|
| | MinScoreScoreFunction () |
| | ctor More...
|
| |
| | MinScoreScoreFunction (utility::options::OptionCollection const &options) |
| | ctor More...
|
| |
| | MinScoreScoreFunction (ScoreFunction const &src, core::Real const) |
| |
| | MinScoreScoreFunction (ScoreFunction const &src, core::Real const, utility::options::OptionCollection const &options) |
| |
| | MinScoreScoreFunction (core::Real const) |
| |
| | MinScoreScoreFunction (core::Real const, utility::options::OptionCollection const &options) |
| |
| void | assign (ScoreFunction const &src) override |
| | INTERNAL USE ONLY. More...
|
| |
| virtual void | assign (MinScoreScoreFunction const &src) |
| | INTERNAL USE ONLY. More...
|
| |
| ScoreFunctionOP | clone () const override |
| | Create a copy of the scorefunction Virtual to keep subclass information. More...
|
| |
| Real | operator() (pose::Pose &pose) const override |
| | Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction. More...
|
| |
| | ScoreFunction () |
| | default ctor that initializes its EnergyMethodOptions object from the global option collection More...
|
| |
| | ScoreFunction (utility::options::OptionCollection const &options) |
| | ctor that initializes its EnergyMethodOptions object from a (possibly local) option collection More...
|
| |
| | ~ScoreFunction () override |
| |
| ScoreFunctionCOP | get_self_ptr () const |
| | self pointers More...
|
| |
| ScoreFunctionOP | get_self_ptr () |
| |
| ScoreFunctionOP | clone_as_base_class () const |
| | If you want to discard subclass information, the following function is availible. More...
|
| |
| void | reset () |
| | Resets the ScoreFunction to default values, reading from the global options collection. More...
|
| |
| void | reset (utility::options::OptionCollection const &options) |
| | Resets the ScoreFunction to default values, reading from a (possibly local) options collection. More...
|
| |
| void | perturb_weights () |
| | Randomly perturbs non-zero score function weights. More...
|
| |
| std::string | serialize_weights () const |
| | Serializes the non-zero score function term weights Format: { term : weight, ... }. More...
|
| |
| void | add_weights_from_file (std::string const &filename) |
| | Initializes this ScoreFunction from the given <filename> More...
|
| |
| void | _add_weights_from_file (std::string const &filename, bool patch=false) |
| | Initializes this ScoreFunction from the given <filename> no lookup in database directory. More...
|
| |
| void | _add_weights_from_stream (std::istream &data, bool patch=false, std::string const &filename="") |
| |
| void | initialize_from_file (std::string const &filename) |
| | Resets everything before reading the <filename> More...
|
| |
| void | apply_patch_from_file (std::string const &filename) |
| | Applies a patch from the given <filename> More...
|
| |
| void | set_etable (std::string const &etable_name) |
| | Given a <filename> (represented by a std::string), set the e_table for this ScoreFunction. More...
|
| |
| void | set_method_weights (ScoreType const &t, utility::vector1< Real > const &wts) |
| |
| methods::EnergyMethodOptions const & | energy_method_options () const |
| | Returns the EnergyMethodOptions object contained in this ScoreFunction (const access) More...
|
| |
| void | set_energy_method_options (methods::EnergyMethodOptions const &energy_method_options_in) |
| | Sets the EnergyMethodOptions object contained in this ScoreFunction. with appropriate update of all the energy methods. More...
|
| |
| void | reset_energy_methods () |
| |
| virtual Real | score (pose::Pose &pose) const |
| | Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction. More...
|
| |
| ScoreFunctionInfoOP | info () const |
| | Score the structure and store the component energies in the EnergyGraph without requiring a second evaluation of the short-ranged two body energies. Note: pose copy operations do not copy the EnergyGraph, so cloning or copying a pose that has had it's components scored will not copy over the component energies. More...
|
| |
| Distance | max_atomic_interaction_cutoff () const |
| |
| void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const |
| | find which context graphs the energy methods require More...
|
| |
| bool | are_they_neighbors (pose::Pose const &pose, Size const pos1, Size const pos2) const |
| | Determine if two residues could have non-zero interaction energy after possibly changing rotamers/chi. More...
|
| |
| Real | operator[] (ScoreType const &t) const |
| | Returns the weight of the ScoreType <t> More...
|
| |
| Real | score_by_scoretype (pose::Pose &pose, ScoreType const t, bool const weighted=true) const |
| | Returns the score of the ScoreType <t> More...
|
| |
| EnergyMap const & | weights () const |
| | Returns an EnergyMap of the current set of weights. More...
|
| |
| Real | weighted_sum (EnergyMap const &unweighted) const |
| | Returns the weighted sum of the given energy map, given the current set of weights. More...
|
| |
| bool | has_zero_weight (ScoreType const &t) const |
| | Returns true if the ScoreType <t> has a weight of zero,. More...
|
| |
| bool | has_nonzero_weight (ScoreType const &t) const |
| | Returns true if the ScoreType <t> has a non-zero weight. More...
|
| |
| ScoreTypes const & | get_nonzero_weighted_scoretypes () const |
| | Returns a list of the ScoreTypes which are non-zero with their current weights. More...
|
| |
| void | set_weight (ScoreType const &t, Real const setting) |
| | Sets the weight for ScoreType <t> to <setting> More...
|
| |
| void | set_weight_if_zero (ScoreType const &t, Real const setting) |
| | Sets the weight for ScoreType <t> to <setting> if weight is originally zero. More...
|
| |
| void | add_to_weight (ScoreType const &t, Real const &increment) |
| | Increments the weight for ScoreType <t> by <setting> More...
|
| |
| Real | get_weight (ScoreType const &t) const |
| | Returns the weight for ScoreType <t> More...
|
| |
| void | add_extra_method (ScoreType const &new_type, Real const new_weight, methods::EnergyMethod const &new_method) |
| | Adds a scoring method that is not necessarily included in the core library. More...
|
| |
| void | add_extra_method (std::map< ScoreType, Real > const &new_weights, methods::EnergyMethod const &new_method) |
| | Adds a scoring method that is not necessarily included in the core library. More...
|
| |
| virtual void | setup_for_minimizing (pose::Pose &pose, kinematics::MinimizerMapBase const &min_map) const |
| | Initializes a MinimizationGraph and caches it in Energies object of <pose> More...
|
| |
| virtual void | finalize_after_minimizing (pose::Pose &pose) const |
| | Called after minimization. More...
|
| |
| virtual void | setup_for_minimizing_for_node (MinimizationNode &min_node, conformation::Residue const &rsd, basic::datacache::BasicDataCache &res_data_cache, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool accumulate_fixed_energies, EnergyMap &fixed_energies) const |
| | Initialize a single node of a MinimizationGraph with the one-body and two-body energy methods that are held within this ScoreFunction object. More...
|
| |
| void | reinitialize_minnode_for_residue (MinimizationNode &min_node, conformation::Residue const &rsd, basic::datacache::BasicDataCache &res_data_cache, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose) const |
| |
| void | setup_for_minimizing_sr2b_enmeths_for_minedge (conformation::Residue const &res1, conformation::Residue const &res2, MinimizationEdge &min_edge, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, EnergyEdge const *energy_edge, EnergyMap &fixed_energies, Real const edge_weight=1.0) const |
| | Initialize a single MinimizationEdge for a particular part of residues, storing sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction. More...
|
| |
| void | setup_for_lr2benmeth_minimization_for_respair (conformation::Residue const &res1, conformation::Residue const &res2, methods::LongRangeTwoBodyEnergyCOP lr2benergy, MinimizationGraph &g, kinematics::MinimizerMapBase const &min_map, pose::Pose &p, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, ResidueNeighborConstIteratorOP rni, EnergyMap &fixed_energies, Real const edge_weight=1.0, Real const edge_dweight=1.0) const |
| | Initialize an edge in the MinimizationGraph with a particular long-range two body. More...
|
| |
| void | setup_for_scoring (pose::Pose &pose) const |
| | For external scorers: Let the energy methods prepare for evaluating their scores on a particular structure. More...
|
| |
| void | setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &residues_repacking, utility::vector1< bool > const &residues_designing) const |
| | Lets the scoring functions cache anything they need to calculate energies in a packing step (rotamer_trials or pack_rotamers) More...
|
| |
| void | setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets) const |
| | Lets the scoring functions cache anything they need to calculate energies in a packing step (pack_rotamers) in the context of all available rotamers. More...
|
| |
| void | prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const |
| | Lets the scoring functions cache anything they need to rapidly calculate rotamer pair energies used in packing (like a trie, e.g.) More...
|
| |
| void | update_residue_for_packing (pose::Pose &pose, Size resid) const |
| | If inside packing, the pose changes conformation, inform the scoring functions that any data they have cached in the Energies object is out of date. In particular, this is to update the trie(s) during rotamer trials. More...
|
| |
| virtual void | setup_for_derivatives (pose::Pose &pose) const |
| |
| virtual void | finalize_after_derivatives (pose::Pose &pose) const |
| |
| core::Real | get_sub_score (pose::Pose const &pose, utility::vector1< bool > const &residue_mask) const |
| | Compute the score for subset of residues. More...
|
| |
| void | get_sub_score (pose::Pose const &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const |
| | Compute the score for subset of residues. More...
|
| |
| core::Real | get_sub_score (pose::Pose &pose, utility::vector1< bool > const &residue_mask) const |
| | Compute the score for subset of residues. More...
|
| |
| void | get_sub_score (pose::Pose &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const |
| | Compute the score for subset of residues. More...
|
| |
| core::Real | get_sub_score_exclude_res (pose::Pose const &pose, utility::vector1< core::Size > const &exclude_list) const |
| | Compute the score for subset of residues. More...
|
| |
| void | get_sub_score_exclude_res (pose::Pose const &pose, utility::vector1< core::Size > const &exclude_list, EnergyMap &emap) const |
| | Compute the score for subset of residues. More...
|
| |
| core::Real | get_sub_score_exclude_res (pose::Pose &pose, utility::vector1< core::Size > const &exclude_list) const |
| | Compute the score for subset of residues. More...
|
| |
| void | get_sub_score_exclude_res (pose::Pose &pose, utility::vector1< core::Size > const &exclude_list, EnergyMap &emap) const |
| | Compute the score for subset of residues. More...
|
| |
| virtual void | eval_twobody_neighbor_energies (pose::Pose &pose) const |
| |
| virtual void | eval_long_range_twobody_energies (pose::Pose &pose) const |
| |
| AllMethodsIterator | all_energies_begin () const |
| |
| AllMethodsIterator | all_energies_end () const |
| |
| LR_2B_MethodIterator | long_range_energies_begin () const |
| |
| LR_2B_MethodIterator | long_range_energies_end () const |
| |
| CI_1B_Methods::const_iterator | ci_1b_methods_begin () const |
| |
| CI_1B_Methods::const_iterator | ci_1b_methods_end () const |
| |
| CD_1B_Methods::const_iterator | cd_1b_methods_begin () const |
| |
| CD_1B_Methods::const_iterator | cd_1b_methods_end () const |
| |
| TWO_B_MethodIterator | ci_2b_intrares_begin () const |
| |
| TWO_B_MethodIterator | ci_2b_intrares_end () const |
| |
| TWO_B_MethodIterator | cd_2b_intrares_begin () const |
| |
| TWO_B_MethodIterator | cd_2b_intrares_end () const |
| |
| CI_2B_Methods::const_iterator | ci_2b_begin () const |
| |
| CI_2B_Methods::const_iterator | ci_2b_end () const |
| |
| CD_2B_Methods::const_iterator | cd_2b_begin () const |
| |
| CD_2B_Methods::const_iterator | cd_2b_end () const |
| |
| CI_LR_2B_MethodIterator | ci_lr_2b_methods_begin () const |
| |
| CI_LR_2B_MethodIterator | ci_lr_2b_methods_end () const |
| |
| CD_LR_2B_MethodIterator | cd_lr_2b_methods_begin () const |
| |
| CD_LR_2B_MethodIterator | cd_lr_2b_methods_end () const |
| |
| WS_MethodIterator | ws_methods_begin () const |
| |
| WS_MethodIterator | ws_methods_end () const |
| |
| bool | check_methods_in_right_order (ScoreType const &score_type_in_first_method, ScoreType const &score_type_in_second_method) const |
| | check order of methods More...
|
| |
| virtual void | eval_onebody_energies (pose::Pose &pose) const |
| |
| void | show (std::ostream &out) const |
| |
| void | merge (const ScoreFunction &scorefxn_to_be_merged) |
| | Merges in the weights of another score function. More...
|
| |
| void | show (std::ostream &out, pose::Pose &pose) const |
| | Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType. More...
|
| |
| void | show_pretty (std::ostream &out) const |
| | similar output as show( ostream, pose ) but without the pose More...
|
| |
| void | show (pose::Pose &pose) const |
| | Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType. More...
|
| |
| void | show_line_headers (std::ostream &out) const |
| |
| void | show_line (std::ostream &out, pose::Pose const &pose) const |
| |
| void | show_additional (std::ostream &out, pose::Pose &pose, bool verbose=false) const |
| |
| void | name (std::string const &weights_tag) |
| | Accumulates the unweighted one body energies of all context independent one body energies for <pose> Residue <rsd> into EnergyMap <emap> More...
|
| |
| std::string | get_name () const |
| |
| void | eval_ci_1b (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| |
| virtual void | eval_cd_1b (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted one body energies of all context dependent one body energies for <pose> Residue <rsd> into EnergyMap <emap> More...
|
| |
| void | eval_ci_2b (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted context independent two body interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More...
|
| |
| void | eval_ci_2b_bb_bb (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted context independent two body interaction energies of <pose> between the backbones of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More...
|
| |
| void | eval_ci_2b_bb_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted short range context independent two body interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap> More...
|
| |
| void | eval_ci_2b_sc_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted short range context dependent two body interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into Energymap <emap> More...
|
| |
| virtual void | eval_cd_2b (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulate the unweighted short range context dependent two body interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More...
|
| |
| void | eval_cd_2b_bb_bb (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the backbones of Residue <rsd1> and <rsd2> into EnergyMap <emap> More...
|
| |
| void | eval_cd_2b_bb_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap> More...
|
| |
| void | eval_cd_2b_sc_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More...
|
| |
| void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates for rsd the unweighted intra-residue one body energies for all context dependent and context independent two body terms that define intra-residue energies. More...
|
| |
| void | eval_ci_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted intra-residue one body energies for all context independent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap> More...
|
| |
| virtual void | eval_cd_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| | Accumulates the unweighted intra-residue one body energies for all context dependent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap> More...
|
| |
| void | bump_check_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | score the sidechain from rsd1 against the entirety of rsd2 More...
|
| |
| void | bump_check_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| | Scores the sidechain from <pose> Residue <rsd1> against the backbone of Residue <rsd2> More...
|
| |
| void | evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, utility::vector1< core::PackerEnergy > &energies) const |
| |
| void | evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, utility::vector1< EnergyMap > &emaps) const |
| |
| void | evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const |
| |
| void | evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set1, conformation::Residue const &residue2, pose::Pose const &pose, utility::vector1< core::PackerEnergy > &energy_vector) const |
| |
| bool | any_lr_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const |
| |
| virtual void | eval_npd_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, Vector &F1, Vector &F2) const |
| |
| Real | eval_dof_derivative (id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose) const |
| |
| ScoreTypes const & | score_types_by_method_type (methods::EnergyMethodType const &t) const |
| |
| ScoreTypes const & | ci_1b_types () const |
| | convenience access to all ci 1b score types More...
|
| |
| ScoreTypes const & | cd_1b_types () const |
| | convenience access to all cd 1b score types More...
|
| |
| ScoreTypes const & | ci_2b_types () const |
| | convenience access to all ci 2b score types More...
|
| |
| ScoreTypes const & | cd_2b_types () const |
| | convenience access to all cd 2b score types More...
|
| |
| ScoreTypes const & | ci_lr_2b_types () const |
| |
| ScoreTypes const & | cd_lr_2b_types () const |
| |
| ScoreTypes const & | whole_structure_types () const |
| |
| bool | ready_for_nonideal_scoring () const |
| |
| AllMethods const & | all_methods () const |
| |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const |
| | Provide citations to the passed CitationCollectionList This allows the scorefunciton to provide citaitons for itself itself and for any modules that it invokes (particularl energy methods). More...
|
| |
Public Member Functions inherited from core::scoring::ScoreFunction