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protocols::antibody::Antibody Class Reference

antibody definition More...

#include <AntibodyClass.hh>

Collaboration diagram for protocols::antibody::Antibody:
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Public Member Functions

 Antibody ()
 default constructor More...
 
 Antibody (core::pose::Pose &pose_in)
 constructor with arguments More...
 
 Antibody (core::pose::Pose &pose_in, bool camelid)
 constructor with arguments More...
 
 Antibody (core::pose::Pose &pose_in, std::string cdr_name)
 constructor with arguments More...
 
void set_defaults ()
 
void set_Fv (core::pose::Pose &pose_in)
 
void set_Fv (core::pose::Pose &pose_in, bool camelid)
 
void populate_all_cdrs ()
 
void all_cdr_fold_tree ()
 
void align_to_native (antibody::Antibody &native)
 align current Fv to native.Fv More...
 

Public Attributes

core::Size cdrl_ [4][3]
 
core::Size cdrh_ [4][3]
 
core::Size lfr_ [8][3]
 
core::Size hfr_ [7][3]
 
core::Size current_start
 
core::Size current_end
 
core::pose::Pose Fv
 
bool kinked_
 
bool extended_
 
utility::vector1< char > Fv_sequence_
 
loops::Loops all_cdr_loops
 
core::kinematics::MoveMap ab_movemap
 

Private Member Functions

void detect_CDR_H3_stem_type ()
 
void detect_camelid_CDR_H3_stem_type ()
 
void detect_regular_CDR_H3_stem_type ()
 
void update_sequence ()
 

Private Attributes

core::Size cdr_h3_cut_
 
bool camelid_
 

Detailed Description

antibody definition

Definition at line 33 of file AntibodyClass.hh.

Constructor & Destructor Documentation

protocols::antibody::Antibody::Antibody ( )

default constructor

Definition at line 41 of file AntibodyClass.cc.

References camelid_, cdrh_, cdrl_, current_end, current_start, extended_, hfr_, kinked_, and lfr_.

protocols::antibody::Antibody::Antibody ( core::pose::Pose &  pose_in)

constructor with arguments

Definition at line 58 of file AntibodyClass.cc.

References camelid_, current_end, current_start, detect_CDR_H3_stem_type(), extended_, Fv, kinked_, set_defaults(), and update_sequence().

protocols::antibody::Antibody::Antibody ( core::pose::Pose &  pose_in,
bool  camelid 
)

constructor with arguments

Definition at line 72 of file AntibodyClass.cc.

References camelid_, current_end, current_start, detect_CDR_H3_stem_type(), extended_, Fv, kinked_, set_defaults(), and update_sequence().

protocols::antibody::Antibody::Antibody ( core::pose::Pose &  pose_in,
std::string  cdr_name 
)

constructor with arguments

Definition at line 86 of file AntibodyClass.cc.

References camelid_, cdrh_, cdrl_, current_end, current_start, Fv, and core::pose::Pose::pdb_info().

Member Function Documentation

void protocols::antibody::Antibody::align_to_native ( antibody::Antibody &  native)

align current Fv to native.Fv

Definition at line 447 of file AntibodyClass.cc.

References core::id::BOGUS_ATOM_ID, Fv, hfr_, core::pose::initialize_atomid_map(), and core::scoring::superimpose_pose().

Referenced by protocols::antibody::AntibodyModeler::apply(), and protocols::antibody::GraftMover::apply().

void protocols::antibody::Antibody::all_cdr_fold_tree ( )

Definition at line 412 of file AntibodyClass.cc.

References all_cdr_loops, protocols::loops::Loops::begin(), core::kinematics::FoldTree::clear(), protocols::loops::Loops::end(), core::pose::Pose::fold_tree(), Fv, protocols::loops::Loops::sequential_order(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody::AntibodyModeler::relax_cdrs(), and set_defaults().

void protocols::antibody::Antibody::detect_camelid_CDR_H3_stem_type ( )
private

Definition at line 285 of file AntibodyClass.cc.

References cdrh_, extended_, Fv_sequence_, kinked_, and protocols::TR().

Referenced by detect_CDR_H3_stem_type().

void protocols::antibody::Antibody::detect_CDR_H3_stem_type ( )
private

Definition at line 276 of file AntibodyClass.cc.

References camelid_, detect_camelid_CDR_H3_stem_type(), and detect_regular_CDR_H3_stem_type().

Referenced by Antibody(), and set_Fv().

void protocols::antibody::Antibody::detect_regular_CDR_H3_stem_type ( )
private

Definition at line 326 of file AntibodyClass.cc.

References cdrh_, extended_, Fv, Fv_sequence_, kinked_, core::conformation::Residue::name1(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and protocols::TR().

Referenced by detect_CDR_H3_stem_type().

void protocols::antibody::Antibody::populate_all_cdrs ( )

Definition at line 216 of file AntibodyClass.cc.

References protocols::loops::Loops::add_loop(), all_cdr_loops, camelid_, cdr_h3_cut_, cdrh_, cdrl_, core::sequence::end, protocols::loops::Loops::sequential_order(), and core::io::serialization::size().

Referenced by set_defaults().

void protocols::antibody::Antibody::set_defaults ( )

Definition at line 138 of file AntibodyClass.cc.

References all_cdr_fold_tree(), camelid_, cdr_h3_cut_, cdrh_, cdrl_, Fv, hfr_, lfr_, core::pose::Pose::pdb_info(), and populate_all_cdrs().

Referenced by Antibody(), and set_Fv().

void protocols::antibody::Antibody::set_Fv ( core::pose::Pose &  pose_in)

Definition at line 188 of file AntibodyClass.cc.

References camelid_, current_end, current_start, detect_CDR_H3_stem_type(), extended_, Fv, kinked_, set_defaults(), and update_sequence().

Referenced by protocols::antibody::CDRH3Modeler::apply(), and protocols::antibody::AntibodyModeler::init_on_new_input().

void protocols::antibody::Antibody::set_Fv ( core::pose::Pose &  pose_in,
bool  camelid 
)

Definition at line 202 of file AntibodyClass.cc.

References camelid_, current_end, current_start, detect_CDR_H3_stem_type(), extended_, Fv, kinked_, set_defaults(), and update_sequence().

void protocols::antibody::Antibody::update_sequence ( )
private

Definition at line 270 of file AntibodyClass.cc.

References Fv, Fv_sequence_, core::conformation::Residue::name1(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by Antibody(), and set_Fv().

Member Data Documentation

core::kinematics::MoveMap protocols::antibody::Antibody::ab_movemap

Definition at line 76 of file AntibodyClass.hh.

loops::Loops protocols::antibody::Antibody::all_cdr_loops

Definition at line 74 of file AntibodyClass.hh.

Referenced by all_cdr_fold_tree(), protocols::antibody::AntibodyModeler::apply(), protocols::antibody::CDRH3Modeler::cutpoints_separation(), populate_all_cdrs(), and protocols::antibody::AntibodyModeler::relax_cdrs().

bool protocols::antibody::Antibody::camelid_
private

Definition at line 81 of file AntibodyClass.hh.

Referenced by Antibody(), detect_CDR_H3_stem_type(), populate_all_cdrs(), set_defaults(), and set_Fv().

core::Size protocols::antibody::Antibody::cdr_h3_cut_
private

Definition at line 80 of file AntibodyClass.hh.

Referenced by populate_all_cdrs(), and set_defaults().

core::Size protocols::antibody::Antibody::cdrh_[4][3]

Definition at line 58 of file AntibodyClass.hh.

Referenced by Antibody(), protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::antibody::AntibodyModeler::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), protocols::antibody::CDRH3Modeler::build_fullatom_loop(), detect_camelid_CDR_H3_stem_type(), detect_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyModeler::display_constraint_residues(), protocols::antibody::AntibodyModeler::global_loop_rmsd(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), populate_all_cdrs(), protocols::antibody::AntibodyModeler::read_and_store_fragments(), protocols::antibody::read_H3_cter_fragment(), protocols::antibody::CDRH3Modeler::scored_frag_close(), and set_defaults().

core::Size protocols::antibody::Antibody::cdrl_[4][3]

Definition at line 57 of file AntibodyClass.hh.

Referenced by Antibody(), protocols::antibody::GraftMover::apply(), protocols::antibody::AntibodyModeler::global_loop_rmsd(), populate_all_cdrs(), and set_defaults().

core::Size protocols::antibody::Antibody::current_end

Definition at line 65 of file AntibodyClass.hh.

Referenced by Antibody(), protocols::antibody::GraftOneMover::set_default(), and set_Fv().

core::Size protocols::antibody::Antibody::current_start

Definition at line 63 of file AntibodyClass.hh.

Referenced by Antibody(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), protocols::antibody::GraftOneMover::set_default(), and set_Fv().

bool protocols::antibody::Antibody::extended_

Definition at line 71 of file AntibodyClass.hh.

Referenced by Antibody(), protocols::antibody::CDRH3Modeler::apply(), detect_camelid_CDR_H3_stem_type(), detect_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyModeler::display_constraint_residues(), protocols::antibody::read_H3_cter_fragment(), protocols::antibody::CDRH3Modeler::scored_frag_close(), and set_Fv().

core::pose::Pose protocols::antibody::Antibody::Fv

Definition at line 68 of file AntibodyClass.hh.

Referenced by align_to_native(), all_cdr_fold_tree(), Antibody(), protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::antibody::AntibodyModeler::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), protocols::antibody::CDRH3Modeler::build_fullatom_loop(), protocols::antibody::CDRH3Modeler::cutpoints_separation(), detect_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyModeler::display_constraint_residues(), protocols::antibody::AntibodyModeler::global_loop_rmsd(), protocols::antibody::AntibodyModeler::read_and_store_fragments(), protocols::antibody::AntibodyModeler::relax_cdrs(), set_defaults(), set_Fv(), and update_sequence().

utility::vector1< char > protocols::antibody::Antibody::Fv_sequence_

Definition at line 72 of file AntibodyClass.hh.

Referenced by detect_camelid_CDR_H3_stem_type(), detect_regular_CDR_H3_stem_type(), protocols::antibody::read_H3_cter_fragment(), and update_sequence().

core::Size protocols::antibody::Antibody::hfr_[7][3]

Definition at line 60 of file AntibodyClass.hh.

Referenced by align_to_native(), Antibody(), and set_defaults().

bool protocols::antibody::Antibody::kinked_

Definition at line 70 of file AntibodyClass.hh.

Referenced by Antibody(), protocols::antibody::CDRH3Modeler::apply(), detect_camelid_CDR_H3_stem_type(), detect_regular_CDR_H3_stem_type(), protocols::antibody::read_H3_cter_fragment(), and set_Fv().

core::Size protocols::antibody::Antibody::lfr_[8][3]

Definition at line 59 of file AntibodyClass.hh.

Referenced by Antibody(), and set_defaults().

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