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protocols::match::output::CloudPDBWriter Class Reference

an output writer that uses a grouper to group matches and then writes out one pdb file per group, with the different hits from the group in different MODEL sections More...

#include <PDBWriter.hh>

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

Public Types

typedef PDBWriter parent
 
typedef utility::vector1
< std::set< upstream_hit > > 
UpstreamHitSets
 
typedef utility::vector1
< std::set< downstream_hit > > 
DownstreamHitSets
 
- Public Types inherited from protocols::match::output::PDBWriter
typedef std::pair< core::Size,
core::Size
SizePair
 
typedef OutputWriter Parent
 

Public Member Functions

 CloudPDBWriter (MatchGrouperOP grouper)
 
 ~CloudPDBWriter () override
 
void prepare_for_output_writing () override
 
void end_output_writing () override
 
void record_match (match const &m, MatchEvaluatorOP evaluator, MatchScoreWriterOP match_score_writer) override
 no writing in this function, only saving the hits according to what group they belong to More...
 
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 write_match_groups ()
 this is where the actual writing happens More...
 
utility::vector1
< UpstreamHitSets > const & 
match_groups_ushits () const
 
utility::vector1
< DownstreamHitSets > const & 
match_groups_dshits () const
 
utility::vector1< match_dspos1 >
const & 
representative_group_matches () const
 
utility::vector1< std::set
< downstream_hit >
::const_iterator > const & 
ds_hitset_its () const
 
utility::vector1< std::set
< downstream_hit >
::const_iterator > const & 
ds_hitset_end_its () const
 
- Public Member Functions inherited from protocols::match::output::PDBWriter
 PDBWriter ()
 
 ~PDBWriter () override
 
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...
 

Protected Member Functions

void setup_hitset_iterators_for_group (core::Size const group)
 
void clear_match_data ()
 
- Protected Member Functions inherited from protocols::match::output::PDBWriter
UpstreamHitCacherOP coordinate_cacher ()
 
utility::vector1
< downstream::DownstreamBuilderCOP >
const & 
dsbuilders ()
 
std::string assemble_outtag (utility::vector1< core::conformation::ResidueCOP > const &upstream_matchres)
 

Private Attributes

MatchGrouperOP grouper_
 
utility::vector1< UpstreamHitSetsmatch_groups_ushits_
 
utility::vector1
< DownstreamHitSets
match_groups_dshits_
 
utility::vector1< std::string > unique_match_names_
 
utility::vector1< match_dspos1representative_group_matches_
 
utility::vector1< std::set
< upstream_hit >
::const_iterator > 
us_hitset_its_
 
utility::vector1< std::set
< upstream_hit >
::const_iterator > 
us_hitset_end_its_
 
utility::vector1< std::set
< downstream_hit >
::const_iterator > 
ds_hitset_its_
 
utility::vector1< std::set
< downstream_hit >
::const_iterator > 
ds_hitset_end_its_
 

Detailed Description

an output writer that uses a grouper to group matches and then writes out one pdb file per group, with the different hits from the group in different MODEL sections

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::match::output::CloudPDBWriter::CloudPDBWriter ( MatchGrouperOP  grouper)

References clear_match_data().

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

Member Function Documentation

void protocols::match::output::CloudPDBWriter::clear_match_data ( )
protected
utility::vector1< std::set< downstream_hit >::const_iterator > const & protocols::match::output::CloudPDBWriter::ds_hitset_end_its ( ) const

References ds_hitset_end_its_.

utility::vector1< std::set< downstream_hit >::const_iterator > const & protocols::match::output::CloudPDBWriter::ds_hitset_its ( ) const

References ds_hitset_its_.

void protocols::match::output::CloudPDBWriter::end_output_writing ( )
overridevirtual

this class writes output in a form that has no link between a downstream conformation and the upstream conf that it came from.

Reimplemented from protocols::match::output::OutputWriter.

Reimplemented in protocols::match::output::PoseMatchOutputWriter.

References clear_match_data(), match_groups_dshits_, match_groups_ushits_, protocols::match::output::PDBWriter::num_geom_cst(), protocols::match::output::TR(), and write_match_groups().

utility::vector1< CloudPDBWriter::DownstreamHitSets > const & protocols::match::output::CloudPDBWriter::match_groups_dshits ( ) const
utility::vector1< CloudPDBWriter::UpstreamHitSets > const & protocols::match::output::CloudPDBWriter::match_groups_ushits ( ) const
void protocols::match::output::CloudPDBWriter::prepare_for_output_writing ( )
overridevirtual
void protocols::match::output::CloudPDBWriter::record_match ( match const &  m,
MatchEvaluatorOP  evaluator,
MatchScoreWriterOP  match_score_writer 
)
overridevirtual
void protocols::match::output::CloudPDBWriter::record_match ( match_dspos1 const &  m)
overridevirtual

evaluator and score writer are not passed in because single-downstream-position match currently have no way of being evaluated

Reimplemented from protocols::match::output::PDBWriter.

utility::vector1< match_dspos1 > const & protocols::match::output::CloudPDBWriter::representative_group_matches ( ) const
void protocols::match::output::CloudPDBWriter::setup_hitset_iterators_for_group ( core::Size const  group)
protected
void protocols::match::output::CloudPDBWriter::write_match_groups ( )

Member Data Documentation

utility::vector1< std::set< downstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::ds_hitset_end_its_
private
utility::vector1< std::set< downstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::ds_hitset_its_
private
MatchGrouperOP protocols::match::output::CloudPDBWriter::grouper_
private
utility::vector1< DownstreamHitSets > protocols::match::output::CloudPDBWriter::match_groups_dshits_
private
utility::vector1< UpstreamHitSets > protocols::match::output::CloudPDBWriter::match_groups_ushits_
private
utility::vector1< match_dspos1 > protocols::match::output::CloudPDBWriter::representative_group_matches_
private
utility::vector1< std::string > protocols::match::output::CloudPDBWriter::unique_match_names_
private
utility::vector1< std::set< upstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::us_hitset_end_its_
private
utility::vector1< std::set< upstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::us_hitset_its_
private

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