class used for picking/caching fragments More...
#include <Picker.hh>
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
◆ FragmentMap
| typedef std::map< std::string, core::fragment::FrameCOP > protocols::denovo_design::components::Picker::FragmentMap |
Constructor & Destructor Documentation
◆ Picker()
| protocols::denovo_design::components::Picker::Picker | ( | ) |
◆ ~Picker()
|
virtualdefault |
Member Function Documentation
◆ fragments_for_permutation()
| 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().
◆ fragments_for_permutation_take_X_from_pose()
| 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().
◆ get_framelist()
|
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().
◆ pick_and_cache_fragments() [1/3]
| 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().
◆ pick_and_cache_fragments() [2/3]
| 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().
◆ pick_and_cache_fragments() [3/3]
| 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 core::scoring::abego, protocols::denovo_design::abego_vector(), and get_framelist().
Referenced by protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover().
◆ pick_fragments_for_resid()
|
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().
◆ set_nfrags()
| void protocols::denovo_design::components::Picker::set_nfrags | ( | core::Size const | nfrags | ) |
References n_frags_.
◆ ss_key()
|
protected |
generates a key based on secondary structure to be used in fragcache
References protocols::cluster::calibur::aa, core::scoring::abego, protocols::loops::stop, and protocols::TR().
Referenced by pick_fragments_for_resid().
Member Data Documentation
◆ fragcache_
|
private |
Referenced by pick_fragments_for_resid().
◆ n_frags_
|
private |
number of fragments to pick for each position (default = 200)
Referenced by pick_fragments_for_resid(), and set_nfrags().
◆ vlb_
|
private |
Referenced by pick_fragments_for_resid().
The documentation for this class was generated from the following files:
