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, bool freeze_ligand_backbone=false, bool freeze_ligand=false)
void	init_params ()
void	initialize (core::pose::PoseCOP pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > movingscs, bool freeze_ligand_backbone, bool freeze_ligand)
bool	defined () const
void	update_conf (core::pose::PoseCOP pose)
void	update_ligand_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, TorsionSamplerCOP 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	density_score (core::Real scorein)
core::Real	density_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
void	superimpose_to_ref_pose (utility::vector1< core::id::AtomID > const &ids)
void	set_has_density_map (bool setting)
bool	has_density_map () const
bool	is_ligand_frozen () const
bool	is_ligand_bb_frozen () const

Private Attributes
core::pose::PoseCOP	ref_pose_
core::pose::PoseCOP	ref_pose_ligand_
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_
bool	freeze_ligand_backbone_
bool	freeze_ligand_
core::Real	score_
core::Real	density_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_
std::map< core::Size, core::chemical::ResidueTypeCOP >	ligid_restype_map_
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_
bool	has_density_map_ = false

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

LigandConformer() [1/2]

protocols::ligand_docking::ga_ligand_dock::LigandConformer::LigandConformer

(

)

References init_params().

~LigandConformer()

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

override

LigandConformer() [2/2]

protocols::ligand_docking::ga_ligand_dock::LigandConformer::LigandConformer	(	core::pose::PoseCOP	pose,
		utility::vector1< core::Size > const &	ligids,
		utility::vector1< core::Size >	movingscs,
		bool	freeze_ligand_backbone = false,
		bool	freeze_ligand = false
	)

References init_params(), and initialize().

Member Function Documentation

assign_ligand_trans()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::assign_ligand_trans

(

core::Vector

transv

)

defined()

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

inline

References rb_.

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

density_score() [1/2]

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::density_score ( ) const

inline

References density_score_.

density_score() [2/2]

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::density_score ( core::Real  scorein )

inline

References density_score_.

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

dump_pose()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::dump_pose

(

std::string

pdbname

)

const

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

generation_tag()

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().

get_jumpid()

core::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_jumpid ( ) const

inline

References jumpid_.

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

get_ligandchi()

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

inline

References ligandchis_.

get_ligandchis()

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

inline

References ligandchis_.

get_ligchi_type()

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

inline

References ligandchi_types_.

get_ligchi_types()

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

inline

References ligandchi_types_.

get_protein_chis()

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

get_protein_restype()

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().

get_ref_pose()

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::MCSAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

get_reference_ft()

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

inline

References ref_pose_.

has_density_map()

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

inline

References has_density_map_.

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

init_params()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::init_params

(

)

References freeze_ligand_, freeze_ligand_backbone_, generation_tag_, jumpid_, ligchimutWidth_, negTdS_, rg_, rotmutWidth_, rtmutationRate_, sample_ring_conformers_, torsmutationRate_, and transmutWidth_.

Referenced by LigandConformer().

initialize()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::initialize	(	core::pose::PoseCOP	pose,
		utility::vector1< core::Size > const &	ligids,
		utility::vector1< core::Size >	movingscs,
		bool	freeze_ligand_backbone,
		bool	freeze_ligand
	)

References core::pose::addVirtualResAsRoot(), freeze_ligand_, freeze_ligand_backbone_, jumpid_, ligand_typenames_, ligids_, movingscs_, ref_pose_, ref_pose_ligand_, and update_conf().

Referenced by LigandConformer().

is_ligand_bb_frozen()

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

inline

References freeze_ligand_, and freeze_ligand_backbone_.

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

is_ligand_frozen()

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

inline

References freeze_ligand_.

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

is_ligand_terminal()

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

inline

References ligids_, and ref_pose_.

ligand_ids()

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::MCSAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score(), 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_ligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin_helper(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_optH(), 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_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_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().

ligand_residue()

core::conformation::Residue protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_residue

(

core::Size

ires

)

const

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

ligand_rg()

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

inline

References rg_.

ligand_typename() [1/2]

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(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

ligand_typename() [2/2]

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

inline

References ligand_typenames_.

ligand_xyz()

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

(

)

moving_scs()

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::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin(), 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(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

n_ligandchis()

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

inline

References ligandchis_.

neg_Tds()

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

inline

References negTdS_.

protein_residue()

core::conformation::Residue protocols::ligand_docking::ga_ligand_dock::LigandConformer::protein_residue

(

core::Size

ires

)

const

quat()

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

inline

References rb_.

randomize()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize

(

core::Real

transmax

)

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

receptor()

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::receptor

(

)

const

rms() [1/2]

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

inline

References rms_.

rms() [2/2]

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

inline

References rms_.

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

sample_conformation()

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

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

sample_ring_conformers()

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

inline

References sample_ring_conformers_.

score() [1/2]

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

inline

References score_.

score() [2/2]

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::GALigandDock::load_template_pool(), and protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status().

set_chiwidth()

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

inline

References ligchimutWidth_.

set_generation_tag()

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::GAOptimizer::next_generation().

set_has_density_map()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_has_density_map ( bool  setting )

inline

References has_density_map_.

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

set_ligandchi()

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

inline

References ligandchis_.

set_moving_scs()

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

inline

References movingscs_.

set_negTds()

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

inline

References negTdS_.

set_protein_chis()

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().

set_protein_restype()

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().

set_rotwidth()

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

inline

References rotmutWidth_.

set_rtmutrate()

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

inline

References rtmutationRate_.

set_sample_ring_conformers()

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::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply().

set_torsmutrate()

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

inline

References torsmutationRate_.

set_transwidth()

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

inline

References transmutWidth_.

superimpose_to_ref_pose()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_ref_pose

(

utility::vector1< core::id::AtomID > const &

ids

)

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

to_minipose()

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().

to_pose()

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(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score_init(), to_minipose(), and update_conf_from_minipose().

to_string()

std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_string

(

)

const

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

trans()

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

inline

References rb_.

update_conf()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf

(

core::pose::PoseCOP

pose

)

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(), core::id::AtomID::atomno(), core::id::BB, 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(), core::id::CHI, protocols::membrane::com(), freeze_ligand_, freeze_ligand_backbone_, core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), jumpid_, ligandchi_types_, ligandchis_, ligandnus_, ligandtaus_, ligandtorsionids_, ligandxyz_, ligandxyz_synced_, ligid_restype_map_, ligids_, core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), movingscs_, core::chemical::ResidueType::n_rings(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), 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(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::conformation::Residue::xyz().

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

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().

update_ligand_conf()

void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf

(

core::pose::PoseCOP

pose

)

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(), core::id::AtomID::atomno(), core::id::BB, 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(), core::id::CHI, protocols::membrane::com(), freeze_ligand_, freeze_ligand_backbone_, ligandchi_types_, ligandchis_, ligandnus_, ligandtaus_, ligandtorsionids_, ligandxyz_, ligandxyz_synced_, ligid_restype_map_, ligids_, core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), core::chemical::ResidueType::n_rings(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::id::NU, core::chemical::ResidueType::nu_atoms(), rg_, core::chemical::ResidueType::ring_atoms(), sample_ring_conformers_, protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::conformation::Residue::xyz().

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

update_ligchi_types()

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

crossover

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

friend

distance_fast

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

friend

distance_internal

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

friend

distance_slow

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

friend

mutate

LigandConformer mutate ( LigandConformer const &  l )

friend

Member Data Documentation

density_score_

core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::density_score_

private

Referenced by density_score().

freeze_ligand_

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::freeze_ligand_

private

Referenced by init_params(), initialize(), is_ligand_bb_frozen(), is_ligand_frozen(), update_conf(), and update_ligand_conf().

freeze_ligand_backbone_

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::freeze_ligand_backbone_

private

Referenced by init_params(), initialize(), is_ligand_bb_frozen(), update_conf(), and update_ligand_conf().

generation_tag_

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

private

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

has_density_map_

bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::has_density_map_ = false

private

Referenced by has_density_map(), and set_has_density_map().

jumpid_

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().

ligand_typenames_

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

private

Referenced by initialize(), and ligand_typename().

ligandchi_types_

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

private

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

ligandchis_

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

private

Referenced by get_ligandchi(), get_ligandchis(), n_ligandchis(), set_ligandchi(), to_pose(), to_string(), update_conf(), and update_ligand_conf().

ligandnus_

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

private

Referenced by to_pose(), update_conf(), and update_ligand_conf().

ligandtaus_

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

private

Referenced by to_pose(), update_conf(), and update_ligand_conf().

ligandtorsionids_

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

private

Referenced by to_pose(), update_conf(), and update_ligand_conf().

ligandxyz_

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

private

Referenced by update_conf(), and update_ligand_conf().

ligandxyz_synced_

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

private

Referenced by set_protein_chis(), set_protein_restype(), update_conf(), and update_ligand_conf().

ligchimutWidth_

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

private

Referenced by init_params(), and set_chiwidth().

ligid_restype_map_

std::map< core::Size, core::chemical::ResidueTypeCOP > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligid_restype_map_

private

Referenced by update_conf(), and update_ligand_conf().

ligids_

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

private

Referenced by initialize(), is_ligand_terminal(), ligand_ids(), to_minipose(), to_pose(), update_conf(), update_conf_from_minipose(), and update_ligand_conf().

movingscs_

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().

negTdS_

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

private

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

proteinchis_

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().

proteinrestypes_

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().

rb_

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

private

Referenced by defined(), quat(), to_pose(), to_string(), trans(), and update_conf().

ref_pose_

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

private

Referenced by get_ref_pose(), get_reference_ft(), initialize(), is_ligand_terminal(), and to_pose().

ref_pose_ligand_

core::pose::PoseCOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::ref_pose_ligand_

private

Referenced by initialize().

rg_

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

private

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

rms_

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

private

Referenced by rms().

rotmutWidth_

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

private

Referenced by init_params(), and set_rotwidth().

rtmutationRate_

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

private

Referenced by init_params(), and set_rtmutrate().

sample_ring_conformers_

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

private

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

score_

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

private

Referenced by score().

torsmutationRate_

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

private

Referenced by init_params(), and set_torsmutrate().

transmutWidth_

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

private

Referenced by init_params(), and set_transwidth().

---

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