Nonmember functions for evaluating some or all energy methods on residues or residue pairs.
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| static basic::Tracer | TR ("core.scoring.utils") |
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| void | core::scoring::eval_scsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1sc_centroid, Vector const &r2sc_centroid, Real const &r1sc_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| | With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...
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| void | core::scoring::eval_bbsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2sc_centroid, Real const &r1bb_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| | With two bounding spheres for a backbone and a sidechain, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_sidechain_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...
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| void | core::scoring::eval_bbbb_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2bb_centroid, Real const &r1bb_radius, Real const &r2bb_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| | With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...
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| Vector | core::scoring::compute_bb_centroid (conformation::Residue const &r1) |
| | Compute the average coordinate of the backbone heavy atoms (aka center of mass). More...
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| Real | core::scoring::compute_bb_radius (conformation::Residue const &r1, Vector const &r1bb_centroid) |
| | Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point. More...
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| Vector | core::scoring::compute_sc_centroid (conformation::Residue const &r1) |
| | Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone. More...
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| Real | core::scoring::compute_sc_radius (conformation::Residue const &r1, Vector const &r1sc_centroid) |
| | Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point. More...
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| bool | core::scoring::check_score_function_sanity (utility::options::OptionCollection const &options, std::string const &scorefxn_key, bool throw_exception=false) |
| | Check if a score function is requested with incompatible option flags Will return true if scorefunction is "sane" and false if not. If throw_exception is true, will raise an exception instead of returning false. More...
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| std::map< id::AtomID, utility::vector1< Real > > | core::scoring::get_single_atom_energies (core::pose::Pose &pose, ScoreFunction const &scorefxn, ScoreTypes const &types, select::residue_selector::ResidueSubsetOP subset=nullptr) |
| | Get the (pseudo-one-body) energies for a set of atoms. Only atoms with non-zero energies will be present in the returned map. The output vector will be ordered by the types in the passed ScoreTypes If subset is passed, only atoms in residues from the subset will be considered. More...
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| std::map< std::pair< id::AtomID, id::AtomID >, utility::vector1< Real > > | core::scoring::get_pairwise_atom_energies (core::pose::Pose &pose, ScoreFunction const &scorefxn, ScoreTypes const &types, select::residue_selector::ResidueSubsetOP subset1=nullptr, select::residue_selector::ResidueSubsetOP subset2=nullptr) |
| | Get the pairwise energies for a set of atoms. Only atom pairs with non-zero energies will be present in the returned map. The output vector will be ordered by the types in the passed ScoreTypes If both subsets are passed, only pairwise interactions between atoms in residues across the two sets will be considered If just subset1 is passed, only pairwise interactions which involve at least one atom in a residue in the set will be considered If neither is passed, all pairwise interactions will be considered. More...
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| std::map< id::AtomID, utility::vector1< Real > > | core::scoring::get_atomistic_energies (core::pose::Pose &pose, ScoreFunction const &scorefxn, ScoreTypes const &types, select::residue_selector::ResidueSubsetOP subset=nullptr) |
| | Get the per-atom contributions to the energy. This differs from get_single_atom_energies() in that it also considers the atoms' contributions to pairwise energies. The output vector will be ordered by the types in the passed ScoreTypes If subset is passed, only atoms in residues from the subset will be considered. More...
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Nonmember functions for evaluating some or all energy methods on residues or residue pairs.
- Author
- Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)
