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ExposedStrandMover Class Reference
Inheritance diagram for ExposedStrandMover:
Inheritance graph
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Public Member Functions

 ExposedStrandMover ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual void print_sheets (core::pose::Pose &pose, core::Size &start_sheet, core::Size &end_sheet, core::Size &nhbonds)
 
virtual void print_sheets_extras (core::pose::Pose &pose, core::pose::Pose &native_pose, core::Size &start_sheet, core::Size &end_sheet, core::Size &nhbonds, Real &rmsd, Real &energy, Size &match_res)
 
virtual void parse_strand_ids (core::pose::Pose &pose, utility::vector1< std::string > &strand_id)
 
virtual Real bb_score (pose::Pose &pose, core::Size aligned_chain_num, core::scoring::ScoreFunctionOP &scorefxn)
 
virtual pose::Pose move_superimpose (core::pose::Pose &pose1, core::pose::Pose &pose2, core::Size &start_res1, core::Size &start_res2, core::Size &end_res1, core::Size &end_res2)
 
virtual Real bb_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
 
virtual bool is_exposed (pose::Pose &pose, Size &resid, vector1< Real > sasa_values)
 
virtual MoverOP clone () const
 
virtual std::string get_name () const
 
virtual MoverOP fresh_instance () const
 

Private Attributes

core::scoring::ScoreFunctionOP scorefxn_
 
bool check_rmsd_
 
vector1< std::string > strand_def_vector_
 
vector1< core::Size > strand_pose_nums_
 
core::pose::Pose native_pose_
 
Size beta_length_
 
Size sat_allow_
 
Size num_satisfied_
 
core::Real maxE_
 
core::Real maxRMSD_
 
char chain_char_
 
std::string struct_filename_
 
vector1< core::Real > best_rmsd_values_
 
utility::vector1< core::Size > res_to_loose_
 
vector1< pose::Pose > master_poses_
 
vector1< Real > full_scores_
 
vector1< Size > start_res_list_
 
vector1< Size > end_res_list_
 

Detailed Description

Definition at line 110 of file exposed_strand_finder.cc.

Constructor & Destructor Documentation

ExposedStrandMover::ExposedStrandMover ( )

Definition at line 179 of file exposed_strand_finder.cc.

References beta_length, check_rmsd, option, and sat_allow.

Member Function Documentation

void ExposedStrandMover::apply ( core::pose::Pose &  pose)
virtual

Definition at line 419 of file exposed_strand_finder.cc.

References app.surface_docking.surface_docking::combined_pose, assign_charges::first, test.T200_Scoring::hbond_set, test.T200_Scoring::ii, max(), max_E_allow, max_RMSD, min(), ContactMap::native, basic::options::option, option, app.surface_docking.surface_docking::pose, strand_span, struct_file, TR(), utility::options::OptionKeys::options::user, utility_exit_with_message_status, and basic::MetricValue< T >::value().

Referenced by src.protocols.jd2.RosettaScriptWrapper::apply_to_failure().

core::Real ExposedStrandMover::bb_rmsd ( const core::pose::Pose &  pose1,
const core::pose::Pose &  pose2 
)
virtual

Definition at line 251 of file exposed_strand_finder.cc.

References loops_kic::rms.

core::Real ExposedStrandMover::bb_score ( pose::Pose &  pose,
core::Size  aligned_chain_num,
core::scoring::ScoreFunctionOP &  scorefxn 
)
virtual

Definition at line 311 of file exposed_strand_finder.cc.

References numeric::distance_squared(), test.T200_Scoring::ii, app.delta_score_per_mutation::res, TR(), and numeric::crick_equations::xyz().

virtual MoverOP ExposedStrandMover::clone ( ) const
inlinevirtual

Definition at line 147 of file exposed_strand_finder.cc.

virtual MoverOP ExposedStrandMover::fresh_instance ( ) const
inlinevirtual

Definition at line 155 of file exposed_strand_finder.cc.

References clone().

virtual std::string ExposedStrandMover::get_name ( ) const
inlinevirtual

Definition at line 151 of file exposed_strand_finder.cc.

bool ExposedStrandMover::is_exposed ( pose::Pose &  pose,
Size &  resid,
vector1< Real >  sasa_values 
)
virtual

Definition at line 389 of file exposed_strand_finder.cc.

References TR().

pose::Pose ExposedStrandMover::move_superimpose ( core::pose::Pose &  pose1,
core::pose::Pose &  pose2,
core::Size &  start_res1,
core::Size &  start_res2,
core::Size &  end_res1,
core::Size &  end_res2 
)
virtual

Definition at line 258 of file exposed_strand_finder.cc.

References test.T200_Scoring::ii, make_symmdef_file_denovo::length, test.T010_LoadPDB::pose2, and runtime_assert.

void ExposedStrandMover::parse_strand_ids ( core::pose::Pose &  pose,
utility::vector1< std::string > &  strand_id 
)
virtual

Definition at line 190 of file exposed_strand_finder.cc.

References chain_index, end_index, start_index, and TR().

void ExposedStrandMover::print_sheets ( core::pose::Pose &  pose,
core::Size &  start_sheet,
core::Size &  end_sheet,
core::Size &  nhbonds 
)
virtual

Definition at line 207 of file exposed_strand_finder.cc.

References test.G202_Module_PythonPDB::filename, and TRout().

void ExposedStrandMover::print_sheets_extras ( core::pose::Pose &  pose,
core::pose::Pose &  native_pose,
core::Size &  start_sheet,
core::Size &  end_sheet,
core::Size &  nhbonds,
Real &  rmsd,
Real &  energy,
Size &  match_res 
)
virtual

Definition at line 223 of file exposed_strand_finder.cc.

References test.G202_Module_PythonPDB::filename, and TRout().

Member Data Documentation

vector1<core::Real> ExposedStrandMover::best_rmsd_values_
private

Definition at line 172 of file exposed_strand_finder.cc.

Size ExposedStrandMover::beta_length_
private

Definition at line 165 of file exposed_strand_finder.cc.

char ExposedStrandMover::chain_char_
private

Definition at line 170 of file exposed_strand_finder.cc.

bool ExposedStrandMover::check_rmsd_
private

Definition at line 161 of file exposed_strand_finder.cc.

vector1<Size> ExposedStrandMover::end_res_list_
private

Definition at line 176 of file exposed_strand_finder.cc.

vector1<Real> ExposedStrandMover::full_scores_
private

Definition at line 175 of file exposed_strand_finder.cc.

vector1<pose::Pose> ExposedStrandMover::master_poses_
private

Definition at line 174 of file exposed_strand_finder.cc.

core::Real ExposedStrandMover::maxE_
private

Definition at line 168 of file exposed_strand_finder.cc.

core::Real ExposedStrandMover::maxRMSD_
private

Definition at line 169 of file exposed_strand_finder.cc.

core::pose::Pose ExposedStrandMover::native_pose_
private

Definition at line 164 of file exposed_strand_finder.cc.

Size ExposedStrandMover::num_satisfied_
private

Definition at line 167 of file exposed_strand_finder.cc.

utility::vector1< core::Size > ExposedStrandMover::res_to_loose_
private

Definition at line 173 of file exposed_strand_finder.cc.

Size ExposedStrandMover::sat_allow_
private

Definition at line 166 of file exposed_strand_finder.cc.

core::scoring::ScoreFunctionOP ExposedStrandMover::scorefxn_
private

Definition at line 160 of file exposed_strand_finder.cc.

vector1<Size> ExposedStrandMover::start_res_list_
private

Definition at line 176 of file exposed_strand_finder.cc.

vector1< std::string > ExposedStrandMover::strand_def_vector_
private

Definition at line 162 of file exposed_strand_finder.cc.

vector1< core::Size > ExposedStrandMover::strand_pose_nums_
private

Definition at line 163 of file exposed_strand_finder.cc.

std::string ExposedStrandMover::struct_filename_
private

Definition at line 171 of file exposed_strand_finder.cc.

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