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protocols::denovo_design::task_operations::ConsensusLoopDesignOperation Class Reference

#include <ConsensusLoopDesignOperation.hh>

Inheritance diagram for protocols::denovo_design::task_operations::ConsensusLoopDesignOperation:
Inheritance graph
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Public Types

typedef std::string AAs
 
- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef pose::Pose Pose
 

Public Member Functions

 ConsensusLoopDesignOperation ()
 default constructor More...
 
 ~ConsensusLoopDesignOperation () override
 destructor More...
 
core::pack::task::operation::TaskOperationOP clone () const override
 make clone More...
 
void apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
 apply More...
 
virtual std::string get_name () const
 Returns the name of the class. More...
 
void set_secstruct (std::string const &secstruct)
 Sets the secondary structure to be used for selection of loops. If a residue selector is set, this is ignored. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelector const &selector_val)
 Sets residue selector. If set, only selected residues will be operated upon. (default = select by secondary structure type L) More...
 
void parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
 Used to parse an xml-like tag to load parameters and properties. More...
 
AAFrequencies const & aa_frequencies (LoopInfo const &info, core::Size const resid) const
 
AAs forbidden_aas (AAFrequencies const &frequencies) const
 
void disallow_aas (core::pack::task::PackerTask &task, LoopInfo const &info) const
 
LoopInfoVec get_loop_info (core::pose::Pose const &pose) const
 
LoopInfoVec loop_info_from_subset (core::pose::Pose const &pose, std::string const &ss, core::select::residue_selector::ResidueSubset const &subset) const
 
void set_include_adjacent_residues (bool const include_res)
 if true, residues adjacent to loops will be restricted. Otherwise, just the loop. (default=false) More...
 
void set_secstruct_from_blueprint (std::string const &bp_file)
 Reads/parses a blueprint file and calls set_secstruct() on the resulting secondary structure. Length of blueprint file must match the length of the input pose. More...
 
void set_enrichment_threshold (core::Real const threshold)
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
 ~TaskOperation () override
 
virtual bool task_operation_provides_citation_info () const
 Does this task operation 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 task_operation_is_unpublished () const
 Does this task_operation 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 class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

std::string get_secstruct (core::pose::Pose const &pose) const
 Gets secondary structure to be used for determining what is surrounding the loops. More...
 
core::select::residue_selector::ResidueSelectorCOP residue_selector (std::string const &secstruct) const
 Returns a residue selector to be used to choose loops. More...
 
AAs compute_aas_after_disallowing (AAs const &aas, core::pack::task::ResidueLevelTask const &task) const
 
AAs compute_best_allowed_aas (AAFrequencies const &aa_freqs, core::pack::task::ResidueLevelTask const &task) const
 

Private Attributes

std::string secstruct_
 
bool include_adjacent_residues_
 
bool use_dssp_
 
core::Real enrichment_threshold_
 
core::select::residue_selector::ResidueSelectorCOP selector_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::ConsensusLoopDesignOperation ( )

default constructor

protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::~ConsensusLoopDesignOperation ( )
overridedefault

destructor

Member Function Documentation

AAFrequencies const & protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::aa_frequencies ( LoopInfo const &  info,
core::Size const  resid 
) const
void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::apply ( core::pose::Pose const &  pose,
core::pack::task::PackerTask task 
) const
overridevirtual
std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::class_name ( )
static
core::pack::task::operation::TaskOperationOP protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::clone ( ) const
overridevirtual
ConsensusLoopDesignOperation::AAs protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_aas_after_disallowing ( AAs const &  aas,
core::pack::task::ResidueLevelTask const &  task 
) const
private
ConsensusLoopDesignOperation::AAs protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_best_allowed_aas ( AAFrequencies const &  aa_freqs,
core::pack::task::ResidueLevelTask const &  task 
) const
private
void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas ( core::pack::task::PackerTask task,
LoopInfo const &  info 
) const
ConsensusLoopDesignOperation::AAs protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::forbidden_aas ( AAFrequencies const &  frequencies) const

References enrichment_threshold_.

Referenced by disallow_aas().

LoopInfoVec protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_loop_info ( core::pose::Pose const &  pose) const
std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_name ( ) const
virtual

Returns the name of the class.

References class_name().

std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_secstruct ( core::pose::Pose const &  pose) const
private

Gets secondary structure to be used for determining what is surrounding the loops.

Parameters
[in]poseinput pose
Returns
Secondary structure string according to the following rules:
  1. If secstruct_ is set, return that.
  2. If use_dssp_ is set, return string computed from DSSP.
  3. return pose.secstruct()

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::Pose::secstruct(), secstruct_, protocols::TR(), and use_dssp_.

Referenced by get_loop_info().

LoopInfoVec protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::loop_info_from_subset ( core::pose::Pose const &  pose,
std::string const &  ss,
core::select::residue_selector::ResidueSubset const &  subset 
) const
void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::residue_selector ( std::string const &  secstruct) const
private

Returns a residue selector to be used to choose loops.

Parameters
[in]secstructSecondary structure to be used, if default selector is used

If selector_ is provided, simply return that. If not, create a default secondary structure selector using the given secstruct

References selector_.

Referenced by get_loop_info().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_enrichment_threshold ( core::Real const  threshold)

References enrichment_threshold_.

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_include_adjacent_residues ( bool const  include_res)

if true, residues adjacent to loops will be restricted. Otherwise, just the loop. (default=false)

References include_adjacent_residues_.

Referenced by parse_tag().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_residue_selector ( core::select::residue_selector::ResidueSelector const &  selector_val)

Sets residue selector. If set, only selected residues will be operated upon. (default = select by secondary structure type L)

Parameters
[in]selector_valResidue selector to be used. Cloned by this function and set as selector_

References core::select::residue_selector::ResidueSelector::clone(), and selector_.

Referenced by parse_tag().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_secstruct ( std::string const &  secstruct)

Sets the secondary structure to be used for selection of loops. If a residue selector is set, this is ignored.

Parameters
[in]secstructSecondary structure to be used. Must match pose length

References secstruct_.

Referenced by parse_tag(), and set_secstruct_from_blueprint().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_secstruct_from_blueprint ( std::string const &  bp_file)

Reads/parses a blueprint file and calls set_secstruct() on the resulting secondary structure. Length of blueprint file must match the length of the input pose.

References protocols::parser::BluePrint::secstruct(), and set_secstruct().

Referenced by parse_tag().

Member Data Documentation

core::Real protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::enrichment_threshold_
private
bool protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::include_adjacent_residues_
private
std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::secstruct_
private
core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::selector_
private
bool protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::use_dssp_
private

Referenced by get_secstruct(), and parse_tag().


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