protocols::antibody2 Namespace Reference

Classes
class	Ab_TemplateInfo
	antibody2 definition More...
struct	FrameWork
class	AntibodyInfo
class	AntibodyModelerProtocol
class	CDRsMinPackMin
class	CloseOneCDRLoop
	Closes only one CDR onto a framework. More...
class	GraftCDRLoopsProtocol
class	GraftOneCDRLoop
	Grafts only one CDR onto a framework. More...
class	H3CterInsert
	H3 CDR, Fragment Insertion and CCD. More...
class	H3PerturbCCD
class	H3RefineCCD
class	LHRepulsiveRamp
class	LHRepulsiveRampLegacy
class	LHSnugFitLegacy
class	ModelCDRH3
	Ab initio modeling of CDR H3 loop. More...
class	RefineBetaBarrel
class	RefineOneCDRLoop
class	RefineOneCDRLoopCentroid
class	SnugDock
class	SnugDockProtocol

Typedefs
typedef utility::pointer::owning_ptr < Ab_TemplateInfo >	Ab_TemplateInfoOP
typedef utility::pointer::owning_ptr < Ab_TemplateInfo const >	Ab_TemplateInfoCOP
typedef utility::pointer::owning_ptr < AntibodyInfo >	AntibodyInfoOP
typedef utility::pointer::owning_ptr < AntibodyInfo const >	AntibodyInfoCOP
typedef utility::pointer::owning_ptr < AntibodyModelerProtocol >	AntibodyModelerProtocolOP
typedef utility::pointer::owning_ptr < AntibodyModelerProtocol const >	AntibodyModelerProtocolCOP
typedef utility::pointer::owning_ptr < CDRsMinPackMin >	CDRsMinPackMinOP
typedef utility::pointer::owning_ptr < CDRsMinPackMin const >	CDRsMinPackMinCOP
typedef utility::pointer::owning_ptr < CloseOneCDRLoop >	CloseOneCDRLoopOP
typedef utility::pointer::owning_ptr < CloseOneCDRLoop const >	CloseOneCDRLoopCOP
typedef utility::pointer::owning_ptr < GraftCDRLoopsProtocol >	GraftCDRLoopsProtocolOP
typedef utility::pointer::owning_ptr < GraftCDRLoopsProtocol const >	GraftCDRLoopsProtocolCOP
typedef utility::pointer::owning_ptr < GraftOneCDRLoop >	GraftOneCDRLoopOP
typedef utility::pointer::owning_ptr < const GraftOneCDRLoop >	GraftOneCDRLoopCOP
typedef utility::pointer::owning_ptr < H3CterInsert >	H3CterInsertOP
typedef utility::pointer::owning_ptr < H3CterInsert const >	H3CterInsertCOP
typedef utility::pointer::owning_ptr < H3PerturbCCD >	H3PerturbCCDOP
typedef utility::pointer::owning_ptr < H3PerturbCCD const >	H3PerturbCCDCOP
typedef utility::pointer::owning_ptr < H3RefineCCD >	H3RefineCCDOP
typedef utility::pointer::owning_ptr < H3RefineCCD const >	H3RefineCCDCOP
typedef utility::pointer::owning_ptr < LHRepulsiveRamp >	LHRepulsiveRampOP
typedef utility::pointer::owning_ptr < LHRepulsiveRamp const >	LHRepulsiveRampCOP
typedef utility::pointer::owning_ptr < LHRepulsiveRampLegacy >	LHRepulsiveRampLegacyOP
typedef utility::pointer::owning_ptr < LHRepulsiveRampLegacy const >	LHRepulsiveRampLegacyCOP
typedef utility::pointer::owning_ptr < LHSnugFitLegacy >	LHSnugFitLegacyOP
typedef utility::pointer::owning_ptr < LHSnugFitLegacy const >	LHSnugFitLegacyCOP
typedef utility::pointer::owning_ptr < ModelCDRH3 >	ModelCDRH3OP
typedef utility::pointer::owning_ptr < ModelCDRH3 const >	ModelCDRH3COP
typedef utility::pointer::owning_ptr < RefineBetaBarrel >	RefineBetaBarrelOP
typedef utility::pointer::owning_ptr < RefineBetaBarrel const >	RefineBetaBarrelCOP
typedef utility::pointer::owning_ptr < RefineOneCDRLoop >	RefineOneCDRLoopOP
typedef utility::pointer::owning_ptr < RefineOneCDRLoop const >	RefineOneCDRLoopCOP
typedef utility::pointer::owning_ptr < RefineOneCDRLoopCentroid >	RefineOneCDRLoopCentroidOP
typedef utility::pointer::owning_ptr < RefineOneCDRLoopCentroid const >	RefineOneCDRLoopCentroidCOP
typedef utility::pointer::owning_ptr < SnugDock >	SnugDockOP
typedef utility::pointer::owning_ptr < SnugDock const >	SnugDockCOP
typedef utility::pointer::owning_ptr < SnugDockProtocol >	SnugDockProtocolOP
typedef utility::pointer::owning_ptr < SnugDockProtocol const >	SnugDockProtocolCOP

Enumerations
enum	AntibodyCDRNameEnum {   start_cdr_loop = 1, h1 = start_cdr_loop, h2, h3,   H_chain_last_loop = h3, camelid_last_loop = h3, l1, l2,   l3, L_chain_last_loop = l3, num_cdr_loops = l3 }
enum	AntibodyNumberingEnum {   Aroop = 1, Chothia, Kabat, Enhanced_Chothia,   AHO, IMGT }
enum	BeginEndEnum { Begin = 1, End, Pack_Angle_Begin, Pack_Angle_End }
enum	H3BaseTypeEnum { Kinked = 1, Extended, Neutral }

Functions
std::ostream &	operator<< (std::ostream &out, const Ab_TemplateInfo &ab_t_info)
scoring::ScoreFunctionCOP	get_Pack_ScoreFxn (void)
scoring::ScoreFunctionCOP	get_Dock_ScoreFxn (void)
scoring::ScoreFunctionCOP	get_LoopCentral_ScoreFxn (void)
scoring::ScoreFunctionCOP	get_LoopHighRes_ScoreFxn (void)
std::ostream &	operator<< (std::ostream &out, const AntibodyInfo &ab_info)
std::ostream &	operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m)
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)
bool	CDR_H3_filter_legacy_code_with_old_rule (const pose::Pose &pose_in, loops::Loop &input_loop, bool is_camelid)
	tests if a loop has H3 like base charachteristics More...
bool	CDR_H3_cter_filter (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
core::pack::task::TaskFactoryOP	setup_packer_task (pose::Pose &pose_in)
bool	cutpoints_separation (core::pose::Pose &pose, AntibodyInfoOP &antibody_info)
	return false if any cdr cutpoint is broken More...
Real	cutpoint_separation (pose::Pose &pose_in, Size cutpoint)
Real	global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop)
Real	vl_vh_packing_angle (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
void	align_to_native (core::pose::Pose &pose, core::pose::Pose &native_pose, AntibodyInfoOP ab_info, AntibodyInfoOP native_ab_info)
	align current Fv to native.Fv More...
std::ostream &	operator<< (std::ostream &out, const CDRsMinPackMin &ab_m_2)
std::ostream &	operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2)
std::ostream &	operator<< (std::ostream &out, SnugDock const &)
std::ostream &	operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)

Typedef Documentation

typedef utility::pointer::owning_ptr< Ab_TemplateInfo const > protocols::antibody2::Ab_TemplateInfoCOP

Definition at line 29 of file Ab_TemplateInfo.fwd.hh.

typedef utility::pointer::owning_ptr< Ab_TemplateInfo > protocols::antibody2::Ab_TemplateInfoOP

Definition at line 26 of file Ab_TemplateInfo.fwd.hh.

typedef utility::pointer::owning_ptr< AntibodyInfo const > protocols::antibody2::AntibodyInfoCOP

Definition at line 31 of file AntibodyInfo.fwd.hh.

typedef utility::pointer::owning_ptr< AntibodyInfo > protocols::antibody2::AntibodyInfoOP

Definition at line 28 of file AntibodyInfo.fwd.hh.

typedef utility::pointer::owning_ptr< AntibodyModelerProtocol const > protocols::antibody2::AntibodyModelerProtocolCOP

Definition at line 25 of file AntibodyModelerProtocol.fwd.hh.

typedef utility::pointer::owning_ptr< AntibodyModelerProtocol > protocols::antibody2::AntibodyModelerProtocolOP

Definition at line 23 of file AntibodyModelerProtocol.fwd.hh.

typedef utility::pointer::owning_ptr< CDRsMinPackMin const > protocols::antibody2::CDRsMinPackMinCOP

Definition at line 25 of file CDRsMinPackMin.fwd.hh.

typedef utility::pointer::owning_ptr< CDRsMinPackMin > protocols::antibody2::CDRsMinPackMinOP

Definition at line 23 of file CDRsMinPackMin.fwd.hh.

typedef utility::pointer::owning_ptr< CloseOneCDRLoop const > protocols::antibody2::CloseOneCDRLoopCOP

Definition at line 24 of file CloseOneCDRLoop.fwd.hh.

typedef utility::pointer::owning_ptr< CloseOneCDRLoop > protocols::antibody2::CloseOneCDRLoopOP

Definition at line 22 of file CloseOneCDRLoop.fwd.hh.

typedef utility::pointer::owning_ptr< GraftCDRLoopsProtocol const > protocols::antibody2::GraftCDRLoopsProtocolCOP

Definition at line 25 of file GraftCDRLoopsProtocol.fwd.hh.

typedef utility::pointer::owning_ptr< GraftCDRLoopsProtocol > protocols::antibody2::GraftCDRLoopsProtocolOP

Definition at line 23 of file GraftCDRLoopsProtocol.fwd.hh.

typedef utility::pointer::owning_ptr<const GraftOneCDRLoop> protocols::antibody2::GraftOneCDRLoopCOP

Definition at line 24 of file GraftOneCDRLoop.fwd.hh.

typedef utility::pointer::owning_ptr< GraftOneCDRLoop > protocols::antibody2::GraftOneCDRLoopOP

Definition at line 22 of file GraftOneCDRLoop.fwd.hh.

typedef utility::pointer::owning_ptr< H3CterInsert const > protocols::antibody2::H3CterInsertCOP

Definition at line 34 of file H3CterInsert.fwd.hh.

typedef utility::pointer::owning_ptr< H3CterInsert > protocols::antibody2::H3CterInsertOP

Definition at line 32 of file H3CterInsert.fwd.hh.

typedef utility::pointer::owning_ptr< H3PerturbCCD const > protocols::antibody2::H3PerturbCCDCOP

Definition at line 25 of file H3PerturbCCD.fwd.hh.

typedef utility::pointer::owning_ptr< H3PerturbCCD > protocols::antibody2::H3PerturbCCDOP

Definition at line 23 of file H3PerturbCCD.fwd.hh.

typedef utility::pointer::owning_ptr< H3RefineCCD const > protocols::antibody2::H3RefineCCDCOP

Definition at line 25 of file H3RefineCCD.fwd.hh.

typedef utility::pointer::owning_ptr< H3RefineCCD > protocols::antibody2::H3RefineCCDOP

Definition at line 23 of file H3RefineCCD.fwd.hh.

typedef utility::pointer::owning_ptr< LHRepulsiveRamp const > protocols::antibody2::LHRepulsiveRampCOP

Definition at line 25 of file LHRepulsiveRamp.fwd.hh.

typedef utility::pointer::owning_ptr< LHRepulsiveRampLegacy const > protocols::antibody2::LHRepulsiveRampLegacyCOP

Definition at line 25 of file LHRepulsiveRampLegacy.fwd.hh.

typedef utility::pointer::owning_ptr< LHRepulsiveRampLegacy > protocols::antibody2::LHRepulsiveRampLegacyOP

Definition at line 23 of file LHRepulsiveRampLegacy.fwd.hh.

typedef utility::pointer::owning_ptr< LHRepulsiveRamp > protocols::antibody2::LHRepulsiveRampOP

Definition at line 23 of file LHRepulsiveRamp.fwd.hh.

typedef utility::pointer::owning_ptr< LHSnugFitLegacy const > protocols::antibody2::LHSnugFitLegacyCOP

Definition at line 25 of file LHSnugFitLegacy.fwd.hh.

typedef utility::pointer::owning_ptr< LHSnugFitLegacy > protocols::antibody2::LHSnugFitLegacyOP

Definition at line 23 of file LHSnugFitLegacy.fwd.hh.

typedef utility::pointer::owning_ptr< ModelCDRH3 const > protocols::antibody2::ModelCDRH3COP

Definition at line 28 of file ModelCDRH3.fwd.hh.

typedef utility::pointer::owning_ptr< ModelCDRH3 > protocols::antibody2::ModelCDRH3OP

Definition at line 26 of file ModelCDRH3.fwd.hh.

typedef utility::pointer::owning_ptr< RefineBetaBarrel const > protocols::antibody2::RefineBetaBarrelCOP

Definition at line 27 of file RefineBetaBarrel.fwd.hh.

typedef utility::pointer::owning_ptr< RefineBetaBarrel > protocols::antibody2::RefineBetaBarrelOP

Definition at line 25 of file RefineBetaBarrel.fwd.hh.

typedef utility::pointer::owning_ptr< RefineOneCDRLoopCentroid const > protocols::antibody2::RefineOneCDRLoopCentroidCOP

Definition at line 25 of file RefineOneCDRLoopCentroid.fwd.hh.

typedef utility::pointer::owning_ptr< RefineOneCDRLoopCentroid > protocols::antibody2::RefineOneCDRLoopCentroidOP

Definition at line 23 of file RefineOneCDRLoopCentroid.fwd.hh.

typedef utility::pointer::owning_ptr< RefineOneCDRLoop const > protocols::antibody2::RefineOneCDRLoopCOP

Definition at line 25 of file RefineOneCDRLoop.fwd.hh.

typedef utility::pointer::owning_ptr< RefineOneCDRLoop > protocols::antibody2::RefineOneCDRLoopOP

Definition at line 23 of file RefineOneCDRLoop.fwd.hh.

typedef utility::pointer::owning_ptr< SnugDock const > protocols::antibody2::SnugDockCOP

Definition at line 26 of file SnugDock.fwd.hh.

typedef utility::pointer::owning_ptr< SnugDock > protocols::antibody2::SnugDockOP

Definition at line 24 of file SnugDock.fwd.hh.

typedef utility::pointer::owning_ptr< SnugDockProtocol const > protocols::antibody2::SnugDockProtocolCOP

Definition at line 26 of file SnugDockProtocol.fwd.hh.

typedef utility::pointer::owning_ptr< SnugDockProtocol > protocols::antibody2::SnugDockProtocolOP

Definition at line 24 of file SnugDockProtocol.fwd.hh.

Enumeration Type Documentation

enum protocols::antibody2::AntibodyCDRNameEnum

Enumerator
start_cdr_loop
h1
h2
h3
H_chain_last_loop
camelid_last_loop
l1
l2
l3
L_chain_last_loop
num_cdr_loops

Definition at line 36 of file AntibodyInfo.hh.

enum protocols::antibody2::AntibodyNumberingEnum

Enumerator
Aroop
Chothia
Kabat
Enhanced_Chothia
AHO
IMGT

Definition at line 50 of file AntibodyInfo.hh.

enum protocols::antibody2::BeginEndEnum

Enumerator
Begin
End
Pack_Angle_Begin
Pack_Angle_End

Definition at line 59 of file AntibodyInfo.hh.

enum protocols::antibody2::H3BaseTypeEnum

Enumerator
Kinked
Extended
Neutral

Definition at line 66 of file AntibodyInfo.hh.

Function Documentation

void protocols::antibody2::align_to_native	(	core::pose::Pose &	pose,
		core::pose::Pose &	native_pose,
		AntibodyInfoOP	ab_info,
		AntibodyInfoOP	native_ab_info
	)

align current Fv to native.Fv

Definition at line 682 of file AntibodyUtil.cc.

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), protocols::loops::start, and core::scoring::superimpose_pose().

Referenced by protocols::antibody2::GraftCDRLoopsProtocol::apply(), and protocols::antibody2::AntibodyModelerProtocol::apply().

bool protocols::antibody2::CDR_H3_cter_filter	(	const pose::Pose &	pose_in,
		AntibodyInfoOP	ab_info
	)

Definition at line 386 of file AntibodyUtil.cc.

References protocols::frag_picker::CA, Extended, h3, Kinked, core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::loops::start, protocols::loops::stop, core::TR(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody2::H3CterInsert::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::antibody2::H3RefineCCD::apply(), and protocols::antibody2::RefineOneCDRLoop::apply().

bool protocols::antibody2::CDR_H3_filter_legacy_code_with_old_rule	(	const pose::Pose &	pose_in,
		loops::Loop &	input_loop,
		bool	is_camelid
	)

tests if a loop has H3 like base charachteristics

CDR_H3_filter

Detailed: Uses the Shirai rules to find out if the dihedral angle

formed by CA atoms of residues n-2,n-1,n and n+1 conform to a kinked/extended structure in accordance with the sequence. If there is a match, a true value is returned

Parameters

[in]

pose,:

full actual protein loop_begin: seq numbered loop begin corresponding to pose size: size of loop to compute loop_end

Global Read: reads -command line flag -base stored in dle_ns

to determine to do the complete H3 filter check or just do a prediction of the H3 base type based on the aforementioned dihedral angle

References: Structural classification of CDR-H3 in antibodies

Hiroki Shirai, Akinori Kidera, Haruki Nakamura FEBS Letters 399 (1996) 1-8

Authors

Aroop 02/04/2010

Last Modified: 02/04/2010

Definition at line 198 of file AntibodyUtil.cc.

References protocols::frag_picker::CA, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, core::TR(), and core::conformation::Residue::xyz().

core::Real protocols::antibody2::cutpoint_separation	(	pose::Pose &	pose_in,
		Size	cutpoint
	)

Definition at line 594 of file AntibodyUtil.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::C, protocols::forge::build::SegmentInsertConnectionScheme::N, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by cutpoints_separation().

bool protocols::antibody2::cutpoints_separation	(	core::pose::Pose &	pose,
		AntibodyInfoOP &	antibody_info
	)

return false if any cdr cutpoint is broken

Definition at line 574 of file AntibodyUtil.cc.

References cutpoint_separation().

Referenced by protocols::antibody2::ModelCDRH3::apply(), and protocols::antibody2::H3RefineCCD::apply().

scoring::ScoreFunctionCOP protocols::antibody2::get_Dock_ScoreFxn

(

void

)

Definition at line 1451 of file AntibodyInfo.cc.

References core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), and core::scoring::overlap_chainbreak.

scoring::ScoreFunctionCOP protocols::antibody2::get_LoopCentral_ScoreFxn

(

void

)

Definition at line 1460 of file AntibodyInfo.cc.

References core::scoring::chainbreak, and core::scoring::ScoreFunctionFactory::create_score_function().

scoring::ScoreFunctionCOP protocols::antibody2::get_LoopHighRes_ScoreFxn

(

void

)

Definition at line 1468 of file AntibodyInfo.cc.

References core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, and core::scoring::overlap_chainbreak.

scoring::ScoreFunctionCOP protocols::antibody2::get_Pack_ScoreFxn

(

void

)

Definition at line 1444 of file AntibodyInfo.cc.

References core::scoring::ScoreFunctionFactory::create_score_function().

core::Real protocols::antibody2::global_loop_rmsd	(	const pose::Pose &	pose_in,
		const pose::Pose &	native_pose,
		loops::LoopsOP	current_loop
	)

Definition at line 614 of file AntibodyUtil.cc.

References core::scoring::is_protein_backbone_including_O(), core::scoring::rmsd_no_super_subset(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody2::AntibodyModelerProtocol::apply().

std::ostream& protocols::antibody2::operator<<	(	std::ostream &	out,
		const Ab_TemplateInfo &	ab_t_info
	)

Definition at line 185 of file Ab_TemplateInfo.cc.

References protocols::comparative_modeling::features::A, protocols::antibody2::Ab_TemplateInfo::H1_t_name_, protocols::antibody2::Ab_TemplateInfo::H1_t_pose_, protocols::antibody2::Ab_TemplateInfo::H2_t_name_, protocols::antibody2::Ab_TemplateInfo::H2_t_pose_, protocols::antibody2::Ab_TemplateInfo::H3_t_name_, protocols::antibody2::Ab_TemplateInfo::H3_t_pose_, protocols::antibody2::Ab_TemplateInfo::L1_t_name_, protocols::antibody2::Ab_TemplateInfo::L1_t_pose_, protocols::antibody2::Ab_TemplateInfo::L2_t_name_, protocols::antibody2::Ab_TemplateInfo::L2_t_pose_, protocols::antibody2::Ab_TemplateInfo::L3_t_name_, protocols::antibody2::Ab_TemplateInfo::L3_t_pose_, protocols::antibody2::Ab_TemplateInfo::load_H1_, protocols::antibody2::Ab_TemplateInfo::load_H2_, protocols::antibody2::Ab_TemplateInfo::load_H3_, protocols::antibody2::Ab_TemplateInfo::load_L1_, protocols::antibody2::Ab_TemplateInfo::load_L2_, and protocols::antibody2::Ab_TemplateInfo::load_L3_.

std::ostream& protocols::antibody2::operator<<	(	std::ostream &	out,
		SnugDockProtocol const &	snugdockprotocol
	)

Definition at line 227 of file SnugDockProtocol.cc.

References protocols::antibody2::SnugDockProtocol::antibody_info_, and protocols::antibody2::SnugDockProtocol::get_name().

std::ostream& protocols::antibody2::operator<<	(	std::ostream &	out,
		const CDRsMinPackMin &	ab_m_2
	)

Definition at line 230 of file CDRsMinPackMin.cc.

References protocols::comparative_modeling::features::A, protocols::antibody2::CDRsMinPackMin::rt_min_, and protocols::antibody2::CDRsMinPackMin::sc_min_.

std::ostream& protocols::antibody2::operator<<	(	std::ostream &	out,
		SnugDock const &
	)

Definition at line 299 of file SnugDock.cc.

std::ostream& protocols::antibody2::operator<<	(	std::ostream &	out,
		const GraftCDRLoopsProtocol &	ab_m_2
	)

Definition at line 409 of file GraftCDRLoopsProtocol.cc.

References protocols::comparative_modeling::features::A, protocols::antibody2::GraftCDRLoopsProtocol::camelid_, protocols::antibody2::GraftCDRLoopsProtocol::graft_h1_, protocols::antibody2::GraftCDRLoopsProtocol::graft_h2_, protocols::antibody2::GraftCDRLoopsProtocol::graft_h3_, protocols::antibody2::GraftCDRLoopsProtocol::graft_l1_, protocols::antibody2::GraftCDRLoopsProtocol::graft_l2_, and protocols::antibody2::GraftCDRLoopsProtocol::graft_l3_.

std::ostream& protocols::antibody2::operator<<	(	std::ostream &	out,
		const AntibodyModelerProtocol &	ab_m
	)

Definition at line 560 of file AntibodyModelerProtocol.cc.

References protocols::comparative_modeling::features::A, protocols::antibody2::AntibodyModelerProtocol::camelid_, protocols::antibody2::AntibodyModelerProtocol::cter_insert_, protocols::antibody2::AntibodyModelerProtocol::h3_filter_, protocols::antibody2::AntibodyModelerProtocol::h3_filter_tolerance_, protocols::antibody2::AntibodyModelerProtocol::h3_perturb_type_, protocols::antibody2::AntibodyModelerProtocol::h3_refine_type_, protocols::antibody2::AntibodyModelerProtocol::LH_repulsive_ramp_, protocols::antibody2::AntibodyModelerProtocol::model_h3_, protocols::antibody2::AntibodyModelerProtocol::refine_h3_, and protocols::antibody2::AntibodyModelerProtocol::snugfit_.

std::ostream& protocols::antibody2::operator<<	(	std::ostream &	out,
		const AntibodyInfo &	ab_info
	)

Definition at line 1491 of file AntibodyInfo.cc.

References protocols::comparative_modeling::features::A, protocols::antibody2::AntibodyInfo::get_CDR_loop(), protocols::antibody2::AntibodyInfo::get_CDR_Name(), protocols::antibody2::AntibodyInfo::get_CDR_Sequence_with_Stem(), protocols::antibody2::AntibodyInfo::get_Predicted_H3BaseType(), protocols::antibody2::AntibodyInfo::get_string_h3_base_type(), protocols::antibody2::AntibodyInfo::is_Camelid(), protocols::loops::Loop::length(), start_cdr_loop, and protocols::antibody2::AntibodyInfo::total_cdr_loops_.

core::pack::task::TaskFactoryOP protocols::antibody2::setup_packer_task

(

pose::Pose &

pose_in)

Definition at line 466 of file AntibodyUtil.cc.

References core::pack::dunbrack::load_unboundrot(), and core::TR().

Referenced by protocols::antibody2::H3RefineCCD::apply(), protocols::antibody2::RefineBetaBarrel::finalize_setup(), protocols::antibody2::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody2::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody2::H3RefineCCD::finalize_setup(), protocols::antibody2::AntibodyInfo::get_TaskFactory_AllCDRs(), and protocols::antibody2::AntibodyInfo::get_TaskFactory_OneCDR().

void protocols::antibody2::simple_fold_tree	(	pose::Pose &	pose_in,
		Size	jumppoint1,
		Size	cutpoint,
		Size	jumppoint2
	)

Definition at line 120 of file AntibodyUtil.cc.

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

Referenced by protocols::antibody2::RefineOneCDRLoop::apply(), and protocols::antibody2::H3RefineCCD::finalize_setup().

void protocols::antibody2::simple_one_loop_fold_tree	(	pose::Pose &	pose_in,
		loops::Loop const &	loop
	)

Definition at line 85 of file AntibodyUtil.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 core::TR().

Referenced by protocols::antibody2::CloseOneCDRLoop::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::antibody2::H3PerturbCCD::apply(), and protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax().

core::Real protocols::antibody2::vl_vh_packing_angle	(	const pose::Pose &	pose_in,
		AntibodyInfoOP	ab_info
	)

Definition at line 632 of file AntibodyUtil.cc.

References core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody2::AntibodyModelerProtocol::apply().