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, utility::vector1< core::Size > const &ligids, std::string method="MCEntropy")

	~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::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, 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 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::pose::Pose const &pose, utility::vector1< core::Real > &chis, bool const &ligonly) 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

core::Real	MCEntropy (core::pose::Pose const &pose) const

core::Real	SimpleEntropy (core::pose::Pose const &pose) const

Private Attributes
std::string	method_

utility::vector1< core::Size >	ligids_

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< std::pair< int, int > >	chimapping_

utility::vector1< std::pair< int, int > >	ligpose_chimapping_

utility::vector1< core::Real >	chiweights_

core::Size	jumpid_

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

◆ EntropyEstimator()

protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::EntropyEstimator	(	core::scoring::ScoreFunctionOP	sfxn,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	ligids,
		std::string	method = `"MCEntropy"`
	)

References core::pose::Pose::fold_tree(), get_chi_weight(), core::kinematics::FoldTree::get_jump_edges(), jumpid_, and ligids_.

◆ ~EntropyEstimator()

protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::~EntropyEstimator ( )

inline

Member Function Documentation

◆ analyze_trajectory()

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::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 chimapping_, 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, ligpose_chimapping_, core::conformation::Residue::name(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::recchis, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::element::S, and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by estimate_Stors().

◆ apply()

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply ( core::pose::Pose const & pose ) const

References MCEntropy(), method_, SimpleEntropy(), and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

◆ chis2rotid()

core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::chis2rotid ( utility::vector1< core::Real > const & chis ) const

private

Referenced by analyze_trajectory().

◆ estimate_Stors()

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::estimate_Stors	(	core::pose::Pose	pose,
		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::comparative_modeling::features::E, protocols::ligand_docking::ga_ligand_dock::ChiInfo::E, get_temperature(), iter_collect_begin_, jumpid_, protocols::ligand_docking::ga_ligand_dock::ChiInfo::ligchis, ligids_, minimize_, niter_, perturb(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::recchis, core::scoring::rg, sample_every_iter_, sfxn_, update_chis(), and update_flexscs().

Referenced by MCEntropy().

◆ get_chi_weight()

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(), chimapping_, chiweights_, core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), ligids_, ligpose_chimapping_, protocols::mean_field::min(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::omega(), core::scoring::omega, core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), weighted_, protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by EntropyEstimator().

◆ get_contacting_reslist()

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(), protocols::membrane::com(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::is_proton_chi(), ligids_, protocols::mean_field::min(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by setup_trj().

◆ get_temperature()

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().

◆ MCEntropy()

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::MCEntropy ( core::pose::Pose const & pose ) const

private

References core::pose::addVirtualResAsRoot(), core::pose::Pose::delete_residue_slow(), estimate_Stors(), ligids_, niter_, core::pose::Pose::residue(), run_apostate_, run_holostate_, setup_trj(), temp_f_, protocols::ligand_docking::ga_ligand_dock::TR(), wRG_, and wtors_.

Referenced by apply().

◆ perturb()

void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::perturb	(	core::pose::Pose &	pose,
		core::Size const	nligchi,
		utility::vector1< core::Size > const &	flexscs,
		bool &	pert_ligand
	)		const

private

main perturb function in MC

References core::pose::Pose::chi(), ligpose_chimapping_, maxpert_, core::conformation::Residue::nchi(), core::pose::Pose::omega(), P_randomize_, core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by estimate_Stors().

◆ set_niter()

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::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

◆ setup_trj()

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 chimapping_, get_contacting_reslist(), protocols::ligand_docking::ga_ligand_dock::ChiInfo::ligchis, ligids_, protocols::ligand_docking::ga_ligand_dock::ChiInfo::recchis, update_chis(), and update_flexscs().

Referenced by MCEntropy().

◆ SimpleEntropy()

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::SimpleEntropy ( core::pose::Pose const & pose ) const

private

References core::chemical::ResidueType::is_proton_chi(), ligids_, core::conformation::Residue::nchi(), core::pose::Pose::residue(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::type().

Referenced by apply().

◆ update_chis()

void protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::update_chis	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	chis,
		bool const &	ligonly
	)		const

private

perturb ligand chis

References core::pose::Pose::chi(), chimapping_, ligpose_chimapping_, core::pose::Pose::omega(), core::pose::Pose::phi(), and core::pose::Pose::psi().

Referenced by estimate_Stors(), and setup_trj().

◆ update_flexscs()

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

◆ chimapping_

utility::vector1< std::pair< int, int > > protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::chimapping_

private

Referenced by analyze_trajectory(), get_chi_weight(), setup_trj(), and update_chis().

◆ chiweights_

utility::vector1< core::Real > protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::chiweights_

private

Referenced by analyze_trajectory(), and get_chi_weight().

◆ iter_collect_begin_

core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::iter_collect_begin_

private

Referenced by estimate_Stors().

◆ jumpid_

core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::jumpid_

private

Referenced by EntropyEstimator(), and estimate_Stors().

◆ ligids_

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

private

Referenced by EntropyEstimator(), estimate_Stors(), get_chi_weight(), get_contacting_reslist(), MCEntropy(), setup_trj(), and SimpleEntropy().

◆ ligpose_chimapping_

utility::vector1< std::pair< int, int > > protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::ligpose_chimapping_

private

Referenced by analyze_trajectory(), get_chi_weight(), perturb(), and update_chis().

◆ maxpert_

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::maxpert_

private

Referenced by perturb().

◆ method_

std::string protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::method_

private

Referenced by apply().

◆ minimize_

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

private

Referenced by estimate_Stors().

◆ niter_

core::Size protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::niter_

private

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

◆ P_randomize_

core::Real protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::P_randomize_

private

Referenced by perturb().

◆ run_apostate_

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

private

Referenced by MCEntropy().

◆ run_holostate_

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

private

Referenced by MCEntropy().

◆ sample_every_iter_

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

private

Referenced by estimate_Stors().

◆ sfxn_

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

private

Referenced by estimate_Stors().

◆ temp_f_

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

private

Referenced by get_temperature(), and MCEntropy().

◆ temp_i_

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

private

Referenced by get_temperature().

◆ weighted_

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

private

Referenced by get_chi_weight().

◆ wRG_

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

private

Referenced by MCEntropy().

◆ wtors_

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

private

Referenced by MCEntropy().

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EntropyEstimator()

◆ ~EntropyEstimator()

Member Function Documentation

◆ analyze_trajectory()

◆ apply()

◆ chis2rotid()

◆ estimate_Stors()

◆ get_chi_weight()

◆ get_contacting_reslist()

◆ get_temperature()

◆ MCEntropy()

◆ perturb()

◆ set_niter()

◆ setup_trj()

◆ SimpleEntropy()

◆ update_chis()

◆ update_flexscs()

Member Data Documentation

◆ chimapping_

◆ chiweights_

◆ iter_collect_begin_

◆ jumpid_

◆ ligids_

◆ ligpose_chimapping_

◆ maxpert_

◆ method_

◆ minimize_

◆ niter_

◆ P_randomize_

◆ run_apostate_

◆ run_holostate_

◆ sample_every_iter_

◆ sfxn_

◆ temp_f_

◆ temp_i_

◆ weighted_

◆ wRG_

◆ wtors_