helper class for the MatcherMover that will put a match into a supplied pose More...
#include <PDBWriter.hh>
Inheritance diagram for protocols::match::output::PoseMatchOutputWriter:
Public Types | |
| typedef CloudPDBWriter | parent |
 Public Types inherited from protocols::match::output::CloudPDBWriter | |
| 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 | |
| PoseMatchOutputWriter (MatchGrouperOP grouper) | |
| ~PoseMatchOutputWriter () override | |
| void | insert_match_into_pose (core::pose::Pose &pose, core::Size match_group) |
| void | insert_match_into_pose (core::pose::Pose &pose) |
| void | end_output_writing () override |
| this function doesn't do anything, but needs to exist to suppress the unwanted call to the base class function More... | |
| Public Member Functions inherited from protocols::match::output::CloudPDBWriter | |
| CloudPDBWriter (MatchGrouperOP grouper) | |
| ~CloudPDBWriter () override | |
| void | prepare_for_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... | |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::match::output::CloudPDBWriter | |
| 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) |
Detailed Description
helper class for the MatcherMover that will put a match into a supplied pose
Member Typedef Documentation
◆ parent
Constructor & Destructor Documentation
◆ PoseMatchOutputWriter()
| protocols::match::output::PoseMatchOutputWriter::PoseMatchOutputWriter | ( | MatchGrouperOP | grouper | ) |
◆ ~PoseMatchOutputWriter()
|
overridedefault |
Member Function Documentation
◆ end_output_writing()
|
overridevirtual |
this function doesn't do anything, but needs to exist to suppress the unwanted call to the base class function
Reimplemented from protocols::match::output::CloudPDBWriter.
◆ insert_match_into_pose() [1/2]
| void protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose | ( | core::pose::Pose & | pose | ) |
◆ insert_match_into_pose() [2/2]
| void protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose | ( | core::pose::Pose & | pose, |
| core::Size | match_group | ||
| ) |
References core::pose::Pose::append_residue_by_jump(), protocols::match::output::PDBWriter::assemble_remark_lines(), protocols::match::output::PDBWriter::coordinate_cacher(), protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(), protocols::match::output::PDBWriter::dsbuilders(), core::sequence::end, protocols::match::fake_hit(), protocols::match::full_hit(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::match::output::CloudPDBWriter::match_groups_dshits(), protocols::match::output::PDBWriter::num_geom_cst(), protocols::match::match_dspos1::originating_geom_cst_for_dspos, core::pose::Pose::pdb_info(), core::pose::Pose::replace_residue(), protocols::match::output::CloudPDBWriter::representative_group_matches(), core::pose::Pose::size(), and protocols::match::match_dspos1::upstream_hits.
Referenced by insert_match_into_pose().
The documentation for this class was generated from the following files:
- src/protocols/match/output/PDBWriter.hh
- src/protocols/match/output/PDBWriter.cc
