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< ChiInfo >	setup_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::Size >	get_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::Size >	chiweights_

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
	)

References get_chi_weight(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

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

torsion entropy calculation function inside estimate_Stors

References core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::chi_atoms(), chis2rotid(), chiweights_, protocols::ligand_docking::ga_ligand_dock::ChiInfo::E, core::chemical::element::F, core::chemical::element::I, core::chemical::ResidueType::is_proton_chi(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::ligchis, core::conformation::Residue::name(), core::chemical::ResidueType::nchi(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::recchis, core::pose::Pose::residue(), core::chemical::element::S, and core::conformation::Residue::type().

Referenced by estimate_Stors().

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply

(

core::pose::Pose const &

pose

)

const

References core::pose::addVirtualResAsRoot(), core::pose::Pose::delete_residue_slow(), estimate_Stors(), ligid_, niter_, core::pose::Pose::residue(), run_apostate_, run_holostate_, setup_trj(), core::pose::Pose::size(), temp_f_, wRG_, and wtors_.

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

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

Runs MC and returns torsion entropy change.

References analyze_trajectory(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::E, protocols::comparative_modeling::features::E, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), get_temperature(), iter_collect_begin_, protocols::ligand_docking::ga_ligand_dock::ChiInfo::ligchis, minimize_, niter_, perturb(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::recchis, core::pose::Pose::residue(), core::scoring::rg, sample_every_iter_, sfxn_, core::pose::Pose::size(), update_chis(), and update_flexscs().

Referenced by apply().

void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight ( core::pose::Pose const &  pose_ref )

private

Estimates per-chiangle weights used for per-chiangle-weighted entropy estimation mode.

References core::conformation::Residue::chi(), chiweights_, ligid_, core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::set_chi(), weighted_, protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by EntropyEstimator().

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

get list of sidechains contacting to ligand

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::is_proton_chi(), ligid_, core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by setup_trj().

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

main perturb function in MC

References core::conformation::Residue::chi(), maxpert_, core::conformation::Residue::nchi(), P_randomize_, core::pose::Pose::residue(), core::scoring::rg, and core::pose::Pose::set_chi().

Referenced by estimate_Stors().

void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::set_niter ( core::Size  setting )

inline

References niter_.

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

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

initialize MC trj datastructure

References get_contacting_reslist(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::ligchis, ligid_, core::conformation::Residue::nchi(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::recchis, core::pose::Pose::residue(), update_chis(), and update_flexscs().

Referenced by apply().

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

Referenced by analyze_trajectory(), and get_chi_weight().

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

Referenced by apply(), get_chi_weight(), get_contacting_reslist(), and setup_trj().

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

Referenced by apply(), estimate_Stors(), get_temperature(), and set_niter().

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:

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