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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:
Inheritance graph
[legend]

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

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 
)
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 
)
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_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]complete_ssThe complete secondary structure string, typically from a Pose.
[in]complete_abegoThe complete abego string, typically from a setter, set_abego
[in]intervalThe interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]frag_lengthThe desired length of the fragments
[in]n_fragsThe 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_ssThe complete secondary structure string, typically from a Pose.
[in]chain_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]chain_abegoThe complete abego string, typically from a setter, set_abego
[in]residThe starting residue to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]frag_lengthThe desired length of the fragments
[in]n_fragsThe number of fragments to pick per position.
[in]chain_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]chain_ssThe complete secondary structure string, typically from a Pose.
[in]chain_abegoThe complete abego string, typically from a setter, set_abego
[in]residThe starting residue to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]frag_lengthThe desired length of the fragments
[in]n_fragsThe 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
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

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