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core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty Class Reference

BuriedUnsatPenalty, an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors or acceptors. More...

#include <BuriedUnsatPenalty.hh>

Inheritance diagram for core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty:
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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 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

Constructor & Destructor Documentation

core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::BuriedUnsatPenalty ( core::scoring::methods::EnergyMethodOptions const &  options)

Options constructor.

core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::~BuriedUnsatPenalty ( )
override

Default destructor.

Member Function Documentation

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::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
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().

core::Real core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_energy ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
utility::vector1< core::Size > const &  rotamer_ids,
core::Size const  substitution_position = 0 
) const
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_, unsat_acceptor_and_donor_count_lastaccepted_, unsat_acceptor_count_lastaccepted_, unsat_donor_count_lastaccepted_, and unsat_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
core::Real core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_from_scratch ( core::pose::Pose const &  pose) const
void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::clean_up_residuearrayannealableenergy_after_packing ( core::pose::Pose pose)
overridevirtual
core::scoring::methods::EnergyMethodOP core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::clone ( ) const
overridevirtual

Clone: create a copy of this object, and return an owning pointer to the copy.

Implements core::scoring::methods::EnergyMethod.

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::commit_considered_substitution ( )
overridevirtual

What to do when a substitution that was considered is accepted.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.

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().

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::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
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_, and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts().

Referenced by calculate_energy().

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::finalize_after_minimizing ( core::pose::Pose pose) const
overridevirtual

Re-enable this scoreterm after a minimization trajectory.

Reimplemented from core::scoring::methods::EnergyMethod.

References disabled_.

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::finalize_total_energy ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  sfxn,
core::scoring::EnergyMap totals 
) const
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_.

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::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
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().

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const
overridevirtual

BuriedUnsatPenalty is context-independent and thus indicates that no context graphs need to be maintained by class Energies.

Implements core::scoring::methods::EnergyMethod.

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::initialize_curstate_graph ( core::pose::Pose const &  pose)
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(), and nres_.

Referenced by set_up_residuearrayannealableenergy_for_packing().

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::initialize_curstate_graph ( utility::vector1< core::conformation::ResidueCOP > const &  resvect)
private
void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const
overridevirtual

Provide the citation.

Reimplemented from core::scoring::methods::EnergyMethod.

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 unsat_graph_.

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::report ( ) const

Get a summary of all loaded data.

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_prevent_pruning ( bool const  setting)
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_.

void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing ( core::pose::Pose pose,
core::pack::rotamer_set::RotamerSets const &  rotamersets,
core::scoring::ScoreFunction const &  sfxn 
)
overridevirtual
void core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::setup_for_minimizing ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  sfxn,
core::kinematics::MinimizerMapBase const &  minmap 
) const
overridevirtual

Disable this scoreterm during minimization trajectory.

Reimplemented from core::scoring::methods::EnergyMethod.

References disabled_.

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::version ( ) const
overridevirtual

BuriedUnsatPenalty is version 1.0 right now.

Implements core::scoring::methods::EnergyMethod.

Friends And Related Function Documentation

friend class ::BuriedUnsatPenaltySymmetricTests
friend
friend class ::BuriedUnsatPenaltyTests
friend

Member Data Documentation

graph::BuriedUnsatPenaltyGraphOP core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::curstate_graph_
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().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::disabled_
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::BuriedUnsatPenaltyGraphOptionsOP core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::graph_options_
private
core::scoring::hbonds::HBondOptionsOP core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::hbond_options_
private
core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::nres_
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().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::num_symmetric_copies_
private

The number of symmetry copies. Used for packing only.

Referenced by calculate_energy(), and set_up_residuearrayannealableenergy_for_packing().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::oversat_acceptor_and_donor_count_lastaccepted_
mutableprivate

The oversat acceptor and donor counts last accepted.

Referenced by calculate_energy(), and initialize_curstate_graph().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::oversat_acceptor_count_lastaccepted_
mutableprivate

The oversat acceptor counts last accepted.

Referenced by calculate_energy(), and initialize_curstate_graph().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::oversat_donor_count_lastaccepted_
mutableprivate

The oversat donor counts last accepted.

Referenced by calculate_energy(), and initialize_curstate_graph().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::prevent_pruning_
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().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::symmetric_
private

Is this pose symmetric? Used during packing only.

Referenced by calculate_energy(), and set_up_residuearrayannealableenergy_for_packing().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::unsat_acceptor_and_donor_count_lastaccepted_
mutableprivate

The unsat acceptor and donor counts last accepted.

Referenced by calculate_energy(), and initialize_curstate_graph().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::unsat_acceptor_count_lastaccepted_
mutableprivate

The unsat acceptor counts last accepted.

Referenced by calculate_energy(), and initialize_curstate_graph().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::unsat_donor_count_lastaccepted_
mutableprivate

The unsat donor counts last accepted.

Referenced by calculate_energy(), and initialize_curstate_graph().

graph::BuriedUnsatPenaltyGraphCOP core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::unsat_graph_
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: