BuriedUnsatPenalty, an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors or acceptors. More...
#include <BuriedUnsatPenalty.hh>
Public Types | |
| typedef core::scoring::methods::WholeStructureEnergy | parent1 |
| typedef core::scoring::annealing::ResidueArrayAnnealableEnergy | parent2 |
 Public Types inherited from core::scoring::methods::WholeStructureEnergy | |
| typedef EnergyMethod | parent |
| Public Types inherited from core::scoring::methods::EnergyMethod | |
| typedef utility::VirtualBase | parent |
Public Member Functions | |
| BuriedUnsatPenalty (core::scoring::methods::EnergyMethodOptions const &options) | |
| Options constructor. More... | |
| ~BuriedUnsatPenalty () override | |
| Default destructor. More... | |
| core::scoring::methods::EnergyMethodOP | clone () const override |
| Clone: create a copy of this object, and return an owning pointer to the copy. More... | |
| void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const override |
| BuriedUnsatPenalty is context-independent and thus indicates that no context graphs need to be maintained by class Energies. More... | |
| core::Size | version () const override |
| BuriedUnsatPenalty is version 1.0 right now. More... | |
| void | finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap &totals) const override |
| Actually calculate the total energy. More... | |
| core::Real | calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &rotamer_ids, core::Size const substitution_position=0) const override |
| Calculate the total energy given a vector of const owning pointers to residues. More... | |
| void | commit_considered_substitution () override |
| What to do when a substitution that was considered is accepted. More... | |
| void | report () const |
| Get a summary of all loaded data. More... | |
| void | set_up_residuearrayannealableenergy_for_packing (core::pose::Pose &pose, core::pack::rotamer_set::RotamerSets const &rotamersets, core::scoring::ScoreFunction const &sfxn) override |
| Cache data from the pose in this EnergyMethod in anticipation of packing. More... | |
| void | clean_up_residuearrayannealableenergy_after_packing (core::pose::Pose &pose) override |
| Delete cached data from the pose and from this EnergyMethod after packing. More... | |
| void | setup_for_minimizing (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MinimizerMapBase const &minmap) const override |
| Disable this scoreterm during minimization trajectory. More... | |
| void | finalize_after_minimizing (core::pose::Pose &pose) const override |
| Re-enable this scoreterm after a minimization trajectory. More... | |
| core::Real | compute_penalty (core::Size const unsat_acceptor_count, core::Size const unsat_donor_count, core::Size const unsat_acceptor_and_donor_count, core::Size const oversat_acceptor_count, core::Size const oversat_donor_count, core::Size const oversat_acceptor_and_donor_count) const |
| Given the counts of various unsaturateds, return a penalty value. More... | |
| core::Real | calculate_penalty_once_almost_from_scratch_using_reference_graph (utility::vector1< core::conformation::ResidueCOP > const &resvect, graph::BuriedUnsatPenaltyGraph const &reference_graph, core::Size const symm_multiplier) const |
| Given a residue vector, calculate the penalty energy using a reference graph. More... | |
| core::Real | calculate_penalty_once_from_scratch (core::pose::Pose const &pose) const |
| Given a pose, calculate the penalty energy. More... | |
| void | provide_pymol_commands_to_show_groups (std::ostream &out, core::pose::Pose const &pose) const |
| Provide Pymol commands to colour the pose grey, non-buried donor and acceptor groups cyan, and buried acceptor and donor groups orange. Useful for debugging degree of burial. More... | |
| void | set_prevent_pruning (bool const setting) |
| Should the graph setup-for-packing skip the step in which groups that are not packable and not able to hydrogen bond to a packable residue are pruned? Default false; this function allows this to be set, though. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| Provide the citation. More... | |
| Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy | |
| WholeStructureEnergy (EnergyMethodCreatorOP) | |
| Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More... | |
| ~WholeStructureEnergy () override | |
| EnergyMethodType | method_type () const override |
| Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More... | |
| virtual Distance | atomic_interaction_cutoff () const |
| how far apart must two heavy atoms be to have a zero interaction energy? More... | |
| Public Member Functions inherited from core::scoring::methods::EnergyMethod | |
| EnergyMethod (EnergyMethodCreatorOP creator) | |
| Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More... | |
| virtual void | setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const |
| if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
| virtual void | setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const |
| if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More... | |
| virtual void | prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const |
| If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
| virtual void | update_residue_for_packing (pose::Pose &, Size resid) const |
| If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More... | |
| virtual void | setup_for_scoring (pose::Pose &, ScoreFunction const &) const |
| if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing. More... | |
| virtual bool | requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const |
| Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More... | |
| virtual void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const |
| Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More... | |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More... | |
| virtual void | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
| called at the end of derivatives evaluation More... | |
| virtual bool | minimize_in_whole_structure_context (pose::Pose const &) const |
| Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More... | |
| virtual bool | defines_high_order_terms (pose::Pose const &) const |
| Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More... | |
| virtual bool | has_atomistic_energies () const |
| Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method? Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it's not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods. More... | |
| virtual bool | has_atomistic_pairwise_energies () const |
| Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method? NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. More... | |
| virtual void | atomistic_energy (core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const |
| Evaluate the (one body) energy associated with a particular atom This may be a "self" energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies() More... | |
| virtual void | atomistic_pair_energy (core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const |
| Evaluate the energy for a particular pair of atoms This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies() More... | |
| virtual void | eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const |
| Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More... | |
| ScoreTypes const & | score_types () const |
| Returns the score types that this energy method computes. More... | |
| virtual void | show_additional_info (std::ostream &, pose::Pose &, bool) const |
| show additional information of the energy method More... | |
| Public Member Functions inherited from core::scoring::annealing::ResidueArrayAnnealableEnergy | |
| ResidueArrayAnnealableEnergy () | |
| Constructor. More... | |
| ResidueArrayAnnealableEnergy (ResidueArrayAnnealableEnergy const &src) | |
| Copy constructor. More... | |
| virtual | ~ResidueArrayAnnealableEnergy () |
| Destructor. More... | |
Private Member Functions | |
| void | initialize_curstate_graph (core::pose::Pose const &pose) |
| Called from set_up_residuearrayannelableenergy_for_packing(). Initializes the graph structure representing the current state during the packing trajectory. More... | |
| void | initialize_curstate_graph (utility::vector1< core::conformation::ResidueCOP > const &resvect) |
| Initialize the graph structure representing the current state during the packing trajectory from a vector of residues. Called from the first step of calculate_energy(). More... | |
| void | add_to_list_of_partners_of_changed_nodes (graph::BuriedUnsatPenaltyGraphCOP curstate_graph, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > &changed_node_partners) const |
| Given a list of changed node indices and a graph of the current state, determine which nodes share edges with the changed nodes, and add their indices to a list of partners. More... | |
| void | increment_counts (core::Size &unsat_acceptor_count_lastconsidered, core::Size &unsat_donor_count_lastconsidered, core::Size &unsat_acceptor_and_donor_count_lastconsidered, core::Size &oversat_acceptor_count_lastconsidered, core::Size &oversat_donor_count_lastconsidered, core::Size &oversat_acceptor_and_donor_count_lastconsidered, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > const &changed_node_partners) const |
| Increment the counts based on the current state of the curstate_graph_ and the current changed_node_indices_ and changed_node_partners_ vectors. More... | |
| void | decrement_counts (core::Size &unsat_acceptor_count_lastconsidered, core::Size &unsat_donor_count_lastconsidered, core::Size &unsat_acceptor_and_donor_count_lastconsidered, core::Size &oversat_acceptor_count_lastconsidered, core::Size &oversat_donor_count_lastconsidered, core::Size &oversat_acceptor_and_donor_count_lastconsidered, utility::vector1< graph::BuriedUnsatPenaltyNodeDataCOP > const &old_data, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > const &changed_node_partners) const |
| Decrement the counts based on the current state of the curstate_graph_ and the current changed_node_indices_ and changed_node_partners_ vectors. More... | |
Private Attributes | |
| bool | disabled_ |
| Is this scoreterm currently disabled (e.g. for a minimization trajectory)? More... | |
| graph::BuriedUnsatPenaltyGraphCOP | unsat_graph_ |
| Pointer to buried unsaturated penalty graph in the pose. Stored during packing to avoid repeated lookups. More... | |
| graph::BuriedUnsatPenaltyGraphOptionsOP | graph_options_ |
| Options for the BruiedUnsatPenaltyGraph. More... | |
| core::scoring::hbonds::HBondOptionsOP | hbond_options_ |
| Options for hydrogen bonds. More... | |
| bool | symmetric_ |
| Is this pose symmetric? Used during packing only. More... | |
| core::Size | nres_ |
| How many residues are in the asymmetric unit of a symmetric pose (symmetric case) or in a pose (asymmetric case)? Used during packing only. More... | |
| core::Size | num_symmetric_copies_ |
| The number of symmetry copies. Used for packing only. More... | |
| bool | prevent_pruning_ |
| Should the graph setup-for-packing skip the step in which groups that are not packable and not able to hydrogen bond to a packable residue are pruned? Default false. More... | |
| graph::BuriedUnsatPenaltyGraphOP | curstate_graph_ |
| The graph representing the last accepted state during the packer trajectory. More... | |
| core::Size | unsat_acceptor_count_lastaccepted_ |
| The unsat acceptor counts last accepted. More... | |
| core::Size | unsat_donor_count_lastaccepted_ |
| The unsat donor counts last accepted. More... | |
| core::Size | unsat_acceptor_and_donor_count_lastaccepted_ |
| The unsat acceptor and donor counts last accepted. More... | |
| core::Size | oversat_acceptor_count_lastaccepted_ |
| The oversat acceptor counts last accepted. More... | |
| core::Size | oversat_donor_count_lastaccepted_ |
| The oversat donor counts last accepted. More... | |
| core::Size | oversat_acceptor_and_donor_count_lastaccepted_ |
| The oversat acceptor and donor counts last accepted. More... | |
Friends | |
| class | ::BuriedUnsatPenaltyTests |
| class | ::BuriedUnsatPenaltySymmetricTests |
Additional Inherited Members | |
| Protected Member Functions inherited from core::scoring::methods::EnergyMethod | |
| void | set_score_types (EnergyMethodCreatorOP creator) |
| Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More... | |
Detailed Description
BuriedUnsatPenalty, an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors or acceptors.
This class is derived from base class WholeStructureEnergy, which is meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of scorefunction evaluation.
Member Typedef Documentation
◆ parent1
| typedef core::scoring::methods::WholeStructureEnergy core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::parent1 |
◆ parent2
| typedef core::scoring::annealing::ResidueArrayAnnealableEnergy core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::parent2 |
Constructor & Destructor Documentation
◆ BuriedUnsatPenalty()
| core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::BuriedUnsatPenalty | ( | core::scoring::methods::EnergyMethodOptions const & | options | ) |
Options constructor.
◆ ~BuriedUnsatPenalty()
|
override |
Default destructor.
Member Function Documentation
◆ add_to_list_of_partners_of_changed_nodes()
|
private |
Given a list of changed node indices and a graph of the current state, determine which nodes share edges with the changed nodes, and add their indices to a list of partners.
Don't add indices that are in the changed_node_indices list or already in the changed_node_partners list.
Referenced by calculate_energy().
◆ calculate_energy()
|
overridevirtual |
Calculate the total energy given a vector of const owning pointers to residues.
Called directly by the ResidueArrayAnnealingEvaluator during packer runs.
- Note
- Outside of the context of the packer, this doesn't behave as expected (and finalize_total_energy() should be called instead).
Called directly by the ResidueArrayAnnealingEvaluator during packer runs. Requires that set_up_residuearrayannealablenergy_for_packing() be called first.
- Note
- Outside of the context of the packer, this doesn't behave as expected (and finalize_total_energy() should be called instead).
Implements core::scoring::annealing::ResidueArrayAnnealableEnergy.
References add_to_list_of_partners_of_changed_nodes(), calculate_penalty_once_almost_from_scratch_using_reference_graph(), compute_penalty(), curstate_graph_, decrement_counts(), disabled_, increment_counts(), nres_, num_symmetric_copies_, oversat_acceptor_and_donor_count_lastaccepted_, oversat_acceptor_count_lastaccepted_, oversat_donor_count_lastaccepted_, symmetric_, core::pack::guidance_scoreterms::buried_unsat_penalty::TR(), unsat_acceptor_and_donor_count_lastaccepted_, unsat_acceptor_count_lastaccepted_, unsat_donor_count_lastaccepted_, and unsat_graph_.
◆ calculate_penalty_once_almost_from_scratch_using_reference_graph()
| core::Real core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_almost_from_scratch_using_reference_graph | ( | utility::vector1< core::conformation::ResidueCOP > const & | resvect, |
| graph::BuriedUnsatPenaltyGraph const & | reference_graph, | ||
| core::Size const | symm_multiplier | ||
| ) | const |
Given a residue vector, calculate the penalty energy using a reference graph.
References compute_penalty(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_all_nodes(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::copy_node_and_connected_edges(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::get_node_index(), graph_options_, hbond_options_, increment_counts(), and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().
Referenced by calculate_energy().
◆ calculate_penalty_once_from_scratch()
| core::Real core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_from_scratch | ( | core::pose::Pose const & | pose | ) | const |
Given a pose, calculate the penalty energy.
References compute_penalty(), core::pose::Pose::conformation_ptr(), graph_options_, hbond_options_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts(), core::pose::symmetry::is_symmetric(), core::pose::Pose::total_residue(), and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().
Referenced by finalize_total_energy().
◆ clean_up_residuearrayannealableenergy_after_packing()
|
overridevirtual |
Delete cached data from the pose and from this EnergyMethod after packing.
Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.
References core::scoring::EnergiesCacheableDataType::BURIED_UNSAT_HBOND_GRAPH, curstate_graph_, core::scoring::Energies::data(), core::pose::Pose::energies(), core::pack::guidance_scoreterms::buried_unsat_penalty::TR(), and unsat_graph_.
◆ clone()
|
overridevirtual |
Clone: create a copy of this object, and return an owning pointer to the copy.
Implements core::scoring::methods::EnergyMethod.
◆ commit_considered_substitution()
|
overridevirtual |
What to do when a substitution that was considered is accepted.
Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.
◆ compute_penalty()
| core::Real core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::compute_penalty | ( | core::Size const | unsat_acceptor_count, |
| core::Size const | unsat_donor_count, | ||
| core::Size const | unsat_acceptor_and_donor_count, | ||
| core::Size const | oversat_acceptor_count, | ||
| core::Size const | oversat_donor_count, | ||
| core::Size const | oversat_acceptor_and_donor_count | ||
| ) | const |
Given the counts of various unsaturateds, return a penalty value.
Referenced by calculate_energy(), calculate_penalty_once_almost_from_scratch_using_reference_graph(), and calculate_penalty_once_from_scratch().
◆ decrement_counts()
|
private |
Decrement the counts based on the current state of the curstate_graph_ and the current changed_node_indices_ and changed_node_partners_ vectors.
Decrement the counts based on the current state of the curstate_graph_ and the current changed_node_indices and changed_node_partners vectors.
References curstate_graph_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::stored_data().
Referenced by calculate_energy().
◆ finalize_after_minimizing()
|
overridevirtual |
Re-enable this scoreterm after a minimization trajectory.
Reimplemented from core::scoring::methods::EnergyMethod.
References disabled_, and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().
◆ finalize_total_energy()
|
overridevirtual |
Actually calculate the total energy.
Called by the scoring machinery. The update_residue_neighbors() function of the pose must be called first.
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::buried_unsatisfied_penalty, calculate_penalty_once_from_scratch(), and disabled_.
◆ increment_counts()
|
private |
Increment the counts based on the current state of the curstate_graph_ and the current changed_node_indices_ and changed_node_partners_ vectors.
Increment the counts based on the current state of the curstate_graph_ and the current changed_node_indices and changed_node_partners vectors.
References curstate_graph_, and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts().
Referenced by calculate_energy(), calculate_penalty_once_almost_from_scratch_using_reference_graph(), and initialize_curstate_graph().
◆ indicate_required_context_graphs()
|
overridevirtual |
BuriedUnsatPenalty is context-independent and thus indicates that no context graphs need to be maintained by class Energies.
Implements core::scoring::methods::EnergyMethod.
◆ initialize_curstate_graph() [1/2]
|
private |
Called from set_up_residuearrayannelableenergy_for_packing(). Initializes the graph structure representing the current state during the packing trajectory.
References core::pose::Pose::conformation(), nres_, and core::conformation::Conformation::residue_cop().
Referenced by set_up_residuearrayannealableenergy_for_packing().
◆ initialize_curstate_graph() [2/2]
|
private |
Initialize the graph structure representing the current state during the packing trajectory from a vector of residues. Called from the first step of calculate_energy().
References curstate_graph_, graph_options_, hbond_options_, increment_counts(), nres_, oversat_acceptor_and_donor_count_lastaccepted_, oversat_acceptor_count_lastaccepted_, oversat_donor_count_lastaccepted_, unsat_acceptor_and_donor_count_lastaccepted_, unsat_acceptor_count_lastaccepted_, unsat_donor_count_lastaccepted_, and unsat_graph_.
◆ provide_citation_info()
|
overridevirtual |
Provide the citation.
Reimplemented from core::scoring::methods::EnergyMethod.
◆ provide_pymol_commands_to_show_groups()
| void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::provide_pymol_commands_to_show_groups | ( | std::ostream & | out, |
| core::pose::Pose const & | pose | ||
| ) | const |
Provide Pymol commands to colour the pose grey, non-buried donor and acceptor groups cyan, and buried acceptor and donor groups orange. Useful for debugging degree of burial.
To use, pass in a pose. If this graph contains residues corresponding to those in the pose, commands for colouring them will be written out. Calls BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups(). Must be called only after set_up_residuearrayannealableenergy_for_packing.
References core::conformation::membrane::out, and unsat_graph_.
Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate().
◆ report()
| void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::report | ( | ) | const |
Get a summary of all loaded data.
References core::pack::guidance_scoreterms::buried_unsat_penalty::TR().
◆ set_prevent_pruning()
|
inline |
Should the graph setup-for-packing skip the step in which groups that are not packable and not able to hydrogen bond to a packable residue are pruned? Default false; this function allows this to be set, though.
References prevent_pruning_.
Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate().
◆ set_up_residuearrayannealableenergy_for_packing()
|
overridevirtual |
Cache data from the pose in this EnergyMethod in anticipation of packing.
Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.
References core::scoring::EnergiesCacheableDataType::BURIED_UNSAT_HBOND_GRAPH, core::pose::Pose::clone(), core::pose::Pose::conformation_ptr(), core::scoring::Energies::data(), core::pose::Pose::energies(), graph_options_, hbond_options_, initialize_curstate_graph(), core::pose::symmetry::is_symmetric(), nres_, num_symmetric_copies_, prevent_pruning_, symmetric_, core::pose::Pose::total_residue(), core::pack::guidance_scoreterms::buried_unsat_penalty::TR(), and unsat_graph_.
Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate().
◆ setup_for_minimizing()
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overridevirtual |
Disable this scoreterm during minimization trajectory.
Reimplemented from core::scoring::methods::EnergyMethod.
References disabled_, and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().
◆ version()
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overridevirtual |
BuriedUnsatPenalty is version 1.0 right now.
Implements core::scoring::methods::EnergyMethod.
Friends And Related Function Documentation
◆ ::BuriedUnsatPenaltySymmetricTests
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friend |
◆ ::BuriedUnsatPenaltyTests
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friend |
Member Data Documentation
◆ curstate_graph_
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mutableprivate |
The graph representing the last accepted state during the packer trajectory.
Referenced by calculate_energy(), clean_up_residuearrayannealableenergy_after_packing(), decrement_counts(), increment_counts(), and initialize_curstate_graph().
◆ disabled_
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mutableprivate |
Is this scoreterm currently disabled (e.g. for a minimization trajectory)?
Referenced by calculate_energy(), finalize_after_minimizing(), finalize_total_energy(), and setup_for_minimizing().
◆ graph_options_
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private |
Options for the BruiedUnsatPenaltyGraph.
Referenced by calculate_penalty_once_almost_from_scratch_using_reference_graph(), calculate_penalty_once_from_scratch(), initialize_curstate_graph(), and set_up_residuearrayannealableenergy_for_packing().
◆ hbond_options_
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private |
Options for hydrogen bonds.
Referenced by calculate_penalty_once_almost_from_scratch_using_reference_graph(), calculate_penalty_once_from_scratch(), initialize_curstate_graph(), and set_up_residuearrayannealableenergy_for_packing().
◆ nres_
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private |
How many residues are in the asymmetric unit of a symmetric pose (symmetric case) or in a pose (asymmetric case)? Used during packing only.
Referenced by calculate_energy(), initialize_curstate_graph(), and set_up_residuearrayannealableenergy_for_packing().
◆ num_symmetric_copies_
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private |
The number of symmetry copies. Used for packing only.
Referenced by calculate_energy(), and set_up_residuearrayannealableenergy_for_packing().
◆ oversat_acceptor_and_donor_count_lastaccepted_
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mutableprivate |
The oversat acceptor and donor counts last accepted.
Referenced by calculate_energy(), and initialize_curstate_graph().
◆ oversat_acceptor_count_lastaccepted_
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mutableprivate |
The oversat acceptor counts last accepted.
Referenced by calculate_energy(), and initialize_curstate_graph().
◆ oversat_donor_count_lastaccepted_
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mutableprivate |
The oversat donor counts last accepted.
Referenced by calculate_energy(), and initialize_curstate_graph().
◆ prevent_pruning_
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private |
Should the graph setup-for-packing skip the step in which groups that are not packable and not able to hydrogen bond to a packable residue are pruned? Default false.
Referenced by set_prevent_pruning(), and set_up_residuearrayannealableenergy_for_packing().
◆ symmetric_
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private |
Is this pose symmetric? Used during packing only.
Referenced by calculate_energy(), and set_up_residuearrayannealableenergy_for_packing().
◆ unsat_acceptor_and_donor_count_lastaccepted_
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mutableprivate |
The unsat acceptor and donor counts last accepted.
Referenced by calculate_energy(), and initialize_curstate_graph().
◆ unsat_acceptor_count_lastaccepted_
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mutableprivate |
The unsat acceptor counts last accepted.
Referenced by calculate_energy(), and initialize_curstate_graph().
◆ unsat_donor_count_lastaccepted_
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mutableprivate |
The unsat donor counts last accepted.
Referenced by calculate_energy(), and initialize_curstate_graph().
◆ unsat_graph_
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private |
Pointer to buried unsaturated penalty graph in the pose. Stored during packing to avoid repeated lookups.
Referenced by calculate_energy(), clean_up_residuearrayannealableenergy_after_packing(), initialize_curstate_graph(), provide_pymol_commands_to_show_groups(), and set_up_residuearrayannealableenergy_for_packing().
The documentation for this class was generated from the following files:
- src/core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenalty.hh
- src/core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenalty.cc
