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

#include <LigandConformer.hh>

Inheritance diagram for protocols::ligand_docking::ga_ligand_dock::LigandConformer:

Public Member Functions
	LigandConformer ()
	~LigandConformer () override
	LigandConformer (core::pose::PoseCOP pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > movingscs)
void	init_params ()
void	initialize (core::pose::PoseCOP pose, utility::vector1< core::Size > const &ligids, 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 (core::Size ires) const
core::conformation::Residue	protein_residue (core::Size ires) const
core::pose::PoseOP	receptor () const
utility::vector1< core::Size >	ligand_ids () const
utility::vector1< core::Real > const &	get_ligandchis () const
core::Real	get_ligandchi (core::Size ichi) const
void	set_ligandchi (core::Size ichi, core::Real value)
core::Size	n_ligandchis () 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	sample_conformation (core::Real transmax, TorsionSampler const &sampler)
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
core::Size	get_jumpid () const
bool	is_ligand_terminal () const
std::string	ligand_typename () const
std::string	ligand_typename (core::Size i) const
void	set_negTds (core::Real inval)
core::Real	neg_Tds () const
core::pose::PoseCOP	get_ref_pose () const
void	update_ligchi_types (core::conformation::Residue const &ligres)
TorsionType const &	get_ligchi_type (core::Size ndx) const
utility::vector1< TorsionType > const &	get_ligchi_types () const

Private Attributes
core::pose::PoseCOP	ref_pose_
utility::vector1< core::Size >	ligids_
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< TorsionType >	ligandchi_types_
utility::vector1 < core::id::TorsionID >	ligandtorsionids_
utility::vector1< core::Real >	ligandnus_
utility::vector1< core::Real >	ligandtaus_
core::Real	rg_
core::Size	jumpid_
bool	ligandxyz_synced_
utility::vector1< core::Vector >	ligandxyz_
core::Real	torsmutationRate_
core::Real	rtmutationRate_
core::Real	transmutWidth_
core::Real	rotmutWidth_
core::Real	ligchimutWidth_
std::string	generation_tag_
utility::vector1< std::string >	ligand_typenames_
core::Real	negTdS_

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

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,
		utility::vector1< core::Size > const &	ligids,
		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::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_jumpid ( ) const

inline

References jumpid_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().

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().

TorsionType const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligchi_type ( core::Size  ndx ) const

inline

References ligandchi_types_.

utility::vector1< TorsionType > const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligchi_types ( ) const

inline

References ligandchi_types_.

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::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_, jumpid_, ligchimutWidth_, negTdS_, 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,
		utility::vector1< core::Size > const &	ligids,
		utility::vector1< core::Size >	movingscs
	)

References jumpid_, ligand_typenames_, ligids_, movingscs_, ref_pose_, and update_conf().

Referenced by LigandConformer().

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

inline

References ligids_, and ref_pose_.

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids ( ) const

inline

References ligids_.

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), 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::GALigandDock::load_reference_pool(), 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

(

core::Size

ires

)

const

References ligids_, 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_typenames_.

Referenced by 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().

std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename ( core::Size  i ) const

inline

References ligand_typenames_.

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

(

)

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

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

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::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::n_ligandchis ( ) const

inline

References ligandchis_.

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_, ligids_, 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 ligids_, 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_.

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_conformation	(	core::Real	transmax,
		TorsionSampler const &	sampler
	)

References protocols::ligand_docking::ga_ligand_dock::TorsionType::at1, protocols::ligand_docking::ga_ligand_dock::TorsionType::at2, protocols::ligand_docking::ga_ligand_dock::TorsionType::at3, protocols::ligand_docking::ga_ligand_dock::TorsionType::at4, protocols::ligand_docking::ga_ligand_dock::TorsionType::bn, protocols::ligand_docking::ga_ligand_dock::TorsionType::br, ligand_xyz(), ligandchi_types_, ligandchis_, ligandnus_, ligandtaus_, ligandxyz_synced_, ligids_, 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(), protocols::ligand_docking::ga_ligand_dock::TorsionSampler::sample(), sample_ring_conformers_, and protocols::ligand_docking::ga_ligand_dock::TR().

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

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

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_ligandchi ( core::Size  ichi, core::Real  value  )

inline

References ligandchis_.

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::to_minipose	(	core::pose::PoseOP	pose,
		LigandConformer &	minilig
	)		const

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

References core::pose::addVirtualResAsRoot(), jumpid_, ligids_, 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 jumpid_, ligandchis_, ligandnus_, ligandtaus_, ligandtorsionids_, ligids_, 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(), 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::GALigandDock::load_reference_pool(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protein_residue(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), 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 core::conformation::Residue::atom_type_index(), core::id::BB, core::chemical::ResidueType::bond_ringness(), core::chemical::ResidueType::bond_type(), core::id::CHI, core::conformation::Residue::chi(), protocols::membrane::com(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), jumpid_, ligandchi_types_, ligandchis_, ligandnus_, ligandtaus_, ligandtorsionids_, ligandxyz_, ligandxyz_synced_, ligids_, core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), movingscs_, core::chemical::ResidueType::n_rings(), core::conformation::Residue::nchi(), core::id::NU, core::chemical::ResidueType::nu_atoms(), proteinchis_, proteinrestypes_, protocols::simple_filters::R2quat(), rb_, rg_, core::chemical::ResidueType::ring_atoms(), sample_ring_conformers_, protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::type().

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), initialize(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), 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 ligids_, 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().

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types

(

core::conformation::Residue const &

ligres

)

References protocols::ligand_docking::ga_ligand_dock::TorsionType::at1, protocols::ligand_docking::ga_ligand_dock::TorsionType::at2, protocols::ligand_docking::ga_ligand_dock::TorsionType::at3, protocols::ligand_docking::ga_ligand_dock::TorsionType::at4, core::conformation::Residue::atom_type_index(), protocols::ligand_docking::ga_ligand_dock::TorsionType::bn, core::chemical::ResidueType::bond_ringness(), core::chemical::ResidueType::bond_type(), protocols::ligand_docking::ga_ligand_dock::TorsionType::br, core::conformation::Residue::chi_atoms(), ligandchi_types_, core::conformation::Residue::nchi(), and core::conformation::Residue::type().

Friends And Related Function Documentation

LigandConformer crossover ( LigandConformer const &  l1, LigandConformer const &  l2  )

friend

core::Real distance_fast ( LigandConformer &  gene1, LigandConformer &  gene2  )

friend

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

std::pair< core::Real, core::Real > distance_internal ( LigandConformer const &  gene1, LigandConformer const &  gene2  )

friend

core::Real distance_slow ( LigandConformer &  gene1, LigandConformer &  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().

core::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::jumpid_

private

Referenced by get_jumpid(), init_params(), initialize(), to_minipose(), to_pose(), and update_conf().

utility::vector1<std::string> protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typenames_

private

Referenced by initialize(), and ligand_typename().

utility::vector1< TorsionType > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandchi_types_

private

Referenced by get_ligchi_type(), get_ligchi_types(), sample_conformation(), update_conf(), and update_ligchi_types().

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

private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), get_ligandchi(), get_ligandchis(), protocols::ligand_docking::ga_ligand_dock::mutate(), n_ligandchis(), randomize(), sample_conformation(), set_ligandchi(), 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(), sample_conformation(), 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(), sample_conformation(), to_pose(), and update_conf().

utility::vector1< core::id::TorsionID > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandtorsionids_

private

Referenced by 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 ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), sample_conformation(), 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().

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligids_

private

Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), protocols::ligand_docking::ga_ligand_dock::distance_slow(), initialize(), is_ligand_terminal(), ligand_ids(), ligand_residue(), ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), receptor(), sample_conformation(), 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().

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(), sample_conformation(), 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(), sample_conformation(), 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_conformation(), 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().

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

• src/protocols/ligand_docking/GALigandDock/LigandConformer.hh
• src/protocols/ligand_docking/GALigandDock/LigandConformer.cc