protocols::antibody_legacy 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::shared_ptr< CDRH3Modeler >	CDRH3ModelerOP
typedef utility::pointer::shared_ptr< const CDRH3Modeler >	CDRH3ModelerCOP
typedef utility::pointer::shared_ptr< GraftMover >	GraftMoverOP
typedef utility::pointer::shared_ptr< const GraftMover >	GraftMoverCOP
typedef utility::pointer::shared_ptr< GraftOneMover >	GraftOneMoverOP
typedef utility::pointer::shared_ptr< const GraftOneMover >	GraftOneMoverCOP
typedef utility::pointer::shared_ptr< CloseOneMover >	CloseOneMoverOP
typedef utility::pointer::shared_ptr< const CloseOneMover >	CloseOneMoverCOP
typedef utility::pointer::shared_ptr< LoopRlxMover >	LoopRlxMoverOP
typedef utility::pointer::shared_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, core::Size jumppoint1, core::Size cutpoint, core::Size jumppoint2)
void	read_H3_cter_fragment (Antibody &antibody_in, utility::vector1< fragment::FragData > &H3_base_library, bool is_camelid)
void	read_H3_cter_fragment (Antibody &antibody_in, utility::vector1< core::fragment::FragData > &H3_base_library, bool is_camelid)

Typedef Documentation

CDRH3ModelerCOP

typedef utility::pointer::shared_ptr< const CDRH3Modeler > protocols::antibody_legacy::CDRH3ModelerCOP

CDRH3ModelerOP

typedef utility::pointer::shared_ptr< CDRH3Modeler > protocols::antibody_legacy::CDRH3ModelerOP

CloseOneMoverCOP

typedef utility::pointer::shared_ptr<const CloseOneMover> protocols::antibody_legacy::CloseOneMoverCOP

CloseOneMoverOP

typedef utility::pointer::shared_ptr< CloseOneMover > protocols::antibody_legacy::CloseOneMoverOP

GraftMoverCOP

typedef utility::pointer::shared_ptr< const GraftMover > protocols::antibody_legacy::GraftMoverCOP

GraftMoverOP

typedef utility::pointer::shared_ptr< GraftMover > protocols::antibody_legacy::GraftMoverOP

GraftOneMoverCOP

typedef utility::pointer::shared_ptr<const GraftOneMover> protocols::antibody_legacy::GraftOneMoverCOP

GraftOneMoverOP

typedef utility::pointer::shared_ptr< GraftOneMover > protocols::antibody_legacy::GraftOneMoverOP

LoopRlxMoverCOP

typedef utility::pointer::shared_ptr<const LoopRlxMover> protocols::antibody_legacy::LoopRlxMoverCOP

LoopRlxMoverOP

typedef utility::pointer::shared_ptr< LoopRlxMover > protocols::antibody_legacy::LoopRlxMoverOP

Function Documentation

read_H3_cter_fragment() [1/2]

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

References protocols::antibody_legacy::Antibody::cdrh_, protocols::antibody_legacy::Antibody::extended_, protocols::antibody_legacy::Antibody::Fv_sequence_, protocols::antibody_legacy::CDRH3Modeler::H3_base_library, protocols::antibody_legacy::Antibody::kinked_, core::scoring::omega, and protocols::TR().

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

read_H3_cter_fragment() [2/2]

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

References protocols::antibody_legacy::Antibody::cdrh_, protocols::antibody_legacy::Antibody::extended_, protocols::antibody_legacy::Antibody::Fv_sequence_, protocols::antibody_legacy::CDRH3Modeler::H3_base_library, protocols::antibody_legacy::Antibody::kinked_, core::scoring::omega, and protocols::TR().

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

simple_fold_tree()

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

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax().

simple_one_loop_fold_tree()

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

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), protocols::loops::Loop::cut(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::TR().

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