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core::pack::guidance_scoreterms::sap::SapConstraintHelper Class Reference

#include <SapConstraintHelper.hh>

Public Member Functions

 SapConstraintHelper (SapConstraintOptionsCOP const &options)
 
core::Real calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position)
 
void commit_considered_substitution ()
 
SapConstraintOptionsCOP options () const
 
core::pack::rotamer_set::RotamerSets init_with_pose (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
Real current_score () const
 
Real set_accurate_sasa_and_recalc (pose::Pose const &pose)
 
void report ()
 
void report_final_score (Real actual_sap) const
 
core::id::AtomID_Map< Realget_per_atom_sap (pose::Pose const &pose) const
 

Protected Types

typedef std::pair< Size,
uint8_t[ATOM_WITHIN_5_ELEMS]> 
atom_within_5_value
 
typedef std::unordered_map
< std::pair
< conformation::Residue const
*, conformation::Residue const * >
, atom_within_5_value,
RotamerRotamerHasher
type_atom_within_5_map
 
typedef float atom_sasa_score_value [ATOM_SASA_SCORE_ELEMS]
 
typedef std::unordered_map
< conformation::Residue const
*, atom_sasa_score_value
atom_sasa_score_map
 

Protected Member Functions

void restore_from_shadow ()
 
void save_to_shadow ()
 
core::Real symm_calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position)
 
void recalculate_saps (utility::vector1< Size > const &positions_to_update)
 
void recalculate_sasa ()
 
void update_neighbors_sap (float const *delta_sasa_score, Size seqpos, bool invert, bool skip_self)
 
void add_to_sap (float amount, Size seqpos, Size iat)
 
void add_remove_rotamer (utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add)
 
void add_remove_rotamer_fast (utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add)
 
void add_remove_rotamer_lightning (utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add)
 
void lightning_update_neighbors_sap (Size seqpos, bool invert, bool dont_update_self)
 
void lightning_add_to_sap (float amount, Size seqpos)
 
void store_sasa_blocks (Size &offset, Size seqpos, bool add, bool mark_dirty)
 
void reinit_with_resvect (utility::vector1< core::conformation::ResidueCOP > const &resvect, bool skip_reset=false)
 
void reset_calculation ()
 
void apply_residue_selectors (core::pose::Pose const &pose)
 
void resize_arrays (core::pose::Pose const &pose)
 
void fill_block_params (core::pose::Pose const &pose, pack::rotamer_set::RotamerSets const &rotamer_sets)
 
Real calculate_block (Real dist2, Real radius_us, Real radius_them)
 
void fill_atom_neighbor_stuff (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
void convert_block_sasa_to_sasa_score (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
float & lightning_1b_lookup (chemical::AA aa, Size seqpos)
 
std::pair< float, float > & lightning_2b_lookup (chemical::AA aa1, Size seqpos1, chemical::AA aa2, Size seqpos2)
 
Real find_lightning_2b (conformation::ResidueCOP const &from_rot, conformation::ResidueCOP const &to_rot)
 
core::pack::rotamer_set::RotamerSets setup_lightning (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
void setup_fast (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
void add_sap_data (conformation::Residue const *key1, conformation::Residue const *key2, utility::vector1< utility::vector1< uint8_t >> const &sap_positions, Size natoms, Size first_sidechain)
 
core::pack::rotamer_set::RotamerSets setup_for_symmetry (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotsets)
 
Size my_natoms (core::conformation::ResidueCOP const &res) const
 
Size my_natoms (core::conformation::Residue const *res) const
 
void init ()
 

Private Attributes

SapConstraintOptionsCOP options_
 
bool fast_
 
bool lightning_
 
bool heavy_
 
utility::vector1< boolscore_positions_
 
utility::vector1< boolsap_calculate_positions_
 
utility::vector1< boolsasa_positions_
 
core::conformation::ResidueCOP fake_rotamer_
 
core::scoring::ScoreFunctionOP fake_lr_scorefxn_
 
core::scoring::ScoreFunctionOP fake_sr_scorefxn_
 
Size max_rotamer_atoms_
 
utility::vector1
< utility::vector1< Size > > 
check_positions_sap_
 
utility::vector1
< utility::vector1< Size > > 
check_positions_block_
 
std::unordered_map
< conformation::Residue const
*, Size
rotamer_to_block_param_offset_
 
utility::vector1< BlockParamall_block_params_
 
atom_sasa_score_map rotamer_to_sasa_data_
 
std::unordered_map< std::pair
< conformation::Residue const
*, conformation::Residue const * >
, Size, RotamerRotamerHasher
interacting_block_offset_
 
utility::vector1< uint8_t > interacting_block_
 
type_atom_within_5_map atom_within_5_map_
 
utility::vector1< uint8_t > atom_within_5_
 
utility::vector1
< core::conformation::ResidueCOP
internal_resvect_
 
utility::vector1< Sizeblock_param_offset_
 
utility::vector1
< utility::vector0< uint16_t > > 
sasa_blocks_
 
utility::vector1
< utility::vector0< float > > 
atom_sasa_score_
 
utility::vector1
< utility::vector0< float > > 
atom_sap_
 
float current_score_
 
utility::vector1< float * > atom_sasa_score_fast_
 
utility::vector1< boolshadow_mismatch_
 
utility::vector1
< utility::vector0< bool > > 
dirty_sasa_
 
utility::vector1
< utility::vector0< float > > 
atom_sasa_score_shadow_
 
utility::vector1
< utility::vector0< uint16_t > > 
sasa_blocks_shadow_
 
utility::vector1
< utility::vector0< float > > 
atom_sap_shadow_
 
float current_score_shadow_
 
utility::vector1< Sizeblock_param_offset_shadow_
 
utility::vector1
< core::conformation::ResidueCOP
internal_resvect_shadow_
 
utility::vector1< float * > atom_sasa_score_fast_shadow_
 
utility::vector1< uint16_t > lightning_aa_2_index_
 
Size lightning_num_aas_
 
Size lightning_num_aas_sq_
 
utility::vector1< uint32_t > lightning_seqpos_2_index_
 
Size lightning_num_seqpos_
 
utility::vector0< float > lightning_rotamer_1b_sap_
 
utility::vector0< std::pair
< float, float > > 
lightning_rotamer_2b_sap_
 
utility::vector1< Reallightning_current_res_sap_
 
utility::vector1< Reallightning_current_res_sap_shadow_
 
utility::vector1< Sizerecalc_positions_scratch_
 
utility::vector0< float > delta_sasa_scratch_
 
utility::vector0< float > delta_sasa_zeros_
 
conformation::symmetry::SymmetryInfoCOP symm_info_
 
std::unordered_map
< core::conformation::Residue
const *, utility::vector1
< core::conformation::ResidueCOP > > 
symm_rotamer_to_other_rotamers_
 
utility::vector1
< core::conformation::ResidueCOP
symm_work_resvect_
 
utility::vector1
< core::conformation::ResidueCOP
symm_work_resvect_shadow_
 
bool symm_debug_
 

Friends

class ::SapConstraintEnergyTests
 

Member Typedef Documentation

typedef float core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_value[ATOM_SASA_SCORE_ELEMS]
protected

Constructor & Destructor Documentation

core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper ( SapConstraintOptionsCOP const &  options)

References init().

Member Function Documentation

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
Size const  substitution_position,
bool  add 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer_fast ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
Size const  substitution_position,
bool  add 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer_lightning ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
Size const  substitution_position,
bool  add 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_sap_data ( conformation::Residue const *  key1,
conformation::Residue const *  key2,
utility::vector1< utility::vector1< uint8_t >> const &  sap_positions,
Size  natoms,
Size  first_sidechain 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_to_sap ( float  amount,
Size  seqpos,
Size  iat 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::apply_residue_selectors ( core::pose::Pose const &  pose)
protected
Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::calculate_block ( Real  dist2,
Real  radius_us,
Real  radius_them 
)
protected
core::Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::calculate_energy ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
core::Size const  substitution_position 
)
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::commit_considered_substitution ( )

References save_to_shadow().

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::convert_block_sasa_to_sasa_score ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected
Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::current_score ( ) const

References current_score_shadow_.

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_block_params ( core::pose::Pose const &  pose,
pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected
Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::find_lightning_2b ( conformation::ResidueCOP const &  from_rot,
conformation::ResidueCOP const &  to_rot 
)
protected
core::id::AtomID_Map< Real > core::pack::guidance_scoreterms::sap::SapConstraintHelper::get_per_atom_sap ( pose::Pose const &  pose) const
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::init ( )
protected
core::pack::rotamer_set::RotamerSets core::pack::guidance_scoreterms::sap::SapConstraintHelper::init_with_pose ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
float & core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_1b_lookup ( chemical::AA  aa,
Size  seqpos 
)
protected
std::pair< float, float > & core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_2b_lookup ( chemical::AA  aa1,
Size  seqpos1,
chemical::AA  aa2,
Size  seqpos2 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_add_to_sap ( float  amount,
Size  seqpos 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_update_neighbors_sap ( Size  seqpos,
bool  invert,
bool  dont_update_self 
)
protected
Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_natoms ( core::conformation::ResidueCOP const &  res) const
protected
Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_natoms ( core::conformation::Residue const *  res) const
protected
SapConstraintOptionsCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::options ( ) const

References options_.

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::recalculate_saps ( utility::vector1< Size > const &  positions_to_update)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::recalculate_sasa ( )
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::reinit_with_resvect ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
bool  skip_reset = false 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::report ( )
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::report_final_score ( Real  actual_sap) const
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::reset_calculation ( )
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::resize_arrays ( core::pose::Pose const &  pose)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::restore_from_shadow ( )
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::save_to_shadow ( )
protected
Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc ( pose::Pose const &  pose)
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_fast ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected
core::pack::rotamer_set::RotamerSets core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotsets 
)
protected
core::pack::rotamer_set::RotamerSets core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_lightning ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::store_sasa_blocks ( Size offset,
Size  seqpos,
bool  add,
bool  mark_dirty 
)
protected
core::Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_calculate_energy ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
core::Size const  substitution_position 
)
protected
void core::pack::guidance_scoreterms::sap::SapConstraintHelper::update_neighbors_sap ( float const *  delta_sasa_score,
Size  seqpos,
bool  invert,
bool  skip_self 
)
protected

Friends And Related Function Documentation

friend class ::SapConstraintEnergyTests
friend

Member Data Documentation

utility::vector1<BlockParam> core::pack::guidance_scoreterms::sap::SapConstraintHelper::all_block_params_
private
utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sap_
private
utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sap_shadow_
private
utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_
private
utility::vector1<float *> core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_fast_
private
utility::vector1<float *> core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_fast_shadow_
private
utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_shadow_
private
utility::vector1<uint8_t> core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_within_5_
private
type_atom_within_5_map core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_within_5_map_
private
utility::vector1<Size> core::pack::guidance_scoreterms::sap::SapConstraintHelper::block_param_offset_
private
utility::vector1<Size> core::pack::guidance_scoreterms::sap::SapConstraintHelper::block_param_offset_shadow_
private
utility::vector1<utility::vector1<Size> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::check_positions_block_
private
utility::vector1<utility::vector1<Size> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::check_positions_sap_
private
float core::pack::guidance_scoreterms::sap::SapConstraintHelper::current_score_
private
float core::pack::guidance_scoreterms::sap::SapConstraintHelper::current_score_shadow_
private
utility::vector0<float> core::pack::guidance_scoreterms::sap::SapConstraintHelper::delta_sasa_scratch_
private

Referenced by recalculate_sasa(), and resize_arrays().

utility::vector0<float> core::pack::guidance_scoreterms::sap::SapConstraintHelper::delta_sasa_zeros_
private

Referenced by reset_calculation(), and resize_arrays().

utility::vector1<utility::vector0<bool> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::dirty_sasa_
private
core::scoring::ScoreFunctionOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::fake_lr_scorefxn_
private

Referenced by fill_atom_neighbor_stuff(), and init().

core::conformation::ResidueCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::fake_rotamer_
private
core::scoring::ScoreFunctionOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::fake_sr_scorefxn_
private
bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::fast_
private
bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::heavy_
private

Referenced by init(), and my_natoms().

utility::vector1<uint8_t> core::pack::guidance_scoreterms::sap::SapConstraintHelper::interacting_block_
private
std::unordered_map< std::pair< conformation::Residue const *, conformation::Residue const *>, Size, RotamerRotamerHasher > core::pack::guidance_scoreterms::sap::SapConstraintHelper::interacting_block_offset_
private
utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::internal_resvect_
private
utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::internal_resvect_shadow_
private
bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_
private
utility::vector1< uint16_t > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_aa_2_index_
private
utility::vector1< Real > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_current_res_sap_
private
utility::vector1< Real > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_current_res_sap_shadow_
private
Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_num_aas_
private
Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_num_aas_sq_
private
Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_num_seqpos_
private
utility::vector0< float > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_rotamer_1b_sap_
private
utility::vector0< std::pair< float, float > > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_rotamer_2b_sap_
private
utility::vector1< uint32_t > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_seqpos_2_index_
private
Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::max_rotamer_atoms_
private
SapConstraintOptionsCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::options_
private
utility::vector1<Size> core::pack::guidance_scoreterms::sap::SapConstraintHelper::recalc_positions_scratch_
private

Referenced by calculate_energy(), and init().

std::unordered_map< conformation::Residue const*, Size > core::pack::guidance_scoreterms::sap::SapConstraintHelper::rotamer_to_block_param_offset_
private
atom_sasa_score_map core::pack::guidance_scoreterms::sap::SapConstraintHelper::rotamer_to_sasa_data_
private
utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::sap_calculate_positions_
private
utility::vector1<utility::vector0<uint16_t> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::sasa_blocks_
private
utility::vector1<utility::vector0<uint16_t> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::sasa_blocks_shadow_
private
utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::sasa_positions_
private
utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::score_positions_
private
utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::shadow_mismatch_
private
bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_debug_
private

Referenced by init(), and setup_for_symmetry().

conformation::symmetry::SymmetryInfoCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_info_
private
std::unordered_map< core::conformation::Residue const *, utility::vector1< core::conformation::ResidueCOP > > core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_rotamer_to_other_rotamers_
private
utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_work_resvect_
private
utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_work_resvect_shadow_
private

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