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Public Member Functions | Private Attributes | List of all members
protocols::loophash::LoopHashSampler Class Reference

#include <LoopHashSampler.hh>

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

 LoopHashSampler (LoopHashLibraryOP library, LocalInserterOP inserter)
 
virtual ~LoopHashSampler ()
 
void set_defaults ()
 
void build_structures (const core::pose::Pose &start_pose, std::vector< core::io::silent::SilentStructOP > &lib_structs)
 create a set of structures for a the given range of residues and other parameters stored int his class. More...
 
void close_gaps (const core::pose::Pose &start_pose, std::vector< core::pose::Pose > &lib_structs, core::Size loop_size)
 create a set of structures with closed gaps More...
 
void set_start_res (core::Size value)
 
void set_stop_res (core::Size value)
 
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)
 

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_
 (fpd) pre-filtering options More...
 
core::scoring::ScoreFunctionOP score_filt_
 

Detailed Description

Definition at line 40 of file LoopHashSampler.hh.

Constructor & Destructor Documentation

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

Definition at line 51 of file LoopHashSampler.cc.

References set_defaults().

protocols::loophash::LoopHashSampler::~LoopHashSampler ( )
virtual

Definition at line 71 of file LoopHashSampler.cc.

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 a the given range of residues and other parameters stored int his class.

Definition at line 181 of file LoopHashSampler.cc.

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(), core::io::silent::SilentStructFactory::get_instance(), protocols::loophash::LoopHashMap::get_loop_size(), protocols::loophash::LoopHashMap::get_peptide(), protocols::loophash::get_rmsd(), protocols::loophash::get_rt_over_leap(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), protocols::loophash::LeapIndex::index, inserter_, protocols::loophash::is_valid_backbone(), library_, 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, RG(), core::pose::Pose::sequence(), core::kinematics::MoveMap::set_bb(), start_res_, stop_res_, core::pose::Pose::total_residue(), 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 
)

create a set of structures with closed gaps

Definition at line 466 of file LoopHashSampler.cc.

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

Definition at line 86 of file LoopHashSampler.hh.

References filter_by_phipsi_.

Referenced by build_structures().

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

Definition at line 82 of file LoopHashSampler.hh.

References max_bbrms_.

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

Definition at line 85 of file LoopHashSampler.hh.

References max_nstruct_.

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

Definition at line 84 of file LoopHashSampler.hh.

References max_rms_.

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

Definition at line 81 of file LoopHashSampler.hh.

References min_bbrms_.

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

Definition at line 83 of file LoopHashSampler.hh.

References min_rms_.

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

Definition at line 79 of file LoopHashSampler.hh.

References start_res_.

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

Definition at line 80 of file LoopHashSampler.hh.

References stop_res_.

void protocols::loophash::LoopHashSampler::set_defaults ( )

Definition at line 74 of file LoopHashSampler.cc.

References filter_by_phipsi_, set_max_bbrms(), set_max_nstruct(), set_max_radius(), set_max_rms(), set_max_struct(), set_max_struct_per_radius(), set_min_bbrms(), and set_min_rms().

Referenced by LoopHashSampler().

void protocols::loophash::LoopHashSampler::set_filter_by_phipsi ( bool  value)
inline

Definition at line 76 of file LoopHashSampler.hh.

References filter_by_phipsi_.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), and protocols::loophash::LoopHashDiversifier::apply().

void protocols::loophash::LoopHashSampler::set_max_bbrms ( core::Real  value)
inline

Definition at line 68 of file LoopHashSampler.hh.

References max_bbrms_.

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

void protocols::loophash::LoopHashSampler::set_max_nstruct ( core::Size  value)
inline

Definition at line 74 of file LoopHashSampler.hh.

References max_nstruct_.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), and set_defaults().

void protocols::loophash::LoopHashSampler::set_max_radius ( core::Size  value)
inline

Definition at line 71 of file LoopHashSampler.hh.

References max_radius_.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::LoopHashDiversifier::apply(), and set_defaults().

void protocols::loophash::LoopHashSampler::set_max_rms ( core::Real  value)
inline

Definition at line 70 of file LoopHashSampler.hh.

References max_rms_.

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

void protocols::loophash::LoopHashSampler::set_max_struct ( core::Size  value)
inline

Definition at line 72 of file LoopHashSampler.hh.

References max_struct_.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), and set_defaults().

void protocols::loophash::LoopHashSampler::set_max_struct_per_radius ( core::Size  value)
inline

Definition at line 73 of file LoopHashSampler.hh.

References max_struct_per_radius_.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), and set_defaults().

void protocols::loophash::LoopHashSampler::set_min_bbrms ( core::Real  value)
inline

Definition at line 67 of file LoopHashSampler.hh.

References min_bbrms_.

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

void protocols::loophash::LoopHashSampler::set_min_rms ( core::Real  value)
inline

Definition at line 69 of file LoopHashSampler.hh.

References min_rms_.

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

void protocols::loophash::LoopHashSampler::set_nonideal ( bool  value)
inline

Definition at line 75 of file LoopHashSampler.hh.

References nonideal_.

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

void protocols::loophash::LoopHashSampler::set_start_res ( core::Size  value)
inline

Definition at line 65 of file LoopHashSampler.hh.

References start_res_.

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::set_stop_res ( core::Size  value)
inline

Definition at line 66 of file LoopHashSampler.hh.

References stop_res_.

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::use_prefiltering ( core::scoring::ScoreFunctionOP  score_filt,
core::Size  nstruct 
)
inline

Definition at line 91 of file LoopHashSampler.hh.

References nprefilter_, and score_filt_.

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

Member Data Documentation

bool protocols::loophash::LoopHashSampler::filter_by_phipsi_
private

Definition at line 116 of file LoopHashSampler.hh.

Referenced by get_filter_by_phipsi(), set_defaults(), and set_filter_by_phipsi().

LocalInserterOP protocols::loophash::LoopHashSampler::inserter_
private

pointer to the insertion functor which provides the peptide insertion facility

Definition at line 102 of file LoopHashSampler.hh.

Referenced by build_structures().

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

pointer to the library used for insertion

Definition at line 99 of file LoopHashSampler.hh.

Referenced by build_structures().

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

Definition at line 108 of file LoopHashSampler.hh.

Referenced by build_structures(), get_max_bbrms(), and set_max_bbrms().

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

Definition at line 114 of file LoopHashSampler.hh.

Referenced by get_max_nstruct(), and set_max_nstruct().

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

Definition at line 113 of file LoopHashSampler.hh.

Referenced by build_structures(), and set_max_radius().

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

Definition at line 110 of file LoopHashSampler.hh.

Referenced by build_structures(), get_max_rms(), and set_max_rms().

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

Definition at line 111 of file LoopHashSampler.hh.

Referenced by build_structures(), and set_max_struct().

core::Size protocols::loophash::LoopHashSampler::max_struct_per_radius_
private

Definition at line 112 of file LoopHashSampler.hh.

Referenced by set_max_struct_per_radius().

core::Real protocols::loophash::LoopHashSampler::min_bbrms_
private

Definition at line 107 of file LoopHashSampler.hh.

Referenced by build_structures(), get_min_bbrms(), and set_min_bbrms().

core::Real protocols::loophash::LoopHashSampler::min_rms_
private

Definition at line 109 of file LoopHashSampler.hh.

Referenced by build_structures(), get_min_rms(), and set_min_rms().

bool protocols::loophash::LoopHashSampler::nonideal_
private

Definition at line 115 of file LoopHashSampler.hh.

Referenced by build_structures(), and set_nonideal().

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

(fpd) pre-filtering options

Definition at line 119 of file LoopHashSampler.hh.

Referenced by use_prefiltering().

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

Definition at line 120 of file LoopHashSampler.hh.

Referenced by use_prefiltering().

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

parameters for insertion positions

Definition at line 105 of file LoopHashSampler.hh.

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

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

Definition at line 106 of file LoopHashSampler.hh.

Referenced by build_structures(), get_stop_res(), and set_stop_res().

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