#include <PDBWriter.hh>

Inheritance diagram for protocols::match::output::PDBWriter:

Collaboration diagram for protocols::match::output::PDBWriter:

Public Types
typedef std::pair< core::Size, core::Size >	SizePair

typedef OutputWriter	Parent

Public Member Functions
	PDBWriter ()

virtual	~PDBWriter ()

virtual void	prepare_for_output_writing ()

virtual void	record_match (match const &m)

virtual void	record_match (match_dspos1 const &m)

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...

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, SizePair >	signature_map_

utility::vector1< bool >	output_dsgeom_for_geomcst_

std::map< core::Size, core::Size >	upstream_only_geom_cst_

Member Typedef Documentation

typedef OutputWriter protocols::match::output::PDBWriter::Parent

typedef std::pair< core::Size, core::Size > protocols::match::output::PDBWriter::SizePair

Constructor & Destructor Documentation

protocols::match::output::PDBWriter::PDBWriter ( )

References signature_map_, and upstream_only_geom_cst_.

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

virtual

Member Function Documentation

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

protected

References cstfile_name_, prefix_, scaf_name_, signature_map_, and signature_string().

Referenced by record_match().

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

References protocols::toolbox::match_enzdes_util::assemble_remark_line(), downstream_pose_from_task_, core::pose::RemarkInfo::num, orig_upstream_pose_, core::pose::Pose::pdb_info(), upstream_only_geom_cst_, and core::pose::RemarkInfo::value.

Referenced by create_output_upstream_pose(), and protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose().

UpstreamHitCacherOP protocols::match::output::PDBWriter::coordinate_cacher ( )

protected

References coordinate_cacher_.

Referenced by protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::match::output::CloudPDBWriter::record_match(), and protocols::match::output::CloudPDBWriter::write_match_groups().

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
	)

References assemble_remark_lines(), orig_upstream_pose_, and write_matchres_only_.

Referenced by record_match(), and protocols::match::output::CloudPDBWriter::write_match_groups().

std::string protocols::match::output::PDBWriter::cstfile_name ( ) const

References cstfile_name_.

Referenced by protocols::match::output::CloudPDBWriter::record_match().

utility::vector1< downstream::DownstreamBuilderCOP > const & protocols::match::output::PDBWriter::dsbuilders ( )

protected

References dsbuilders_.

Referenced by protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::match::output::CloudPDBWriter::record_match(), and protocols::match::output::CloudPDBWriter::write_match_groups().

void protocols::match::output::PDBWriter::initialize_from_matcher_task ( MatcherTaskCOP mtask)

virtual

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

References cstfile_name_, downstream_pose_from_task_, dsbuilders_, protocols::match::output::OutputWriter::initialize_from_matcher_task(), num_geom_cst_, orig_upstream_pose_, output_dsgeom_for_geomcst_, scaf_name_, upstream_only_geom_cst_, and write_matchres_only_.

core::Size protocols::match::output::PDBWriter::num_geom_cst ( ) const

References num_geom_cst_.

Referenced by protocols::match::output::CloudPDBWriter::end_output_writing(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::match::output::CloudPDBWriter::record_match(), and protocols::match::output::CloudPDBWriter::write_match_groups().

std::string protocols::match::output::PDBWriter::prefix ( ) const

References prefix_.

Referenced by protocols::match::output::CloudPDBWriter::record_match(), and set_prefix().

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

virtual

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

Reimplemented in protocols::match::output::CloudPDBWriter.

References num_written_, and signature_map_.

Referenced by protocols::match::output::CloudPDBWriter::prepare_for_output_writing().

void protocols::match::output::PDBWriter::record_match ( match const & m)

virtual

Implements protocols::match::output::OutputWriter.

Reimplemented in protocols::match::output::CloudPDBWriter.

References assemble_outtag(), coordinate_cacher_, create_output_upstream_pose(), protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(), dsbuilders_, num_written_, and output_dsgeom_for_geomcst_.

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

virtual

Implements protocols::match::output::OutputWriter.

Reimplemented in protocols::match::output::CloudPDBWriter.

References assemble_outtag(), coordinate_cacher_, create_output_upstream_pose(), protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(), dsbuilders_, protocols::match::Hit::external_geom_id(), protocols::match::fake_hit(), protocols::match::full_hit(), num_written_, protocols::match::match_dspos1::originating_geom_cst_for_dspos, output_dsgeom_for_geomcst_, and protocols::match::match_dspos1::upstream_hits.

std::string protocols::match::output::PDBWriter::scaf_name ( ) const

References scaf_name_.

Referenced by protocols::match::output::CloudPDBWriter::record_match().

void protocols::match::output::PDBWriter::set_coordinate_cacher ( UpstreamHitCacherOP cacher)

References coordinate_cacher_.

void protocols::match::output::PDBWriter::set_downstream_builder	(	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

References orig_upstream_pose_.

Referenced by assemble_outtag(), and protocols::match::output::CloudPDBWriter::record_match().