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protocols::hotspot_hashing::HotspotStubSet Class Reference

#include <HotspotStubSet.hh>

Inheritance diagram for protocols::hotspot_hashing::HotspotStubSet:
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Public Types

typedef std::multimap
< core::Real, HotspotStubOP
Hotspots
 
typedef std::map< std::string,
Hotspots
Hs_map
 
typedef std::pair< std::string,
std::pair< core::Real,
HotspotStubOP > > 
Hs_data
 
typedef std::vector< Hs_dataHs_vec
 
typedef Hs_vec::iterator iterator
 
typedef Hs_vec::const_iterator const_iterator
 

Public Member Functions

 HotspotStubSet ()
 
 HotspotStubSet (HotspotStubSet const &init)
 
 HotspotStubSet (HotspotStubSet &&)=default
 Move constructor (mainly for copy/swap idiom) We're just moving the structure from one address to the other, so a default bitwise copy is appropriate. More...
 
HotspotStubSetoperator= (HotspotStubSet &&)=default
 Move assigment operator (mainly for copy/swap idiom) More...
 
HotspotStubSetoperator= (HotspotStubSet const &rhs)
 Assigment operator, needed as copy constructor is specified. More...
 
 ~HotspotStubSet () override
 
void clear ()
 
HotspotStubSet::const_iterator begin () const
 
HotspotStubSet::const_iterator end () const
 
HotspotStubSet::iterator begin ()
 
HotspotStubSet::iterator end ()
 
core::Size hotspot_length () const
 set length of hotspot peptide used for finding stubs. Default=1, Hotspot stored in set will always be only 1 residue More...
 
void hotspot_length (core::Size const length)
 
HotspotStubSetOP colonyE ()
 returns a new stub_set with stub scores recalculated by colony energy (Xiang, Soto, and Honig PNAS 2002) More...
 
HotspotStubSetOP cluster ()
 cluster stubs, returning a new stubset of cluster centers for each residue More...
 
Hotspots retrieve (std::string const &residue_name3)
 retrieve all stubs with a given residue name More...
 
Hotspots::const_iterator get_stub (std::string const &residue_name3, core::Real const score) const
 gets a stub from the stub_set_. A version returning an OP is private More...
 
HotspotStubSetOP subset (std::string const &residue_name3, core::Real const scorecut)
 
HotspotStubSetOP subset (core::Real const scorecut) const
 build a new stubset containing stubs that pass a score cutoff More...
 
HotspotStubCOP get_best_energy_stub () const
 gets the best energy stub in the set More...
 
HotspotStubCOP get_nearest_stub (core::conformation::ResidueCOP stub) const
 get the stub that's nearest to a residue More...
 
std::set< std::pair
< std::string, core::Real > > 
find_neighboring_stubs (HotspotStubCOP stub) const
 finds neighbors to stub based on distance between atoms. More...
 
void remove_stubs_from_set (std::set< std::pair< std::string, core::Real > > const &)
 removes neighbors of stub based on repulsive energy between the pair of residues More...
 
void remove_random_stubs_from_set (int const num_to_remove)
 
bool remove_stub (HotspotStubCOP stub)
 removes a single stub. Reports false if stub is not found More...
 
void read_data (std::string const &filename)
 add to stubset by reading from a file More...
 
void fill (core::pose::Pose const &reference_pose, core::scoring::ScoreFunctionCOP scorefxn_in, std::string const &residue_name3, core::Size const n_stubs)
 fill the stub set with n_stubs by Rosetta residue name More...
 
void fill (core::pose::Pose const &reference_pose, core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const target, core::Real const distance, std::string const &residue_name3, core::Size const n_stubs)
 only keep stubs within a certain distance of a residue on the target pose. More...
 
HotspotStubSetOP rescore (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn)
 rescore all stubs in this set based on current flags (eg - sc_only() ) More...
 
void autofill (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const n_stubs)
 fill the stub set with n_stubs each of A, R, N, D, E, Q, H, I, L, K, M, P, F, S, T, W, Y, and V More...
 
void autofill (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const target, core::Real const distance, core::Size const n_stubs)
 
void score_threshold (core::Real const threshold)
 only accept stubs that score better than this threshold (default is -1.0) More...
 
void write_all (std::string const &filename) const
 write all stubs contained in this set to filename More...
 
void write_stub (utility::io::ozstream &outstream, HotspotStubCOP stub, std::string const &tag) const
 write one stub with a user-supplied tag More...
 
void pair_with_scaffold (core::pose::Pose const &pose, core::Size const partner, protocols::filters::FilterCOP filter)
 associate all stubs in the set with a scaffold partner More...
 
void filter (protocols::filters::FilterCOP filter)
 set the filter to use for scaffold matching within this set More...
 
bool sc_only () const
 true if these stubs are sidechain-only (defaults true) More...
 
void sc_only (bool sc_switch)
 set whether or not sidechains are included More...
 
core::Size size () const
 how many total stubs are in the set (all residues)? More...
 
core::Size size (std::string const &resname)
 how many stubs are in the set by residue? More...
 
HotspotStubOP random_stub ()
 returns a random stub either from the entire set or based on residue name More...
 
HotspotStubOP random_stub (std::string const &resname)
 
void add_hotspot_constraints_to_pose (core::pose::Pose &pose, core::Size const partner, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
 Sets up constraints using a given partner (auto choose packer task and fixed reference atom) More...
 
void add_hotspot_constraints_to_wholepose (core::pose::Pose &pose, core::Size const partner, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
 utility function to add hotspot bbcst's to a pose More...
 
void add_hotspot_constraints_to_pose (core::pose::Pose &pose, core::id::AtomID const &fixed_atom, core::pack::task::PackerTaskCOP const packer_task, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
 Sets up constraints with user-supplied packer task and fixed reference atom. More...
 
void add_hotspot_constraints_to_wholepose (core::pose::Pose &pose, core::id::AtomID const &fixed_atom, core::pack::task::PackerTaskCOP const packer_task, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
 Sets up constraints with user-supplied packer task and fixed reference atom. More...
 
bool remove_all_hotspot_constraints (core::pose::Pose &pose) const
 remove all ambiguous constraints that contain backbone_stub_constraints from the supplied pose More...
 
void set_chain_to_design (core::Size const chain_to_design=2)
 
core::pack::task::PackerTaskOP prepare_hashing_packer_task_ (core::pose::Pose const &pose, core::Size const chain_to_redesign=2)
 
core::scoring::constraints::ConstraintCOPs constraints () const
 return bbcst's associatied with this stub set More...
 
void add_stub_ (HotspotStubCOP stub)
 
void add_stub_set (HotspotStubSet const &stubset)
 

Private Member Functions

void handshake_stub_sets (void)
 clears stub_set_vec_ and inserts all the elements in stub_set_ to it. More...
 
void create_hotspot_after_pose (core::pose::Pose &pose, std::string const &resname)
 
void setup_hotspot_foldtree_ (core::pose::Pose &pose)
 set up foldtree for residue docking. If target_res is defined, takes that as connection point. Assumes hotspot to dock is last res in the pose! Assumes monomeric fold_tree! More...
 
core::Size stub_offset ()
 utility function to find distance of stub from the end of the pose. More...
 
core::Real get_residue_score_ (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const seqpos)
 utility function to calculate interaction energy for a single residue More...
 
core::Real evaluate_stub_bumps_ (core::conformation::Residue const &placed_stub_residue, core::pose::Pose const &unbound_pose, core::Size const resnum, core::scoring::TenANeighborGraph const &unbound_neighbor_graph, core::scoring::ScoreFunctionCOP const &bump_scorefxn, core::Real const &max_bump_energy)
 
core::Real evaluate_stub_self_energy_ (core::conformation::Residue const &stub_residue, core::pose::Pose const &unbound_pose, core::Size const resnum, core::scoring::TenANeighborGraph const &unbound_neighbor_graph, core::scoring::ScoreFunctionCOP const &full_scorefxn)
 
void generate_unbound_pose_ (core::pose::Pose &pose)
 

Private Attributes

Hs_map stub_set_
 
Hs_vec stub_set_vec_
 
bool sc_only_
 
core::Size target_resnum_
 
core::Real target_distance_
 
core::Size chain_to_design_
 
core::pose::PoseCOP pose_
 
core::Real score_threshold_
 
protocols::filters::FilterCOP filter_
 
core::Size hotspot_length_
 
core::scoring::constraints::ConstraintCOPs constraints_
 

Friends

class HotspotStub
 

Member Typedef Documentation

typedef std::pair< std::string, std::pair< core::Real, HotspotStubOP > > protocols::hotspot_hashing::HotspotStubSet::Hs_data

Constructor & Destructor Documentation

protocols::hotspot_hashing::HotspotStubSet::HotspotStubSet ( )

References set_chain_to_design().

protocols::hotspot_hashing::HotspotStubSet::HotspotStubSet ( HotspotStubSet const &  init)
protocols::hotspot_hashing::HotspotStubSet::HotspotStubSet ( HotspotStubSet &&  )
default

Move constructor (mainly for copy/swap idiom) We're just moving the structure from one address to the other, so a default bitwise copy is appropriate.

protocols::hotspot_hashing::HotspotStubSet::~HotspotStubSet ( )
overridedefault

Member Function Documentation

void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose ( core::pose::Pose pose,
core::Size const  partner,
HotspotStubSetOP  hotspot_stub_set,
core::Real const &  CB_force_constant,
core::Real const &  worst_allowed_stub_bonus,
bool const  apply_self_energies,
core::Real const &  bump_cutoff,
bool const  apply_ambiguous_constraints = false 
)

Sets up constraints using a given partner (auto choose packer task and fixed reference atom)

utility function to add hotspot bbcst's to a pose

References core::conformation::Residue::atom_index(), prepare_hashing_packer_task_(), core::pose::Pose::residue(), and core::pose::Pose::size().

void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose ( core::pose::Pose pose,
core::id::AtomID const &  fixed_atom,
core::pack::task::PackerTaskCOP const  packer_task,
HotspotStubSetOP  hotspot_stub_set,
core::Real const &  CB_force_constant,
core::Real const &  worst_allowed_stub_bonus,
bool const  apply_self_energies,
core::Real const &  bump_cutoff,
bool const  apply_ambiguous_constraints = false 
)
void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose ( core::pose::Pose pose,
core::Size const  partner,
HotspotStubSetOP  hotspot_stub_set,
core::Real const &  CB_force_constant,
core::Real const &  worst_allowed_stub_bonus,
bool const  apply_self_energies,
core::Real const &  bump_cutoff,
bool const  apply_ambiguous_constraints = false 
)
void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose ( core::pose::Pose pose,
core::id::AtomID const &  fixed_atom,
core::pack::task::PackerTaskCOP const  packer_task,
HotspotStubSetOP  hotspot_stub_set,
core::Real const &  CB_force_constant,
core::Real const &  worst_allowed_stub_bonus,
bool const  apply_self_energies,
core::Real const &  bump_cutoff,
bool const  apply_ambiguous_constraints = false 
)
void protocols::hotspot_hashing::HotspotStubSet::add_stub_ ( HotspotStubCOP  stub)

References handshake_stub_sets(), and stub_set_.

Referenced by add_stub_set(), fill(), and read_data().

void protocols::hotspot_hashing::HotspotStubSet::add_stub_set ( HotspotStubSet const &  stubset)

References add_stub_().

void protocols::hotspot_hashing::HotspotStubSet::autofill ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
core::Size const  n_stubs 
)

fill the stub set with n_stubs each of A, R, N, D, E, Q, H, I, L, K, M, P, F, S, T, W, Y, and V

References fill().

Referenced by autofill().

void protocols::hotspot_hashing::HotspotStubSet::autofill ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
core::Size const  target,
core::Real const  distance,
core::Size const  n_stubs 
)
HotspotStubSet::const_iterator protocols::hotspot_hashing::HotspotStubSet::begin ( ) const
inline

References size(), and stub_set_vec_.

HotspotStubSet::iterator protocols::hotspot_hashing::HotspotStubSet::begin ( )
inline

References size(), and stub_set_vec_.

void protocols::hotspot_hashing::HotspotStubSet::clear ( )
HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::cluster ( )

cluster stubs, returning a new stubset of cluster centers for each residue

clusters all residues within this stubset on a per-restype basis and returns a new clustered stubset

References protocols::antibody::lambda, protocols::hotspot_hashing::residue_sc_rmsd_no_super(), retrieve(), core::scoring::rms, protocols::hybridization::score, and protocols::hotspot_hashing::TR().

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::colonyE ( )

returns a new stub_set with stub scores recalculated by colony energy (Xiang, Soto, and Honig PNAS 2002)

E = -ln (sum exp( -E(j) - rmsd(ij)^3/6L ) )

References chain_to_design_, filter_, pose_, protocols::hotspot_hashing::residue_sc_rmsd_no_super(), retrieve(), core::scoring::rms, and protocols::hotspot_hashing::TR().

core::scoring::constraints::ConstraintCOPs protocols::hotspot_hashing::HotspotStubSet::constraints ( ) const

return bbcst's associatied with this stub set

References constraints_.

void protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose ( core::pose::Pose pose,
std::string const &  resname 
)
private
HotspotStubSet::const_iterator protocols::hotspot_hashing::HotspotStubSet::end ( ) const
inline
HotspotStubSet::iterator protocols::hotspot_hashing::HotspotStubSet::end ( )
inline

References stub_set_vec_.

core::Real protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_bumps_ ( core::conformation::Residue const &  placed_stub_residue,
core::pose::Pose const &  unbound_pose,
core::Size const  resnum,
core::scoring::TenANeighborGraph const &  unbound_neighbor_graph,
core::scoring::ScoreFunctionCOP const &  bump_scorefxn,
core::Real const &  max_bump_energy 
)
private
core::Real protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_self_energy_ ( core::conformation::Residue const &  stub_residue,
core::pose::Pose const &  unbound_pose,
core::Size const  resnum,
core::scoring::TenANeighborGraph const &  unbound_neighbor_graph,
core::scoring::ScoreFunctionCOP const &  full_scorefxn 
)
private
void protocols::hotspot_hashing::HotspotStubSet::fill ( core::pose::Pose const &  reference_pose,
core::scoring::ScoreFunctionCOP  scorefxn_in,
std::string const &  residue_name3,
core::Size const  n_stubs 
)
void protocols::hotspot_hashing::HotspotStubSet::fill ( core::pose::Pose const &  reference_pose,
core::scoring::ScoreFunctionCOP  scorefxn_in,
core::Size const  target,
core::Real const  distance,
std::string const &  residue_name3,
core::Size const  n_stubs 
)

only keep stubs within a certain distance of a residue on the target pose.

References core::kinematics::distance(), fill(), core::pose::Pose::size(), target_distance_, and target_resnum_.

void protocols::hotspot_hashing::HotspotStubSet::filter ( protocols::filters::FilterCOP  filter)

set the filter to use for scaffold matching within this set

References filter_.

Referenced by pair_with_scaffold().

std::set< std::pair< std::string, core::Real > > protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs ( HotspotStubCOP  stub) const

finds neighbors to stub based on distance between atoms.

References core::conformation::Residue::atom_begin(), core::conformation::Residue::atom_end(), and stub_set_.

void protocols::hotspot_hashing::HotspotStubSet::generate_unbound_pose_ ( core::pose::Pose pose)
private
HotspotStubCOP protocols::hotspot_hashing::HotspotStubSet::get_best_energy_stub ( ) const

gets the best energy stub in the set

References stub_set_.

HotspotStubCOP protocols::hotspot_hashing::HotspotStubSet::get_nearest_stub ( core::conformation::ResidueCOP  residue) const

get the stub that's nearest to a residue

find stub nearest to residue based on CA-CA distance

References core::kinematics::distance(), and stub_set_.

core::Real protocols::hotspot_hashing::HotspotStubSet::get_residue_score_ ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
core::Size const  seqpos 
)
private
HotspotStubSet::Hotspots::const_iterator protocols::hotspot_hashing::HotspotStubSet::get_stub ( std::string const &  residue_name3,
core::Real const  score 
) const

gets a stub from the stub_set_. A version returning an OP is private

References stub_set_.

Referenced by remove_stubs_from_set().

void protocols::hotspot_hashing::HotspotStubSet::handshake_stub_sets ( void  )
private

clears stub_set_vec_ and inserts all the elements in stub_set_ to it.

remove all stubs from stub_set_vec_ and repopulate it with stub_set_

References stub_set_, and stub_set_vec_.

Referenced by add_stub_(), clear(), remove_stub(), and remove_stubs_from_set().

core::Size protocols::hotspot_hashing::HotspotStubSet::hotspot_length ( ) const

set length of hotspot peptide used for finding stubs. Default=1, Hotspot stored in set will always be only 1 residue

References hotspot_length_.

Referenced by create_hotspot_after_pose(), get_residue_score_(), setup_hotspot_foldtree_(), and stub_offset().

void protocols::hotspot_hashing::HotspotStubSet::hotspot_length ( core::Size const  length)

References hotspot_length_.

HotspotStubSet& protocols::hotspot_hashing::HotspotStubSet::operator= ( HotspotStubSet &&  )
default

Move assigment operator (mainly for copy/swap idiom)

HotspotStubSet& protocols::hotspot_hashing::HotspotStubSet::operator= ( HotspotStubSet const &  rhs)
inline

Assigment operator, needed as copy constructor is specified.

References core::id::swap().

void protocols::hotspot_hashing::HotspotStubSet::pair_with_scaffold ( core::pose::Pose const &  pose,
core::Size const  partner,
protocols::filters::FilterCOP  filter 
)

associate all stubs in the set with a scaffold partner

set up scaffold_status_ for each stub included in this set

References chain_to_design_, filter(), filter_, pose_, stub_set_, protocols::hotspot_hashing::TR(), and protocols::hotspot_hashing::unchecked.

core::pack::task::PackerTaskOP protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_ ( core::pose::Pose const &  pose,
core::Size const  chain_to_redesign = 2 
)
HotspotStubOP protocols::hotspot_hashing::HotspotStubSet::random_stub ( )

returns a random stub either from the entire set or based on residue name

References HotspotStub, core::scoring::rg, size(), and stub_set_.

HotspotStubOP protocols::hotspot_hashing::HotspotStubSet::random_stub ( std::string const &  resname)
void protocols::hotspot_hashing::HotspotStubSet::read_data ( std::string const &  filename)
bool protocols::hotspot_hashing::HotspotStubSet::remove_all_hotspot_constraints ( core::pose::Pose pose) const

remove all ambiguous constraints that contain backbone_stub_constraints from the supplied pose

References constraints_, and core::pose::Pose::remove_constraints().

void protocols::hotspot_hashing::HotspotStubSet::remove_random_stubs_from_set ( int const  num_to_remove)
bool protocols::hotspot_hashing::HotspotStubSet::remove_stub ( HotspotStubCOP  stub)

removes a single stub. Reports false if stub is not found

removes the first occurence of stub in the stubset

References handshake_stub_sets(), stub_set_, and protocols::hotspot_hashing::TR().

Referenced by remove_random_stubs_from_set().

void protocols::hotspot_hashing::HotspotStubSet::remove_stubs_from_set ( std::set< std::pair< std::string, core::Real > > const &  stubs)

removes neighbors of stub based on repulsive energy between the pair of residues

removes a set of stubs from the stub_set_

References get_stub(), handshake_stub_sets(), and stub_set_.

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::rescore ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn 
)
HotspotStubSet::Hotspots protocols::hotspot_hashing::HotspotStubSet::retrieve ( std::string const &  residue_name3)

retrieve all stubs with a given residue name

References stub_set_, and protocols::hotspot_hashing::TR().

Referenced by cluster(), colonyE(), random_stub(), size(), and subset().

bool protocols::hotspot_hashing::HotspotStubSet::sc_only ( ) const

true if these stubs are sidechain-only (defaults true)

References sc_only_.

void protocols::hotspot_hashing::HotspotStubSet::sc_only ( bool  sc_switch)

set whether or not sidechains are included

References sc_only_.

void protocols::hotspot_hashing::HotspotStubSet::score_threshold ( core::Real const  threshold)

only accept stubs that score better than this threshold (default is -1.0)

References score_threshold_.

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply().

void protocols::hotspot_hashing::HotspotStubSet::set_chain_to_design ( core::Size const  chain_to_design = 2)

References chain_to_design_.

Referenced by HotspotStubSet().

void protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_ ( core::pose::Pose pose)
private

set up foldtree for residue docking. If target_res is defined, takes that as connection point. Assumes hotspot to dock is last res in the pose! Assumes monomeric fold_tree!

References core::pose::Pose::fold_tree(), hotspot_length(), core::pose::Pose::num_jump(), core::pose::residue_center_of_mass(), core::pose::Pose::size(), core::kinematics::FoldTree::slide_jump(), stub_offset(), target_distance_, target_resnum_, and protocols::hotspot_hashing::TR().

Referenced by fill().

core::Size protocols::hotspot_hashing::HotspotStubSet::size ( ) const
core::Size protocols::hotspot_hashing::HotspotStubSet::size ( std::string const &  resname)

how many stubs are in the set by residue?

References retrieve(), and size().

core::Size protocols::hotspot_hashing::HotspotStubSet::stub_offset ( )
private

utility function to find distance of stub from the end of the pose.

utility function to find distance of a hotspot from the end of the current pose. Should be in middle or more C-terminal if hotspot_length is even

References hotspot_length().

Referenced by fill(), and setup_hotspot_foldtree_().

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::subset ( std::string const &  residue_name3,
core::Real const  scorecut 
)
HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::subset ( core::Real const  scorecut) const

build a new stubset containing stubs that pass a score cutoff

References sc_only_, stub_set_, and protocols::hotspot_hashing::TR().

void protocols::hotspot_hashing::HotspotStubSet::write_all ( std::string const &  filename) const

write all stubs contained in this set to filename

References stub_set_, protocols::hotspot_hashing::TR(), and write_stub().

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply().

void protocols::hotspot_hashing::HotspotStubSet::write_stub ( utility::io::ozstream &  outstream,
HotspotStubCOP  stub,
std::string const &  tag 
) const

write one stub with a user-supplied tag

References core::io::pdb::dump_pdb_residue().

Referenced by write_all().

Friends And Related Function Documentation

friend class HotspotStub
friend

Referenced by random_stub().

Member Data Documentation

core::Size protocols::hotspot_hashing::HotspotStubSet::chain_to_design_
private
core::scoring::constraints::ConstraintCOPs protocols::hotspot_hashing::HotspotStubSet::constraints_
private
protocols::filters::FilterCOP protocols::hotspot_hashing::HotspotStubSet::filter_
private
core::Size protocols::hotspot_hashing::HotspotStubSet::hotspot_length_
private

Referenced by hotspot_length().

core::pose::PoseCOP protocols::hotspot_hashing::HotspotStubSet::pose_
private

Referenced by colonyE(), and pair_with_scaffold().

bool protocols::hotspot_hashing::HotspotStubSet::sc_only_
private
core::Real protocols::hotspot_hashing::HotspotStubSet::score_threshold_
private

Referenced by fill(), and score_threshold().

Hs_map protocols::hotspot_hashing::HotspotStubSet::stub_set_
private
Hs_vec protocols::hotspot_hashing::HotspotStubSet::stub_set_vec_
private
core::Real protocols::hotspot_hashing::HotspotStubSet::target_distance_
private
core::Size protocols::hotspot_hashing::HotspotStubSet::target_resnum_
private

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