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Public Types | Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::match::output::PDBWriter Class Reference

#include <PDBWriter.hh>

Inheritance diagram for protocols::match::output::PDBWriter:
Inheritance graph
[legend]

Public Types

typedef std::pair< core::Size,
core::Size
SizePair
 
typedef OutputWriter Parent
 

Public Member Functions

 PDBWriter ()
 
 ~PDBWriter () override
 
void prepare_for_output_writing () override
 
void record_match (match const &m, MatchEvaluatorOP evaluator, MatchScoreWriterOP match_score_writer) override
 
void record_match (match_dspos1 const &m) override
 evaluator and score writer are not passed in because single-downstream-position match currently have no way of being evaluated More...
 
void set_coordinate_cacher (UpstreamHitCacherOP)
 
void set_prefix (std::string const &prefix)
 
void initialize_from_matcher_task (MatcherTaskCOP mtask) override
 
void set_downstream_builder (core::Size geomcst_id, downstream::DownstreamBuilderCOP dsbuilder)
 
void assemble_remark_lines (core::pose::Pose &outpose, utility::vector1< core::conformation::ResidueCOP > const &upstream_matchres, std::map< core::Size, core::Size > const &redundant_upstream_res, utility::vector1< core::Size > const &ex_geom_ids_for_upstream_res) const
 
core::pose::PoseCOP create_output_upstream_pose (utility::vector1< core::conformation::ResidueCOP > const &upstream_matchres, std::map< core::Size, core::Size > const &redundant_upstream_res, utility::vector1< core::Size > const &ex_geom_ids_for_upstream_res)
 
std::string signature_string (utility::vector1< core::conformation::ResidueCOP > const &upstream_matchres) const
 
core::Size num_geom_cst () const
 
std::string scaf_name () const
 
std::string cstfile_name () const
 
std::string prefix () const
 
- Public Member Functions inherited from protocols::match::output::OutputWriter
 OutputWriter ()
 
 ~OutputWriter () override
 
protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP cst_io () const
 
void determine_redundant_upstream_matchres (match_dspos1 const &m, std::map< core::Size, core::Size > &redundant_upstream_res) const
 determine if any upstream res are at the same scaffold position, i.e. if one of them is a backbone interaction the redundant_upstream_res map is a mapping from the redundant geometric constraint id of the redundant residue to the geomcst_id of the "nonredundant" res i.e. if cstres 1 happens to be a cys at position 10 and cstres 3 is a gly at position 10 (and it's backbone is used in satisfying constraint 3), the mapping will contain the 3,1 pair. More...
 
virtual void end_output_writing ()
 

Protected Member Functions

UpstreamHitCacherOP coordinate_cacher ()
 
utility::vector1
< downstream::DownstreamBuilderCOP >
const & 
dsbuilders ()
 
std::string assemble_outtag (utility::vector1< core::conformation::ResidueCOP > const &upstream_matchres)
 

Private Attributes

UpstreamHitCacherOP coordinate_cacher_
 
bool write_matchres_only_
 
std::string scaf_name_
 
std::string cstfile_name_
 
std::string prefix_
 
core::Size num_written_
 
core::Size num_geom_cst_
 
utility::vector1
< downstream::DownstreamBuilderCOP
dsbuilders_
 
core::pose::PoseCOP orig_upstream_pose_
 
core::pose::PoseCOP downstream_pose_from_task_
 
std::map< std::string, SizePairsignature_map_
 
utility::vector1< booloutput_dsgeom_for_geomcst_
 
std::map< core::Size, core::Sizeupstream_only_geom_cst_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::match::output::PDBWriter::PDBWriter ( )
protocols::match::output::PDBWriter::~PDBWriter ( )
overridedefault

Member Function Documentation

std::string protocols::match::output::PDBWriter::assemble_outtag ( utility::vector1< core::conformation::ResidueCOP > const &  upstream_matchres)
protected
void protocols::match::output::PDBWriter::assemble_remark_lines ( core::pose::Pose outpose,
utility::vector1< core::conformation::ResidueCOP > const &  upstream_matchres,
std::map< core::Size, core::Size > const &  redundant_upstream_res,
utility::vector1< core::Size > const &  ex_geom_ids_for_upstream_res 
) const
UpstreamHitCacherOP protocols::match::output::PDBWriter::coordinate_cacher ( )
protected
core::pose::PoseCOP protocols::match::output::PDBWriter::create_output_upstream_pose ( utility::vector1< core::conformation::ResidueCOP > const &  upstream_matchres,
std::map< core::Size, core::Size > const &  redundant_upstream_res,
utility::vector1< core::Size > const &  ex_geom_ids_for_upstream_res 
)
std::string protocols::match::output::PDBWriter::cstfile_name ( ) const
utility::vector1< downstream::DownstreamBuilderCOP > const & protocols::match::output::PDBWriter::dsbuilders ( )
protected
void protocols::match::output::PDBWriter::initialize_from_matcher_task ( MatcherTaskCOP  mtask)
overridevirtual
core::Size protocols::match::output::PDBWriter::num_geom_cst ( ) const
std::string protocols::match::output::PDBWriter::prefix ( ) const
void protocols::match::output::PDBWriter::prepare_for_output_writing ( )
overridevirtual
void protocols::match::output::PDBWriter::record_match ( match const &  m,
MatchEvaluatorOP  evaluator,
MatchScoreWriterOP  match_score_writer 
)
overridevirtual
void protocols::match::output::PDBWriter::record_match ( match_dspos1 const &  m)
overridevirtual
std::string protocols::match::output::PDBWriter::scaf_name ( ) const
void protocols::match::output::PDBWriter::set_coordinate_cacher ( UpstreamHitCacherOP  cacher)

References coordinate_cacher_.

void protocols::match::output::PDBWriter::set_downstream_builder ( core::Size  geomcst_id,
downstream::DownstreamBuilderCOP  dsbuilder 
)

References dsbuilders_.

void protocols::match::output::PDBWriter::set_prefix ( std::string const &  prefix)

References prefix(), and prefix_.

std::string protocols::match::output::PDBWriter::signature_string ( utility::vector1< core::conformation::ResidueCOP > const &  upstream_matchres) const

Member Data Documentation

UpstreamHitCacherOP protocols::match::output::PDBWriter::coordinate_cacher_
private
std::string protocols::match::output::PDBWriter::cstfile_name_
private
core::pose::PoseCOP protocols::match::output::PDBWriter::downstream_pose_from_task_
private
utility::vector1< downstream::DownstreamBuilderCOP > protocols::match::output::PDBWriter::dsbuilders_
private
core::Size protocols::match::output::PDBWriter::num_geom_cst_
private
core::Size protocols::match::output::PDBWriter::num_written_
private
core::pose::PoseCOP protocols::match::output::PDBWriter::orig_upstream_pose_
private
utility::vector1< bool > protocols::match::output::PDBWriter::output_dsgeom_for_geomcst_
private
std::string protocols::match::output::PDBWriter::prefix_
private

Referenced by assemble_outtag(), prefix(), and set_prefix().

std::string protocols::match::output::PDBWriter::scaf_name_
private
std::map< std::string, SizePair > protocols::match::output::PDBWriter::signature_map_
private
std::map< core::Size, core::Size > protocols::match::output::PDBWriter::upstream_only_geom_cst_
private
bool protocols::match::output::PDBWriter::write_matchres_only_
private

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