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>

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)
virtual	~CloudPDBWriter ()
virtual void	prepare_for_output_writing ()
void	end_output_writing ()
virtual void	record_match (match const &m, MatchEvaluatorOP evaluator, MatchScoreWriterOP match_score_writer)
	no writing in this function, only saving the hits according to what group they belong to More...
virtual void	record_match (match_dspos1 const &m)
	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 ()
virtual	~PDBWriter ()
void	set_coordinate_cacher (UpstreamHitCacherOP)
void	set_prefix (std::string const &prefix)
void	initialize_from_matcher_task (MatcherTaskCOP mtask)
void	set_downstream_builder (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 ()
virtual	~OutputWriter ()
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< UpstreamHitSets >	match_groups_ushits_
utility::vector1 < DownstreamHitSets >	match_groups_dshits_
utility::vector1< std::string >	unique_match_names_
utility::vector1< match_dspos1 >	representative_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

typedef utility::vector1< std::set< downstream_hit > > protocols::match::output::CloudPDBWriter::DownstreamHitSets

typedef PDBWriter protocols::match::output::CloudPDBWriter::parent

typedef utility::vector1< std::set< upstream_hit > > protocols::match::output::CloudPDBWriter::UpstreamHitSets

Constructor & Destructor Documentation

protocols::match::output::CloudPDBWriter::CloudPDBWriter

(

MatchGrouperOP

grouper

)

References clear_match_data().

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

virtual

Member Function Documentation

void protocols::match::output::CloudPDBWriter::clear_match_data ( )

protected

References ds_hitset_end_its_, ds_hitset_its_, match_groups_dshits_, match_groups_ushits_, representative_group_matches_, unique_match_names_, us_hitset_end_its_, and us_hitset_its_.

Referenced by CloudPDBWriter(), end_output_writing(), and prepare_for_output_writing().

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 ( )

virtual

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

References match_groups_dshits_.

Referenced by protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose().

utility::vector1< CloudPDBWriter::UpstreamHitSets > const & protocols::match::output::CloudPDBWriter::match_groups_ushits

(

)

const

References match_groups_ushits_.

Referenced by protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose().

void protocols::match::output::CloudPDBWriter::prepare_for_output_writing ( )

virtual

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

References clear_match_data(), grouper_, and protocols::match::output::PDBWriter::prepare_for_output_writing().

void protocols::match::output::CloudPDBWriter::record_match ( match const &  m, MatchEvaluatorOP  evaluator, MatchScoreWriterOP  match_score_writer  )

virtual

no writing in this function, only saving the hits according to what group they belong to

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

References protocols::match::output::PDBWriter::coordinate_cacher(), protocols::match::output::PDBWriter::cstfile_name(), protocols::match::output::PDBWriter::dsbuilders(), end, grouper_, match_groups_dshits_, match_groups_ushits_, protocols::match::output::PDBWriter::num_geom_cst(), protocols::match::output::PDBWriter::prefix(), representative_group_matches_, runtime_assert, protocols::match::output::PDBWriter::scaf_name(), protocols::match::output::PDBWriter::signature_string(), utility::to_string(), and unique_match_names_.

void protocols::match::output::CloudPDBWriter::record_match ( match_dspos1 const &  m )

virtual

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.

References utility_exit_with_message.

utility::vector1< match_dspos1 > const & protocols::match::output::CloudPDBWriter::representative_group_matches

(

)

const

References representative_group_matches_.

Referenced by protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose().

void protocols::match::output::CloudPDBWriter::setup_hitset_iterators_for_group ( core::Size const  group )

protected

References begin, ds_hitset_end_its_, ds_hitset_its_, end, match_groups_dshits_, match_groups_ushits_, runtime_assert, us_hitset_end_its_, and us_hitset_its_.

Referenced by write_match_groups().

void protocols::match::output::CloudPDBWriter::write_match_groups

(

)

this is where the actual writing happens

References protocols::match::output::PDBWriter::coordinate_cacher(), protocols::match::output::PDBWriter::create_output_upstream_pose(), protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(), ds_hitset_end_its_, ds_hitset_its_, protocols::match::output::PDBWriter::dsbuilders(), core::io::pdb::dump_pdb_residue(), protocols::match::fake_hit(), protocols::match::full_hit(), match_groups_dshits_, match_groups_ushits_, protocols::match::output::PDBWriter::num_geom_cst(), protocols::match::match_dspos1::originating_geom_cst_for_dspos, representative_group_matches_, runtime_assert, setup_hitset_iterators_for_group(), utility::to_string(), protocols::match::output::TR, unique_match_names_, protocols::match::match_dspos1::upstream_hits, us_hitset_end_its_, us_hitset_its_, and utility_exit_with_message.

Referenced by end_output_writing().

Member Data Documentation

utility::vector1< std::set< downstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::ds_hitset_end_its_

private

Referenced by clear_match_data(), ds_hitset_end_its(), setup_hitset_iterators_for_group(), and write_match_groups().

utility::vector1< std::set< downstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::ds_hitset_its_

private

Referenced by clear_match_data(), ds_hitset_its(), setup_hitset_iterators_for_group(), and write_match_groups().

MatchGrouperOP protocols::match::output::CloudPDBWriter::grouper_

private

Referenced by prepare_for_output_writing(), and record_match().

utility::vector1< DownstreamHitSets > protocols::match::output::CloudPDBWriter::match_groups_dshits_

private

Referenced by clear_match_data(), end_output_writing(), match_groups_dshits(), record_match(), setup_hitset_iterators_for_group(), and write_match_groups().

utility::vector1< UpstreamHitSets > protocols::match::output::CloudPDBWriter::match_groups_ushits_

private

Referenced by clear_match_data(), end_output_writing(), match_groups_ushits(), record_match(), setup_hitset_iterators_for_group(), and write_match_groups().

utility::vector1< match_dspos1 > protocols::match::output::CloudPDBWriter::representative_group_matches_

private

Referenced by clear_match_data(), record_match(), representative_group_matches(), and write_match_groups().

utility::vector1< std::string > protocols::match::output::CloudPDBWriter::unique_match_names_

private

Referenced by clear_match_data(), record_match(), and write_match_groups().

utility::vector1< std::set< upstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::us_hitset_end_its_

private

Referenced by clear_match_data(), setup_hitset_iterators_for_group(), and write_match_groups().

utility::vector1< std::set< upstream_hit >::const_iterator > protocols::match::output::CloudPDBWriter::us_hitset_its_

private

Referenced by clear_match_data(), setup_hitset_iterators_for_group(), and write_match_groups().

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

• src/protocols/match/output/PDBWriter.hh
• src/protocols/match/output/PDBWriter.cc