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protocols::stepwise::monte_carlo::submotif::SubMotifLibrary Class Reference

#include <SubMotifLibrary.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::submotif::SubMotifLibrary:
Inheritance graph
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Public Member Functions

 SubMotifLibrary (core::chemical::ResidueTypeSetCOP rsd_set, bool const include_submotifs_from_jump_library=false, bool const use_first_jump_for_submotif=false, utility::vector1< std::string > const &exclude_submotif_list=utility::vector1< std::string >())
 
 ~SubMotifLibrary () override
 
core::pose::PoseOP create_new_submotif (SequenceMapping const &sequence_mapping, PoseTag const &submotif_tag, core::pose::Pose const &pose, bool const &seed=false) const
 
utility::vector1
< monte_carlo::mover::StepWiseMove
get_submotif_moves (core::pose::Pose const &pose) const
 

Private Member Functions

void initialize ()
 
void initialize_from_directory (std::string const &dir_name)
 
void initialize_from_jump_library ()
 
SubMotifSequenceSet get_submotif_sequence_set (core::pose::Pose const &pose, bool sort_sequences=true) const
 
void save_pose_as_submotif (core::pose::PoseOP pose, std::string const &tag)
 
utility::vector1< SequenceMappingget_matches_for_one_submotif_sequence_set (SubMotifSequenceSet const &submotif_sequence_set, core::pose::Pose const &pose, bool const use_full_model_info=true) const
 
void get_moves_for_one_submotif (core::pose::PoseCOP submotif_pose, core::pose::Pose const &pose) const
 
void get_matches (utility::vector1< SequenceMapping > &all_matches, SequenceMapping const &matching_residues, std::string const &submotif_sequence, utility::vector1< core::Size > const &submotif_cutpoints, std::string const &pose_sequence, utility::vector1< core::Size > const &pose_cutpoints, utility::vector1< core::Size > const &pose_domain_map) const
 
void output_tags () const
 

Private Attributes

core::chemical::ResidueTypeSetCOP rsd_set_
 
bool const include_submotifs_from_jump_library_
 
bool const use_first_jump_for_submotif_
 
utility::vector1< PoseTagexclude_submotif_list_
 
std::set< SubMotifSequenceSetsubmotif_sequence_sets_
 
std::map< SubMotifSequenceSet,
utility::vector1< std::pair
< PoseTag, SequenceMapping > > > 
submotif_mappings_by_sequence_set_
 
std::map< PoseTag,
core::pose::PoseCOP
submotif_poses_by_tag_
 

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::SubMotifLibrary ( core::chemical::ResidueTypeSetCOP  rsd_set,
bool const  include_submotifs_from_jump_library = false,
bool const  use_first_jump_for_submotif = false,
utility::vector1< std::string > const &  exclude_submotif_list = utility::vector1< std::string >() 
)

References initialize().

protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::~SubMotifLibrary ( )
overridedefault

Member Function Documentation

pose::PoseOP protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif ( SequenceMapping const &  sequence_mapping,
PoseTag const &  submotif_tag,
core::pose::Pose const &  pose,
bool const &  seed = false 
) const
void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches ( utility::vector1< SequenceMapping > &  all_matches,
SequenceMapping const &  matching_residues,
std::string const &  submotif_sequence,
utility::vector1< core::Size > const &  submotif_cutpoints,
std::string const &  pose_sequence,
utility::vector1< core::Size > const &  pose_cutpoints,
utility::vector1< core::Size > const &  pose_domain_map 
) const
private
utility::vector1< SequenceMapping > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set ( SubMotifSequenceSet const &  submotif_sequence_set,
core::pose::Pose const &  pose,
bool const  use_full_model_info = true 
) const
private
void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_moves_for_one_submotif ( core::pose::PoseCOP  submotif_pose,
core::pose::Pose const &  pose 
) const
private
utility::vector1< StepWiseMove > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_submotif_moves ( core::pose::Pose const &  pose) const
SubMotifSequenceSet protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_submotif_sequence_set ( core::pose::Pose const &  pose,
bool  sort_sequences = true 
) const
private
void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize ( )
private
void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_directory ( std::string const &  dir_name)
private
void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library ( )
private
void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::output_tags ( ) const
private
void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::save_pose_as_submotif ( core::pose::PoseOP  pose,
std::string const &  tag 
)
private

Member Data Documentation

utility::vector1< PoseTag > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::exclude_submotif_list_
private
bool const protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::include_submotifs_from_jump_library_
private

Referenced by initialize().

core::chemical::ResidueTypeSetCOP protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::rsd_set_
private
std::map< SubMotifSequenceSet, utility::vector1< std::pair< PoseTag, SequenceMapping > > > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::submotif_mappings_by_sequence_set_
private
std::map< PoseTag, core::pose::PoseCOP > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::submotif_poses_by_tag_
private
std::set< SubMotifSequenceSet > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::submotif_sequence_sets_
private
bool const protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::use_first_jump_for_submotif_
private

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