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protocols::aa_composition::AddHelixSequenceConstraintsMover Class Reference

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:
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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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

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

Constructors ///.

Default constructor

References initialize_types_to_avoid().

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

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

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

Member Function Documentation

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().

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().

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().

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().

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().

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().

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().

void protocols::aa_composition::AddHelixSequenceConstraintsMover::apply ( core::pose::Pose pose)
overridevirtual
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().

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().

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().

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

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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().

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().

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().

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().

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().

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().

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

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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().

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().

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().

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().

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().

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().

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().

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

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().

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(), and set_up_overall_constraints().

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().

void protocols::aa_composition::AddHelixSequenceConstraintsMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::aa_composition::AddHelixSequenceConstraintsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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().

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().

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().

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().

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_.

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().

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().

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_.

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().

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().

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_max_count(), overall_max_count_, and types_to_avoid_.

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().

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().

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().

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().

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().

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().

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().

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<<().

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_up_overall_constraints().

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

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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: