Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::pose_length_moves::PossibleLoop Class Reference

#include <NearNativeLoopCloser.hh>

Inheritance diagram for protocols::pose_length_moves::PossibleLoop:
Inheritance graph
[legend]

Public Member Functions

 PossibleLoop (int resAdjustmentBeforeLoop, int resAdjustmentAfterLoop, core::Size loopLength, core::Size resBeforeLoop, core::Size resAfterLoop, char resTypeBeforeLoop, char resTypeAfterLoop, core::Size insertedBeforeLoopRes, core::Size insertedAfterLoopRes, core::pose::PoseOP fullLengthPoseOP, core::pose::PoseOP orig_atom_type_fullLengthPoseOP)
 
 ~PossibleLoop () override
 
void evaluate_distance_closure ()
 
void generate_stub_rmsd ()
 
void generate_uncached_stub_rmsd ()
 
void generate_output_pose (bool output_closed, bool ideal_loop, core::Real rms_threshold, std::string allowed_loop_abegos, std::string closure_type)
 
core::pose::PoseOP get_finalPoseOP ()
 
core::Real get_stubRMSD ()
 
core::Real get_uncached_stubRMSD ()
 
core::Real get_final_RMSD ()
 
bool outputed ()
 
void outputed (bool outputed)
 
bool get_below_distance_threshold ()
 
std::string get_description ()
 

Private Member Functions

void trimRegion (core::pose::PoseOP &poseOP, core::Size resStart, core::Size resStop)
 
void extendRegion (bool towardCTerm, core::Size resStart, core::Size numberAddRes, core::pose::PoseOP &poseOP)
 
bool check_loop_abego (core::pose::PoseOP &poseOP, core::Size loopStart, core::Size loopStop, std::string allowed_loop_abegos, core::Real loop_rmsd)
 
void assign_phi_psi_omega_from_lookback (core::Size db_index, core::Size fragment_index, core::pose::PoseOP &poseOP)
 
std::vector< core::Realget_center_of_mass (const core::Real *coordinates, int number_of_atoms)
 
void output_fragment_debug (std::vector< numeric::xyzVector< numeric::Real > > coordinates, std::string filename)
 
void add_coordinate_csts_from_lookback (core::Size stub_ss_index_match, core::Size fragment_index, core::Size pose_residue, bool match_stub_alone, core::pose::PoseOP &poseOP)
 
void add_dihedral_csts_from_lookback (core::Size stub_ss_index_match, core::Size fragment_index, core::Size pose_residue, core::pose::PoseOP &poseOP)
 
core::Size get_valid_resid (int resid, core::pose::Pose const pose)
 
std::vector
< numeric::xyzVector
< numeric::Real > > 
get_coordinates_from_pose (core::pose::PoseOP const poseOP, core::Size resid, core::Size length)
 
core::Real rmsd_between_coordinates (std::vector< numeric::xyzVector< numeric::Real > > fragCoordinates, std::vector< numeric::xyzVector< numeric::Real > > coordinates)
 
bool kic_closure (core::scoring::ScoreFunctionOP scorefxn_, core::pose::PoseOP &poseOP, core::Size firstLoopRes, core::Size lastLoopRes, core::Size numb_kic_cycles)
 
void minimize_loop (core::scoring::ScoreFunctionOP scorefxn, bool ideal_loop, core::pose::PoseOP &poseOP)
 

Private Attributes

core::Size insertedBeforeLoopRes_
 
core::Size insertedAfterLoopRes_
 
int resAdjustmentBeforeLoop_
 
int resAdjustmentAfterLoop_
 
char resTypeBeforeLoop_
 
char resTypeAfterLoop_
 
core::Size loopLength_
 
core::Size resBeforeLoop_
 
core::Size resAfterLoop_
 
core::Size fullLength_resBeforeLoop_
 
bool below_distance_threshold_
 
core::Real stub_rmsd_match_
 
core::Size stub_index_match_
 
core::Size stub_ss_index_match_
 
core::Real uncached_stub_rmsd_
 
core::Size uncached_stub_index_
 
bool outputed_
 
core::pose::PoseOP original_atom_type_fullLengthPoseOP_
 
core::pose::PoseOP fullLengthPoseOP_
 
core::pose::PoseOP finalPoseOP_
 
protocols::indexed_structure_store::SSHashedFragmentStoreSSHashedFragmentStore_
 
core::Real final_rmsd_
 

Constructor & Destructor Documentation

protocols::pose_length_moves::PossibleLoop::PossibleLoop ( int  resAdjustmentBeforeLoop,
int  resAdjustmentAfterLoop,
core::Size  loopLength,
core::Size  resBeforeLoop,
core::Size  resAfterLoop,
char  resTypeBeforeLoop,
char  resTypeAfterLoop,
core::Size  insertedBeforeLoopRes,
core::Size  insertedAfterLoopRes,
core::pose::PoseOP  fullLengthPoseOP,
core::pose::PoseOP  orig_atom_type_fullLengthPoseOP 
)

References protocols::TR().

protocols::pose_length_moves::PossibleLoop::~PossibleLoop ( )
overridedefault

Member Function Documentation

void protocols::pose_length_moves::PossibleLoop::add_coordinate_csts_from_lookback ( core::Size  stub_ss_index_match,
core::Size  fragment_index,
core::Size  pose_residue,
bool  match_stub_alone,
core::pose::PoseOP poseOP 
)
private
void protocols::pose_length_moves::PossibleLoop::add_dihedral_csts_from_lookback ( core::Size  stub_ss_index_match,
core::Size  fragment_index,
core::Size  pose_residue,
core::pose::PoseOP poseOP 
)
private
void protocols::pose_length_moves::PossibleLoop::assign_phi_psi_omega_from_lookback ( core::Size  db_index,
core::Size  fragment_index,
core::pose::PoseOP poseOP 
)
private
bool protocols::pose_length_moves::PossibleLoop::check_loop_abego ( core::pose::PoseOP poseOP,
core::Size  loopStart,
core::Size  loopStop,
std::string  allowed_loop_abegos,
core::Real  loop_rmsd 
)
private
void protocols::pose_length_moves::PossibleLoop::evaluate_distance_closure ( )
void protocols::pose_length_moves::PossibleLoop::extendRegion ( bool  towardCTerm,
core::Size  resStart,
core::Size  numberAddRes,
core::pose::PoseOP poseOP 
)
private
void protocols::pose_length_moves::PossibleLoop::generate_output_pose ( bool  output_closed,
bool  ideal_loop,
core::Real  rms_threshold,
std::string  allowed_loop_abegos,
std::string  closure_type 
)
void protocols::pose_length_moves::PossibleLoop::generate_stub_rmsd ( )
void protocols::pose_length_moves::PossibleLoop::generate_uncached_stub_rmsd ( )
bool protocols::pose_length_moves::PossibleLoop::get_below_distance_threshold ( )
inline
vector< Real > protocols::pose_length_moves::PossibleLoop::get_center_of_mass ( const core::Real coordinates,
int  number_of_atoms 
)
private
std::vector< numeric::xyzVector< numeric::Real > > protocols::pose_length_moves::PossibleLoop::get_coordinates_from_pose ( core::pose::PoseOP const  poseOP,
core::Size  resid,
core::Size  length 
)
private
std::string protocols::pose_length_moves::PossibleLoop::get_description ( )
core::Real protocols::pose_length_moves::PossibleLoop::get_final_RMSD ( )
inline

References final_rmsd_.

core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::get_finalPoseOP ( )
core::Real protocols::pose_length_moves::PossibleLoop::get_stubRMSD ( )
inline

References stub_rmsd_match_.

core::Real protocols::pose_length_moves::PossibleLoop::get_uncached_stubRMSD ( )
inline

References uncached_stub_rmsd_.

Size protocols::pose_length_moves::PossibleLoop::get_valid_resid ( int  resid,
core::pose::Pose const  pose 
)
private
bool protocols::pose_length_moves::PossibleLoop::kic_closure ( core::scoring::ScoreFunctionOP  scorefxn_,
core::pose::PoseOP poseOP,
core::Size  firstLoopRes,
core::Size  lastLoopRes,
core::Size  numb_kic_cycles 
)
private
void protocols::pose_length_moves::PossibleLoop::minimize_loop ( core::scoring::ScoreFunctionOP  scorefxn,
bool  ideal_loop,
core::pose::PoseOP poseOP 
)
private
void protocols::pose_length_moves::PossibleLoop::output_fragment_debug ( std::vector< numeric::xyzVector< numeric::Real > >  coordinates,
std::string  filename 
)
private
bool protocols::pose_length_moves::PossibleLoop::outputed ( )
inline

References outputed_.

void protocols::pose_length_moves::PossibleLoop::outputed ( bool  outputed)
inline

References outputed(), and outputed_.

Referenced by outputed().

Real protocols::pose_length_moves::PossibleLoop::rmsd_between_coordinates ( std::vector< numeric::xyzVector< numeric::Real > >  fragCoordinates,
std::vector< numeric::xyzVector< numeric::Real > >  coordinates 
)
private
void protocols::pose_length_moves::PossibleLoop::trimRegion ( core::pose::PoseOP poseOP,
core::Size  resStart,
core::Size  resStop 
)
private

Member Data Documentation

bool protocols::pose_length_moves::PossibleLoop::below_distance_threshold_
private
core::Real protocols::pose_length_moves::PossibleLoop::final_rmsd_
private

Referenced by get_final_RMSD().

core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::finalPoseOP_
private
core::Size protocols::pose_length_moves::PossibleLoop::fullLength_resBeforeLoop_
private
core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::fullLengthPoseOP_
private
core::Size protocols::pose_length_moves::PossibleLoop::insertedAfterLoopRes_
private
core::Size protocols::pose_length_moves::PossibleLoop::insertedBeforeLoopRes_
private
core::Size protocols::pose_length_moves::PossibleLoop::loopLength_
private
core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::original_atom_type_fullLengthPoseOP_
private
bool protocols::pose_length_moves::PossibleLoop::outputed_
private

Referenced by outputed().

int protocols::pose_length_moves::PossibleLoop::resAdjustmentAfterLoop_
private
int protocols::pose_length_moves::PossibleLoop::resAdjustmentBeforeLoop_
private
core::Size protocols::pose_length_moves::PossibleLoop::resAfterLoop_
private
core::Size protocols::pose_length_moves::PossibleLoop::resBeforeLoop_
private
char protocols::pose_length_moves::PossibleLoop::resTypeAfterLoop_
private
char protocols::pose_length_moves::PossibleLoop::resTypeBeforeLoop_
private
protocols::indexed_structure_store::SSHashedFragmentStore* protocols::pose_length_moves::PossibleLoop::SSHashedFragmentStore_
private
core::Size protocols::pose_length_moves::PossibleLoop::stub_index_match_
private
core::Real protocols::pose_length_moves::PossibleLoop::stub_rmsd_match_
private

Referenced by get_stubRMSD().

core::Size protocols::pose_length_moves::PossibleLoop::stub_ss_index_match_
private
core::Size protocols::pose_length_moves::PossibleLoop::uncached_stub_index_
private
core::Real protocols::pose_length_moves::PossibleLoop::uncached_stub_rmsd_
private

Referenced by get_uncached_stubRMSD().


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