Rosetta 3.4
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protocols::hotspot_hashing::HotspotStubSet Class Reference

#include <HotspotStubSet.hh>

Inheritance diagram for protocols::hotspot_hashing::HotspotStubSet:
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List of all members.

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 ()
void clear ()
HotspotStubSet::const_iterator begin () const
HotspotStubSet::const_iterator end () const
HotspotStubSet::iterator begin ()
HotspotStubSet::iterator end ()
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
void hotspot_length (Size const length)
HotspotStubSetOP colonyE ()
 returns a new stub_set with stub scores recalculated by colony energy (Xiang, Soto, and Honig PNAS 2002)
HotspotStubSetOP cluster ()
 cluster stubs, returning a new stubset of cluster centers for each residue
Hotspots retrieve (std::string const &residue_name3)
 retrieve all stubs with a given residue name
HotspotStubOP 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
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
HotspotStubCOP get_best_energy_stub () const
 gets the best energy stub in the set
HotspotStubCOP get_nearest_stub (core::conformation::ResidueCOP stub) const
 get the stub that's nearest to a residue
std::set< std::pair
< std::string, core::Real > > 
find_neighboring_stubs (HotspotStubCOP stub) const
 finds neighbors to stub based on distance between atoms.
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
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
void read_data (std::string const filename)
 add to stubset by reading from a file
void fill (core::pose::Pose const &reference_pose, core::scoring::ScoreFunctionCOP scorefxn_in, std::string const residue_name3, Size const n_stubs)
 fill the stub set with n_stubs by Rosetta residue name
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, Size const n_stubs)
 only keep stubs within a certain distance of a residue on the target pose.
HotspotStubSetOP rescore (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn)
 rescore all stubs in this set based on current flags (eg - sc_only() )
void autofill (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, 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
void autofill (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const target, core::Real const distance, Size const n_stubs)
void score_threshold (core::Real const threshold)
 only accept stubs that score better than this threshold (default is -1.0)
void write_all (std::string const &filename) const
 write all stubs contained in this set to filename
void write_stub (utility::io::ozstream &outstream, HotspotStubCOP stub, std::string const &tag) const
 write one stub with a user-supplied tag
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
void filter (protocols::filters::FilterCOP filter)
 set the filter to use for scaffold matching within this set
bool sc_only () const
 true if these stubs are sidechain-only (defaults true)
void sc_only (bool sc_switch)
 set whether or not sidechains are included
core::Size size () const
 how many total stubs are in the set (all residues)?
core::Size size (std::string const resname)
 how many stubs are in the set by residue?
HotspotStubOP random_stub ()
 returns a random stub either from the entire set or based on residue name
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)
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.
bool remove_all_hotspot_constraints (core::pose::Pose &pose) const
 remove all ambiguous constraints that contain backbone_stub_constraints from the supplied pose
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
void add_stub_ (HotspotStubCOP stub)
void add_stub_set (HotspotStubSet const &stubset)

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().

Referenced by rescore(), and subset().

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

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::total_residue().

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_stub_ ( HotspotStubCOP  stub)
void protocols::hotspot_hashing::HotspotStubSet::add_stub_set ( HotspotStubSet const &  stubset)
void protocols::hotspot_hashing::HotspotStubSet::autofill ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
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,
Size const  n_stubs 
)
HotspotStubSet::iterator protocols::hotspot_hashing::HotspotStubSet::begin ( ) [inline]

References size().

HotspotStubSet::const_iterator protocols::hotspot_hashing::HotspotStubSet::begin ( ) const [inline]

References size().

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::hotspot_hashing::residue_sc_rmsd_no_super(), retrieve(), core::scoring::rms, 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)

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

References HotspotStub, 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

HotspotStubSet::iterator protocols::hotspot_hashing::HotspotStubSet::end ( ) [inline]
HotspotStubSet::const_iterator protocols::hotspot_hashing::HotspotStubSet::end ( ) const [inline]
void protocols::hotspot_hashing::HotspotStubSet::fill ( core::pose::Pose const &  reference_pose,
core::scoring::ScoreFunctionCOP  scorefxn_in,
std::string const  residue_name3,
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,
Size const  n_stubs 
)

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

References core::kinematics::distance(), fill(), and core::pose::Pose::total_residue().

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

set the filter to use for scaffold matching within this set

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(), and core::conformation::Residue::atom_end().

HotspotStubCOP protocols::hotspot_hashing::HotspotStubSet::get_best_energy_stub ( ) const

gets the best energy stub in the set

References HotspotStub.

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

get the stub that's nearest to a residue

Detailed: find stub nearest to residue based on CA-CA distance

References core::kinematics::distance().

HotspotStubOP 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

Referenced by remove_stubs_from_set().

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

void protocols::hotspot_hashing::HotspotStubSet::hotspot_length ( core::Size const  length)
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 filter(), 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, protocols::RG(), and size().

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 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 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().

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 protocols::hotspot_hashing::TR().

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

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

set whether or not sidechains are included

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

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

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

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

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)

Referenced by HotspotStubSet().

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().

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 HotspotStubSet(), 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 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]

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