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protocols::ligand_docking::ga_ligand_dock::EntropyEstimator Class Reference

Estimates entropy change by ligand binding using short MC simulation. More...

#include <EntropyEstimator.hh>

Public Member Functions

 EntropyEstimator (core::scoring::ScoreFunctionOP sfxn, core::pose::Pose const &pose, core::Size const ligid)
 
 ~EntropyEstimator ()
 
core::Real apply (core::pose::Pose const &pose) const
 
void set_niter (core::Size setting)
 

Private Member Functions

void get_chi_weight (core::pose::Pose const &pose_ref)
 Estimates per-chiangle weights used for per-chiangle-weighted entropy estimation mode. More...
 
core::Real analyze_trajectory (utility::vector1< ChiInfo > const &chitrj, core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > const &chidefs, core::Size const ligid, core::Real const Emin, core::Real const RT, bool const run_on_ligand, bool const run_on_receptor) const
 torsion entropy calculation function inside estimate_Stors More...
 
core::Real estimate_Stors (core::pose::Pose pose, core::Size const ligid, utility::vector1< ChiInfo > &chitrj, utility::vector1< core::Size > const &flexscs, utility::vector1< std::pair< core::Size, core::Size > > const &chidefs, bool const run_on_ligand, bool const run_on_receptor) const
 Runs MC and returns torsion entropy change. More...
 
void perturb (core::pose::Pose &pose, core::Size const ligid, core::Size const nligchi, utility::vector1< core::Size > const &flexscs, bool &pert_ligand) const
 main perturb function in MC More...
 
utility::vector1< ChiInfosetup_trj (core::pose::Pose const &pose, utility::vector1< core::Size > &flexscs, utility::vector1< std::pair< core::Size, core::Size > > &chidefs) const
 initialize MC trj datastructure More...
 
utility::vector1< core::Sizeget_contacting_reslist (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > &chidefs) const
 get list of sidechains contacting to ligand More...
 
core::Real get_temperature (core::Size const it) const
 
void update_chis (core::conformation::Residue const &rsd, utility::vector1< core::Real > &chis) const
 perturb ligand chis More...
 
void update_flexscs (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > const &chidefs, std::map< core::Size, utility::vector1< core::Real > > &chis) const
 perturb receptor sidechains More...
 
core::Size chis2rotid (utility::vector1< core::Real > const &chis) const
 

Private Attributes

core::Size ligid_
 
core::scoring::ScoreFunctionOP sfxn_
 
core::Real run_apostate_
 
core::Real run_holostate_
 
core::Real P_randomize_
 
core::Real maxpert_
 
bool minimize_
 
core::Size sample_every_iter_
 
core::Real temp_i_
 
core::Real temp_f_
 
core::Size niter_
 
core::Size iter_collect_begin_
 
core::Real wRG_
 
core::Real wtors_
 
bool weighted_
 
utility::vector1< core::Sizechiweights_
 

Detailed Description

Estimates entropy change by ligand binding using short MC simulation.

This class takes a full complex pose and ligand seqpos index to calculate entropy change upon ligand binding. MC simulation perturbs chi angles defined for the ligand at free state, and estimates effective entropy loss by binding by processing torsion probability during simulation assuming that ligand gets completely after binding.

Constructor & Destructor Documentation

protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::EntropyEstimator ( core::scoring::ScoreFunctionOP  sfxn,
core::pose::Pose const &  pose,
core::Size const  ligid 
)
protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::~EntropyEstimator ( )
inline

Member Function Documentation

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory ( utility::vector1< ChiInfo > const &  chitrj,
core::pose::Pose const &  pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  chidefs,
core::Size const  ligid,
core::Real const  Emin,
core::Real const  RT,
bool const  run_on_ligand,
bool const  run_on_receptor 
) const
private
core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply ( core::pose::Pose const &  pose) const
core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::chis2rotid ( utility::vector1< core::Real > const &  chis) const
private

Referenced by analyze_trajectory().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::estimate_Stors ( core::pose::Pose  pose,
core::Size const  ligid,
utility::vector1< ChiInfo > &  chitrj,
utility::vector1< core::Size > const &  flexscs,
utility::vector1< std::pair< core::Size, core::Size > > const &  chidefs,
bool const  run_on_ligand,
bool const  run_on_receptor 
) const
private
void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight ( core::pose::Pose const &  pose_ref)
private
utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist ( core::pose::Pose const &  pose,
utility::vector1< std::pair< core::Size, core::Size > > &  chidefs 
) const
private
core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_temperature ( core::Size const  it) const
private

References niter_, temp_f_, and temp_i_.

Referenced by estimate_Stors().

void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::perturb ( core::pose::Pose pose,
core::Size const  ligid,
core::Size const  nligchi,
utility::vector1< core::Size > const &  flexscs,
bool pert_ligand 
) const
private
void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::set_niter ( core::Size  setting)
inline
utility::vector1< ChiInfo > protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::setup_trj ( core::pose::Pose const &  pose,
utility::vector1< core::Size > &  flexscs,
utility::vector1< std::pair< core::Size, core::Size > > &  chidefs 
) const
private
void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::update_chis ( core::conformation::Residue const &  rsd,
utility::vector1< core::Real > &  chis 
) const
private

perturb ligand chis

References core::conformation::Residue::chi().

Referenced by estimate_Stors(), and setup_trj().

void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::update_flexscs ( core::pose::Pose const &  pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  chidefs,
std::map< core::Size, utility::vector1< core::Real > > &  chis 
) const
private

perturb receptor sidechains

References core::conformation::Residue::chi(), and core::pose::Pose::residue().

Referenced by estimate_Stors(), and setup_trj().

Member Data Documentation

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::chiweights_
private
core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::iter_collect_begin_
private

Referenced by estimate_Stors().

core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::ligid_
private
core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::maxpert_
private

Referenced by perturb().

bool protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::minimize_
private

Referenced by estimate_Stors().

core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::niter_
private
core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::P_randomize_
private

Referenced by perturb().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::run_apostate_
private

Referenced by apply().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::run_holostate_
private

Referenced by apply().

core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::sample_every_iter_
private

Referenced by estimate_Stors().

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::sfxn_
private

Referenced by estimate_Stors().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::temp_f_
private

Referenced by apply(), and get_temperature().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::temp_i_
private

Referenced by get_temperature().

bool protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::weighted_
private

Referenced by get_chi_weight().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::wRG_
private

Referenced by apply().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::wtors_
private

Referenced by apply().


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