_helix_assignments_, core::pose::Pose::total_residue(), protocols::helical_bundle_predict::HBPHelixAssignments::try_retracting_helix(), and user_helix_assignments_.

Referenced by generate_monte_carlo_move().

bool protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves	(	core::pose::Pose const &	pose,
		protocols::rosetta_scripts::ParsedProtocol &	protocol
	)		const

private

Add movers to the move list to update the helices based on the helix assignments.

Returns true for FAILURE (due to inability to generate helix from parameters), false for success.

References protocols::rosetta_scripts::ParsedProtocol::add_step(), core::id::BB, candidate_helix_assignments_, current_helix_assignments_, protocols::helical_bundle_predict::HBPHelixAssignments::generate_torsion_values_for_helices(), protocols::helical_bundle_predict::HBPHelixAssignments::get_containing_helix_index(), protocols::helical_bundle_predict::HBPHelixAssignments::is_in_helix(), core::pose::Pose::residue(), core::id::to_string(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by generate_monte_carlo_move().

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_local_parameter_perturbations ( core::pose::Pose const & pose ) const

private

Add local parameter perturbations.

References candidate_helix_assignments_, and protocols::helical_bundle_predict::HBPHelixAssignments::try_perturbing_local_helix_parameters().

Referenced by generate_monte_carlo_move().

void protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_nonhelix_small_moves	(	core::pose::Pose const &	pose,
		protocols::rosetta_scripts::ParsedProtocol &	protocol
	)		const

private

Add the SmallMover moves to the protocol, at non-helix positions.

References protocols::rosetta_scripts::ParsedProtocol::add_step(), candidate_helix_assignments_, protocols::helical_bundle_predict::HBPHelixAssignments::is_in_helix(), ramaprepro_sfxn_, and core::pose::Pose::total_residue().

Referenced by generate_monte_carlo_move().

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

Tentatively-considered helix assignments.

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

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:

src/protocols/helical_bundle_predict/HBP_HelixCoilMoveGenerator.hh
src/protocols/helical_bundle_predict/HBP_HelixCoilMoveGenerator.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation