#include <EnvPairPotential.hh>
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 |
Static Public Member Functions | |
| static CenListInfo const & | cenlist_from_pose (pose::Pose const &) |
| static CenListInfo & | nonconst_cenlist_from_pose (pose::Pose &) |
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 | |
| Real const | cen_dist_cutoff2 |
| ObjexxFCL::FArray2D< Real > | env_log_ |
| ObjexxFCL::FArray1D< Real > | cbeta_den6_ |
| ObjexxFCL::FArray1D< Real > | cbeta_den12_ |
| ObjexxFCL::FArray3D< Real > | pair_log_ |
| ObjexxFCL::FArray1D< Real > | cenpack_log_ |
| 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
◆ EnvPairPotential()
| core::scoring::EnvPairPotential::EnvPairPotential | ( | ) |
References protocols::cluster::calibur::aa, cbeta_den12_, cbeta_den6_, cenpack_log_, env_log_, and pair_log_.
Member Function Documentation
◆ cenlist_from_pose()
|
static |
Pose must already contain a cenlist object or this method will fail.
References core::pose::Pose::data().
Referenced by protocols::simple_moves::StructProfileMover::calc_cenlist(), core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::MembranePotential::evaluate_env(), evaluate_env_and_cbeta_scores(), and protocols::scoring::InterchainPotential::evaluate_env_score().
◆ compute_centroid_environment()
| void core::scoring::EnvPairPotential::compute_centroid_environment | ( | pose::Pose & | pose | ) | const |
References core::scoring::CenListInfo::calculated(), cen_dist_cutoff_12_pad, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_cenlist(), core::scoring::CenListInfo::initialize(), core::conformation::Residue::is_protein(), nonconst_cenlist_from_pose(), core::pose::Pose::residue(), and truncate_cenlist_values().
Referenced by protocols::scoring::methods::InterchainEnvEnergy::setup_for_scoring(), protocols::scoring::methods::InterchainPairEnergy::setup_for_scoring(), core::energy_methods::CenPairEnergy::setup_for_scoring(), core::energy_methods::EnvEnergy::setup_for_scoring(), core::energy_methods::MembraneCbetaEnergy::setup_for_scoring(), core::energy_methods::MembraneCenPairEnergy::setup_for_scoring(), core::energy_methods::MembraneEnvEnergy::setup_for_scoring(), core::energy_methods::MembraneLipo::setup_for_scoring(), core::energy_methods::MPCbetaEnergy::setup_for_scoring(), core::energy_methods::MPEnvEnergy::setup_for_scoring(), and core::energy_methods::MPPairEnergy::setup_for_scoring().
◆ evaluate_env_and_cbeta_scores()
| 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 |
References core::conformation::Residue::aa(), cbeta_den12_, cbeta_den6_, cenlist_from_pose(), env_log_, core::scoring::CenListInfo::fcen10(), core::scoring::CenListInfo::fcen12(), core::scoring::CenListInfo::fcen6(), core::chemical::get_L_equivalent(), core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_or_gly(), core::conformation::Residue::is_protein(), and core::conformation::Residue::seqpos().
Referenced by core::energy_methods::EnvEnergy::residue_energy().
◆ evaluate_pair_and_cenpack_score()
| 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 |
References core::conformation::Residue::aa(), cen_dist10_pad_hinv, cen_dist10_pad_minus, cen_dist10_pad_plus, cen_dist12_pad_hinv, cen_dist12_pad_minus, cen_dist5_pad_hinv, cen_dist5_pad_minus, cen_dist5_pad_plus, cen_dist7_pad_hinv, cen_dist7_pad_minus, cen_dist7_pad_plus, cenpack_log_, core::chemical::DISULFIDE, core::chemical::get_L_equivalent(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_bonded(), core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_or_gly(), core::chemical::ResidueType::is_disulfide_bonded(), core::conformation::Residue::is_protein(), pair_log_, core::conformation::Residue::polymeric_sequence_distance(), and core::conformation::Residue::type().
Referenced by core::energy_methods::CenPairEnergy::residue_pair_energy().
◆ fill_cenlist()
|
private |
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(), core::scoring::CenListInfo::fcen6(), and protocols::mean_field::min().
Referenced by compute_centroid_environment().
◆ finalize()
| void core::scoring::EnvPairPotential::finalize | ( | pose::Pose & | pose | ) | const |
◆ nonconst_cenlist_from_pose()
|
static |
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::membrane::MembraneData::finalize(), core::scoring::Membrane_FAPotential::finalize(), and core::scoring::MembranePotential::finalize().
◆ truncate_cenlist_values()
|
private |
Member Data Documentation
◆ cbeta_den12_
|
private |
Referenced by EnvPairPotential(), and evaluate_env_and_cbeta_scores().
◆ cbeta_den6_
|
private |
Referenced by EnvPairPotential(), and evaluate_env_and_cbeta_scores().
◆ cen_dist10_pad
|
private |
◆ cen_dist10_pad_hinv
|
private |
Referenced by evaluate_pair_and_cenpack_score(), and fill_cenlist().
◆ cen_dist10_pad_minus
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist10_pad_plus
|
private |
Referenced by evaluate_pair_and_cenpack_score(), and fill_cenlist().
◆ cen_dist12_pad
|
private |
◆ cen_dist12_pad_hinv
|
private |
Referenced by evaluate_pair_and_cenpack_score(), and fill_cenlist().
◆ cen_dist12_pad_minus
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist12_pad_plus
|
private |
Referenced by fill_cenlist().
◆ cen_dist5_pad
|
private |
◆ cen_dist5_pad_hinv
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist5_pad_minus
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist5_pad_plus
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist6_pad
|
private |
◆ cen_dist6_pad_hinv
|
private |
Referenced by fill_cenlist().
◆ cen_dist6_pad_plus
|
private |
Referenced by fill_cenlist().
◆ cen_dist7_pad
|
private |
◆ cen_dist7_pad_hinv
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist7_pad_minus
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist7_pad_plus
|
private |
Referenced by evaluate_pair_and_cenpack_score().
◆ cen_dist_cutoff2
|
private |
◆ cen_dist_cutoff_12_pad
|
private |
Referenced by compute_centroid_environment().
◆ cenpack_log_
|
private |
Referenced by EnvPairPotential(), and evaluate_pair_and_cenpack_score().
◆ env_log_
|
private |
Referenced by EnvPairPotential(), and evaluate_env_and_cbeta_scores().
◆ pair_log_
|
private |
Referenced by EnvPairPotential(), and evaluate_pair_and_cenpack_score().
The documentation for this class was generated from the following files:
- src/core/scoring/EnvPairPotential.hh
- src/core/scoring/EnvPairPotential.cc
