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protocols::loophash::LoopHashSampler Class Reference

Create candidate structures where some residues have been sampled by loophash. More...

#include <LoopHashSampler.hh>

Inheritance diagram for protocols::loophash::LoopHashSampler:
Inheritance graph
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Public Member Functions

 LoopHashSampler (LoopHashLibraryOP library, LocalInserterOP inserter)
 
 ~LoopHashSampler () override
 
void set_defaults ()
 Load default values from the command line. More...
 
void build_structures (const core::pose::Pose &start_pose, std::vector< core::io::silent::SilentStructOP > &lib_structs)
 Create a set of structures for the given range of residues and other parameters stored in this class. More...
 
void close_gaps (const core::pose::Pose &start_pose, std::vector< core::pose::Pose > &lib_structs, core::Size loop_size)
 Not implemented! Create a set of structures with closed gaps. More...
 
void set_start_res (core::Size value)
 Set the first residue to sample. More...
 
void set_stop_res (core::Size value)
 Set the last residue to sample. More...
 
void set_min_bbrms (core::Real value)
 
void set_max_bbrms (core::Real value)
 
void set_min_rms (core::Real value)
 
void set_max_rms (core::Real value)
 
void set_max_radius (core::Size value)
 
void set_max_struct (core::Size value)
 
void set_max_struct_per_radius (core::Size value)
 
void set_max_nstruct (core::Size value)
 
void set_nonideal (bool value)
 
void set_filter_by_phipsi (bool value)
 
core::Size get_start_res ()
 
core::Size get_stop_res ()
 
core::Real get_min_bbrms ()
 
core::Real get_max_bbrms ()
 
core::Real get_min_rms ()
 
core::Real get_max_rms ()
 
core::Size get_max_nstruct ()
 
bool get_filter_by_phipsi ()
 
void use_prefiltering (core::scoring::ScoreFunctionOP score_filt, core::Size nstruct)
 Pre-filter structures with a scorefunction. More...
 

Private Attributes

LoopHashLibraryOP library_
 Pointer to the library used for insertion. More...
 
LocalInserterOP inserter_
 Pointer to the insertion functor which provides the peptide insertion facility. More...
 
core::Size start_res_
 Parameters for insertion positions. More...
 
core::Size stop_res_
 
core::Real min_bbrms_
 
core::Real max_bbrms_
 
core::Real min_rms_
 
core::Real max_rms_
 
core::Size max_struct_
 
core::Size max_struct_per_radius_
 
core::Size max_radius_
 
core::Size max_nstruct_
 
bool nonideal_
 
bool filter_by_phipsi_
 
core::Size nprefilter_
 Pre-filtering options. More...
 
core::scoring::ScoreFunctionOP score_filt_
 

Detailed Description

Create candidate structures where some residues have been sampled by loophash.

Constructor & Destructor Documentation

protocols::loophash::LoopHashSampler::LoopHashSampler ( LoopHashLibraryOP  library,
LocalInserterOP  inserter 
)

References set_defaults().

protocols::loophash::LoopHashSampler::~LoopHashSampler ( )
overridedefault

Member Function Documentation

void protocols::loophash::LoopHashSampler::build_structures ( const core::pose::Pose start_pose,
std::vector< core::io::silent::SilentStructOP > &  lib_structs 
)

Create a set of structures for the given range of residues and other parameters stored in this class.

Parameters
[in]start_poseThe pose to sample.
[out]lib_structsThe resulting structures.

The algorithm, in pseudocode:

  • For each residue between start_res and stop_res:
    • For each loop length in the database
      • Calculate the rigid-body transformation between the ends of a loop starting at the current residue and extending the current length.
      • For each radius from 0 to max_radius:
        • Do a radial hashmap search for that radius.
        • For each hit:
          • Discard if the RMSD to the starting pose is either too low or too high
          • Discard if there are Ramachandran outliers.
          • Otherwise, keep!
        • For each remaining hit:
          • Insert the hit into a copy of the starting pose.
          • Create a silent file representation of that pose and some information describing to how it was generated, and add it to lib_structs.

References protocols::loophash::FilterBucket::BBrms, protocols::loophash::BBData::extra_key, protocols::loophash::FilterBucket::filter_beta, protocols::loophash::FilterBucket::filter_gly, protocols::loophash::FilterBucket::filter_pro, get_filter_by_phipsi(), protocols::loophash::LoopHashMap::get_loop_size(), protocols::loophash::LoopHashMap::get_peptide(), protocols::loophash::get_rmsd(), protocols::loophash::get_rt_over_leap(), protocols::loophash::LeapIndex::index, inserter_, protocols::loophash::is_valid_backbone(), library_, protocols::mean_field::max(), max_bbrms_, max_radius_, max_rms_, max_struct_, min_bbrms_, min_rms_, nonideal_, protocols::loophash::LeapIndex::offset, protocols::loophash::BBExtraData::pdb_id, protocols::loophash::BackboneSegment::phi(), protocols::loophash::BackboneSegment::psi(), protocols::loophash::LoopHashMap::radial_lookup(), protocols::loophash::BackboneSegment::read_from_pose(), protocols::loophash::FilterBucket::retrieve_index, core::scoring::rg, core::pose::Pose::sequence(), core::kinematics::MoveMap::set_bb(), core::pose::Pose::size(), start_res_, stop_res_, core::id::to_string(), protocols::loophash::TR(), core::pose::transfer_jumps(), and core::pose::transfer_phi_psi().

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), and protocols::loophash::WorkUnit_LoopHash::run().

void protocols::loophash::LoopHashSampler::close_gaps ( const core::pose::Pose start_pose,
std::vector< core::pose::Pose > &  lib_structs,
core::Size  loop_size 
)

Not implemented! Create a set of structures with closed gaps.

bool protocols::loophash::LoopHashSampler::get_filter_by_phipsi ( )
inline

References filter_by_phipsi_.

Referenced by build_structures().

core::Real protocols::loophash::LoopHashSampler::get_max_bbrms ( )
inline

References max_bbrms_.

core::Size protocols::loophash::LoopHashSampler::get_max_nstruct ( )
inline

References max_nstruct_.

core::Real protocols::loophash::LoopHashSampler::get_max_rms ( )
inline

References max_rms_.

core::Real protocols::loophash::LoopHashSampler::get_min_bbrms ( )
inline

References min_bbrms_.

core::Real protocols::loophash::LoopHashSampler::get_min_rms ( )
inline

References min_rms_.

core::Size protocols::loophash::LoopHashSampler::get_start_res ( )
inline

References start_res_.

core::Size protocols::loophash::LoopHashSampler::get_stop_res ( )
inline

References stop_res_.

void protocols::loophash::LoopHashSampler::set_defaults ( )
void protocols::loophash::LoopHashSampler::set_filter_by_phipsi ( bool  value)
inline
void protocols::loophash::LoopHashSampler::set_max_bbrms ( core::Real  value)
inline
void protocols::loophash::LoopHashSampler::set_max_nstruct ( core::Size  value)
inline
void protocols::loophash::LoopHashSampler::set_max_radius ( core::Size  value)
inline
void protocols::loophash::LoopHashSampler::set_max_rms ( core::Real  value)
inline
void protocols::loophash::LoopHashSampler::set_max_struct ( core::Size  value)
inline
void protocols::loophash::LoopHashSampler::set_max_struct_per_radius ( core::Size  value)
inline
void protocols::loophash::LoopHashSampler::set_min_bbrms ( core::Real  value)
inline
void protocols::loophash::LoopHashSampler::set_min_rms ( core::Real  value)
inline
void protocols::loophash::LoopHashSampler::set_nonideal ( bool  value)
inline
void protocols::loophash::LoopHashSampler::set_start_res ( core::Size  value)
inline
void protocols::loophash::LoopHashSampler::set_stop_res ( core::Size  value)
inline
void protocols::loophash::LoopHashSampler::use_prefiltering ( core::scoring::ScoreFunctionOP  score_filt,
core::Size  nstruct 
)
inline

Pre-filter structures with a scorefunction.

This is done using a chainbroken pose (before constraint minimization!) and is useful for experimentally derived scorefunctions (eg density).

References nprefilter_, and score_filt_.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply().

Member Data Documentation

bool protocols::loophash::LoopHashSampler::filter_by_phipsi_
private
LocalInserterOP protocols::loophash::LoopHashSampler::inserter_
private

Pointer to the insertion functor which provides the peptide insertion facility.

Referenced by build_structures().

LoopHashLibraryOP protocols::loophash::LoopHashSampler::library_
private

Pointer to the library used for insertion.

Referenced by build_structures().

core::Real protocols::loophash::LoopHashSampler::max_bbrms_
private
core::Size protocols::loophash::LoopHashSampler::max_nstruct_
private

Referenced by get_max_nstruct(), and set_max_nstruct().

core::Size protocols::loophash::LoopHashSampler::max_radius_
private

Referenced by build_structures(), and set_max_radius().

core::Real protocols::loophash::LoopHashSampler::max_rms_
private
core::Size protocols::loophash::LoopHashSampler::max_struct_
private

Referenced by build_structures(), and set_max_struct().

core::Size protocols::loophash::LoopHashSampler::max_struct_per_radius_
private
core::Real protocols::loophash::LoopHashSampler::min_bbrms_
private
core::Real protocols::loophash::LoopHashSampler::min_rms_
private
bool protocols::loophash::LoopHashSampler::nonideal_
private

Referenced by build_structures(), and set_nonideal().

core::Size protocols::loophash::LoopHashSampler::nprefilter_
private

Pre-filtering options.

Referenced by use_prefiltering().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashSampler::score_filt_
private

Referenced by use_prefiltering().

core::Size protocols::loophash::LoopHashSampler::start_res_
private

Parameters for insertion positions.

Referenced by build_structures(), get_start_res(), and set_start_res().

core::Size protocols::loophash::LoopHashSampler::stop_res_
private

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