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protocols::evolution::AlignmentGapInserter Class Reference

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...

#include <AlignmentGapInserterFilter.hh>

Inheritance diagram for protocols::evolution::AlignmentGapInserter:
Inheritance graph
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Public Member Functions

 AlignmentGapInserter ()
 
 ~AlignmentGapInserter () override
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
utility::vector0< core::Sizefind_char_location_in_string (std::string const &string, char const findIt) const
 
bool apply (core::pose::Pose const &p) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
std::string alignment_file () const
 
void alignment_file (std::string const &a)
 
std::string available_AAs_file () const
 
void available_AAs_file (std::string const &a)
 
std::string cleaned_alignment_file () const
 
void cleaned_alignment_file (std::string const &a)
 
core::Real nbr_e_threshold () const
 
void nbr_e_threshold (core::Real const &t)
 
utility::vector1< core::Realloop_seqid_thresholds () const
 
void loop_seqid_thresholds (utility::vector1< core::Real > const &v)
 
core::Size indel_motif_radius () const
 
void indel_motif_radius (core::Size const &r)
 
core::Size only_clean_seq_num () const
 
void only_clean_seq_num (core::Size const &t)
 
core::scoring::ScoreFunctionOP scorefxn () const
 
void scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
utility::vector1< core::Realmax_score_diffs () const
 
void max_score_diffs (utility::vector1< core::Real > const &v)
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter 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 filter_is_unpublished () const
 Does this filter 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 Attributes

std::string alignment_file_
 
std::string available_AAs_file_
 
std::string cleaned_alignment_file_
 
core::Real nbr_e_threshold_
 
utility::vector1< core::Realloop_seqid_thresholds_
 
core::Size indel_motif_radius_
 
core::Real only_clean_seq_num_
 
core::scoring::ScoreFunctionOP scorefxn_
 
utility::vector1< core::Realmax_score_diffs_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Detailed Description

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts.

Constructor & Destructor Documentation

protocols::evolution::AlignmentGapInserter::AlignmentGapInserter ( )
protocols::evolution::AlignmentGapInserter::~AlignmentGapInserter ( )
overridedefault

Member Function Documentation

std::string protocols::evolution::AlignmentGapInserter::alignment_file ( ) const
inline

References alignment_file_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::alignment_file ( std::string const &  a)
inline
bool protocols::evolution::AlignmentGapInserter::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::evolution::AlignmentGapInserter::available_AAs_file ( ) const
inline

References available_AAs_file_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::available_AAs_file ( std::string const &  a)
inline
std::string protocols::evolution::AlignmentGapInserter::class_name ( )
static
std::string protocols::evolution::AlignmentGapInserter::cleaned_alignment_file ( ) const
inline

References cleaned_alignment_file_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::cleaned_alignment_file ( std::string const &  a)
inline
filters::FilterOP protocols::evolution::AlignmentGapInserter::clone ( ) const
inlineoverridevirtual
utility::vector0< core::Size > protocols::evolution::AlignmentGapInserter::find_char_location_in_string ( std::string const &  string,
char const  findIt 
) const

Referenced by apply().

filters::FilterOP protocols::evolution::AlignmentGapInserter::fresh_instance ( ) const
inlineoverridevirtual
core::Size protocols::evolution::AlignmentGapInserter::indel_motif_radius ( ) const
inline

References indel_motif_radius_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::indel_motif_radius ( core::Size const &  r)
inline

References indel_motif_radius_.

utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds ( ) const
inline

References loop_seqid_thresholds_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds ( utility::vector1< core::Real > const &  v)
inline
utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::max_score_diffs ( ) const
inline

References max_score_diffs_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::max_score_diffs ( utility::vector1< core::Real > const &  v)
inline

References max_score_diffs_.

std::string protocols::evolution::AlignmentGapInserter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

core::Real protocols::evolution::AlignmentGapInserter::nbr_e_threshold ( ) const
inline

References nbr_e_threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::nbr_e_threshold ( core::Real const &  t)
inline
core::Size protocols::evolution::AlignmentGapInserter::only_clean_seq_num ( ) const
inline

References only_clean_seq_num_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::only_clean_seq_num ( core::Size const &  t)
inline
void protocols::evolution::AlignmentGapInserter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::evolution::AlignmentGapInserter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::evolution::AlignmentGapInserter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

core::Real protocols::evolution::AlignmentGapInserter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

core::scoring::ScoreFunctionOP protocols::evolution::AlignmentGapInserter::scorefxn ( ) const
inline

References scorefxn_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentGapInserter::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
inline

References scorefxn(), and scorefxn_.

Referenced by scorefxn().

Member Data Documentation

std::string protocols::evolution::AlignmentGapInserter::alignment_file_
private

Referenced by alignment_file().

std::string protocols::evolution::AlignmentGapInserter::available_AAs_file_
private

Referenced by available_AAs_file().

std::string protocols::evolution::AlignmentGapInserter::cleaned_alignment_file_
private

Referenced by cleaned_alignment_file().

core::Size protocols::evolution::AlignmentGapInserter::indel_motif_radius_
private

Referenced by indel_motif_radius().

utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds_
private
utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::max_score_diffs_
private
core::Real protocols::evolution::AlignmentGapInserter::nbr_e_threshold_
private

Referenced by nbr_e_threshold().

core::Real protocols::evolution::AlignmentGapInserter::only_clean_seq_num_
private

Referenced by only_clean_seq_num().

core::scoring::ScoreFunctionOP protocols::evolution::AlignmentGapInserter::scorefxn_
private

Referenced by scorefxn().


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