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:

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_pose	The pose to sample.
[out]	lib_structs	The 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

(

)

Load default values from the command line.

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

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

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

References max_nstruct_.

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

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

inline

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

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

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

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

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

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

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

Set the first residue to sample.

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

Set the last residue to sample.

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

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

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.

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

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

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

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

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

Referenced by set_max_struct_per_radius().

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

private

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

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

private

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

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

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

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

• src/protocols/loophash/LoopHashSampler.hh
• src/protocols/loophash/LoopHashSampler.cc