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protocols::hbnet::HBNetStapleInterface Class Reference

#include <HBNetStapleInterface.hh>

Inheritance diagram for protocols::hbnet::HBNetStapleInterface:
Inheritance graph
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Public Member Functions

 HBNetStapleInterface ()
 
 HBNetStapleInterface (std::string const name)
 
 HBNetStapleInterface (core::scoring::ScoreFunctionCOP scorefxn, core::Size max_unsat_Hpol, core::Size min_network_size=3, core::Real hb_threshold=-0.5, core::Size max_network_size=15, std::string des_residues="STRKHYWNQDE", bool find_native=false, bool only_native=false, bool keep_existing=false, bool extend_existing=false, bool only_extend=false)
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
 ~HBNetStapleInterface () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void setup_packer_task_and_starting_residues (core::pose::Pose const &pose) override
 
void prepare_output () override
 
std::string print_additional_info_for_net (HBondNetStruct &i, core::pose::Pose const &pose) override
 
std::string print_additional_headers () override
 
bool network_meets_initial_criteria (HBondNetStruct const &network) override
 initial criteria for screening that just reuqires HBondNetStruct (no scoring or placement of rotamers on the pose) More...
 
bool network_meets_final_criteria (core::pose::Pose const &pose, HBondNetStruct &network) override
 final criteria that reuqires network rotamers placed on pose More...
 
bool state_is_starting_aa_type (core::Size const res, core::Size const rot_id) override
 
bool pair_meets_starting_criteria (core::Size const res1, core::Size const rot1, core::Size const res2, core::Size const rot2) override
 
core::Real scale_twobody_energy (core::Real input_twobody_energy, char res1, char res2) override
 
bool same_helix (utility::vector1< std::pair< core::Size, core::Size > > const helix_boundaries, core::Size const r1, core::Size const r2)
 
bool interhelical_contact (utility::vector1< std::pair< core::Size, core::Size > > const helix_boundaries, core::Size const r1, core::Size const r2, core::pose::Pose const &pose)
 
core::Size get_helix_id (core::Size r1) const
 
void rec_add_staple (std::vector< HBondNetStructOP >::const_iterator netit, std::set< core::Size > net_ids, core::Size staple_count)
 
bool network_spans_all_helices (HBondNetStruct const &i) const
 
core::Size num_helices_w_hbond (HBondNetStruct const &i) const
 
core::Size num_helices_w_hbond (utility::vector1< HBondResStructCOP > const &residues) const
 
bool has_pH_His (core::pose::Pose const &pose, HBondNetStruct &i)
 
bool residues_are_interface_pairs (core::Size const res1, core::Size const res2)
 
core::Size num_intermolecular_hbonds (HBondNetStruct &i, core::pose::Pose const &pose)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::hbnet::HBNet
 HBNet ()
 
 HBNet (std::string const name)
 
 HBNet (core::scoring::ScoreFunctionCOP scorefxn, core::Size max_unsat, core::Size min_network_size=3, core::Real hb_threshold=-0.75, core::Size max_network_size=15, std::string des_residues="STRKHYWNQDE", bool find_native=false, bool only_native=false, bool keep_existing=false, bool extend_existing=false, bool only_extend=false)
 
 ~HBNet () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
virtual void trim_additional_rotamers (core::pose::Pose &)
 
virtual void search_IG_for_networks (core::pose::Pose &pose)
 
core::Real upweight_starting_twobody_energy ()
 
virtual core::Size ligand ()
 
bool symmetric () const
 
void symmetric (bool const is_symmetric_pose)
 
core::conformation::symmetry::SymmetryInfoCOP get_symm_info () const
 
void set_symm_info (core::conformation::symmetry::SymmetryInfoCOP const &symminfo)
 
bool multi_component () const
 
void multi_component (bool const multi_component)
 
bool verbose () const
 
void verbose (bool const set_verbose)
 
bool pdb_numbering () const
 
void pdb_numbering (bool const pdb_numbering)
 
std::set< core::Sizeget_start_res_vec ()
 
void add_start_res (core::Size res)
 
void set_start_res_vec (std::set< core::Size > const start_resnums)
 
void set_start_resnums (std::set< core::Size > const start_resnums)
 
core::pack::task::PackerTaskOP get_task () const
 
void set_task (core::pack::task::PackerTaskOP const &task)
 
void task_factory (core::pack::task::TaskFactoryOP const &task_factory)
 
core::pack::task::TaskFactoryOP task_factory () const
 
void set_core_residues (core::select::residue_selector::ResidueSubset core_residues)
 
core::select::residue_selector::ResidueSubset get_core_residues ()
 
core::select::residue_selector::ResidueSelectorOP get_core_selector ()
 
void set_boundary_residues (core::select::residue_selector::ResidueSubset boundary_residues)
 
core::select::residue_selector::ResidueSubset get_boundary_residues ()
 
core::select::residue_selector::ResidueSelectorOP get_boundary_selector ()
 
void update_core_and_boundary_residues (core::pose::Pose const &pose)
 
void set_upweight_starting_twobody (core::Real upweight_factor)
 
std::vector< HBondNetStructOP > & get_net_vec ()
 return all hbond networks, sorted with best networks at the front, THIS SHOULD RETURN A POINTER (OP) More...
 
std::vector< HBondNetStructOP > & get_native_vec ()
 
std::vector< std::set
< core::Size > > & 
get_output_vector ()
 
HBondNetStructOP get_network_by_id (core::Size id)
 
core::pose::Pose const & get_orig_pose ()
 
void set_orig_pose (core::pose::Pose &pose)
 
core::pose::Pose const & get_ala_pose ()
 
void set_ala_pose (core::pose::Pose &pose)
 
char get_aa_for_state (core::Size const res, core::Size const rot) const
 
bool res_is_boundary (core::Size const res) const
 
bool res_is_core (core::Size const res) const
 
void set_min_networks_size (core::Size min)
 
void set_max_networks_size (core::Size max)
 
void set_max_unsat (core::Size max)
 
core::Size get_min_networks_size ()
 
core::Size get_max_networks_size ()
 
core::Size get_max_unsat ()
 
void set_find_native (bool native)
 
bool find_native ()
 
void set_find_only_native (bool only)
 
bool only_native ()
 
void set_keep_existing_networks (bool keep_existing_networks)
 
bool get_keep_existing_networks ()
 
void set_extend_existing_networks (bool extend_existing_networks)
 
bool get_extend_existing_networks ()
 
void set_only_extend_existing (bool only_extend_existing)
 
bool get_only_extend_existing ()
 
utility::graph::GraphOP get_packer_graph ()
 
core::Size num_core_res (HBondNetStruct const &network)
 
core::Size num_boundary_res (HBondNetStruct const &network)
 
void select_best_networks ()
 
std::vector< HBondNetStructOPget_networks ()
 
void set_score_function (core::scoring::ScoreFunctionCOP const &sf)
 
bool net_clash (HBondNetStruct const &i, HBondNetStruct const &j)
 checks if two h-bond networks clash; returns true if they do clash More...
 
void set_symmetry (core::pose::Pose &pose)
 
core::Size get_ind_res (core::pose::Pose const &pose, core::Size const res_i)
 
bool quick_and_dirty_network_has_heavy_atom_unsat (core::pose::Pose const &pose, HBondNetStruct const &network)
 
bool quick_and_dirty_heavy_atom_is_unsat (core::pose::Pose const &pose, core::id::AtomID const at_id)
 
bool atom_hbonds_to_bridging_water (core::pose::Pose const &pose, core::id::AtomID const at_id)
 
void find_unsats (core::pose::Pose const &pose, HBondNetStruct &i)
 
utility::vector1< core::Sizeplace_rots_on_pose (core::pose::Pose &pose, HBondNetStruct &residues, bool use_pose=false)
 places the rotamers of the provided h-bond network onto the provided pose More...
 
core::Size get_num_native_rot (core::pose::Pose &pose, utility::vector1< HBondResStructCOP > const &residues, core::Real sc_rmsd_cut=0.25, bool super=true)
 return the number of rotamers in a network that are identical in seq or rot to the original input pose: More...
 
core::Size get_num_native_seq (core::pose::Pose &pose, utility::vector1< HBondResStructCOP > const &residues)
 
bool water_clashes (core::pose::Pose const &pose, core::Vector const water_O)
 
bool water_oxygen_clashes_with_residue (core::Vector const water_oxygen, core::Size const resnum, int const rot_state)
 
bool water_oxygen_clashes_with_residue (core::Vector const water_oxygen, core::conformation::Residue const &res)
 
core::pose::PoseOP get_additional_output () override
 used by the job distributor and MultiplePoseMover (MPM) to return poses OTF as requested (without need to store in memory) More...
 
std::string get_file_name (core::Size id, std::string prefix, std::string extension)
 
void set_monte_carlo_branch (bool setting)
 turn on or off the monte carlo branching protocol More...
 
void set_total_num_mc_runs (core::Size setting)
 set number of monte carlo runs to be divided over all the seed hbonds. A single monte carlo run appears to take roughly 1 ms (very loose estimate). More...
 
void set_monte_carlo_seed_threshold (core::Real setting)
 Maybe you only want to branch from strong hbonds. If this value is -1.2, then only hbonds with a strength of -1.2 or lower will be branched from. More...
 
void set_monte_carlo_seed_must_be_buried (bool setting)
 Only branch from hbonds where at least one residue is buried. Effectively, this results in only finding networks that have at least one buried residue. More...
 
void set_monte_carlo_seed_must_be_fully_buried (bool setting)
 Only branch from hbonds where both residues are buried. This results in only finding networks that have at least one buried hbond but this does not prevent having additional exposed hbonds. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::hbnet::HBNet
static std::string mover_name ()
 
static void attributes_for_hbnet (utility::tag::AttributeList &)
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Protected Member Functions

bool edge_can_yield_monte_carlo_seed (core::Size resid1, core::Size resid2) const override
 The edge_can_yield_monte_carlo_seed() methods determine if a hydrogen bond can be used as a seed for monte carlo branching. Examples of when this might fail include when the hbond does not cross the interface (for HBNetStapleInterface) or when the hbond is not buried to the level of the user's specifications. More...
 
- Protected Member Functions inherited from protocols::hbnet::HBNet
void setup (core::pose::Pose const &pose)
 sets up rotamer_sets and makes preparations for populating the IG based on task_ops More...
 
void get_native_networks (core::pose::Pose const &pose)
 
void run (core::pose::Pose &pose)
 run common steps universal to all HBNet, e.g. finalize rotamer sets and scoring then populate and search IG for networks. More...
 
void trim_rotamers (core::pose::Pose &pose)
 remove unwanted rotamers from rotamer_sets_ before IG is populated and searched. calls virtual trim_additional_rotamers() that can be overriden by specialized HBNet classes to remove additional rotmaers More...
 
void traverse_native (core::pose::Pose const &pose, core::Real const hb_threshold)
 Do a recursive traversal of an EnergyGraph of a static pose; will find and store all native h-bond networks, regardless of score/parameters. More...
 
void rec_trav_native (core::pose::Pose const &pose, core::Size new_res, core::Size prev_res, utility::vector1< HBondResStructCOP > residues, core::Real const hb_threshold)
 
void traverse_IG (core::Real const hb_threshold)
 Recursively traverse the Interaction Graph ig_, and find all possible h-bond networks, given the parameters that have been set. More...
 
void recursive_traverse (int const new_node_ind, int const newstate, core::Size const newres, core::Size const prevres, utility::vector1< HBondResStructCOP > residues, core::Size network_rec_count, core::Real init_sc, core::Real const hb_threshold, bool const second_search=false)
 
void MC_traverse_IG ()
 A monte carlo alternative to traverse_IG() and recursive_traverse(). Basically just populates hbond_graph_. More...
 
bool network_already_stored (utility::vector1< HBondResStructCOP > &residues, utility::vector1< HBondResStructCOP > &i_residues)
 for efficiency, makes sure that an equivalent network has not already been stored More...
 
void store_network (utility::vector1< HBondResStructCOP > residues, core::Real init_score=0.0, bool term_w_start=false, bool term_w_cycle=false, bool score_now=false, bool native=false)
 
void score_network_on_pose (core::pose::Pose &pose, HBondNetStruct &i)
 void score_networks( bool minimize=false); More...
 
void minimize_network (core::pose::Pose &pose, HBondNetStruct &network, bool residues_already_placed=true)
 
bool check_clash (utility::vector1< HBondResStructCOP > const &residues, platform::uint my_node_ind, core::Size mystate, core::Size myres, core::Real &init_score, bool &cycle)
 check if a residue clashes with other reisdues in the network before adding it to the h-bond network. true = clashes More...
 
bool net_clash (utility::vector1< HBondResStructCOP > const &residues_i, utility::vector1< HBondResStructCOP > const &residues_j)
 used by net_clash( HBondNetStruct & i, HBondNetStruct & j ), should not be called externally! More...
 
bool monte_carlo_net_clash (utility::vector1< HBondResStructCOP > const &residues_i, utility::vector1< HBondResStructCOP > const &residues_j) const
 monte carlo protocol needs to use a different net_clash call because its IG is not populated More...
 
void branch_overlapping_networks ()
 This function finds all networks that share a common rotamer, and then for ones that do not clash, branches them together in all possible combination to find all possible networks. More...
 
void rec_set_intersection (std::vector< core::Size > add_index_vec, std::vector< core::Size > next_index_list, core::Size pos)
 used by branch_overlapping() to efficiently search for all combinations of compatible networks that can be merged More...
 
void MC_branch_overlapping_networks ()
 monte carlo alternative to branch_overlapping_networks(). Requires MC_traverse_IG() to be called ahead of time. Theoretically O( total_num_mc_runs_ ) More...
 
void merge_2_branched_networks (HBondNetStruct const &i, HBondNetStruct const &j, HBondNetStructOP new_network)
 Merges 2 networks (i,j) into a single h-bond network, new_network. More...
 
void merge_2_branched_networks (utility::vector1< HBondResStructCOP > const &residues1, utility::vector1< HBondResStructCOP > const &residues2, utility::vector1< HBondResStructCOP > &new_residues)
 
bool networks_unique (HBondNetStruct const &i, HBondNetStruct const &j, bool no_surface=true)
 
bool networks_identical_aa_sequence (HBondNetStruct const &i, HBondNetStruct const &j)
 
bool residues_identical (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)
 
bool residues_not_unique (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)
 
bool is_sub_residues (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)
 Returns true if a network is a subset of another; it's symmetric, i.e. returns true if i is subset of j, or if j is a subset of i. More...
 
bool is_sub_residues (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2, bool &branch, bool true_if_identical=true)
 
void remove_replicate_networks (core::Size same_max=1)
 Sorts all networks by score, removes replicate networks and networks > upper_score_limit; also removes subnetworks if store_subnetworks=false. More...
 
void output_networks (bool finalize=false)
 Writes h-bond networks out to TR, and stores them in output_net_vec_ if finalize=true so they can be returned by get_additional_output(). More...
 
core::pack::task::PackerTaskOP create_ptask (core::pose::Pose const &pose, bool initialize_from_commandline=false)
 
bool task_is_valid (core::pose::Pose const &pose) const
 
bool store_network_scores_in_pose () const
 
void store_network_scores_in_pose (bool setting)
 
void write_network_pdb (HBondNetStructOP &p)
 
void set_constraints (core::pose::Pose &pose, core::scoring::constraints::ConstraintSet &constraints, HBondNetStruct &p, bool write_cst_file=false)
 
core::Size chain_for_resid (core::Size resid) const
 
core::Size chain_for_moltenres (core::Size mres) const
 
void set_monte_carlo_data_to_default ()
 
void initialize_hbond_graph ()
 This transfers rotamer sets data to hbond_graph_. Need to call this before traversing the IG. More...
 
void register_clash (core::Size rotamerA, core::Size rotamerB)
 
virtual bool edge_can_yield_monte_carlo_seed (core::pack::interaction_graph::EdgeBase const *) const
 
core::scoring::hbonds::graph::HBondNodeget_next_node (NetworkState &current_state)
 get_next_node() randomly decides how the current_state will grow during the monte carlo branching protocol More...
 
bool monte_carlo_seed_is_dead_end (core::scoring::hbonds::graph::HBondEdge const *monte_carlo_seed)
 returns true if this hbond can not create a network More...
 
void append_to_network_vector (utility::vector1< DecoratedNetworkState > const &designed_networks)
 called at the end of the monte carlo branching protocol. Adds all of the monte carlo networks to the data elements used by the traditional HBNet protocol More...
 
void add_residue_to_network_state (NetworkState &current_state, core::scoring::hbonds::graph::HBondNode *node_being_added) const
 
bool network_state_is_satisfied (NetworkState &current_state) const
 quick and dirty satisfaction check More...
 
void score_network_state (NetworkState &state) const
 evaluates state and stores the score in state.score More...
 
bool register_new_network (NetworkState &current_network_state, utility::vector0< std::list< utility::vector1< core::Size > > > &hash_table, std::list< NetworkState > &designed_networks) const
 
bool node_is_compatible (NetworkState const &current_state, core::scoring::hbonds::graph::HBondNode const *node_being_added)
 returns false if there is a clash between the node_being_added and any node currently in the current_state More...
 
bool network_state_is_done_growing (NetworkState const &current_state, core::scoring::hbonds::graph::HBondGraphCOP hbond_graph)
 This is only being used for debug purposes right now. Makes sure that there are no possible nodes that can be added to current_state. More...
 
core::Real estimate_saturation (NetworkState const &) const
 TODO. More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Private Attributes

bool all_helices_
 
bool span_all_helices_
 
bool only_symm_interfaces_
 
bool allow_onebody_networks_
 
bool his_tyr_
 
bool pH_His_
 
bool at_least_one_net_w_aromatic_sc_
 
bool at_least_one_net_spans_all_helices_
 
bool at_least_one_net_fully_satisfied_
 
bool boundary_his_must_to_hbond_pos_charge_
 
bool only_start_at_interface_pairs_
 
bool use_aa_dependent_weights_
 
core::Size min_networks_per_pose_
 
core::Size max_networks_per_pose_
 
core::Size combos_
 
core::Size min_intermolecular_hbonds_
 
core::Size min_helices_contacted_by_network_
 
core::Size min_asp_glu_hbonds_
 
core::Real interf_distance_
 
utility::vector1< core::Sizejump_nums_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
helix_boundaries_
 
utility::vector1< std::list
< core::Size > > 
pair_lists_vec_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Constructor & Destructor Documentation

protocols::hbnet::HBNetStapleInterface::HBNetStapleInterface ( )
protocols::hbnet::HBNetStapleInterface::HBNetStapleInterface ( std::string const  name)
protocols::hbnet::HBNetStapleInterface::HBNetStapleInterface ( core::scoring::ScoreFunctionCOP  scorefxn,
core::Size  max_unsat_Hpol,
core::Size  min_network_size = 3,
core::Real  hb_threshold = -0.5,
core::Size  max_network_size = 15,
std::string  des_residues = "STRKHYWNQDE",
bool  find_native = false,
bool  only_native = false,
bool  keep_existing = false,
bool  extend_existing = false,
bool  only_extend = false 
)
protocols::hbnet::HBNetStapleInterface::~HBNetStapleInterface ( )
overridedefault

Member Function Documentation

moves::MoverOP protocols::hbnet::HBNetStapleInterface::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::hbnet::HBNet.

bool protocols::hbnet::HBNetStapleInterface::edge_can_yield_monte_carlo_seed ( core::Size  resid1,
core::Size  resid2 
) const
inlineoverrideprotectedvirtual

The edge_can_yield_monte_carlo_seed() methods determine if a hydrogen bond can be used as a seed for monte carlo branching. Examples of when this might fail include when the hbond does not cross the interface (for HBNetStapleInterface) or when the hbond is not buried to the level of the user's specifications.

Reimplemented from protocols::hbnet::HBNet.

References all_helices_, protocols::hbnet::HBNet::chain_for_resid(), protocols::hbnet::HBNet::edge_can_yield_monte_carlo_seed(), and protocols::hbnet::HBNet::symmetric().

moves::MoverOP protocols::hbnet::HBNetStapleInterface::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::hbnet::HBNet.

Size protocols::hbnet::HBNetStapleInterface::get_helix_id ( core::Size  r1) const

returns false if residues is not part of a helix

References helix_boundaries_.

Referenced by num_helices_w_hbond().

std::string protocols::hbnet::HBNetStapleInterface::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Reimplemented from protocols::hbnet::HBNet.

References mover_name().

bool protocols::hbnet::HBNetStapleInterface::has_pH_His ( core::pose::Pose const &  pose,
HBondNetStruct i 
)
bool protocols::hbnet::HBNetStapleInterface::interhelical_contact ( utility::vector1< std::pair< core::Size, core::Size > > const  helix_boundaries,
core::Size const  r1,
core::Size const  r2,
core::pose::Pose const &  pose 
)

returns false if either of the residues are not Helix (H); returns true if residues contact eachother from different helices (interhelical contact)

References interf_distance_, core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and same_helix().

Referenced by setup_packer_task_and_starting_residues().

std::string protocols::hbnet::HBNetStapleInterface::mover_name ( )
static
bool protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria ( core::pose::Pose const &  ,
HBondNetStruct  
)
overridevirtual
bool protocols::hbnet::HBNetStapleInterface::network_meets_initial_criteria ( HBondNetStruct const &  )
overridevirtual

initial criteria for screening that just reuqires HBondNetStruct (no scoring or placement of rotamers on the pose)

Reimplemented from protocols::hbnet::HBNet.

References min_helices_contacted_by_network_, num_helices_w_hbond(), and protocols::hbnet::HBNet::symmetric().

bool protocols::hbnet::HBNetStapleInterface::network_spans_all_helices ( HBondNetStruct const &  i) const

References helix_boundaries_, and num_helices_w_hbond().

Referenced by prepare_output().

Size protocols::hbnet::HBNetStapleInterface::num_helices_w_hbond ( HBondNetStruct const &  i) const
Size protocols::hbnet::HBNetStapleInterface::num_helices_w_hbond ( utility::vector1< HBondResStructCOP > const &  residues) const
Size protocols::hbnet::HBNetStapleInterface::num_intermolecular_hbonds ( HBondNetStruct i,
core::pose::Pose const &  pose 
)
bool protocols::hbnet::HBNetStapleInterface::pair_meets_starting_criteria ( core::Size const  res1,
core::Size const  rot1,
core::Size const  res2,
core::Size const  rot2 
)
overridevirtual
void protocols::hbnet::HBNetStapleInterface::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::hbnet::HBNetStapleInterface::prepare_output ( )
overridevirtual
std::string protocols::hbnet::HBNetStapleInterface::print_additional_headers ( )
overridevirtual
std::string protocols::hbnet::HBNetStapleInterface::print_additional_info_for_net ( HBondNetStruct i,
core::pose::Pose const &  pose 
)
overridevirtual
void protocols::hbnet::HBNetStapleInterface::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::hbnet::HBNetStapleInterface::rec_add_staple ( std::vector< HBondNetStructOP >::const_iterator  netit,
std::set< core::Size net_ids,
core::Size  staple_count 
)
bool protocols::hbnet::HBNetStapleInterface::residues_are_interface_pairs ( core::Size const  res1,
core::Size const  res2 
)
bool protocols::hbnet::HBNetStapleInterface::same_helix ( utility::vector1< std::pair< core::Size, core::Size > > const  helix_boundaries,
core::Size const  r1,
core::Size const  r2 
)

Referenced by interhelical_contact().

Real protocols::hbnet::HBNetStapleInterface::scale_twobody_energy ( core::Real  input_twobody_energy,
char  res1,
char  res2 
)
overridevirtual

Reimplemented from protocols::hbnet::HBNet.

References use_aa_dependent_weights_.

void protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues ( core::pose::Pose const &  pose)
overridevirtual
bool protocols::hbnet::HBNetStapleInterface::state_is_starting_aa_type ( core::Size const  res,
core::Size const  rot_id 
)
overridevirtual

Member Data Documentation

bool protocols::hbnet::HBNetStapleInterface::all_helices_
private
bool protocols::hbnet::HBNetStapleInterface::allow_onebody_networks_
private

Referenced by parse_my_tag().

bool protocols::hbnet::HBNetStapleInterface::at_least_one_net_fully_satisfied_
private

Referenced by parse_my_tag(), and prepare_output().

bool protocols::hbnet::HBNetStapleInterface::at_least_one_net_spans_all_helices_
private
bool protocols::hbnet::HBNetStapleInterface::at_least_one_net_w_aromatic_sc_
private

Referenced by parse_my_tag(), and prepare_output().

bool protocols::hbnet::HBNetStapleInterface::boundary_his_must_to_hbond_pos_charge_
private

Referenced by parse_my_tag().

core::Size protocols::hbnet::HBNetStapleInterface::combos_
private

Referenced by parse_my_tag(), and rec_add_staple().

utility::vector1< std::pair< core::Size, core::Size > > protocols::hbnet::HBNetStapleInterface::helix_boundaries_
private
bool protocols::hbnet::HBNetStapleInterface::his_tyr_
private
core::Real protocols::hbnet::HBNetStapleInterface::interf_distance_
private
utility::vector1< core::Size > protocols::hbnet::HBNetStapleInterface::jump_nums_
private
core::Size protocols::hbnet::HBNetStapleInterface::max_networks_per_pose_
private
core::Size protocols::hbnet::HBNetStapleInterface::min_asp_glu_hbonds_
private
core::Size protocols::hbnet::HBNetStapleInterface::min_helices_contacted_by_network_
private
core::Size protocols::hbnet::HBNetStapleInterface::min_intermolecular_hbonds_
private
core::Size protocols::hbnet::HBNetStapleInterface::min_networks_per_pose_
private
bool protocols::hbnet::HBNetStapleInterface::only_start_at_interface_pairs_
private
bool protocols::hbnet::HBNetStapleInterface::only_symm_interfaces_
private
utility::vector1< std::list< core::Size > > protocols::hbnet::HBNetStapleInterface::pair_lists_vec_
private
bool protocols::hbnet::HBNetStapleInterface::pH_His_
private
bool protocols::hbnet::HBNetStapleInterface::span_all_helices_
private
bool protocols::hbnet::HBNetStapleInterface::use_aa_dependent_weights_
private

The documentation for this class was generated from the following files: