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protocols::features::strand_assembly::StrandBundleFeatures Class Reference

#include <StrandBundleFeatures.hh>

Inheritance diagram for protocols::features::strand_assembly::StrandBundleFeatures:
Inheritance graph
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Public Member Functions

 StrandBundleFeatures ()
 
void init_from_options ()
 
virtual std::string type_name () const
 
virtual void write_schema_to_db (utility::sql_database::sessionOP db_session) const
 generate the table schemas and write them to the database More...
 
utility::vector1< std::string > features_reporter_dependencies () const
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
virtual core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
 collect all the feature data for the pose More...
 
utility::vector1< StrandFragment > get_full_strands (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< StrandFragment > get_selected_strands (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< StrandFragment > get_strand_pairs (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< StrandFragment > get_strand_from_bss_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size bss_id)
 
bool find_antiparallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
bool find_parallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
bool check_strand_too_closeness (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
core::Real get_avg_dis_CA_CA (core::pose::Pose const &pose, core::Size i_resnum, core::Size i_resnum_1, core::Size i_resnum_2, core::Size i_resnum_3, core::Size j_resnum, core::Size j_resnum_1, core::Size j_resnum_2, core::Size j_resnum_3)
 
core::Real check_sw_by_dis (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j, bool antiparalell)
 
bool final_check_sw_by_dis (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j, bool antiparalell)
 
bool judge_sw_dis_too_close (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j)
 
bool judge_sw_torsion (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j)
 
core::Real judge_sw_inter_dis (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j)
 
core::Size round (core::Real x)
 
core::Size get_nearest_res_from_strand (core::pose::Pose const &pose, StrandFragment strand_to_be_searched, core::Size rounded_resnum)
 
core::Real sheet_torsion (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
bool judge_facing (core::pose::Pose const &pose, StrandFragment strand_ii_i, StrandFragment strand_ii_j, StrandFragment strand_jj_i, StrandFragment strand_jj_j)
 
core::Real shortest_dis_sidechain (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
core::Real get_shortest_among_4 (core::Real val_shortest_dis_sidechain_1, core::Real val_shortest_dis_sidechain_2, core::Real val_shortest_dis_sidechain_3, core::Real val_shortest_dis_sidechain_4)
 
core::Real sheet_dis_by_terminals (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 FeaturesReporter ()
 
virtual ~FeaturesReporter ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
virtual std::string schema () const
 return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator More...
 
core::Size report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 
virtual void load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
virtual void delete_record (StructureID, utility::sql_database::sessionOP)
 
void set_relevant_residues_mode (RelevantResiduesMode::T setting)
 
RelevantResiduesMode::T get_relevant_residues_mode () const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const
 

Private Attributes

core::Size min_num_strands_to_deal_
 
core::Size max_num_strands_to_deal_
 
bool extract_native_only_
 
core::Size min_res_in_strand_
 
core::Size max_res_in_strand_
 
core::Real min_O_N_dis_
 
core::Real max_O_N_dis_
 
core::Real min_sheet_dis_
 
core::Real max_sheet_dis_
 
core::Real min_sheet_torsion_
 
core::Real max_sheet_torsion_
 
core::Real min_sheet_angle_
 
core::Real max_sheet_angle_
 
core::Real min_shortest_dis_sidechain_inter_sheet_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::features::FeaturesReporter
std::string find_tag (core::pose::Pose const &pose) const
 
void delete_records_from_table (std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session)
 a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
 
- Protected Attributes inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T relevant_residues_mode_
 

Constructor & Destructor Documentation

protocols::features::strand_assembly::StrandBundleFeatures::StrandBundleFeatures ( )

References init_from_options().

Member Function Documentation

bool protocols::features::strand_assembly::StrandBundleFeatures::check_strand_too_closeness ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by judge_sw_dis_too_close().

Real protocols::features::strand_assembly::StrandBundleFeatures::check_sw_by_dis ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j,
bool  antiparalell 
)

References get_avg_dis_CA_CA(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), and core::pose::Pose::total_residue().

Referenced by final_check_sw_by_dis().

utility::vector1< std::string > protocols::features::strand_assembly::StrandBundleFeatures::features_reporter_dependencies ( ) const
virtual

return the set of features reporters that are required to also already be extracted by the time this one is used.

Reimplemented from protocols::features::FeaturesReporter.

bool protocols::features::strand_assembly::StrandBundleFeatures::final_check_sw_by_dis ( core::pose::Pose const &  pose,
StrandFragment  temp_strand_ii_i,
StrandFragment  temp_strand_ii_j,
StrandFragment  temp_strand_jj_i,
StrandFragment  temp_strand_jj_j,
bool  antiparalell 
)

References check_sw_by_dis().

Referenced by report_features().

bool protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_end(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), max_O_N_dis_, min_O_N_dis_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by report_features().

bool protocols::features::strand_assembly::StrandBundleFeatures::find_parallel ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_end(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), max_O_N_dis_, min_O_N_dis_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::get_avg_dis_CA_CA ( core::pose::Pose const &  pose,
core::Size  i_resnum,
core::Size  i_resnum_1,
core::Size  i_resnum_2,
core::Size  i_resnum_3,
core::Size  j_resnum,
core::Size  j_resnum_1,
core::Size  j_resnum_2,
core::Size  j_resnum_3 
)

References core::conformation::Residue::atom(), max_sheet_dis_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by check_sw_by_dis().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_full_strands ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)

Referenced by report_features().

Size protocols::features::strand_assembly::StrandBundleFeatures::get_nearest_res_from_strand ( core::pose::Pose const &  pose,
StrandFragment  strand_to_be_searched,
core::Size  rounded_resnum 
)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by judge_facing().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_selected_strands ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::get_shortest_among_4 ( core::Real  val_shortest_dis_sidechain_1,
core::Real  val_shortest_dis_sidechain_2,
core::Real  val_shortest_dis_sidechain_3,
core::Real  val_shortest_dis_sidechain_4 
)

Referenced by judge_facing(), and judge_sw_inter_dis().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_strand_from_bss_id ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  bss_id 
)

Referenced by report_features().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_strand_pairs ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)

Referenced by report_features().

void protocols::features::strand_assembly::StrandBundleFeatures::init_from_options ( )

References extract_native_only_, max_num_strands_to_deal_, max_O_N_dis_, max_res_in_strand_, max_sheet_angle_, max_sheet_dis_, max_sheet_torsion_, min_num_strands_to_deal_, min_O_N_dis_, min_res_in_strand_, min_sheet_angle_, min_sheet_dis_, min_sheet_torsion_, and min_shortest_dis_sidechain_inter_sheet_.

Referenced by StrandBundleFeatures().

bool protocols::features::strand_assembly::StrandBundleFeatures::judge_facing ( core::pose::Pose const &  pose,
StrandFragment  strand_ii_i,
StrandFragment  strand_ii_j,
StrandFragment  strand_jj_i,
StrandFragment  strand_jj_j 
)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_end(), get_nearest_res_from_strand(), get_shortest_among_4(), protocols::features::strand_assembly::StrandFragment::get_start(), max_sheet_angle_, min_sheet_angle_, core::pose::Pose::residue(), round(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by report_features().

bool protocols::features::strand_assembly::StrandBundleFeatures::judge_sw_dis_too_close ( core::pose::Pose const &  pose,
StrandFragment  temp_strand_ii_i,
StrandFragment  temp_strand_ii_j,
StrandFragment  temp_strand_jj_i,
StrandFragment  temp_strand_jj_j 
)

References check_strand_too_closeness().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::judge_sw_inter_dis ( core::pose::Pose const &  pose,
StrandFragment  temp_strand_ii_i,
StrandFragment  temp_strand_ii_j,
StrandFragment  temp_strand_jj_i,
StrandFragment  temp_strand_jj_j 
)

References get_shortest_among_4(), min_shortest_dis_sidechain_inter_sheet_, and shortest_dis_sidechain().

Referenced by report_features().

bool protocols::features::strand_assembly::StrandBundleFeatures::judge_sw_torsion ( core::pose::Pose const &  pose,
StrandFragment  temp_strand_ii_i,
StrandFragment  temp_strand_ii_j,
StrandFragment  temp_strand_jj_i,
StrandFragment  temp_strand_jj_j 
)

References max_sheet_torsion_, min_sheet_torsion_, and sheet_torsion().

Referenced by report_features().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References extract_native_only_, final_check_sw_by_dis(), find_antiparallel(), find_parallel(), get_full_strands(), get_selected_strands(), get_strand_from_bss_id(), get_strand_pairs(), judge_facing(), judge_sw_dis_too_close(), judge_sw_inter_dis(), judge_sw_torsion(), max_num_strands_to_deal_, max_res_in_strand_, min_num_strands_to_deal_, min_res_in_strand_, sheet_dis_by_terminals(), and protocols::features::strand_assembly::TR().

Size protocols::features::strand_assembly::StrandBundleFeatures::round ( core::Real  x)

Referenced by judge_facing().

Real protocols::features::strand_assembly::StrandBundleFeatures::sheet_dis_by_terminals ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)

References protocols::features::strand_assembly::StrandFragment::get_end(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)

References protocols::features::strand_assembly::StrandFragment::get_end(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by judge_sw_torsion().

Real protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)

References protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by judge_sw_inter_dis().

virtual std::string protocols::features::strand_assembly::StrandBundleFeatures::type_name ( ) const
inlinevirtual

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::strand_assembly::StrandBundleFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

Member Data Documentation

bool protocols::features::strand_assembly::StrandBundleFeatures::extract_native_only_
private

Referenced by init_from_options(), and report_features().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::max_num_strands_to_deal_
private

Referenced by init_from_options(), and report_features().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_O_N_dis_
private

Referenced by find_antiparallel(), find_parallel(), and init_from_options().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::max_res_in_strand_
private

Referenced by init_from_options(), and report_features().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_angle_
private

Referenced by init_from_options(), and judge_facing().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_dis_
private

Referenced by get_avg_dis_CA_CA(), and init_from_options().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_torsion_
private

Referenced by init_from_options(), and judge_sw_torsion().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::min_num_strands_to_deal_
private

Referenced by init_from_options(), and report_features().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_O_N_dis_
private

Referenced by find_antiparallel(), find_parallel(), and init_from_options().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::min_res_in_strand_
private

Referenced by init_from_options(), and report_features().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_angle_
private

Referenced by init_from_options(), and judge_facing().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_dis_
private

Referenced by init_from_options().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_torsion_
private

Referenced by init_from_options(), and judge_sw_torsion().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_shortest_dis_sidechain_inter_sheet_
private

Referenced by init_from_options(), and judge_sw_inter_dis().

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