protocols::denovo_design::components::Picker Class Reference

class used for picking/caching fragments More...

#include <Picker.hh>

Inheritance diagram for protocols::denovo_design::components::Picker:

Public Types
typedef std::map< std::string, core::fragment::FrameCOP >	FragmentMap

Public Member Functions
	Picker ()
virtual	~Picker ()
void	set_nfrags (core::Size const nfrags)
core::fragment::ConstantLengthFragSetOP	pick_and_cache_fragments (std::string const &ss, std::string const &abego, protocols::loops::Loops const &loops, utility::vector1< core::Size > const &chain_endings, core::Size const frag_size)
	picks and caches fragments for the given segments with size frag_size More...
core::fragment::ConstantLengthFragSetOP	fragments_for_permutation (StructureData const &perm, SegmentNameList const &comp_ids, core::Size const frag_size)
	picks and caches fragments for the listed components with size frag_size More...
core::fragment::ConstantLengthFragSetOP	fragments_for_permutation_take_X_from_pose (StructureData const &perm, core::pose::Pose const &pose, SegmentNames const &comp_ids, core::Size const frag_size)
	picks and caches fragments for the listed components with size frag_size More...
core::fragment::ConstantLengthFragSetOP	pick_and_cache_fragments (std::string const &complete_ss, utility::vector1< std::string > const &complete_abego, utility::vector1< core::Size > const &chain_endings, core::Size const start_res, core::Size const end_res, core::Size const frag_length)
	pick and cache fragments without considering primary sequence More...
core::fragment::ConstantLengthFragSetOP	pick_and_cache_fragments (std::string const &complete_aa, std::string const &complete_ss, utility::vector1< std::string > const &complete_abego, utility::vector1< core::Size > const &chain_endings, core::Size const start_res, core::Size const end_res, core::Size const frag_length)
	pick and cache fragments with a primary sequence in mind More...

Protected Member Functions
std::string	ss_key (std::string const &aa, std::string const &ss, utility::vector1< std::string > const &complete_abego, core::Size const resid, core::Size const fragsize) const
	generates a key based on secondary structure to be used in fragcache More...
core::fragment::FrameOP	pick_fragments_for_resid (std::string const &chain_aa, std::string const &chain_ss, utility::vector1< std::string > const &chain_abego, core::Size const resid, core::Size const frag_length)
	Simply picks fragments for the given position, caching as needed. More...
core::fragment::FrameList	get_framelist (std::string const &complete_aa, std::string const &complete_ss, utility::vector1< std::string > const &complete_abego, utility::vector1< core::Size > const &chain_endings, core::Size const start_res, core::Size const end_res, core::Size const frag_length)
	pick fragments of a given length, padding when necessary – CACHES fragments for all positions More...

Private Attributes
VLBProtected	vlb_
FragmentMap	fragcache_
core::Size	n_frags_
	number of fragments to pick for each position (default = 200) More...

Detailed Description

class used for picking/caching fragments

Member Typedef Documentation

typedef std::map< std::string, core::fragment::FrameCOP > protocols::denovo_design::components::Picker::FragmentMap

Constructor & Destructor Documentation

protocols::denovo_design::components::Picker::Picker

(

)

protocols::denovo_design::components::Picker::~Picker ( )

virtualdefault

Member Function Documentation

core::fragment::ConstantLengthFragSetOP protocols::denovo_design::components::Picker::fragments_for_permutation	(	StructureData const &	perm,
		SegmentNameList const &	comp_ids,
		core::Size const	frag_size
	)

picks and caches fragments for the listed components with size frag_size

picks and caches fragments for the listed components with size frag_size this does cache and should be the primary function called by objects needing fragments

References protocols::denovo_design::components::StructureData::abego(), protocols::denovo_design::abego_vector(), get_framelist(), protocols::denovo_design::components::Segment::has_free_upper_terminus(), protocols::denovo_design::components::Segment::lower(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), protocols::denovo_design::components::StructureData::ss(), and protocols::denovo_design::components::Segment::upper().

core::fragment::ConstantLengthFragSetOP protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose	(	StructureData const &	perm,
		core::pose::Pose const &	pose,
		SegmentNames const &	comp_ids,
		core::Size const	frag_size
	)

picks and caches fragments for the listed components with size frag_size

picks and caches fragments for the listed components with size frag_size this does cache and should be the primary function called by objects needing fragments replaces X in the desired abego with whatever is in the pose

References protocols::denovo_design::components::StructureData::abego(), protocols::denovo_design::abego_vector(), core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), get_framelist(), core::sequence::ABEGOManager::get_symbols(), protocols::denovo_design::components::Segment::lower(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::ss(), protocols::denovo_design::components::Segment::start(), protocols::denovo_design::components::Segment::stop(), and protocols::denovo_design::components::Segment::upper().

core::fragment::FrameList protocols::denovo_design::components::Picker::get_framelist ( std::string const &  complete_aa, std::string const &  complete_ss, utility::vector1< std::string > const &  complete_abego, utility::vector1< core::Size > const &  chain_endings, core::Size const  start_res, core::Size const  end_res, core::Size const  frag_length  )

protected

pick fragments of a given length, padding when necessary – CACHES fragments for all positions

Parameters

[in]	complete_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	complete_ss	The complete secondary structure string, typically from a Pose.
[in]	complete_abego	The complete abego string, typically from a setter, set_abego
[in]	interval	The interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	frag_length	The desired length of the fragments
[in]	n_frags	The number of fragments to pick per position.

References protocols::denovo_design::components::get_closest_chain_ending(), pick_fragments_for_resid(), protocols::TR(), and protocols::denovo_design::components::truncate_abego().

Referenced by fragments_for_permutation(), fragments_for_permutation_take_X_from_pose(), and pick_and_cache_fragments().

core::fragment::ConstantLengthFragSetOP protocols::denovo_design::components::Picker::pick_and_cache_fragments	(	std::string const &	ss,
		std::string const &	abego,
		protocols::loops::Loops const &	loops,
		utility::vector1< core::Size > const &	chain_endings,
		core::Size const	frag_size
	)

picks and caches fragments for the given segments with size frag_size

picks and caches fragments for the listed components with size frag_size this does cache and should be the primary function called by objects needing fragments

References protocols::denovo_design::abego_vector(), and get_framelist().

Referenced by protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover().

core::fragment::ConstantLengthFragSetOP protocols::denovo_design::components::Picker::pick_and_cache_fragments	(	std::string const &	complete_ss,
		utility::vector1< std::string > const &	complete_abego,
		utility::vector1< core::Size > const &	chain_endings,
		core::Size const	start_res,
		core::Size const	end_res,
		core::Size const	frag_length
	)

pick and cache fragments without considering primary sequence

References get_framelist().

core::fragment::ConstantLengthFragSetOP protocols::denovo_design::components::Picker::pick_and_cache_fragments	(	std::string const &	complete_aa,
		std::string const &	complete_ss,
		utility::vector1< std::string > const &	complete_abego,
		utility::vector1< core::Size > const &	chain_endings,
		core::Size const	start_res,
		core::Size const	end_res,
		core::Size const	frag_length
	)

pick and cache fragments with a primary sequence in mind

References get_framelist().

core::fragment::FrameOP protocols::denovo_design::components::Picker::pick_fragments_for_resid ( std::string const &  chain_aa, std::string const &  chain_ss, utility::vector1< std::string > const &  chain_abego, core::Size const  resid, core::Size const  frag_length  )

protected

Simply picks fragments for the given position, caching as needed.

Parameters

[in]	chain_ss	The complete secondary structure string, typically from a Pose.
[in]	chain_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	chain_abego	The complete abego string, typically from a setter, set_abego
[in]	resid	The starting residue to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	frag_length	The desired length of the fragments
[in]	n_frags	The number of fragments to pick per position.
[in]	chain_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	chain_ss	The complete secondary structure string, typically from a Pose.
[in]	chain_abego	The complete abego string, typically from a setter, set_abego
[in]	resid	The starting residue to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	frag_length	The desired length of the fragments
[in]	n_frags	The number of fragments to pick per position.

References fragcache_, n_frags_, protocols::denovo_design::components::VLBProtected::pick_fragments_public(), ss_key(), protocols::TR(), and vlb_.

Referenced by get_framelist().

void protocols::denovo_design::components::Picker::set_nfrags

(

core::Size const

nfrags

)

References n_frags_.

std::string protocols::denovo_design::components::Picker::ss_key ( std::string const &  aa, std::string const &  ss, utility::vector1< std::string > const &  complete_abego, core::Size const  resid, core::Size const  fragsize  ) const

protected

generates a key based on secondary structure to be used in fragcache

References protocols::loops::stop, and protocols::TR().

Referenced by pick_fragments_for_resid().

Member Data Documentation

FragmentMap protocols::denovo_design::components::Picker::fragcache_

private

Referenced by pick_fragments_for_resid().

core::Size protocols::denovo_design::components::Picker::n_frags_

private

number of fragments to pick for each position (default = 200)

Referenced by pick_fragments_for_resid(), and set_nfrags().

VLBProtected protocols::denovo_design::components::Picker::vlb_

private

Referenced by pick_fragments_for_resid().

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

• src/protocols/denovo_design/components/Picker.hh
• src/protocols/denovo_design/components/Picker.cc