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protocols::ligand_docking::ga_ligand_dock::LigandConformer Class Reference

Gene representation of ligand & flexible sidechains in receptor. More...

#include <LigandConformer.hh>

Inheritance diagram for protocols::ligand_docking::ga_ligand_dock::LigandConformer:
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Public Member Functions

 LigandConformer ()
 
 ~LigandConformer () override
 
 LigandConformer (core::pose::PoseCOP pose, core::Size ligid, utility::vector1< core::Size > movingscs)
 
void init_params ()
 
void initialize (core::pose::PoseCOP pose, core::Size ligid, utility::vector1< core::Size > movingscs)
 
bool defined () const
 
void update_conf (core::pose::PoseCOP pose)
 
void to_pose (core::pose::PoseOP pose) const
 
void to_minipose (core::pose::PoseOP pose, LigandConformer &minilig) const
 create a reduced pose representation (to be used in minimization) More...
 
void update_conf_from_minipose (core::pose::PoseCOP pose)
 update internal information from the reduced pose representation More...
 
numeric::Quaternion
< core::Real > const 		quat () const
 
numeric::xyzVector< core::Real >
const 		trans () const
 
utility::vector1< core::Vector >
const & 		ligand_xyz ()
 
core::Real ligand_rg () const
 
core::conformation::Residue ligand_residue () const
 
core::conformation::Residue protein_residue (core::Size ires) const
 
core::pose::PoseOP receptor () const
 
core::Size ligand_id () const
 
utility::vector1< core::Real >
const & 		get_ligandchis () const
 
core::Real get_ligandchi (core::Size ichi) const
 
utility::vector1< core::Size >
const & 		moving_scs () const
 
void set_moving_scs (utility::vector1< core::Size > setting)
 
void set_protein_restype (core::Size ires, core::chemical::ResidueTypeCOP restype)
 
void set_protein_chis (core::Size ires, utility::vector1< core::Real > const &newchis)
 
void set_sample_ring_conformers (bool setting)
 
bool sample_ring_conformers () const
 
core::chemical::ResidueTypeCOP get_protein_restype (core::Size ires) const
 
utility::vector1< core::Real > get_protein_chis (core::Size ires) const
 
void randomize (core::Real transmax)
 
void superimpose_to_alternative_frame (LigandConformer const &refconf)
 
void set_rotwidth (core::Real setting)
 
void set_transwidth (core::Real setting)
 
void set_chiwidth (core::Real setting)
 
void set_torsmutrate (core::Real setting)
 
void set_rtmutrate (core::Real setting)
 
void assign_ligand_trans (core::Vector transv)
 
void score (core::Real scorein)
 
core::Real score () const
 
void rms (core::Real rmsin)
 
core::Real rms () const
 
void dump_pose (std::string pdbname) const
 
void set_generation_tag (std::string tag)
 
std::string generation_tag () const
 
std::string to_string () const
 
core::kinematics::FoldTree const & get_reference_ft () const
 
bool is_ligand_terminal () const
 
void set_typename (std::string name)
 
std::string ligand_typename () const
 
void set_negTds (core::Real inval)
 
core::Real neg_Tds () const
 
core::pose::PoseCOP get_ref_pose () const
 

Private Attributes

core::pose::PoseCOP ref_pose_
 
core::Size ligid_
 
utility::vector1< core::Size > movingscs_
 
utility::vector1
< core::chemical::ResidueTypeCOP > 		proteinrestypes_
 
utility::vector1
< utility::vector1< core::Real > > 		proteinchis_
 
bool sample_ring_conformers_
 
core::Real score_
 
core::Real rms_
 
utility::vector1< core::Real > rb_
 
utility::vector1< core::Real > ligandchis_
 
utility::vector1< core::Real > ligandnus_
 
utility::vector1< core::Real > ligandtaus_
 
utility::vector1
< utility::vector1< core::Size > > 		ligandchi_downstream_
 
core::Real rg_
 
bool ligandxyz_synced_
 
utility::vector1< core::Vector > ligandxyz_
 
core::Real torsmutationRate_
 
core::Real rtmutationRate_
 
core::Real transmutWidth_
 
core::Real rotmutWidth_
 
core::Real ligchimutWidth_
 
core::Real protchimutWidth_
 
std::string generation_tag_
 
std::string ligand_typename_
 
core::Real negTdS_
 

Friends

LigandConformer mutate (LigandConformer const &l)
 
LigandConformer crossover (LigandConformer const &l1, LigandConformer const &l2)
 
LigandConformer crossover_ft (LigandConformer const &l1, LigandConformer const &l2)
 
core::Real distance_fast (LigandConformer &gene1, LigandConformer &gene2)
 
std::pair< core::Real, core::Real > distance_internal (LigandConformer const &gene1, LigandConformer const &gene2)
 
core::Real distance_slow (LigandConformer const &gene1, LigandConformer const &gene2)
 

Detailed Description

Gene representation of ligand & flexible sidechains in receptor.

Gene is preresented by rigid body (rb_), ligandchis, and receptorchis Also has functions to tranform back and forth to pose object Uses friend functions to perform mutation / crossovers with others within gene representation

Constructor & Destructor Documentation

protocols::ligand_docking::ga_ligand_dock::LigandConformer::LigandConformer ( )

References init_params().

protocols::ligand_docking::ga_ligand_dock::LigandConformer::~LigandConformer ( )
override
protocols::ligand_docking::ga_ligand_dock::LigandConformer::LigandConformer ( core::pose::PoseCOP  pose,
core::Size  ligid,
utility::vector1< core::Size >  movingscs 
)

References init_params(), and initialize().

Member Function Documentation

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::assign_ligand_trans ( core::Vector  transv)

References rb_.

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::defined ( ) const
inline

References rb_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::dump_pose ( std::string  pdbname) const

References to_pose().

std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::generation_tag ( ) const
inline

References generation_tag_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchi ( core::Size  ichi) const
inline

References ligandchis_.

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().

utility::vector1< core::Real > const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchis ( ) const
inline

References ligandchis_.

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().

utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_chis ( core::Size  ires) const
inline

References proteinchis_.

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop().

core::chemical::ResidueTypeCOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_restype ( core::Size  ires) const
inline

References proteinrestypes_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop().

core::pose::PoseCOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ref_pose ( ) const
inline

References ref_pose_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

core::kinematics::FoldTree const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_reference_ft ( ) const
inline

References ref_pose_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::init_params ( )

References generation_tag_, ligand_typename_, ligchimutWidth_, negTdS_, protchimutWidth_, rg_, rotmutWidth_, rtmutationRate_, sample_ring_conformers_, torsmutationRate_, and transmutWidth_.

Referenced by LigandConformer().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::initialize ( core::pose::PoseCOP  pose,
core::Size  ligid,
utility::vector1< core::Size >  movingscs 
)

References protocols::sewing::data_storage::ligand, ligand_typename_, ligandchi_downstream_, ligid_, movingscs_, ref_pose_, and update_conf().

Referenced by LigandConformer().

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::is_ligand_terminal ( ) const
inline

References ligid_, and ref_pose_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_optimizer().

core::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_id ( ) const
inline

References ligid_.

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_optimizer(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

core::conformation::Residue protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_residue ( ) const

References ligid_, ref_pose_, and to_pose().

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_slow().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_rg ( ) const
inline

References rg_.

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().

std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename ( ) const
inline

References ligand_typename_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

utility::vector1< core::Vector > const & protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_xyz ( )

References protocols::membrane::com(), ligandxyz_, ligandxyz_synced_, ligid_, ref_pose_, rg_, to_pose(), and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_fast(), and randomize().

utility::vector1< core::Size > const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs ( ) const
inline

References movingscs_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::distance_internal(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_optimizer(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::neg_Tds ( ) const
inline

References negTdS_.

core::conformation::Residue protocols::ligand_docking::ga_ligand_dock::LigandConformer::protein_residue ( core::Size  ires) const

References ref_pose_, and to_pose().

numeric::Quaternion< core::Real > const protocols::ligand_docking::ga_ligand_dock::LigandConformer::quat ( ) const
inline

References rb_.

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize ( core::Real  transmax)

References ligand_xyz(), ligandchis_, ligandnus_, ligandtaus_, ligandxyz_synced_, ligid_, core::chemical::ResidueType::n_rings(), protocols::simple_filters::R2quat(), core::scoring::motif::random_rotation(), rb_, ref_pose_, core::scoring::rg, core::chemical::ResidueType::ring_atoms(), core::chemical::ResidueType::ring_conformer_set(), sample_ring_conformers_, and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::receptor ( ) const

References ligid_, and ref_pose_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::rms ( core::Real  rmsin)
inline

References rms_.

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::rms ( ) const
inline

References rms_.

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_ring_conformers ( ) const
inline

References sample_ring_conformers_.

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), and protocols::ligand_docking::ga_ligand_dock::mutate().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::score ( core::Real  scorein)
inline

References score_.

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status(), and protocols::ligand_docking::ga_ligand_dock::GAOptimizer::update_pool().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::score ( ) const
inline

References score_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_chiwidth ( core::Real  setting)
inline

References ligchimutWidth_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_generation_tag ( std::string  tag)
inline

References generation_tag_.

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover_ft(), protocols::ligand_docking::ga_ligand_dock::mutate(), and protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_moving_scs ( utility::vector1< core::Size >  setting)
inline

References movingscs_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_negTds ( core::Real  inval)
inline

References negTdS_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_protein_chis ( core::Size  ires,
utility::vector1< core::Real > const &  newchis 
)
inline

References ligandxyz_synced_, and proteinchis_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_protein_restype ( core::Size  ires,
core::chemical::ResidueTypeCOP  restype 
)
inline

References ligandxyz_synced_, proteinchis_, and proteinrestypes_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_rotwidth ( core::Real  setting)
inline

References rotmutWidth_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_rtmutrate ( core::Real  setting)
inline

References rtmutationRate_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_sample_ring_conformers ( bool  setting)
inline

References sample_ring_conformers_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_torsmutrate ( core::Real  setting)
inline

References torsmutationRate_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_transwidth ( core::Real  setting)
inline

References transmutWidth_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_typename ( std::string  name)
inline

References ligand_typename_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame ( LigandConformer const &  refconf)

References core::pose::addVirtualResAsRoot(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::id::AtomID::BOGUS_ATOM_ID(), core::conformation::Residue::chi_atoms(), core::pose::initialize_atomid_map(), protocols::sewing::data_storage::ligand, ligandchis_, ligid_, core::conformation::Residue::nbr_atom(), core::conformation::Residue::nheavyatoms(), core::scoring::rg, core::scoring::superimpose_pose(), to_pose(), protocols::ligand_docking::ga_ligand_dock::TR(), update_conf(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose ( core::pose::PoseOP  pose,
LigandConformer &  minilig 
) const

create a reduced pose representation (to be used in minimization)

References core::pose::addVirtualResAsRoot(), ligid_, movingscs_, and to_pose().

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose ( core::pose::PoseOP  pose) const

References ligandchis_, ligandnus_, ligandtaus_, ligid_, movingscs_, core::chemical::ResidueType::n_rings(), core::id::NU, core::chemical::ResidueType::nu_atoms(), proteinchis_, proteinrestypes_, protocols::simple_filters::quat2R(), rb_, ref_pose_, core::chemical::ResidueType::ring_atoms(), sample_ring_conformers_, core::kinematics::Jump::set_rotation(), and core::kinematics::Jump::set_translation().

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), dump_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), ligand_residue(), ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protein_residue(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), superimpose_to_alternative_frame(), to_minipose(), and update_conf_from_minipose().

std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_string ( ) const

References core::chemical::element::F, ligandchis_, and rb_.

numeric::xyzVector< core::Real > const protocols::ligand_docking::ga_ligand_dock::LigandConformer::trans ( ) const
inline

References rb_.

Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf ( core::pose::PoseCOP  pose)

References protocols::membrane::com(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), ligandchis_, ligandnus_, ligandtaus_, ligandxyz_, ligandxyz_synced_, ligid_, movingscs_, core::chemical::ResidueType::n_rings(), core::id::NU, core::chemical::ResidueType::nu_atoms(), proteinchis_, proteinrestypes_, protocols::simple_filters::R2quat(), rb_, rg_, core::chemical::ResidueType::ring_atoms(), and sample_ring_conformers_.

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), initialize(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), superimpose_to_alternative_frame(), and update_conf_from_minipose().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf_from_minipose ( core::pose::PoseCOP  pose)

update internal information from the reduced pose representation

References ligid_, movingscs_, to_pose(), and update_conf().

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().

Friends And Related Function Documentation

LigandConformer crossover ( LigandConformer const &  l1,
LigandConformer const &  l2 
)
friend
LigandConformer crossover_ft ( LigandConformer const &  l1,
LigandConformer const &  l2 
)
friend
core::Real distance_fast ( LigandConformer &  gene1,
LigandConformer &  gene2 
)
friend
std::pair< core::Real, core::Real > distance_internal ( LigandConformer const &  gene1,
LigandConformer const &  gene2 
)
friend
core::Real distance_slow ( LigandConformer const &  gene1,
LigandConformer const &  gene2 
)
friend
LigandConformer mutate ( LigandConformer const &  l)
friend

Member Data Documentation

std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::generation_tag_
private

Referenced by generation_tag(), init_params(), and set_generation_tag().

std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename_
private

Referenced by init_params(), initialize(), ligand_typename(), and set_typename().

utility::vector1< utility::vector1< core::Size > > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandchi_downstream_
private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover_ft(), and initialize().

utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandchis_
private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), protocols::ligand_docking::ga_ligand_dock::crossover_ft(), get_ligandchi(), get_ligandchis(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), superimpose_to_alternative_frame(), to_pose(), to_string(), and update_conf().

utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandnus_
private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), to_pose(), and update_conf().

utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandtaus_
private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), to_pose(), and update_conf().

utility::vector1< core::Vector > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandxyz_
private

Referenced by ligand_xyz(), and update_conf().

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandxyz_synced_
private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover_ft(), ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), set_protein_chis(), set_protein_restype(), and update_conf().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligchimutWidth_
private

Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_chiwidth().

core::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligid_
private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), initialize(), is_ligand_terminal(), ligand_id(), ligand_residue(), ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), receptor(), superimpose_to_alternative_frame(), to_minipose(), to_pose(), update_conf(), and update_conf_from_minipose().

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::LigandConformer::movingscs_
private

Referenced by initialize(), moving_scs(), set_moving_scs(), to_minipose(), to_pose(), update_conf(), and update_conf_from_minipose().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::negTdS_
private

Referenced by init_params(), neg_Tds(), and set_negTds().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::protchimutWidth_
private

Referenced by init_params().

utility::vector1< utility::vector1< core::Real > > protocols::ligand_docking::ga_ligand_dock::LigandConformer::proteinchis_
private

Referenced by get_protein_chis(), set_protein_chis(), set_protein_restype(), to_pose(), and update_conf().

utility::vector1< core::chemical::ResidueTypeCOP > protocols::ligand_docking::ga_ligand_dock::LigandConformer::proteinrestypes_
private

Referenced by get_protein_restype(), set_protein_restype(), to_pose(), and update_conf().

utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::rb_
private

Referenced by assign_ligand_trans(), defined(), protocols::ligand_docking::ga_ligand_dock::mutate(), quat(), randomize(), to_pose(), to_string(), trans(), and update_conf().

core::pose::PoseCOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::ref_pose_
private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), get_ref_pose(), get_reference_ft(), initialize(), is_ligand_terminal(), ligand_residue(), ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::mutate(), protein_residue(), randomize(), receptor(), and to_pose().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::rg_
private

Referenced by init_params(), ligand_rg(), ligand_xyz(), and update_conf().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::rms_
private

Referenced by rms().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::rotmutWidth_
private

Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_rotwidth().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::rtmutationRate_
private

Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_rtmutrate().

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_ring_conformers_
private

Referenced by init_params(), randomize(), sample_ring_conformers(), set_sample_ring_conformers(), to_pose(), and update_conf().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::score_
private

Referenced by score().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::torsmutationRate_
private

Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_torsmutrate().

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::transmutWidth_
private

Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_transwidth().

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