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:

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Collaboration diagram for protocols::match::output::CloudPDBWriter:

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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)
	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)

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

Definition at line 176 of file PDBWriter.hh.