This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues. More...

#include <AddHelixSequenceConstraintsMover.hh>

Inheritance diagram for protocols::aa_composition::AddHelixSequenceConstraintsMover:

[legend]

Public Member Functions
	AddHelixSequenceConstraintsMover ()
	Constructors ///. More...

	AddHelixSequenceConstraintsMover (AddHelixSequenceConstraintsMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~AddHelixSequenceConstraintsMover () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	An optional residue selector. If provided, only helices that have at least one residue in the selection have constraints applied. If unused, all heliecs receive constraints. More...

bool	has_residue_selector () const
	Has a residue selector been specified for this mover? More...

bool	reset_mode () const
	Get whether old composition constraints should be deleted before applying this mover. More...

core::Size	min_helix_length () const
	Get the minimum number of residues in a helix for the helix to be considered. More...

bool	add_n_terminal_constraints () const
	Should this mover add constraints to the N-termini of helices requiring negative charges there? More...

bool	add_c_terminal_constraints () const
	Should this mover add constraints to the C-termini of helices requiring positive charges there? More...

bool	add_overall_constraints () const
	Should this mover add constraints to the helix penalizing helix-disfavouring residue types? More...

bool	add_alanine_constraints () const
	Should this mover add constraints to the helix requiring a certain alanine fraction? More...

bool	add_hydrophobic_constraints () const
	Should this mover add constraints to the helix requiring at minimum fraction of hydrophobic residues? More...

core::Size	min_n_terminal_charges () const
	The number of negative charges required at the N-terminus of each helix. More...

core::Size	n_terminus_size () const
	The number of N-terminal residues in each helix, in which negative charges must be found. More...

core::Real const &	n_terminal_constraint_strength () const
	The weight given to the N-terminal constraints. More...

core::Size	min_c_terminal_charges () const
	The number of positive charges required at the C-terminus of each helix. More...

core::Size	c_terminus_size () const
	The number of C-terminal residues in each helix, in which positive charges must be found. More...

core::Real const &	c_terminal_constraint_strength () const
	The weight given to the C-terminal constraints. More...

utility::vector1< std::string > const &	types_to_avoid () const
	Access the vector of types to avoid. More...

std::string const &	types_to_avoid (core::Size const index) const
	Access an element in the vector of types to avoid. More...

core::Size	overall_max_count () const
	Max number of residues from the types to avoid list per helix. More...

core::Real const &	overall_constraints_strength () const
	Get the strength of the helix constraints that penalize helix-disfavouring residue types. More...

core::Real const &	desired_ala_fraction () const
	Get the desired fractional content of alanine in each helix. More...

core::Real const &	ala_constraint_under_strength () const
	Get the penalty for having 1% less than the desired fractional content of alanine. More...

core::Real const &	ala_constraint_over_strength () const
	Get the penalty for having 1% more than the desired fractional content of alanine. More...

core::Real const &	desired_min_hydrophobic_fraction () const
	Get the desired minimum hydrophobic fraction. More...

core::Real const &	hydrophobic_constraint_strength () const
	Get the strength of the hydrophobic constraint. (The penalty for having more than 1% less than the desired minimum hydrophobic content. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set a residue selector if specified by the user. More...

void	set_reset_mode (bool const setting)
	Set whether old composition constraints should be deleted before applying this mover. More...

void	set_min_helix_length (core::Size const setting)
	Set the minimum number of residues in a helix for the helix to be considered. More...

void	set_add_n_terminal_constraints (bool const setting, core::Size const min_charges, core::Size const nterm_size, core::Real const &strength)
	Set whether this mover should add constraints to the N-termini of helices requiring negative charges there. More...

void	set_add_c_terminal_constraints (bool const setting, core::Size const min_charges, core::Size const cterm_size, core::Real const &strength)
	Set whether this mover should add constraints to the C-termini of helices requiring positive charges there. More...

void	set_add_overall_constraints (bool const setting)
	Set whether this mover should add constraints to the helix penalizing helix-disfavouring residue types. More...

void	set_add_overall_constraints (bool const setting, std::string const &types_to_avoid, core::Size const overall_max_count, core::Real const &overall_constraints_strength)
	Set whether this mover should add constraints to the helix penalizing helix-disfavouring residue types. More...

void	set_add_alanine_constraints (bool const setting)
	Set whether this mover should add constraints to the helix requiring a certain alanine fraction. More...

void	set_add_alanine_constraints (bool const setting, core::Real const &desired_ala_fraction, core::Real const &ala_constraint_under_strength, core::Real const &ala_constraint_over_strength)
	Set whether this mover should add constraints to the helix requiring a certain alanine fraction. More...

void	set_add_hydrophobic_constraints (bool const setting)
	Set whether this mover should add constraints to the helix requiring at minimum fraction of hydrophobic residues. More...

void	set_add_hydrophobic_constraints (bool const setting, core::Real const &desired_min_hydrophobic_fraction, core::Real const &hydrophobic_constraint_strength)
	Set whether this mover should add constraints to the helix requiring at minimum fraction of hydrophobic residues. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
void	check_lengths_sensible () const
	Once the mover has been set up, check that the lengths of termini is sensible compared to the min_helix_length setting. More...

void	initialize_types_to_avoid ()
	Initialize the types to avoid to ASN, ASP, SER, GLU, THR, VAL. More...

void	delete_old_sequence_constraints (core::pose::Pose &pose) const
	Given a pose, remove all sequence constraints from it. More...

void	set_up_terminal_constraints (std::string &setup_string_out, bool const n_terminal) const
	Set up strings defining terminal constraints. More...

void	set_up_overall_constraints (std::string &setup_string_out) const
	Set up strings defining constraints penalizing helix-disfavouring residue types. More...

void	set_up_alanine_constraints (std::string &setup_string_out) const
	Set up strings defining constraints penalizing too few or too many alanines. More...

void	set_up_hydrophobic_constraints (std::string &setup_string_out) const
	Set up strings defining constraints penalizing too few hydrophobics. More...

void	find_helices (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > &helices) const
	Given a pose and an empty vector (that will be cleared by this operation and repopulated), run DSSP and identify all helices longer than a specified length. More...

void	remove_unselected_helices (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > &helices) const
	Given a pose and an already-populated list of helices, remove helices that do not have at least one residue selected by the residue selector associated with this mover. More...

void	do_terminal_constraints (core::pose::Pose &pose, bool const n_terminus, core::Size const start_res, core::Size const end_res, std::string const &constraint_setup) const
	Given a pose and helix start and end points, add constraints for the helix termini requiring charges in the first or last N residues. More...

void	do_overall_or_alanine_constraints (core::pose::Pose &pose, core::Size const start_res, core::Size const end_res, std::string const &constraint_setup) const
	Given a pose and helix start and end points, add constraints for the helix limiting helix-disfavouring residues. More...

Private Attributes
bool	reset_mode_
	Should old composition constraints be deleted before applying this mover? More...

core::Size	min_helix_length_
	The minimum number of residues in a helix for the helix to be considered. More...

bool	add_n_terminal_constraints_
	Should this mover add constraints to the N-termini of helices requiring negative charges there? More...

bool	add_c_terminal_constraints_
	Should this mover add constraints to the C-termini of helices requiring positive charges there? More...

bool	add_overall_constraints_
	Should this mover add constraints to the helix penalizing helix-disfavouring residue types? More...

bool	add_alanine_constraints_
	Should this mover add constraints to the helix requiring a certain alanine fraction? More...

bool	add_hydrophobic_constraints_
	Should this mover add constraints to the helix requiring at minimum fraction of hydrophobic residues? More...

core::Size	min_n_terminal_charges_
	The number of negative charges required at the N-terminus of each helix. More...

core::Size	n_terminus_size_
	The number of N-terminal residues in each helix, in which negative charges must be found. More...

core::Real	n_terminal_constraint_strength_
	The weight given to the N-terminal constraints. More...

core::Size	min_c_terminal_charges_
	The number of positive charges required at the C-terminus of each helix. More...

core::Size	c_terminus_size_
	The number of C-terminal residues in each helix, in which positive charges must be found. More...

core::Real	c_terminal_constraint_strength_
	The weight given to the C-terminal constraints. More...

utility::vector1< std::string >	types_to_avoid_
	The types, listed as three-letter codes, that should be avoided in helices. More...

core::Size	overall_max_count_
	The maximum number of residues from the types_to_avoid_ list that will be tolerated per helix. More...

core::Real	overall_constraints_strength_
	The penalty strength of the overall penalty, which penalizes types from the types_to_avoid_ list. More...

core::Real	desired_ala_fraction_
	The desired fractional content of alanine in each helix. More...

core::Real	ala_constraint_under_strength_
	The penalty for having 1% less than the desired fractional content of alanine. More...

core::Real	ala_constraint_over_strength_
	The penalty for having 1% more than the desired fractional content of alanine. More...

core::Real	desired_min_hydrophobic_fraction_
	The desired minimum hydrophobic content of helices. More...

core::Real	hydrophobic_constraint_strength_
	The strength of the hydrophobic constraint. (The penalty for having more than 1% less than the desired minimum hydrophobic content. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector_
	An optional residue selector. If provided, only helices that have at least one residue in the selection have constraints applied. If unused, all heliecs receive constraints. More...

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues.

Constructor & Destructor Documentation

◆ AddHelixSequenceConstraintsMover() [1/2]

protocols::aa_composition::AddHelixSequenceConstraintsMover::AddHelixSequenceConstraintsMover ( )

Constructors ///.

Default constructor

References initialize_types_to_avoid().

◆ AddHelixSequenceConstraintsMover() [2/2]

protocols::aa_composition::AddHelixSequenceConstraintsMover::AddHelixSequenceConstraintsMover ( AddHelixSequenceConstraintsMover const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~AddHelixSequenceConstraintsMover()

protocols::aa_composition::AddHelixSequenceConstraintsMover::~AddHelixSequenceConstraintsMover ( )

overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ add_alanine_constraints()

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_alanine_constraints ( ) const

inline

Should this mover add constraints to the helix requiring a certain alanine fraction?

Default true.

References add_alanine_constraints_.

Referenced by apply(), and parse_my_tag().

◆ add_c_terminal_constraints()

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_c_terminal_constraints ( ) const

inline

Should this mover add constraints to the C-termini of helices requiring positive charges there?

Default true.

References add_c_terminal_constraints_.

Referenced by apply(), check_lengths_sensible(), and parse_my_tag().

◆ add_hydrophobic_constraints()

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_hydrophobic_constraints ( ) const

inline

Should this mover add constraints to the helix requiring at minimum fraction of hydrophobic residues?

Default true.

References add_hydrophobic_constraints_.

Referenced by apply(), and parse_my_tag().

◆ add_n_terminal_constraints()

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_n_terminal_constraints ( ) const

inline

Should this mover add constraints to the N-termini of helices requiring negative charges there?

Default true.

References add_n_terminal_constraints_.

Referenced by apply(), check_lengths_sensible(), and parse_my_tag().

◆ add_overall_constraints()

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_overall_constraints ( ) const

inline

Should this mover add constraints to the helix penalizing helix-disfavouring residue types?

Default true.

References add_overall_constraints_.

Referenced by apply(), and parse_my_tag().

◆ ala_constraint_over_strength()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::ala_constraint_over_strength ( ) const

inline

Get the penalty for having 1% more than the desired fractional content of alanine.

Penalties ramp quadratically.

References ala_constraint_over_strength_.

Referenced by parse_my_tag(), set_add_alanine_constraints(), and set_up_alanine_constraints().

◆ ala_constraint_under_strength()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::ala_constraint_under_strength ( ) const

inline

Get the penalty for having 1% less than the desired fractional content of alanine.

Penalties ramp quadratically.

References ala_constraint_under_strength_.

Referenced by parse_my_tag(), set_add_alanine_constraints(), and set_up_alanine_constraints().

◆ apply()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover

Apply the mover.

Calls find_helices(), do_terminal_constraints(), do_overall_or_alanine_constraints().

Implements protocols::moves::Mover.

References add_alanine_constraints(), add_c_terminal_constraints(), add_hydrophobic_constraints(), add_n_terminal_constraints(), add_overall_constraints(), check_lengths_sensible(), delete_old_sequence_constraints(), do_overall_or_alanine_constraints(), do_terminal_constraints(), find_helices(), has_residue_selector(), remove_unselected_helices(), reset_mode(), set_up_alanine_constraints(), set_up_hydrophobic_constraints(), set_up_overall_constraints(), set_up_terminal_constraints(), and protocols::TR().

Referenced by remove_unselected_helices().

◆ c_terminal_constraint_strength()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::c_terminal_constraint_strength ( ) const

inline

The weight given to the C-terminal constraints.

The mover applies a quadratic penalty for having fewer than the desired number of positive charges at the C-terminus of each helix. This is the penalty for having one fewer than the desired number. There is no penalty or bonus for having more than the desired number.

References c_terminal_constraint_strength_.

Referenced by parse_my_tag(), and set_up_terminal_constraints().

◆ c_terminus_size()

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::c_terminus_size ( ) const

inline

The number of C-terminal residues in each helix, in which positive charges must be found.

Default 3.

References c_terminus_size_.

Referenced by check_lengths_sensible(), do_terminal_constraints(), and parse_my_tag().

◆ check_lengths_sensible()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::check_lengths_sensible ( ) const

private

Once the mover has been set up, check that the lengths of termini is sensible compared to the min_helix_length setting.

Throws an error if add_n_terminal_constraints or add_c_terminal_constraints is true, and the min_helix_length is less than the lesser of the active termini lenghts.

Throws an error if add_n_terminal_constraints or add_c_terminal_constraints is true, and the min_helix_length is less than the greater of the active termini lenghts.

References add_c_terminal_constraints(), add_n_terminal_constraints(), c_terminus_size(), protocols::mean_field::max(), min_helix_length(), protocols::hybridization::minlen, and n_terminus_size().

Referenced by apply(), and parse_my_tag().

◆ clone()

protocols::moves::MoverOP protocols::aa_composition::AddHelixSequenceConstraintsMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ delete_old_sequence_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::delete_old_sequence_constraints ( core::pose::Pose & pose ) const

private

Given a pose, remove all sequence constraints from it.

References protocols::aa_composition::ClearCompositionConstraintsMover::apply().

Referenced by apply().

◆ desired_ala_fraction()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::desired_ala_fraction ( ) const

inline

Get the desired fractional content of alanine in each helix.

Penalties ramp quadratically.

References desired_ala_fraction_.

Referenced by parse_my_tag(), set_add_alanine_constraints(), and set_up_alanine_constraints().

◆ desired_min_hydrophobic_fraction()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::desired_min_hydrophobic_fraction ( ) const

inline

Get the desired minimum hydrophobic fraction.

References desired_min_hydrophobic_fraction_.

Referenced by parse_my_tag(), set_add_hydrophobic_constraints(), and set_up_hydrophobic_constraints().

◆ do_overall_or_alanine_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::do_overall_or_alanine_constraints	(	core::pose::Pose &	pose,
		core::Size const	start_res,
		core::Size const	end_res,
		std::string const &	constraint_setup
	)		const

private

Given a pose and helix start and end points, add constraints for the helix limiting helix-disfavouring residues.

References core::pose::Pose::add_constraint().

Referenced by apply().

◆ do_terminal_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::do_terminal_constraints	(	core::pose::Pose &	pose,
		bool const	n_terminus,
		core::Size const	start_res,
		core::Size const	end_res,
		std::string const &	constraint_setup
	)		const

private

Given a pose and helix start and end points, add constraints for the helix termini requiring charges in the first or last N residues.

Given a pose, add constraints for the termini requiring charges in the first or last N residues.

If n_terminus is true, this adds the requirement that the N-terminus has negative charges; if it is false, this adds the requirement that the C-terminus has positive charges.

References core::pose::Pose::add_constraint(), c_terminus_size(), and n_terminus_size().

Referenced by apply().

◆ find_helices()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::find_helices	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > &	helices
	)		const

private

Given a pose and an empty vector (that will be cleared by this operation and repopulated), run DSSP and identify all helices longer than a specified length.

Calls protocols::aa_composition::find_helices_over_length(), in util.cc/hh.

References protocols::aa_composition::find_helices_over_length(), and min_helix_length().

Referenced by apply().

◆ fresh_instance()

moves::MoverOP protocols::aa_composition::AddHelixSequenceConstraintsMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::aa_composition::AddHelixSequenceConstraintsMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ has_residue_selector()

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::has_residue_selector ( ) const

inline

Has a residue selector been specified for this mover?

References residue_selector_.

Referenced by apply(), and remove_unselected_helices().

◆ hydrophobic_constraint_strength()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::hydrophobic_constraint_strength ( ) const

inline

Get the strength of the hydrophobic constraint. (The penalty for having more than 1% less than the desired minimum hydrophobic content.

References hydrophobic_constraint_strength_.

Referenced by parse_my_tag(), set_add_hydrophobic_constraints(), and set_up_hydrophobic_constraints().

◆ initialize_types_to_avoid()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::initialize_types_to_avoid ( )

private

Initialize the types to avoid to ASN, ASP, SER, GLU, THR, VAL.

Initialize the types to avoid to ASN, ASP, SER, GLY, THR, VAL.

References types_to_avoid_.

Referenced by AddHelixSequenceConstraintsMover().

◆ min_c_terminal_charges()

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::min_c_terminal_charges ( ) const

inline

The number of positive charges required at the C-terminus of each helix.

Default 2.

References min_c_terminal_charges_.

Referenced by parse_my_tag(), and set_up_terminal_constraints().

◆ min_helix_length()

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::min_helix_length ( ) const

inline

Get the minimum number of residues in a helix for the helix to be considered.

Very short helices (e.g. one turn, five residues) have negligible helix macrodipoles, and can be disregarded. Defaults to 8.

References min_helix_length_.

Referenced by check_lengths_sensible(), find_helices(), and parse_my_tag().

◆ min_n_terminal_charges()

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::min_n_terminal_charges ( ) const

inline

The number of negative charges required at the N-terminus of each helix.

Default 2.

References min_n_terminal_charges_.

Referenced by parse_my_tag(), and set_up_terminal_constraints().

◆ mover_name()

std::string protocols::aa_composition::AddHelixSequenceConstraintsMover::mover_name ( )

static

Referenced by get_name(), protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator::keyname(), and provide_xml_schema().

◆ n_terminal_constraint_strength()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::n_terminal_constraint_strength ( ) const

inline

The weight given to the N-terminal constraints.

The mover applies a quadratic penalty for having fewer than the desired number of negative charges at the N-terminus of each helix. This is the penalty for having one fewer than the desired number. There is no penalty or bonus for having more than the desired number.

References n_terminal_constraint_strength_.

Referenced by parse_my_tag(), and set_up_terminal_constraints().

◆ n_terminus_size()

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::n_terminus_size ( ) const

inline

The number of N-terminal residues in each helix, in which negative charges must be found.

Default 3.

References n_terminus_size_.

Referenced by check_lengths_sensible(), do_terminal_constraints(), and parse_my_tag().

◆ overall_constraints_strength()

core::Real const& protocols::aa_composition::AddHelixSequenceConstraintsMover::overall_constraints_strength ( ) const

inline

Get the strength of the helix constraints that penalize helix-disfavouring residue types.

This is the penalty for having one more than the maximum count of the disfavoured residues. Past this, the penalty ramps quadratically.

References overall_constraints_strength_.

Referenced by parse_my_tag(), set_add_overall_constraints(), and set_up_overall_constraints().

◆ overall_max_count()

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::overall_max_count ( ) const

inline

Max number of residues from the types to avoid list per helix.

References overall_max_count_.

Referenced by parse_my_tag(), set_add_overall_constraints(), and set_up_overall_constraints().

◆ parse_my_tag()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References add_alanine_constraints(), add_c_terminal_constraints(), add_hydrophobic_constraints(), add_n_terminal_constraints(), add_overall_constraints(), ala_constraint_over_strength(), ala_constraint_under_strength(), c_terminal_constraint_strength(), c_terminus_size(), check_lengths_sensible(), desired_ala_fraction(), desired_min_hydrophobic_fraction(), hydrophobic_constraint_strength(), min_c_terminal_charges(), min_helix_length(), min_n_terminal_charges(), n_terminal_constraint_strength(), n_terminus_size(), overall_constraints_strength(), overall_max_count(), core::select::residue_selector::parse_residue_selector(), reset_mode(), set_add_alanine_constraints(), set_add_c_terminal_constraints(), set_add_hydrophobic_constraints(), set_add_n_terminal_constraints(), set_add_overall_constraints(), set_min_helix_length(), set_reset_mode(), and set_residue_selector().

◆ provide_xml_schema()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator::provide_xml_schema().

◆ remove_unselected_helices()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::remove_unselected_helices	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > &	helices
	)		const

private

Given a pose and an already-populated list of helices, remove helices that do not have at least one residue selected by the residue selector associated with this mover.

Does nothing if there's no residue selector.

References apply(), has_residue_selector(), and residue_selector().

Referenced by apply().

◆ reset_mode()

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::reset_mode ( ) const

inline

Get whether old composition constraints should be deleted before applying this mover.

Default false (i.e. new composition constraints are appended to the old).

References reset_mode_.

Referenced by apply(), and parse_my_tag().

◆ residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::aa_composition::AddHelixSequenceConstraintsMover::residue_selector ( ) const

inline

An optional residue selector. If provided, only helices that have at least one residue in the selection have constraints applied. If unused, all heliecs receive constraints.

References residue_selector_.

Referenced by remove_unselected_helices().

◆ set_add_alanine_constraints() [1/2]

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_alanine_constraints ( bool const setting )

Set whether this mover should add constraints to the helix requiring a certain alanine fraction.

Set whether this mover should add constraints to the helix requiring a certain alanine fraction?

Default true.

References add_alanine_constraints_.

Referenced by parse_my_tag().

◆ set_add_alanine_constraints() [2/2]

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_alanine_constraints	(	bool const	setting,
		core::Real const &	desired_ala_fraction,
		core::Real const &	ala_constraint_under_strength,
		core::Real const &	ala_constraint_over_strength
	)

Set whether this mover should add constraints to the helix requiring a certain alanine fraction.

Default true.

References add_alanine_constraints_, ala_constraint_over_strength(), ala_constraint_over_strength_, ala_constraint_under_strength(), ala_constraint_under_strength_, desired_ala_fraction(), and desired_ala_fraction_.

◆ set_add_c_terminal_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_c_terminal_constraints	(	bool const	setting,
		core::Size const	min_charges,
		core::Size const	cterm_size,
		core::Real const &	strength
	)

Set whether this mover should add constraints to the C-termini of helices requiring positive charges there.

Set whether this mover should add constraints to the C-termini of helices requiring negative charges there?

Default true.

References add_c_terminal_constraints_, c_terminal_constraint_strength_, c_terminus_size_, and min_c_terminal_charges_.

Referenced by parse_my_tag().

◆ set_add_hydrophobic_constraints() [1/2]

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_hydrophobic_constraints ( bool const setting )

Set whether this mover should add constraints to the helix requiring at minimum fraction of hydrophobic residues.

Default true.

References add_hydrophobic_constraints_.

Referenced by parse_my_tag().

◆ set_add_hydrophobic_constraints() [2/2]

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_hydrophobic_constraints	(	bool const	setting,
		core::Real const &	desired_min_hydrophobic_fraction,
		core::Real const &	hydrophobic_constraint_strength
	)

Set whether this mover should add constraints to the helix requiring at minimum fraction of hydrophobic residues.

Default true.

References add_hydrophobic_constraints_, desired_min_hydrophobic_fraction(), desired_min_hydrophobic_fraction_, hydrophobic_constraint_strength(), and hydrophobic_constraint_strength_.

◆ set_add_n_terminal_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_n_terminal_constraints	(	bool const	setting,
		core::Size const	min_charges,
		core::Size const	nterm_size,
		core::Real const &	strength
	)

Set whether this mover should add constraints to the N-termini of helices requiring negative charges there.

Set whether this mover should add constraints to the N-termini of helices requiring negative charges there?

References add_n_terminal_constraints_, min_n_terminal_charges_, n_terminal_constraint_strength_, and n_terminus_size_.

Referenced by parse_my_tag().

◆ set_add_overall_constraints() [1/2]

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_overall_constraints ( bool const setting )

Set whether this mover should add constraints to the helix penalizing helix-disfavouring residue types.

Set whether this mover should add constraints to the helix penalizing helix-disfavouring residue types?

Default true.

References add_overall_constraints_.

Referenced by parse_my_tag().

◆ set_add_overall_constraints() [2/2]

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_overall_constraints	(	bool const	setting,
		std::string const &	types_to_avoid,
		core::Size const	overall_max_count,
		core::Real const &	overall_constraints_strength
	)

Set whether this mover should add constraints to the helix penalizing helix-disfavouring residue types.

Default true.

References add_overall_constraints_, overall_constraints_strength(), overall_max_count(), overall_max_count_, types_to_avoid(), and types_to_avoid_.

◆ set_min_helix_length()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_min_helix_length ( core::Size const setting )

Set the minimum number of residues in a helix for the helix to be considered.

Very short helices (e.g. one turn, five residues) have negligible helix macrodipoles, and can be disregarded. Defaults to 8.

References min_helix_length_.

Referenced by parse_my_tag().

◆ set_reset_mode()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_reset_mode ( bool const setting )

Set whether old composition constraints should be deleted before applying this mover.

References reset_mode_.

Referenced by parse_my_tag().

◆ set_residue_selector()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Set a residue selector if specified by the user.

References residue_selector_.

Referenced by parse_my_tag().

◆ set_up_alanine_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_up_alanine_constraints ( std::string & setup_string_out ) const

private

Set up strings defining constraints penalizing too few or too many alanines.

References ala_constraint_over_strength(), ala_constraint_under_strength(), and desired_ala_fraction().

Referenced by apply().

◆ set_up_hydrophobic_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_up_hydrophobic_constraints ( std::string & setup_string_out ) const

private

Set up strings defining constraints penalizing too few hydrophobics.

References desired_min_hydrophobic_fraction(), and hydrophobic_constraint_strength().

Referenced by apply().

◆ set_up_overall_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_up_overall_constraints ( std::string & setup_string_out ) const

private

Set up strings defining constraints penalizing helix-disfavouring residue types.

References overall_constraints_strength(), overall_max_count(), and types_to_avoid().

Referenced by apply().

◆ set_up_terminal_constraints()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::set_up_terminal_constraints	(	std::string &	setup_string_out,
		bool const	n_terminal
	)		const

private

Set up strings defining terminal constraints.

References c_terminal_constraint_strength(), min_c_terminal_charges(), min_n_terminal_charges(), and n_terminal_constraint_strength().

Referenced by apply().

◆ show()

void protocols::aa_composition::AddHelixSequenceConstraintsMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::aa_composition::operator<<().

◆ types_to_avoid() [1/2]

utility::vector1< std::string > const& protocols::aa_composition::AddHelixSequenceConstraintsMover::types_to_avoid ( ) const

inline

Access the vector of types to avoid.

References types_to_avoid_.

Referenced by set_add_overall_constraints(), and set_up_overall_constraints().

◆ types_to_avoid() [2/2]

std::string const& protocols::aa_composition::AddHelixSequenceConstraintsMover::types_to_avoid ( core::Size const index ) const

inline

Access an element in the vector of types to avoid.

Note: no bounds checking!

References types_to_avoid_.

Member Data Documentation

◆ add_alanine_constraints_

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_alanine_constraints_

private

Should this mover add constraints to the helix requiring a certain alanine fraction?

Default true.

Referenced by add_alanine_constraints(), and set_add_alanine_constraints().

◆ add_c_terminal_constraints_

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_c_terminal_constraints_

private

Should this mover add constraints to the C-termini of helices requiring positive charges there?

Default true.

Referenced by add_c_terminal_constraints(), and set_add_c_terminal_constraints().

◆ add_hydrophobic_constraints_

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_hydrophobic_constraints_

private

Should this mover add constraints to the helix requiring at minimum fraction of hydrophobic residues?

Default true.

Referenced by add_hydrophobic_constraints(), and set_add_hydrophobic_constraints().

◆ add_n_terminal_constraints_

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_n_terminal_constraints_

private

Should this mover add constraints to the N-termini of helices requiring negative charges there?

Default true.

Referenced by add_n_terminal_constraints(), and set_add_n_terminal_constraints().

◆ add_overall_constraints_

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::add_overall_constraints_

private

Should this mover add constraints to the helix penalizing helix-disfavouring residue types?

Default true.

Referenced by add_overall_constraints(), and set_add_overall_constraints().

◆ ala_constraint_over_strength_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::ala_constraint_over_strength_

private

The penalty for having 1% more than the desired fractional content of alanine.

Default 0.2.

Referenced by ala_constraint_over_strength(), and set_add_alanine_constraints().

◆ ala_constraint_under_strength_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::ala_constraint_under_strength_

private

The penalty for having 1% less than the desired fractional content of alanine.

Default 0.2.

Referenced by ala_constraint_under_strength(), and set_add_alanine_constraints().

◆ c_terminal_constraint_strength_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::c_terminal_constraint_strength_

private

The weight given to the C-terminal constraints.

The mover applies a quadratic penalty for having fewer than the desired number of positive charges at the C-terminus of each helix. This is the penalty for having one fewer than the desired number. There is no penalty or bonus for having more than the desired number.

Referenced by c_terminal_constraint_strength(), and set_add_c_terminal_constraints().

◆ c_terminus_size_

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::c_terminus_size_

private

The number of C-terminal residues in each helix, in which positive charges must be found.

Default 3.

Referenced by c_terminus_size(), and set_add_c_terminal_constraints().

◆ desired_ala_fraction_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::desired_ala_fraction_

private

The desired fractional content of alanine in each helix.

Referenced by desired_ala_fraction(), and set_add_alanine_constraints().

◆ desired_min_hydrophobic_fraction_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::desired_min_hydrophobic_fraction_

private

The desired minimum hydrophobic content of helices.

Defaults to 0.25.

Referenced by desired_min_hydrophobic_fraction(), and set_add_hydrophobic_constraints().

◆ hydrophobic_constraint_strength_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::hydrophobic_constraint_strength_

private

The strength of the hydrophobic constraint. (The penalty for having more than 1% less than the desired minimum hydrophobic content.

Referenced by hydrophobic_constraint_strength(), and set_add_hydrophobic_constraints().

◆ min_c_terminal_charges_

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::min_c_terminal_charges_

private

The number of positive charges required at the C-terminus of each helix.

Default 2.

Referenced by min_c_terminal_charges(), and set_add_c_terminal_constraints().

◆ min_helix_length_

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::min_helix_length_

private

The minimum number of residues in a helix for the helix to be considered.

Very short helices (e.g. one turn, five residues) have negligible helix macrodipoles, and can be disregarded. Defaults to 8.

Referenced by min_helix_length(), and set_min_helix_length().

◆ min_n_terminal_charges_

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::min_n_terminal_charges_

private

The number of negative charges required at the N-terminus of each helix.

Default 2.

Referenced by min_n_terminal_charges(), and set_add_n_terminal_constraints().

◆ n_terminal_constraint_strength_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::n_terminal_constraint_strength_

private

The weight given to the N-terminal constraints.

The mover applies a quadratic penalty for having fewer than the desired number of negative charges at the N-terminus of each helix. This is the penalty for having one fewer than the desired number. There is no penalty or bonus for having more than the desired number.

Referenced by n_terminal_constraint_strength(), and set_add_n_terminal_constraints().

◆ n_terminus_size_

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::n_terminus_size_

private

The number of N-terminal residues in each helix, in which negative charges must be found.

Default 3.

Referenced by n_terminus_size(), and set_add_n_terminal_constraints().

◆ overall_constraints_strength_

core::Real protocols::aa_composition::AddHelixSequenceConstraintsMover::overall_constraints_strength_

private

The penalty strength of the overall penalty, which penalizes types from the types_to_avoid_ list.

The mover applies a quadratic penalty for having more than the maximum number of residues of these types. There is no penalty or bonus for having fewer. This is the penalty for having one more than the max tolerated. Default 5.0.

Referenced by overall_constraints_strength().

◆ overall_max_count_

core::Size protocols::aa_composition::AddHelixSequenceConstraintsMover::overall_max_count_

private

The maximum number of residues from the types_to_avoid_ list that will be tolerated per helix.

Default 0.

Referenced by overall_max_count(), and set_add_overall_constraints().

◆ reset_mode_

bool protocols::aa_composition::AddHelixSequenceConstraintsMover::reset_mode_

private

Should old composition constraints be deleted before applying this mover?

Default false (i.e. new composition constraints are appended to the old).

Referenced by reset_mode(), and set_reset_mode().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::aa_composition::AddHelixSequenceConstraintsMover::residue_selector_

private

An optional residue selector. If provided, only helices that have at least one residue in the selection have constraints applied. If unused, all heliecs receive constraints.

Referenced by has_residue_selector(), residue_selector(), and set_residue_selector().

◆ types_to_avoid_

utility::vector1< std::string > protocols::aa_composition::AddHelixSequenceConstraintsMover::types_to_avoid_

private

The types, listed as three-letter codes, that should be avoided in helices.

The overall constraints cap the number of residues of these types that are allowed. Defaults to ASN, ASP, SER, GLY, THR, VAL.

Referenced by initialize_types_to_avoid(), set_add_overall_constraints(), and types_to_avoid().

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

src/protocols/aa_composition/AddHelixSequenceConstraintsMover.hh
src/protocols/aa_composition/AddHelixSequenceConstraintsMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AddHelixSequenceConstraintsMover() [1/2]

◆ AddHelixSequenceConstraintsMover() [2/2]

◆ ~AddHelixSequenceConstraintsMover()

Member Function Documentation

◆ add_alanine_constraints()

◆ add_c_terminal_constraints()

◆ add_hydrophobic_constraints()

◆ add_n_terminal_constraints()

◆ add_overall_constraints()

◆ ala_constraint_over_strength()

◆ ala_constraint_under_strength()

◆ apply()

◆ c_terminal_constraint_strength()

◆ c_terminus_size()

◆ check_lengths_sensible()

◆ clone()

◆ delete_old_sequence_constraints()

◆ desired_ala_fraction()

◆ desired_min_hydrophobic_fraction()

◆ do_overall_or_alanine_constraints()

◆ do_terminal_constraints()

◆ find_helices()

◆ fresh_instance()

◆ get_name()

◆ has_residue_selector()

◆ hydrophobic_constraint_strength()

◆ initialize_types_to_avoid()

◆ min_c_terminal_charges()

◆ min_helix_length()

◆ min_n_terminal_charges()

◆ mover_name()

◆ n_terminal_constraint_strength()

◆ n_terminus_size()

◆ overall_constraints_strength()

◆ overall_max_count()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ remove_unselected_helices()

◆ reset_mode()

◆ residue_selector()

◆ set_add_alanine_constraints() [1/2]

◆ set_add_alanine_constraints() [2/2]

◆ set_add_c_terminal_constraints()

◆ set_add_hydrophobic_constraints() [1/2]

◆ set_add_hydrophobic_constraints() [2/2]

◆ set_add_n_terminal_constraints()

◆ set_add_overall_constraints() [1/2]

◆ set_add_overall_constraints() [2/2]

◆ set_min_helix_length()

◆ set_reset_mode()

◆ set_residue_selector()

◆ set_up_alanine_constraints()

◆ set_up_hydrophobic_constraints()

◆ set_up_overall_constraints()

◆ set_up_terminal_constraints()

◆ show()

◆ types_to_avoid() [1/2]

◆ types_to_avoid() [2/2]

Member Data Documentation

◆ add_alanine_constraints_

◆ add_c_terminal_constraints_

◆ add_hydrophobic_constraints_

◆ add_n_terminal_constraints_

◆ add_overall_constraints_

◆ ala_constraint_over_strength_

◆ ala_constraint_under_strength_

◆ c_terminal_constraint_strength_

◆ c_terminus_size_

◆ desired_ala_fraction_

◆ desired_min_hydrophobic_fraction_

◆ hydrophobic_constraint_strength_

◆ min_c_terminal_charges_

◆ min_helix_length_