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protocols::antibody::design::NativeAntibodySeq Class Reference

Class that keeps track of the 'native' sequence during design. Native means that no design has occured. Used for conservative base design to keep it from hopping around residue types. More...

#include <NativeAntibodySeq.hh>

Inheritance diagram for protocols::antibody::design::NativeAntibodySeq:
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Public Member Functions

 NativeAntibodySeq (core::pose::Pose const &pose, AntibodyInfo const &ab_info)
 
void set_sequence (core::pose::Pose const &pose, AntibodyInfo const &ab_info)
 Sets the sequence from the PDB into this class and into the pose. More...
 
void set_to_pose (core::pose::Pose &pose)
 Set this class to the pose datacache. More...
 
void set_from_cdr (core::pose::Pose const &pose, AntibodyInfo const &ab_info, CDRNameEnum cdr)
 Sets the sequence from the CDR of the PDB into this class and into the pose. More...
 
std::map< std::string,
core::chemical::AA > const & 
get_full_sequence () const
 Get a map of PDBInfo residues to AA residues as the sequence. More...
 
std::map< CDRNameEnum,
utility::vector1
< core::chemical::AA > > const & 
get_cdr_sequence () const
 Get a map of each native CDR sequence. More...
 
std::string get_native_sequence_matching_current_length (core::pose::Pose const &pose, AntibodyInfo const &ab_info) const
 Get the full pose sequence, accounting for length changes to the pose. More...
 
basic::datacache::CacheableDataOP clone () const override
 

Private Attributes

std::map< std::string,
core::chemical::AA
seq_
 
std::map< CDRNameEnum,
utility::vector1
< core::chemical::AA > > 
cdr_seq_
 

Detailed Description

Class that keeps track of the 'native' sequence during design. Native means that no design has occured. Used for conservative base design to keep it from hopping around residue types.

Constructor & Destructor Documentation

protocols::antibody::design::NativeAntibodySeq::NativeAntibodySeq ( core::pose::Pose const &  pose,
AntibodyInfo const &  ab_info 
)

References set_sequence().

Member Function Documentation

basic::datacache::CacheableDataOP protocols::antibody::design::NativeAntibodySeq::clone ( ) const
override

Referenced by set_to_pose().

std::map< CDRNameEnum, utility::vector1< core::chemical::AA > > const & protocols::antibody::design::NativeAntibodySeq::get_cdr_sequence ( ) const

Get a map of each native CDR sequence.

References cdr_seq_.

std::map< std::string, core::chemical::AA > const & protocols::antibody::design::NativeAntibodySeq::get_full_sequence ( ) const

Get a map of PDBInfo residues to AA residues as the sequence.

References seq_.

std::string protocols::antibody::design::NativeAntibodySeq::get_native_sequence_matching_current_length ( core::pose::Pose const &  pose,
AntibodyInfo const &  ab_info 
) const
void protocols::antibody::design::NativeAntibodySeq::set_from_cdr ( core::pose::Pose const &  pose,
AntibodyInfo const &  ab_info,
CDRNameEnum  cdr 
)

Sets the sequence from the CDR of the PDB into this class and into the pose.

References core::pose::Pose::aa(), cdr_seq_, protocols::antibody::AntibodyInfo::get_CDR_length(), and protocols::antibody::AntibodyInfo::get_CDR_start().

Referenced by set_sequence().

void protocols::antibody::design::NativeAntibodySeq::set_sequence ( core::pose::Pose const &  pose,
AntibodyInfo const &  ab_info 
)
void protocols::antibody::design::NativeAntibodySeq::set_to_pose ( core::pose::Pose pose)

Member Data Documentation

std::map< CDRNameEnum, utility::vector1< core::chemical::AA > > protocols::antibody::design::NativeAntibodySeq::cdr_seq_
private
std::map< std::string , core::chemical::AA> protocols::antibody::design::NativeAntibodySeq::seq_
private

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