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core::scoring::EnvPairPotential Class Reference

#include <EnvPairPotential.hh>

Inheritance diagram for core::scoring::EnvPairPotential:
Inheritance graph
Collaboration diagram for core::scoring::EnvPairPotential:
Collaboration graph

Public Member Functions

 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

Protected Member Functions

CenListInfo const & cenlist_from_pose (pose::Pose const &) const
CenListInfononconst_cenlist_from_pose (pose::Pose &) const

Protected Attributes

Real const cen_dist_cutoff2

Private Member Functions

void fill_cenlist (CenListInfo &cenlist, Size const res1, Size const res2, Real const cendist) const
 fill the cenlist using interpolation More...
void truncate_cenlist_values (CenListInfo &cenlist) const

Private Attributes

ObjexxFCL::FArray2D< Realenv_log_
ObjexxFCL::FArray1D< Realcbeta_den6_
ObjexxFCL::FArray1D< Realcbeta_den12_
ObjexxFCL::FArray3D< Realpair_log_
ObjexxFCL::FArray1D< Realcenpack_log_
Real const cen_dist6sqr_
Real const cen_dist10sqr_
Real const cen_dist12sqr_
Real const cen_dist5_pad
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
Real const cen_dist_cutoff_12_pad

Constructor & Destructor Documentation

core::scoring::EnvPairPotential::EnvPairPotential ( )

Member Function Documentation

CenListInfo const & core::scoring::EnvPairPotential::cenlist_from_pose ( pose::Pose const &  pose) const
void core::scoring::EnvPairPotential::compute_centroid_environment ( pose::Pose pose) const
void core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores ( pose::Pose const &  pose,
conformation::Residue const &  rsd,
Real env_score,
Real cb_score6,
Real cb_score12 
) const
void core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Real const  cendist,
Real pair_contribution,
Real cenpack_contribution 
) const
void core::scoring::EnvPairPotential::fill_cenlist ( CenListInfo cenlist,
Size const  res1,
Size const  res2,
Real const  cendist 
) const

fill the cenlist using interpolation

cems-----------------------------------------------------------------------— interpolation notes –Historically we have broken the centroid density statistics into three bins: i) pairs less than 6 angstroms ii) pairs less than 10 angstroms ems iii) and pairs between 6 and 12 angstroms the resulting abruptness in the scoring functions due to the arbitrary radius cutoffs has caused some problems during gradient minimization. therefore this was replaced with an interpolated binning schema as follows: When a pairwise distance lies within "+/- dr" of the bin boundary (6,10,12) then partial credit is given to the enclosing bins. So for example, if fgap=0.5 angstroms, and a pair radius were 6.4 angstroms, then a fractional count is given to BOTH the "less-than-6" bin AND to the "between-6-and-10" bin. The sum of these fractions always adds to one. So that we dont have to re-do the statistics we currently use we want to keep "fgap" small. ideally fgap should be large compared to the search algorithm step size, and larger than the expected roundoff error in any refold operation, and otherwise as small as possible. Also we want to cleverly choose the interpolation function so that the average number of counts getting into the bins is the same as under the old schema. As long as dr is small then we can use either r+/-fgap or alternatively r^2+/-fgap^2 and this will be approximately satsified. since the squared from is easier to work we will use this. in the code below the frag^2 term is called a _pad, and we allow for different pad_sizes on the three radii. cems-----------------------------------------------------------------------—

References cen_dist10_pad_hinv, cen_dist10_pad_plus, cen_dist12_pad_hinv, cen_dist12_pad_plus, cen_dist6_pad_hinv, cen_dist6_pad_plus, core::scoring::CenListInfo::fcen10(), core::scoring::CenListInfo::fcen12(), and core::scoring::CenListInfo::fcen6().

Referenced by compute_centroid_environment().

void core::scoring::EnvPairPotential::finalize ( pose::Pose pose) const
CenListInfo & core::scoring::EnvPairPotential::nonconst_cenlist_from_pose ( pose::Pose pose) const

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::datacache::CacheableDataType::CEN_LIST_INFO, and core::pose::Pose::data().

Referenced by compute_centroid_environment(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::scoring::InterchainPotential::finalize(), finalize(), core::scoring::MembranePotential::finalize(), and core::scoring::Membrane_FAPotential::finalize().

void core::scoring::EnvPairPotential::truncate_cenlist_values ( CenListInfo cenlist) const

Member Data Documentation

ObjexxFCL::FArray1D< Real > core::scoring::EnvPairPotential::cbeta_den12_
ObjexxFCL::FArray1D< Real > core::scoring::EnvPairPotential::cbeta_den6_
Real const core::scoring::EnvPairPotential::cen_dist10_pad
Real const core::scoring::EnvPairPotential::cen_dist10_pad_hinv
Real const core::scoring::EnvPairPotential::cen_dist10_pad_minus
Real const core::scoring::EnvPairPotential::cen_dist10_pad_plus
Real const core::scoring::EnvPairPotential::cen_dist10sqr_
Real const core::scoring::EnvPairPotential::cen_dist12_pad
Real const core::scoring::EnvPairPotential::cen_dist12_pad_hinv
Real const core::scoring::EnvPairPotential::cen_dist12_pad_minus
Real const core::scoring::EnvPairPotential::cen_dist12_pad_plus

Referenced by fill_cenlist().

Real const core::scoring::EnvPairPotential::cen_dist12sqr_
Real const core::scoring::EnvPairPotential::cen_dist5_pad
Real const core::scoring::EnvPairPotential::cen_dist5_pad_hinv
Real const core::scoring::EnvPairPotential::cen_dist5_pad_minus
Real const core::scoring::EnvPairPotential::cen_dist5_pad_plus
Real const core::scoring::EnvPairPotential::cen_dist6_pad
Real const core::scoring::EnvPairPotential::cen_dist6_pad_hinv

Referenced by fill_cenlist().

Real const core::scoring::EnvPairPotential::cen_dist6_pad_plus

Referenced by fill_cenlist().

Real const core::scoring::EnvPairPotential::cen_dist6sqr_
Real const core::scoring::EnvPairPotential::cen_dist7_pad
Real const core::scoring::EnvPairPotential::cen_dist7_pad_hinv
Real const core::scoring::EnvPairPotential::cen_dist7_pad_minus
Real const core::scoring::EnvPairPotential::cen_dist7_pad_plus
Real const core::scoring::EnvPairPotential::cen_dist_cutoff2
Real const core::scoring::EnvPairPotential::cen_dist_cutoff_12_pad
ObjexxFCL::FArray1D< Real > core::scoring::EnvPairPotential::cenpack_log_
ObjexxFCL::FArray2D< Real > core::scoring::EnvPairPotential::env_log_
ObjexxFCL::FArray3D< Real > core::scoring::EnvPairPotential::pair_log_

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