protocols::antibody::Antibody Class Reference

antibody definition More...

#include <AntibodyClass.hh>

Collaboration diagram for protocols::antibody::Antibody:

List of all members.

Public Member Functions
	Antibody ()
	default constructor
	Antibody (core::pose::Pose &pose_in)
	constructor with arguments
	Antibody (core::pose::Pose &pose_in, bool camelid)
	constructor with arguments
	Antibody (core::pose::Pose &pose_in, std::string cdr_name)
	constructor with arguments
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
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

---

Detailed Description

antibody definition

---

Constructor & Destructor Documentation

protocols::antibody::Antibody::Antibody

(

)

default constructor

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

protocols::antibody::Antibody::Antibody

(

core::pose::Pose &

pose_in

)

constructor with arguments

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

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

constructor with arguments

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

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

constructor with arguments

References 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

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

Referenced by protocols::antibody::GraftMover::apply().

void protocols::antibody::Antibody::all_cdr_fold_tree

(

)

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

Referenced by set_defaults().

void protocols::antibody::Antibody::populate_all_cdrs

(

)

References protocols::loops::Loops::add_loop(), all_cdr_loops, make_table_of_pilot_apps::begin, cdrh_, cdrl_, core::sequence::end, and protocols::loops::Loops::sequential_order().

Referenced by set_defaults().

void protocols::antibody::Antibody::set_defaults

(

)

References all_cdr_fold_tree(), 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,
		bool	camelid
	)

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

void protocols::antibody::Antibody::set_Fv

(

core::pose::Pose &

pose_in

)

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

---

Member Data Documentation

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

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

Referenced by all_cdr_fold_tree(), and populate_all_cdrs().

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

Referenced by Antibody(), protocols::antibody::GraftMover::apply(), populate_all_cdrs(), protocols::antibody::read_H3_cter_fragment(), and set_defaults().

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

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

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

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

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

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

bool protocols::antibody::Antibody::extended_

Referenced by Antibody(), protocols::antibody::read_H3_cter_fragment(), and set_Fv().

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

Referenced by align_to_native(), all_cdr_fold_tree(), Antibody(), protocols::antibody::GraftMover::apply(), set_defaults(), and set_Fv().

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

Referenced by protocols::antibody::read_H3_cter_fragment().

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

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

bool protocols::antibody::Antibody::kinked_

Referenced by Antibody(), protocols::antibody::read_H3_cter_fragment(), and set_Fv().

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

Referenced by Antibody(), and set_defaults().

---

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

• src/protocols/antibody/AntibodyClass.hh
• src/protocols/antibody/AntibodyClass.cc