Rosetta Membrane Low Resolution Scoring Methods. More...

#include <MembranePotential.hh>

Public Member Functions
	MembranePotential ()
	Default Constructor. More...

void	evaluate_env (pose::Pose const &pose, conformation::Residue const &rsd, Real const MembraneDepth, Real &membrane_env_score) const
	Evalaute Membrane Environment. More...

void	evaluate_env (pose::Pose const &pose, conformation::Residue const &rsd, Real &membrane_env_score) const
	Evaluate Membrane Environment Term (by residue) More...

void	evaluate_cbeta (pose::Pose const &pose, conformation::Residue const &rsd, Real &membrane_cb_score) const
	Evaluate CBeta Score (no idea...?) More...

void	evaluate_pair (pose::Pose const &pose, conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &membrane_pair_score) const
	Evaluate Energy For Two Residues. More...

virtual void	finalize (pose::Pose &pose) const
	I think these methods should be private ///. More...

void	compute_membrane_embedding (pose::Pose &pose) const
	Compute Membrane Embedding from pose and add Membed to Pose Cache. More...

void	init_membrane_center_normal (pose::Pose const &pose, Vector &normal, Vector &center) const
	Initialize Membrane Center/Normal. More...

void	tm_projection_penalty (pose::Pose const &pose, Real &tm_proj) const
	Compute Transmembrane Spanning Projection Penalty (documentation for what this is - se MP potential from refactor) More...

void	tm_projection_penalty (pose::Pose const &pose, Vector const &normal, Vector const &center, Real &tm_proj) const

void	non_helix_in_membrane_penalty (pose::Pose const &pose, Real &non_helix_in_membrane_penalty) const
	Compute penaly for alpha helices that are not tm spanning. More...

void	non_helix_in_membrane_penalty (pose::Pose const &pose, Vector const &normal, Vector const &center, Real &non_helix_in_membrane_penalty) const

void	termini_penalty (pose::Pose const &pose, Real &termini_penalty) const
	Compute penalty for ??? More...

void	termini_penalty (pose::Pose const &pose, Vector const &normal, Vector const &center, Real &termin_penalty) const

bool	Menv_penalties () const
	User Specified use penalties. More...

bool	Membed_init () const
	Initialize Membrane Embedding. More...

Public Member Functions inherited from core::scoring::EnvPairPotential
	EnvPairPotential ()

void	compute_centroid_environment (pose::Pose &pose) const

void	finalize (pose::Pose &pose) const

void	evaluate_env_and_cbeta_scores (pose::Pose const &pose, conformation::Residue const &rsd, Real &env_score, Real &cb_score6, Real &cb_score12) const

void	evaluate_pair_and_cenpack_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &pair_contribution, Real &cenpack_contribution) const

Private Member Functions
void	score_normal_center (pose::Pose const &pose, Vector const &normal, Vector const &center, Real &score) const
	Score normal and center with environment score. More...

void	search_memb_normal (Vector &n, Real const &alpha, Real const &theta) const
	Helper function to determine normal vector. More...

void	search_memb_center (Vector &c, Vector &n, Real const &delta) const
	Helper function to determine membrane center. More...

void	rot_perturb_vector (Vector &v, Real const &std_dev) const
	Randomnly Rotate Vector. More...

void	rigid_perturb_vector (Vector &v, Real const &std_dev) const
	Randomnly Translate Vector. More...

bool	check_spanning (pose::Pose const &pose, Vector const &normal, Vector const &center) const
	Check Spanning ( should use new adapted check spanning in metrics or geom) More...

Private Attributes
ObjexxFCL::FArray3D< Real >	mem_env_log6_
	Membrane Etable Data. More...

ObjexxFCL::FArray3D< Real >	mem_env_log10_

ObjexxFCL::FArray1D< Real >	mem_cbeta_den6_

ObjexxFCL::FArray1D< Real >	mem_cbeta_den12_

ObjexxFCL::FArray1D< Real >	mem_cbeta_2TM_den6_

ObjexxFCL::FArray1D< Real >	mem_cbeta_2TM_den12_

ObjexxFCL::FArray1D< Real >	mem_cbeta_4TM_den6_

ObjexxFCL::FArray1D< Real >	mem_cbeta_4TM_den12_

ObjexxFCL::FArray4D< Real >	mem_pair_log_

Real const	cen_dist5_pad
	Centroid Database. More...

Real const	cen_dist6_pad

Real const	cen_dist7_pad

Real const	cen_dist10_pad

Real const	cen_dist12_pad

Real const	cen_dist5_pad_plus

Real const	cen_dist6_pad_plus

Real const	cen_dist7_pad_plus

Real const	cen_dist10_pad_plus

Real const	cen_dist12_pad_plus

Real const	cen_dist5_pad_minus

Real const	cen_dist7_pad_minus

Real const	cen_dist10_pad_minus

Real const	cen_dist12_pad_minus

Real const	cen_dist5_pad_hinv

Real const	cen_dist6_pad_hinv

Real const	cen_dist7_pad_hinv

Real const	cen_dist10_pad_hinv

Real const	cen_dist12_pad_hinv

bool	calculated_
	User Specified options for Scoring. More...

bool	no_interpolate_Mpair_

bool	Menv_penalties_

bool	Membed_init_

bool	memb_center_search_

bool	memb_normal_search_

Size	membrane_center_max_delta_
	MCM Search Parameters for normal/embed caluclations. More...

Size	membrane_normal_start_angle_

Size	membrane_normal_delta_angle_

Size	membrane_normal_max_angle_

Size	membrane_normal_cycles_

Real	membrane_normal_magnitude_

Real	membrane_center_magnitude_

Real	smooth_move_frac_

Additional Inherited Members
Protected Member Functions inherited from core::scoring::EnvPairPotential
CenListInfo const &	cenlist_from_pose (pose::Pose const &) const

CenListInfo &	nonconst_cenlist_from_pose (pose::Pose &) const

Protected Attributes inherited from core::scoring::EnvPairPotential
Real const	cen_dist_cutoff2

Detailed Description

Rosetta Membrane Low Resolution Scoring Methods.

Compute scoring terms part of the Membrane Low resolution energy function. Developed by Vladmir Yarov-Yaravoy et al. 2006. Includes Menv, MPair, MCBeta, and membrane alpha helical specific penalties. Framework tied.

Constructor & Destructor Documentation

core::scoring::MembranePotential::MembranePotential ( )

Default Constructor.

Construct a Membrane Potential Object - Acts as the base layer for membrane protein scoring.

Member Function Documentation

bool core::scoring::MembranePotential::check_spanning	(	pose::Pose const &	pose,
		Vector const &	normal,
		Vector const &	center
	)		const

private

Check Spanning ( should use new adapted check spanning in metrics or geom)

Should get replaced with the refactored check spanning in metrics.

References core::scoring::MembraneTopology::allow_tmh_scoring(), dot(), core::scoring::MembraneTopology::helix_id(), j, core::scoring::MembraneTopology_from_pose(), core::pose::Pose::residue(), core::scoring::MembraneTopology::span_begin(), core::scoring::MembraneTopology::tmhelix(), and core::conformation::Residue::xyz().

Referenced by compute_membrane_embedding().

void core::scoring::MembranePotential::compute_membrane_embedding ( pose::Pose & pose ) const

Compute Membrane Embedding from pose and add Membed to Pose Cache.

References core::conformation::Residue::atom(), core::scoring::MembraneEmbed::calculated(), center_mag, check_spanning(), cycles, core::pack::interaction_graph::debug, core::scoring::MembraneEmbed::depth(), dot(), basic::options::OptionKeys::membrane::fixed_membrane, init_membrane_center_normal(), core::scoring::MembraneTopology::initialize(), core::scoring::MembraneEmbed::initialize(), core::scoring::CenListInfo::initialize(), core::scoring::MembraneTopology::initialized(), core::pose::symmetry::is_symmetric(), memb_center_search_, memb_normal_search_, Membed_init_, membrane_center_magnitude_, membrane_center_max_delta_, membrane_normal_cycles_, membrane_normal_delta_angle_, membrane_normal_magnitude_, membrane_normal_max_angle_, membrane_normal_start_angle_, core::scoring::EnvPairPotential::nonconst_cenlist_from_pose(), core::scoring::nonconst_MembraneEmbed_from_pose(), core::scoring::nonconst_MembraneTopology_from_pose(), normal_mag, nres, basic::options::option, option, core::pose::Pose::residue(), RG, rigid_perturb_vector(), rot_perturb_vector(), score, score_normal_center(), search_memb_center(), search_memb_normal(), core::scoring::MembraneEmbed::set_center(), core::scoring::MembraneEmbed::set_normal(), spanfile, in::file::spanfile, core::scoring::MembraneEmbed::spanning(), temperature, core::pose::Pose::total_residue(), core::scoring::TR, numeric::random::RandomGenerator::uniform(), user, numeric::xyzVector< class >::x(), xyz, core::conformation::Atom::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::methods::MembraneCenPairEnergy::setup_for_scoring(), and core::scoring::methods::MembraneEnvEnergy::setup_for_scoring().

void core::scoring::MembranePotential::evaluate_cbeta	(	pose::Pose const &	pose,
		conformation::Residue const &	rsd,
		Real &	membrane_cb_score
	)		const

Evaluate CBeta Score (no idea...?)

References core::scoring::EnvPairPotential::cenlist_from_pose(), core::scoring::electron_density::SplineInterp::interp3(), core::scoring::electron_density::SplineInterp::interp4(), mem_cbeta_2TM_den6_, mem_cbeta_4TM_den6_, mem_cbeta_den12_, mem_cbeta_den6_, core::scoring::MembraneTopology_from_pose(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::methods::MembraneCbetaEnergy::residue_energy().

void core::scoring::MembranePotential::evaluate_env	(	pose::Pose const &	pose,
		conformation::Residue const &	rsd,
		Real const	MembraneDepth,
		Real &	membrane_env_score
	)		const

Evalaute Membrane Environment.

Full Evaluate Membrane Env Method (given depth and const menv score)

References core::conformation::Residue::aa(), core::scoring::EnvPairPotential::cenlist_from_pose(), core::conformation::Residue::is_protein(), layer, mem_env_log10_, mem_env_log6_, s2, and core::conformation::Residue::seqpos().

Referenced by evaluate_env(), core::scoring::methods::MembraneEnvEnergy::residue_energy(), and score_normal_center().

void core::scoring::MembranePotential::evaluate_env	(	pose::Pose const &	pose,
		conformation::Residue const &	rsd,
		Real &	membrane_env_score
	)		const

Evaluate Membrane Environment Term (by residue)

References center(), depth, dot(), evaluate_env(), core::scoring::MembraneEmbed_from_pose(), Menv_penalties_, core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::pose::Pose::total_residue(), xyz, and core::conformation::Residue::xyz().

void core::scoring::MembranePotential::evaluate_pair	(	pose::Pose const &	pose,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Real const	cendist,
		Real &	membrane_pair_score
	)		const

void core::scoring::MembranePotential::finalize ( pose::Pose & pose ) const

virtual

I think these methods should be private ///.

Fianlize Setup of MP Scoring.

Finalize Setup of MP Potential Class

References core::scoring::MembraneEmbed::calculated(), core::scoring::CenListInfo::calculated(), core::scoring::EnvPairPotential::nonconst_cenlist_from_pose(), and core::scoring::nonconst_MembraneEmbed_from_pose().

Referenced by core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::methods::MembraneEnvPenalties::finalize_total_energy(), core::scoring::methods::MembraneCbetaEnergy::finalize_total_energy(), core::scoring::methods::MembraneCenPairEnergy::finalize_total_energy(), and core::scoring::methods::MembraneEnvEnergy::finalize_total_energy().

void core::scoring::MembranePotential::init_membrane_center_normal	(	pose::Pose const &	pose,
		Vector &	normal,
		Vector &	center
	)		const

Initialize Membrane Center/Normal.

Initialize Membrane Center and Normal parameters (from starting params)

References core::scoring::MembraneTopology::allow_tmh_scoring(), core::sequence::end, basic::options::OptionKeys::membrane::fixed_membrane, core::scoring::MembraneTopology::helix_id(), basic::options::OptionKeys::membrane::membrane_center, basic::options::OptionKeys::membrane::membrane_normal, core::scoring::MembraneTopology_from_pose(), numeric::xyzVector< class >::normalize(), basic::options::option, core::pose::Pose::residue(), core::scoring::MembraneTopology::span_begin(), core::scoring::MembraneTopology::span_end(), start, core::scoring::MembraneTopology::tmh_inserted(), core::scoring::MembraneTopology::tmhelix(), user, numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), numeric::xyzVector< class >::z(), and numeric::xyzVector< class >::zero().

Referenced by compute_membrane_embedding().

bool core::scoring::MembranePotential::Membed_init ( ) const

inline

Initialize Membrane Embedding.

References Membed_init_.

bool core::scoring::MembranePotential::Menv_penalties ( ) const

inline

User Specified use penalties.

References Menv_penalties_.

Referenced by core::scoring::methods::MembraneEnvPenalties::finalize_total_energy().

void core::scoring::MembranePotential::non_helix_in_membrane_penalty	(	pose::Pose const &	pose,
		Real &	non_helix_in_membrane_penalty
	)		const

Compute penaly for alpha helices that are not tm spanning.

References center(), core::scoring::MembraneEmbed_from_pose(), and Menv_penalties_.

Referenced by core::scoring::methods::MembraneEnvPenalties::finalize_total_energy(), and score_normal_center().

void core::scoring::MembranePotential::non_helix_in_membrane_penalty	(	pose::Pose const &	pose,
		Vector const &	normal,
		Vector const &	center,
		Real &	non_helix_in_membrane_penalty
	)		const

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::MembraneTopology::allow_scoring(), core::conformation::Residue::atom(), core::pose::Pose::conformation(), depth, dot(), core::pose::symmetry::is_symmetric(), core::scoring::MembraneTopology_from_pose(), Menv_penalties_, core::pose::Pose::residue(), core::conformation::Conformation::secstruct(), core::conformation::Residue::seqpos(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::scoring::MembraneTopology::tmregion(), core::pose::Pose::total_residue(), xyz, and core::conformation::Atom::xyz().

void core::scoring::MembranePotential::rigid_perturb_vector	(	Vector &	v,
		Real const &	std_dev
	)		const

private

Randomnly Translate Vector.

References numeric::random::gaussian(), and numeric::xyzVector< class >::normalize().

Referenced by compute_membrane_embedding().

void core::scoring::MembranePotential::rot_perturb_vector	(	Vector &	v,
		Real const &	std_dev
	)		const

private

Randomnly Rotate Vector.

Rotatate Vector (Helper method - randomnly perturb for normal search)

References numeric::random::gaussian(), and rotation_matrix().

Referenced by compute_membrane_embedding().

void core::scoring::MembranePotential::score_normal_center	(	pose::Pose const &	pose,
		Vector const &	normal,
		Vector const &	center,
		Real &	score
	)		const

private

Score normal and center with environment score.

Score Pose using MP Normal and Center.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::MembraneTopology::allow_scoring(), core::conformation::Residue::atom(), core::pose::Pose::conformation(), depth, dot(), evaluate_env(), core::pose::symmetry::is_symmetric(), core::scoring::MembraneTopology_from_pose(), Menv_penalties_, non_helix_in_membrane_penalty(), nres, core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), termini_penalty(), tm_projection_penalty(), core::pose::Pose::total_residue(), xyz, and core::conformation::Atom::xyz().

Referenced by compute_membrane_embedding().

void core::scoring::MembranePotential::search_memb_center	(	Vector &	c,
		Vector &	n,
		Real const &	delta
	)		const

private

Helper function to determine membrane center.

Search for the Membrane Center.

Referenced by compute_membrane_embedding().

void core::scoring::MembranePotential::search_memb_normal	(	Vector &	n,
		Real const &	alpha,
		Real const &	theta
	)		const

private

Helper function to determine normal vector.

Search for the Membrane Normal Parameter.

References numeric::conversions::radians(), and rotation_matrix_degrees().

Referenced by compute_membrane_embedding().

void core::scoring::MembranePotential::termini_penalty	(	pose::Pose const &	pose,
		Real &	termini_penalty
	)		const

Compute penalty for ???

References center(), core::scoring::MembraneEmbed_from_pose(), and Menv_penalties_.

Referenced by core::scoring::methods::MembraneEnvPenalties::finalize_total_energy(), and score_normal_center().

void core::scoring::MembranePotential::termini_penalty	(	pose::Pose const &	pose,
		Vector const &	normal,
		Vector const &	center,
		Real &	termin_penalty
	)		const

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::MembraneTopology::allow_scoring(), core::conformation::Residue::atom(), core::pose::Pose::conformation(), depth, dot(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_terminus(), core::scoring::MembraneTopology_from_pose(), Menv_penalties_, core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), xyz, and core::conformation::Atom::xyz().

void core::scoring::MembranePotential::tm_projection_penalty	(	pose::Pose const &	pose,
		Real &	tm_proj
	)		const

Compute Transmembrane Spanning Projection Penalty (documentation for what this is - se MP potential from refactor)

References center(), core::scoring::MembraneEmbed_from_pose(), and Menv_penalties_.

Referenced by core::scoring::methods::MembraneEnvPenalties::finalize_total_energy(), and score_normal_center().

void core::scoring::MembranePotential::tm_projection_penalty	(	pose::Pose const &	pose,
		Vector const &	normal,
		Vector const &	center,
		Real &	tm_proj
	)		const