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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::Realget_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::Sizemovingscs_
 
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::Realrb_
 
utility::vector1< core::Realligandchis_
 
utility::vector1< core::Realligandnus_
 
utility::vector1< core::Realligandtaus_
 
utility::vector1
< utility::vector1< core::Size > > 
ligandchi_downstream_
 
core::Real rg_
 
bool ligandxyz_synced_
 
utility::vector1< core::Vectorligandxyz_
 
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::Realdistance_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
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
core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchi ( core::Size  ichi) const
inline
utility::vector1< core::Real > const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchis ( ) const
inline
utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_chis ( core::Size  ires) const
inline
core::chemical::ResidueTypeCOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_restype ( core::Size  ires) const
inline
core::pose::PoseCOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ref_pose ( ) const
inline
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 ( )
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::initialize ( core::pose::PoseCOP  pose,
core::Size  ligid,
utility::vector1< core::Size movingscs 
)
bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::is_ligand_terminal ( ) const
inline
core::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_id ( ) const
inline
core::conformation::Residue protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_residue ( ) const
core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_rg ( ) const
inline
std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename ( ) const
inline
utility::vector1< core::Vector > const & protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_xyz ( )
utility::vector1< core::Size > const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs ( ) const
inline
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
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize ( core::Real  transmax)
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
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::score ( core::Real  scorein)
inline
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
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
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_protein_restype ( core::Size  ires,
core::chemical::ResidueTypeCOP  restype 
)
inline
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
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)
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose ( core::pose::PoseOP  pose,
LigandConformer minilig 
) const
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose ( core::pose::PoseOP  pose) const
std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_string ( ) const
numeric::xyzVector< core::Real > const protocols::ligand_docking::ga_ligand_dock::LigandConformer::trans ( ) const
inline
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf ( core::pose::PoseCOP  pose)
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf_from_minipose ( core::pose::PoseCOP  pose)

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
std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename_
private
utility::vector1< utility::vector1< core::Size > > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandchi_downstream_
private
utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandchis_
private
utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandnus_
private
utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandtaus_
private
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
core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligchimutWidth_
private
core::Size protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligid_
private
utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::LigandConformer::movingscs_
private
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
utility::vector1< core::chemical::ResidueTypeCOP > protocols::ligand_docking::ga_ligand_dock::LigandConformer::proteinrestypes_
private
utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::LigandConformer::rb_
private
core::pose::PoseCOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::ref_pose_
private
core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::rg_
private
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
core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::rtmutationRate_
private
bool protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_ring_conformers_
private
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
core::Real protocols::ligand_docking::ga_ligand_dock::LigandConformer::transmutWidth_
private

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