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>
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
◆ NativeAntibodySeq()
| protocols::antibody::design::NativeAntibodySeq::NativeAntibodySeq | ( | core::pose::Pose const & | pose, |
| AntibodyInfo const & | ab_info | ||
| ) |
References set_sequence().
Member Function Documentation
◆ clone()
|
override |
Referenced by set_to_pose().
◆ get_cdr_sequence()
| 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_.
◆ get_full_sequence()
| 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_.
◆ get_native_sequence_matching_current_length()
| std::string protocols::antibody::design::NativeAntibodySeq::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.
References core::pose::Pose::aa(), cdr_seq_, protocols::antibody::AntibodyInfo::get_all_cdrs_present(), protocols::antibody::AntibodyInfo::get_CDR_length(), protocols::antibody::AntibodyInfo::get_CDR_start(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::pdb_info(), seq_, and core::pose::Pose::size().
◆ set_from_cdr()
| 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().
◆ set_sequence()
| void protocols::antibody::design::NativeAntibodySeq::set_sequence | ( | core::pose::Pose const & | pose, |
| AntibodyInfo const & | ab_info | ||
| ) |
Sets the sequence from the PDB into this class and into the pose.
References core::pose::Pose::aa(), protocols::antibody::cdr_region, cdr_seq_, protocols::antibody::AntibodyInfo::get_all_cdrs_present(), protocols::antibody::AntibodyInfo::get_region_of_residue(), core::pose::Pose::pdb_info(), seq_, set_from_cdr(), and core::pose::Pose::size().
Referenced by NativeAntibodySeq().
◆ set_to_pose()
| void protocols::antibody::design::NativeAntibodySeq::set_to_pose | ( | core::pose::Pose & | pose | ) |
Set this class to the pose datacache.
References clone(), core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::NATIVE_ANTIBODY_SEQ.
Member Data Documentation
◆ cdr_seq_
|
private |
Referenced by get_cdr_sequence(), get_native_sequence_matching_current_length(), set_from_cdr(), and set_sequence().
◆ seq_
|
private |
Referenced by get_full_sequence(), get_native_sequence_matching_current_length(), and set_sequence().
The documentation for this class was generated from the following files:
- src/protocols/antibody/design/NativeAntibodySeq.hh
- src/protocols/antibody/design/NativeAntibodySeq.cc
