protocols::antibody Namespace Reference

Classes
class	Antibody
	antibody definition More...
class	AntibodyModeler
class	CDRH3Modeler
	Ab initio modeling of CDR H3 loop. More...
class	GraftMover
	Grafts a series of CDR onto a framework. More...
class	GraftOneMover
	Grafts only one CDR onto a framework. More...
class	CloseOneMover
	Closes only one CDR onto a framework. More...
class	LoopRlxMover
	Closes only one CDR onto a framework. More...

Typedefs
typedef utility::pointer::owning_ptr < CDRH3Modeler >	CDRH3ModelerOP
typedef utility::pointer::owning_ptr < const CDRH3Modeler >	CDRH3ModelerCOP
typedef utility::pointer::owning_ptr < GraftMover >	GraftMoverOP
typedef utility::pointer::owning_ptr < const GraftMover >	GraftMoverCOP
typedef utility::pointer::owning_ptr < GraftOneMover >	GraftOneMoverOP
typedef utility::pointer::owning_ptr < const GraftOneMover >	GraftOneMoverCOP
typedef utility::pointer::owning_ptr < CloseOneMover >	CloseOneMoverOP
typedef utility::pointer::owning_ptr < const CloseOneMover >	CloseOneMoverCOP
typedef utility::pointer::owning_ptr < LoopRlxMover >	LoopRlxMoverOP
typedef utility::pointer::owning_ptr < const LoopRlxMover >	LoopRlxMoverCOP

Functions
void	simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop)
void	simple_fold_tree (pose::Pose &pose_in, Size jumppoint1, Size cutpoint, Size jumppoint2)
void	read_H3_cter_fragment (antibody::Antibody &antibody_in, utility::vector1< fragment::FragData > &H3_base_library, bool is_camelid)

Typedef Documentation

typedef utility::pointer::owning_ptr< const CDRH3Modeler > protocols::antibody::CDRH3ModelerCOP

Definition at line 51 of file CDRH3Modeler.hh.

typedef utility::pointer::owning_ptr< CDRH3Modeler > protocols::antibody::CDRH3ModelerOP

Definition at line 49 of file CDRH3Modeler.hh.

typedef utility::pointer::owning_ptr<const CloseOneMover> protocols::antibody::CloseOneMoverCOP

Definition at line 152 of file GraftMover.hh.

typedef utility::pointer::owning_ptr< CloseOneMover > protocols::antibody::CloseOneMoverOP

Definition at line 150 of file GraftMover.hh.

typedef utility::pointer::owning_ptr< const GraftMover > protocols::antibody::GraftMoverCOP

Definition at line 40 of file GraftMover.hh.

typedef utility::pointer::owning_ptr< GraftMover > protocols::antibody::GraftMoverOP

Definition at line 38 of file GraftMover.hh.

typedef utility::pointer::owning_ptr<const GraftOneMover> protocols::antibody::GraftOneMoverCOP

Definition at line 111 of file GraftMover.hh.

typedef utility::pointer::owning_ptr< GraftOneMover > protocols::antibody::GraftOneMoverOP

Definition at line 109 of file GraftMover.hh.

typedef utility::pointer::owning_ptr<const LoopRlxMover> protocols::antibody::LoopRlxMoverCOP

Definition at line 197 of file GraftMover.hh.

typedef utility::pointer::owning_ptr< LoopRlxMover > protocols::antibody::LoopRlxMoverOP

Definition at line 195 of file GraftMover.hh.

Function Documentation

void protocols::antibody::read_H3_cter_fragment	(	antibody::Antibody &	antibody_in,
		utility::vector1< fragment::FragData > &	H3_base_library,
		bool	is_camelid
	)

Definition at line 435 of file CDRH3Modeler.cc.

References protocols::antibody::Antibody::cdrh_, protocols::antibody::Antibody::extended_, protocols::antibody::Antibody::Fv_sequence_, protocols::antibody::Antibody::kinked_, core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), and protocols::TR().

Referenced by protocols::antibody::AntibodyModeler::init_on_new_input().

void protocols::antibody::simple_fold_tree	(	pose::Pose &	pose_in,
		Size	jumppoint1,
		Size	cutpoint,
		Size	jumppoint2
	)

Definition at line 403 of file CDRH3Modeler.cc.

References core::pose::Pose::fold_tree(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::antibody::CDRH3Modeler::loop_fa_relax(), and protocols::swa::rna::setup_simple_fold_tree().

void protocols::antibody::simple_one_loop_fold_tree	(	pose::Pose &	pose_in,
		loops::Loop const &	loop
	)

Definition at line 371 of file CDRH3Modeler.cc.

References protocols::loops::Loop::cut(), core::pose::Pose::fold_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::antibody::AntibodyModeler::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), and protocols::antibody::CDRH3Modeler::scored_frag_close().