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core::scoring::MembranePotential Class Reference

Rosetta Membrane Low Resolution Scoring Methods. More...

#include <MembranePotential.hh>

Inheritance diagram for core::scoring::MembranePotential:
Inheritance graph
[legend]

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< Realmem_env_log6_
 Membrane Etable Data. More...
 
ObjexxFCL::FArray3D< Realmem_env_log10_
 
ObjexxFCL::FArray1D< Realmem_cbeta_den6_
 
ObjexxFCL::FArray1D< Realmem_cbeta_den12_
 
ObjexxFCL::FArray1D< Realmem_cbeta_2TM_den6_
 
ObjexxFCL::FArray1D< Realmem_cbeta_2TM_den12_
 
ObjexxFCL::FArray1D< Realmem_cbeta_4TM_den6_
 
ObjexxFCL::FArray1D< Realmem_cbeta_4TM_den12_
 
ObjexxFCL::FArray4D< Realmem_pair_log_
 
Real const cen_dist5_pad
 Centroid Database. More...
 
Real const cen_dist7_pad
 
Real const cen_dist10_pad
 
Real const cen_dist12_pad
 
Real const cen_dist5_pad_plus
 
Real const cen_dist7_pad_plus
 
Real const cen_dist10_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_dist7_pad_hinv
 
Real const cen_dist10_pad_hinv
 
Real const cen_dist12_pad_hinv
 
bool no_interpolate_Mpair_
 User Specified options for Scoring. More...
 
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

- Static Public Member Functions inherited from core::scoring::EnvPairPotential
static CenListInfo const & cenlist_from_pose (pose::Pose const &)
 
static CenListInfononconst_cenlist_from_pose (pose::Pose &)
 

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 ( )

Member Function Documentation

bool core::scoring::MembranePotential::check_spanning ( pose::Pose const &  pose,
Vector const &  normal,
Vector const &  center 
) const
private
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(), check_spanning(), core::pack::interaction_graph::debug, core::scoring::MembraneEmbed::depth(), core::chemical::element::F, 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(), protocols::mean_field::max(), 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_, protocols::mean_field::min(), core::scoring::EnvPairPotential::nonconst_cenlist_from_pose(), core::scoring::nonconst_MembraneEmbed_from_pose(), core::scoring::nonconst_MembraneTopology_from_pose(), protocols::simple_moves::bb_sampler::probability, core::pose::Pose::residue(), core::scoring::rg, rigid_perturb_vector(), rot_perturb_vector(), protocols::hybridization::score, score_normal_center(), search_memb_center(), search_memb_normal(), core::scoring::MembraneEmbed::set_center(), core::scoring::MembraneEmbed::set_normal(), core::pose::Pose::size(), core::scoring::MembraneEmbed::spanning(), core::scoring::TR(), protocols::kinmatch::xyz(), and core::conformation::Atom::xyz().

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_embed(), 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
void core::scoring::MembranePotential::evaluate_env ( pose::Pose const &  pose,
conformation::Residue const &  rsd,
Real const  MembraneDepth,
Real membrane_env_score 
) const
void core::scoring::MembranePotential::evaluate_env ( pose::Pose const &  pose,
conformation::Residue const &  rsd,
Real membrane_env_score 
) const
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
void core::scoring::MembranePotential::init_membrane_center_normal ( pose::Pose const &  pose,
Vector normal,
Vector center 
) const
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
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
void core::scoring::MembranePotential::rigid_perturb_vector ( Vector v,
Real const &  std_dev 
) const
private

Randomnly Translate Vector.

References protocols::hybridization::u.

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 protocols::hybridization::u.

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
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 protocols::hybridization::u.

Referenced by compute_membrane_embedding().

void core::scoring::MembranePotential::termini_penalty ( pose::Pose const &  pose,
Real termini_penalty 
) const
void core::scoring::MembranePotential::termini_penalty ( pose::Pose const &  pose,
Vector const &  normal,
Vector const &  center,
Real termin_penalty 
) const
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 core::conformation::membrane::center, core::scoring::MembraneEmbed_from_pose(), Menv_penalties_, and core::conformation::membrane::normal.

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

Member Data Documentation

Real const core::scoring::MembranePotential::cen_dist10_pad
private
Real const core::scoring::MembranePotential::cen_dist10_pad_hinv
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist10_pad_minus
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist10_pad_plus
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist12_pad
private
Real const core::scoring::MembranePotential::cen_dist12_pad_hinv
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist12_pad_minus
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist5_pad
private

Centroid Database.

Real const core::scoring::MembranePotential::cen_dist5_pad_hinv
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist5_pad_minus
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist5_pad_plus
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist7_pad
private
Real const core::scoring::MembranePotential::cen_dist7_pad_hinv
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist7_pad_minus
private

Referenced by evaluate_pair().

Real const core::scoring::MembranePotential::cen_dist7_pad_plus
private

Referenced by evaluate_pair().

ObjexxFCL::FArray1D< Real > core::scoring::MembranePotential::mem_cbeta_2TM_den12_
private

Referenced by MembranePotential().

ObjexxFCL::FArray1D< Real > core::scoring::MembranePotential::mem_cbeta_2TM_den6_
private
ObjexxFCL::FArray1D< Real > core::scoring::MembranePotential::mem_cbeta_4TM_den12_
private

Referenced by MembranePotential().

ObjexxFCL::FArray1D< Real > core::scoring::MembranePotential::mem_cbeta_4TM_den6_
private
ObjexxFCL::FArray1D< Real > core::scoring::MembranePotential::mem_cbeta_den12_
private
ObjexxFCL::FArray1D< Real > core::scoring::MembranePotential::mem_cbeta_den6_
private
ObjexxFCL::FArray3D< Real > core::scoring::MembranePotential::mem_env_log10_
private

Referenced by evaluate_env(), and MembranePotential().

ObjexxFCL::FArray3D< Real > core::scoring::MembranePotential::mem_env_log6_
private

Membrane Etable Data.

Referenced by evaluate_env(), and MembranePotential().

ObjexxFCL::FArray4D< Real > core::scoring::MembranePotential::mem_pair_log_
private

Referenced by evaluate_pair(), and MembranePotential().

bool core::scoring::MembranePotential::memb_center_search_
private
bool core::scoring::MembranePotential::memb_normal_search_
private
bool core::scoring::MembranePotential::Membed_init_
private
Real core::scoring::MembranePotential::membrane_center_magnitude_
private
Size core::scoring::MembranePotential::membrane_center_max_delta_
private

MCM Search Parameters for normal/embed caluclations.

Referenced by compute_membrane_embedding(), and MembranePotential().

Size core::scoring::MembranePotential::membrane_normal_cycles_
private
Size core::scoring::MembranePotential::membrane_normal_delta_angle_
private
Real core::scoring::MembranePotential::membrane_normal_magnitude_
private
Size core::scoring::MembranePotential::membrane_normal_max_angle_
private
Size core::scoring::MembranePotential::membrane_normal_start_angle_
private
bool core::scoring::MembranePotential::Menv_penalties_
private
bool core::scoring::MembranePotential::no_interpolate_Mpair_
private

User Specified options for Scoring.

Referenced by evaluate_pair(), and MembranePotential().

Real core::scoring::MembranePotential::smooth_move_frac_
private

Referenced by MembranePotential().


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