With the traditional scoring hierarchy, classes like this one are created and accessed via the ScoringManager, which is itself a Singleton class. These "potential" classes are only created and initialized when the use of the EnergyMethod these classes correspond is encountered. No point in reading database files for a term if that term is not being used in some score function. However, the surface energy is used when users specify they want to use it on the command line - NOT via a score function. The score/energy is done within an interaction graph. One might ask why I just don't put the logic for reading in the database file to the interaction graph init methods. However, there will be cases where I will want to just score a protein (and not do any design) where I will want the database file to be read in. Scoring doesn't use interaction graphs, so if the code for that was located there, these values would not be read in. Instead, I've decided to implement this as its own separate class. It uses the Singleton design pattern so the database will only get read in once during a run. More...
#include <SurfacePotential.hh>
Public Member Functions | |
| Real | average_residue_hASA (chemical::AA aa_type, Size num_nbs) |
| Returns the average surface energy for the given residue type and number of neighbors. More... | |
| Real | hASA_patch_energy (Real patch_area, Size num_nbs) |
| Returns the energy for a given patch size. The calling function must ensure that an out-of-bounds error will not occur. More... | |
| void | compute_residue_surface_energy (conformation::Residue const &rsd, pose::Pose const &pose, scoring::EnergyMap &emap, Size resid, utility::vector1< Size > num_neighbors_) |
| Calculates the surface energy for a single residue within a Pose object. Used only by the RotamerSet_::compute_one_body_energy_maps function (which, in turn, is only used by the optE protocol). Nowhere else in mini is this function used. More... | |
| void | compute_pose_surface_energy (pose::Pose const &pose, Real &surface_energy_) |
| helper method for computing surface score. in the optE protocol we don't care about the total vs. residue level surface scores. so just call that function but discard the values for those variables. More... | |
| void | compute_pose_surface_energy (pose::Pose const &pose, Real &total_surface_energy_, utility::vector1< Real > &residue_surface_energy_) |
| core::Real | hpatch_score (core::Real patch_area) |
| Returns the score for a given patch size. The calling function must ensure that an out-of-bounds error will not occur. More... | |
| Real | compute_pose_hpatch_score (pose::Pose const &pose) |
| return the hpatch score for an entire pose More... | |
| void | compute_pose_hpatch_score (pose::Pose const &pose, Real &total_hpatch_energy_, std::map< core::Size, std::pair< core::Real, core::Real > > &patch_scores_, std::map< core::Size, utility::vector1< id::AtomID > > &atoms_in_patches_) |
| Uses the src/core/pack/interaction_graph/RotamerDots classes to determine exact SASAs and then uses a graph-based approach to find all the exposed hydrophobic patches on the surface of the pose. Uses the scores in the file scoring/score_functions/SurfacePotential/hpatch_score.txt to assign a score to each patch and puts the score into the passed in Real. More... | |
Static Public Attributes | |
| static const core::Size | MAX_HPATCH_AREA = 1000 |
| static const core::Real | MAX_HPATCH_SCORE = 100.0 |
| static const core::Size | HPATCH_SCORE_BIN_SIZE = 50 |
Private Member Functions | |
| SurfacePotential () | |
| private constructor More... | |
| void | read_average_res_hASA_database_file () |
| Reads in the database file which contains average residue hydrophobic accessible surface areas. More... | |
| void | read_hASA_score_database_file () |
| Reads in the database file which contains the scores for a distribution of patch sizes. More... | |
| void | read_hpatch_score_database_file () |
| Reads in the database file for the hpatch score, yet another version of the surface energy. More... | |
Private Attributes | |
| utility::vector1< utility::vector1< Real > > | res_to_average_hASA_ |
| std::vector< utility::vector1< Real > > | hASA_to_score_ |
| std::vector< core::Real > | patcharea_to_score_ |
Static Private Attributes | |
| static const core::Size | MAX_PATCH_SURFACE_AREA = 1200 |
| static const core::Real | MAX_SURFACE_ENERGY = 25.0 |
| static const core::Size | SURFACE_EXPOSED_CUTOFF = 20 |
| static const core::Real | INTERACTION_RADIUS = 10.0 |
| static const core::Size | SURFACE_SCORE_BIN_SIZE = 25 |
| static const core::Size | BURIED_RESIDUE_NO_HSASA_CUTOFF = 24 |
Friends | |
| class | utility::SingletonBase< SurfacePotential > |
Detailed Description
With the traditional scoring hierarchy, classes like this one are created and accessed via the ScoringManager, which is itself a Singleton class. These "potential" classes are only created and initialized when the use of the EnergyMethod these classes correspond is encountered. No point in reading database files for a term if that term is not being used in some score function. However, the surface energy is used when users specify they want to use it on the command line - NOT via a score function. The score/energy is done within an interaction graph. One might ask why I just don't put the logic for reading in the database file to the interaction graph init methods. However, there will be cases where I will want to just score a protein (and not do any design) where I will want the database file to be read in. Scoring doesn't use interaction graphs, so if the code for that was located there, these values would not be read in. Instead, I've decided to implement this as its own separate class. It uses the Singleton design pattern so the database will only get read in once during a run.
Constructor & Destructor Documentation
◆ SurfacePotential()
|
private |
private constructor
private constructor to guarantee the singleton
References read_average_res_hASA_database_file(), read_hASA_score_database_file(), and read_hpatch_score_database_file().
Member Function Documentation
◆ average_residue_hASA()
| Real core::pack::interaction_graph::SurfacePotential::average_residue_hASA | ( | chemical::AA | aa_type, |
| Size | num_nbs | ||
| ) |
Returns the average surface energy for the given residue type and number of neighbors.
References BURIED_RESIDUE_NO_HSASA_CUTOFF, core::chemical::num_canonical_aas, and res_to_average_hASA_.
Referenced by compute_pose_surface_energy(), and compute_residue_surface_energy().
◆ compute_pose_hpatch_score() [1/2]
| Real core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score | ( | pose::Pose const & | pose | ) |
return the hpatch score for an entire pose
◆ compute_pose_hpatch_score() [2/2]
| void core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score | ( | pose::Pose const & | pose, |
| core::Real & | total_hpatch_score_, | ||
| std::map< core::Size, std::pair< core::Real, core::Real > > & | patch_scores_, | ||
| std::map< core::Size, utility::vector1< id::AtomID > > & | atoms_in_patches_ | ||
| ) |
Uses the src/core/pack/interaction_graph/RotamerDots classes to determine exact SASAs and then uses a graph-based approach to find all the exposed hydrophobic patches on the surface of the pose. Uses the scores in the file scoring/score_functions/SurfacePotential/hpatch_score.txt to assign a score to each patch and puts the score into the passed in Real.
Note: If a Pose object has overlapping atoms anywhere, then this function will fail with the following error:
sin_cos_range ERROR: nan is outside of [-1,+1] sin and cos value legal range sin_cos_range ERROR: nan is outside of [-1,+1] sin and cos value legal range ERROR:: Exit from: src/numeric/trig.functions.hh line: 117
References core::conformation::Residue::atom_name(), core::chemical::ResidueType::atom_type(), core::id::AtomID::atomno(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::chemical::AtomType::element(), hpatch_score(), core::pose::initialize_atomid_map(), core::conformation::Residue::is_protein(), MAX_HPATCH_AREA, MAX_HPATCH_SCORE, core::conformation::Residue::nheavyatoms(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::pose_max_nbr_radius(), core::pack::interaction_graph::RotamerDots::probe_radius_, core::pose::Pose::residue(), core::conformation::residue_point_graph_from_conformation(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::resize(), core::id::AtomID::rsd(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::pose::Pose::size(), and core::pack::interaction_graph::TR().
◆ compute_pose_surface_energy() [1/2]
| void core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy | ( | pose::Pose const & | pose, |
| Real & | surface_energy_ | ||
| ) |
helper method for computing surface score. in the optE protocol we don't care about the total vs. residue level surface scores. so just call that function but discard the values for those variables.
◆ compute_pose_surface_energy() [2/2]
| void core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy | ( | pose::Pose const & | pose, |
| Real & | total_surface_energy_, | ||
| utility::vector1< Real > & | residue_surface_energy_ | ||
| ) |
References core::conformation::Residue::aa(), average_residue_hASA(), BURIED_RESIDUE_NO_HSASA_CUTOFF, core::pose::Pose::conformation(), core::pose::Pose::energies(), hASA_patch_energy(), INTERACTION_RADIUS, core::pose::symmetry::is_symmetric(), MAX_PATCH_SURFACE_AREA, MAX_SURFACE_ENERGY, core::conformation::Residue::nbr_atom(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::pose::Pose::size(), SURFACE_EXPOSED_CUTOFF, core::scoring::Energies::tenA_neighbor_graph(), core::pack::interaction_graph::TR(), and core::conformation::Residue::xyz().
◆ compute_residue_surface_energy()
| void core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| scoring::EnergyMap & | emap, | ||
| Size | resid, | ||
| utility::vector1< Size > | num_neighbors_ | ||
| ) |
Calculates the surface energy for a single residue within a Pose object. Used only by the RotamerSet_::compute_one_body_energy_maps function (which, in turn, is only used by the optE protocol). Nowhere else in mini is this function used.
References core::conformation::Residue::aa(), average_residue_hASA(), BURIED_RESIDUE_NO_HSASA_CUTOFF, core::pose::Pose::energies(), hASA_patch_energy(), INTERACTION_RADIUS, MAX_PATCH_SURFACE_AREA, MAX_SURFACE_ENERGY, core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::pose::Pose::size(), core::scoring::surface, SURFACE_EXPOSED_CUTOFF, core::pack::interaction_graph::TR(), and core::conformation::Residue::xyz().
◆ hASA_patch_energy()
| Real core::pack::interaction_graph::SurfacePotential::hASA_patch_energy | ( | Real | patch_area, |
| Size | num_nbs | ||
| ) |
Returns the energy for a given patch size. The calling function must ensure that an out-of-bounds error will not occur.
References hASA_to_score_, MAX_PATCH_SURFACE_AREA, and SURFACE_SCORE_BIN_SIZE.
Referenced by compute_pose_surface_energy(), and compute_residue_surface_energy().
◆ hpatch_score()
| Real core::pack::interaction_graph::SurfacePotential::hpatch_score | ( | core::Real | patch_area | ) |
Returns the score for a given patch size. The calling function must ensure that an out-of-bounds error will not occur.
References HPATCH_SCORE_BIN_SIZE, MAX_HPATCH_AREA, and patcharea_to_score_.
Referenced by compute_pose_hpatch_score().
◆ read_average_res_hASA_database_file()
|
private |
Reads in the database file which contains average residue hydrophobic accessible surface areas.
References core::chemical::aa_from_name(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, res_to_average_hASA_, and core::pack::interaction_graph::TR().
Referenced by SurfacePotential().
◆ read_hASA_score_database_file()
|
private |
Reads in the database file which contains the scores for a distribution of patch sizes.
Not assuming any particular length to the database file so that if I want to increase the maximum of the distribution or shrink it, the vector will dynamically resize to what it needs to be.
References hASA_to_score_, protocols::hybridization::score, and core::pack::interaction_graph::TR().
Referenced by SurfacePotential().
◆ read_hpatch_score_database_file()
|
private |
Reads in the database file for the hpatch score, yet another version of the surface energy.
Not assuming any particular length to the database file so that if I want to increase the maximum of the distribution or shrink it, the vector will dynamically resize to what it needs to be.
References patcharea_to_score_, protocols::hybridization::score, and core::pack::interaction_graph::TR().
Referenced by SurfacePotential().
Friends And Related Function Documentation
◆ utility::SingletonBase< SurfacePotential >
|
friend |
Member Data Documentation
◆ BURIED_RESIDUE_NO_HSASA_CUTOFF
|
staticprivate |
Referenced by average_residue_hASA(), compute_pose_surface_energy(), and compute_residue_surface_energy().
◆ hASA_to_score_
|
private |
Referenced by hASA_patch_energy(), and read_hASA_score_database_file().
◆ HPATCH_SCORE_BIN_SIZE
|
static |
Referenced by hpatch_score().
◆ INTERACTION_RADIUS
|
staticprivate |
Referenced by compute_pose_surface_energy(), and compute_residue_surface_energy().
◆ MAX_HPATCH_AREA
|
static |
◆ MAX_HPATCH_SCORE
|
static |
◆ MAX_PATCH_SURFACE_AREA
|
staticprivate |
Referenced by compute_pose_surface_energy(), compute_residue_surface_energy(), and hASA_patch_energy().
◆ MAX_SURFACE_ENERGY
|
staticprivate |
Referenced by compute_pose_surface_energy(), and compute_residue_surface_energy().
◆ patcharea_to_score_
|
private |
Referenced by hpatch_score(), and read_hpatch_score_database_file().
◆ res_to_average_hASA_
|
private |
Referenced by average_residue_hASA(), and read_average_res_hASA_database_file().
◆ SURFACE_EXPOSED_CUTOFF
|
staticprivate |
Referenced by compute_pose_surface_energy(), and compute_residue_surface_energy().
◆ SURFACE_SCORE_BIN_SIZE
|
staticprivate |
Referenced by hASA_patch_energy().
The documentation for this class was generated from the following files:
- src/core/pack/interaction_graph/SurfacePotential.hh
- src/core/pack/interaction_graph/SurfacePotential.cc
