protocols::indexed_structure_store::SegmentSequenceProfile Struct Reference

#include <SegmentSequenceProfile.hh>

Public Types
typedef SegmentSequenceProfileConfig	Config

Public Member Functions
	SegmentSequenceProfile ()=default
	SegmentSequenceProfile (Config conf)
SegmentSequenceProfileResult	segment_profile (StructureStore &structure_store, search::StructureDatabase &structure_db, core::pose::Pose &context, core::Size segment_start, core::Size segment_end)

Public Attributes
search::PairQuerySummaryStatistics	query_stats
SegmentSequenceProfileConfig	config

Static Public Attributes
static std::map< core::chemical::AA, core::Real >	aa_background_distribution

Member Typedef Documentation

Config

typedef SegmentSequenceProfileConfig protocols::indexed_structure_store::SegmentSequenceProfile::Config

Constructor & Destructor Documentation

SegmentSequenceProfile() [1/2]

protocols::indexed_structure_store::SegmentSequenceProfile::SegmentSequenceProfile ( )

default

SegmentSequenceProfile() [2/2]

protocols::indexed_structure_store::SegmentSequenceProfile::SegmentSequenceProfile ( Config  conf )

inline

Member Function Documentation

segment_profile()

SegmentSequenceProfileResult protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile	(	StructureStore &	structure_store,
		search::StructureDatabase &	structure_db,
		core::pose::Pose &	context,
		core::Size	segment_start,
		core::Size	segment_end
	)

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), protocols::indexed_structure_store::SegmentSequenceProfileResult::counts, protocols::indexed_structure_store::search::SingleQueryExecutor::execute(), protocols::indexed_structure_store::extract_residue_entry(), core::chemical::first_l_aa, protocols::indexed_structure_store::search::StructureSingleQueryResult::fragment_start, protocols::indexed_structure_store::SegmentSequenceProfileResult::frequencies, protocols::indexed_structure_store::SegmentSequenceProfileResult::log_odds, core::chemical::num_canonical_aas, core::chemical::oneletter_code_from_aa(), protocols::indexed_structure_store::orient_array(), protocols::indexed_structure_store::search::SingleQueryExecutor::query_results, protocols::indexed_structure_store::SegmentSequenceProfileResult::query_results, protocols::indexed_structure_store::search::SingleQueryExecutor::query_stats, core::pose::Pose::residue(), protocols::indexed_structure_store::StructureStore::residue_entries, and protocols::indexed_structure_store::TR().

Referenced by protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply().

Member Data Documentation

aa_background_distribution

std::map< core::chemical::AA, core::Real > protocols::indexed_structure_store::SegmentSequenceProfile::aa_background_distribution

static

Initial value:

= {
{ core::chemical::aa_ala, 0.082949},
{ core::chemical::aa_arg, 0.046585},
{ core::chemical::aa_asn, 0.046900},
{ core::chemical::aa_asp, 0.059111},
{ core::chemical::aa_cys, 0.017223},
{ core::chemical::aa_gln, 0.037391},
{ core::chemical::aa_glu, 0.061225},
{ core::chemical::aa_gly, 0.079431},
{ core::chemical::aa_his, 0.022011},
{ core::chemical::aa_ile, 0.055373},
{ core::chemical::aa_leu, 0.082300},
{ core::chemical::aa_lys, 0.059822},
{ core::chemical::aa_met, 0.021037},
{ core::chemical::aa_phe, 0.040169},
{ core::chemical::aa_pro, 0.046761},
{ core::chemical::aa_ser, 0.061387},
{ core::chemical::aa_thr, 0.058805},
{ core::chemical::aa_trp, 0.014722},
{ core::chemical::aa_tyr, 0.036899},
{ core::chemical::aa_val, 0.069899}
}

config

SegmentSequenceProfileConfig protocols::indexed_structure_store::SegmentSequenceProfile::config

Referenced by protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply().

query_stats

search::PairQuerySummaryStatistics protocols::indexed_structure_store::SegmentSequenceProfile::query_stats

---

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

• src/protocols/indexed_structure_store/SegmentSequenceProfile.hh
• src/protocols/indexed_structure_store/SegmentSequenceProfile.cc