protocols::antibody Namespace Reference

Namespaces
	clusters
	constraints
	design
	grafting
	residue_selector
	snugdock
	task_operations

Classes
class	Ab_TemplateInfo
	Specifically for AntibodyModeling protocol templates. Not for general use. More...
class	AntibodyCDRGrafter
	Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody. Independant of antibody and CDR modeling. Results in 100 percent loop closure if using both graft algorithms. More...
class	AntibodyCDRGrafterCreator
class	AntibodyEnumManager
	Interface to this class is in AntibodyInfo. More...
class	AntibodyFeatures
	Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics. More...
class	AntibodyFeaturesCreator
	creator for the HBondParameterFeatures class More...
struct	FrameWork
class	AntibodyInfo
	This class is used to get all relevant information you would need when dealing with an antibody. More...
class	AntibodyModelerProtocol
class	AntibodyNumberingConverterMover
	Converts numbering schemes of an antibody, independant of AntibodyInfo. By default, works on a SINGLE antibody FAB with chains L and H, as in the rest of Rosetta. More...
class	AntibodyNumberingConverterMoverCreator
struct	AntibodyNumbering
class	AntibodyNumberingParser
	Class responsible for reading database Numbering Scheme definitions and their transforms from the database. More...
class	PDBLandmark
	Class that was once a struct; Used for matching pdb information between numbering schemes and cdr definitions. More...
class	CDRsMinPackMin
class	CloseOneCDRLoop
	Closes only one CDR onto a framework. More...
struct	CDRDBPose
struct	CDRDBSequence
class	AntibodyDatabaseManager
	Class responsible for loading information from the AntibodyDatabase. More...
class	CDRSetOptions
	Class that holds instructions for a single CDR for loading from the antibody database. Default is instructions to load all CDRs from the database. More...
class	CDRSetOptionsParser
	Parses CDRSetOptions for a single CDR at a time from a simple instruction file. More...
class	GraftCDRLoopsProtocol
class	GraftedStemOptimizer
	Grafts only one CDR onto a framework. More...
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
struct	ParatopeMetric
	Convenience struct for passing around paratope data, including individual data for cdrs. CDRs not present default to 0. Templates are used mainly to have core::Size/ Real or string values. More...
class	RefineBetaBarrel
class	LHRepulsiveRampLegacy
class	LHSnugFitLegacy

Typedefs
typedef utility::pointer::shared_ptr< Ab_TemplateInfo >	Ab_TemplateInfoOP
typedef utility::pointer::shared_ptr< Ab_TemplateInfo const >	Ab_TemplateInfoCOP
typedef utility::pointer::shared_ptr< AntibodyCDRGrafter >	AntibodyCDRGrafterOP
typedef utility::pointer::shared_ptr< AntibodyCDRGrafter const >	AntibodyCDRGrafterCOP
typedef utility::pointer::shared_ptr< AntibodyEnumManager >	AntibodyEnumManagerOP
typedef utility::pointer::shared_ptr< AntibodyEnumManager const >	AntibodyEnumManagerCOP
typedef utility::pointer::shared_ptr< AntibodyFeatures >	AntibodyFeaturesOP
typedef utility::pointer::shared_ptr< AntibodyFeatures const >	AntibodyFeaturesCOP
typedef utility::pointer::shared_ptr< AntibodyInfo >	AntibodyInfoOP
typedef utility::pointer::shared_ptr< AntibodyInfo const >	AntibodyInfoCOP
typedef utility::pointer::weak_ptr< AntibodyInfo >	AntibodyInfoAP
typedef utility::pointer::weak_ptr< AntibodyInfo const >	AntibodyInfoCAP
typedef utility::pointer::shared_ptr< AntibodyModelerProtocol >	AntibodyModelerProtocolOP
typedef utility::pointer::shared_ptr< AntibodyModelerProtocol const >	AntibodyModelerProtocolCOP
typedef utility::pointer::shared_ptr< AntibodyNumberingConverterMover >	AntibodyNumberingConverterMoverOP
typedef utility::pointer::shared_ptr< AntibodyNumberingConverterMover const >	AntibodyNumberingConverterMoverCOP
typedef utility::pointer::shared_ptr< AntibodyNumberingParser >	AntibodyNumberingParserOP
typedef utility::pointer::shared_ptr< AntibodyNumberingParser const >	AntibodyNumberingParserCOP
typedef utility::pointer::shared_ptr< PDBLandmark >	PDBLandmarkOP
typedef utility::pointer::shared_ptr< PDBLandmark const >	PDBLandmarkCOP
typedef utility::vector1< utility::vector1< core::Size > >	Vector2DSize
typedef utility::pointer::shared_ptr< CDRsMinPackMin >	CDRsMinPackMinOP
typedef utility::pointer::shared_ptr< CDRsMinPackMin const >	CDRsMinPackMinCOP
typedef utility::pointer::shared_ptr< CloseOneCDRLoop >	CloseOneCDRLoopOP
typedef utility::pointer::shared_ptr< CloseOneCDRLoop const >	CloseOneCDRLoopCOP
typedef std::map< CDRNameEnum, vector1< CDRDBPose > >	CDRDBPoseSet
typedef utility::pointer::shared_ptr< AntibodyDatabaseManager >	AntibodyDatabaseManagerOP
typedef utility::pointer::shared_ptr< AntibodyDatabaseManager const >	AntibodyDatabaseManagerCOP
typedef std::map< CDRNameEnum, utility::vector1< CDRDBSequence > >	CDRDBSequenceSet
typedef std::map< core::chemical::AA, core::Real >	AAProbabilities
typedef utility::pointer::shared_ptr< CDRSetOptions >	CDRSetOptionsOP
typedef utility::pointer::shared_ptr< CDRSetOptions const >	CDRSetOptionsCOP
typedef utility::vector1< CDRSetOptionsOP >	AntibodyCDRSetOptions
typedef utility::pointer::shared_ptr< CDRSetOptionsParser >	CDRSetOptionsParserOP
typedef utility::pointer::shared_ptr< CDRSetOptionsParser const >	CDRSetOptionsParserCOP
typedef utility::pointer::shared_ptr< GraftCDRLoopsProtocol >	GraftCDRLoopsProtocolOP
typedef utility::pointer::shared_ptr< GraftCDRLoopsProtocol const >	GraftCDRLoopsProtocolCOP
typedef utility::pointer::shared_ptr< GraftedStemOptimizer >	GraftedStemOptimizerOP
typedef utility::pointer::shared_ptr< const GraftedStemOptimizer >	GraftedStemOptimizerCOP
typedef utility::pointer::shared_ptr< GraftOneCDRLoop >	GraftOneCDRLoopOP
typedef utility::pointer::shared_ptr< const GraftOneCDRLoop >	GraftOneCDRLoopCOP
typedef utility::pointer::shared_ptr< H3CterInsert >	H3CterInsertOP
typedef utility::pointer::shared_ptr< H3CterInsert const >	H3CterInsertCOP
typedef utility::pointer::shared_ptr< H3PerturbCCD >	H3PerturbCCDOP
typedef utility::pointer::shared_ptr< H3PerturbCCD const >	H3PerturbCCDCOP
typedef utility::pointer::shared_ptr< H3RefineCCD >	H3RefineCCDOP
typedef utility::pointer::shared_ptr< H3RefineCCD const >	H3RefineCCDCOP
typedef utility::pointer::shared_ptr< LHRepulsiveRamp >	LHRepulsiveRampOP
typedef utility::pointer::shared_ptr< LHRepulsiveRamp const >	LHRepulsiveRampCOP
typedef utility::pointer::shared_ptr< RefineBetaBarrel >	RefineBetaBarrelOP
typedef utility::pointer::shared_ptr< RefineBetaBarrel const >	RefineBetaBarrelCOP
typedef utility::pointer::shared_ptr< LHRepulsiveRampLegacy >	LHRepulsiveRampLegacyOP
typedef utility::pointer::shared_ptr< LHRepulsiveRampLegacy const >	LHRepulsiveRampLegacyCOP
typedef utility::pointer::shared_ptr< LHSnugFitLegacy >	LHSnugFitLegacyOP
typedef utility::pointer::shared_ptr< LHSnugFitLegacy const >	LHSnugFitLegacyCOP

Enumerations
enum	CDRNameEnum {   h1 = 1 , h2 , h3 , l1 ,   l2 , l3 , proto_h4 , proto_l4 ,   start_cdr_loop = h1 , H_chain_last_loop = h3 , L_chain_last_loop = l3 , camelid_last_loop = h3 ,   num_cdr_loops = l3 , CDRNameEnum_start = h1 , CDRNameEnum_total = l3 , CDRNameEnum_proto_start = proto_h4 ,   CDRNameEnum_proto_total = proto_l4 , l4 = proto_l4 , h4 = proto_h4 , L1 = l1 ,   L2 = l2 , L3 = l3 , H1 = h1 , H2 = h2 ,   H3 = h3 , L4 = l4 , H4 = h4 }
enum	AntibodyNumberingSchemeEnum {   Chothia_Scheme = 1 , Kabat_Scheme , Enhanced_Chothia_Scheme , IMGT_Scheme ,   AHO_Scheme , AntibodyNumberingSchemeEnum_start = Chothia_Scheme , AntibodyNumberingSchemeEnum_total = AHO_Scheme , NONE }
enum	CDRDefinitionEnum {   Chothia = 1 , Aroop , Kabat , Martin ,   North , CDRDefinitionEnum_start = Chothia , CDRDefinitionEnum_total = North }
enum	LightChainTypeEnum {   lambda =1 , kappa , lambda6 , unknown ,   LightChainTypeEnum_start = lambda , LightChainTypeEnum_total = unknown }
enum	AntibodyRegionEnum {   antigen_region = 1 , cdr_region , framework_region , AntibodyRegionEnum_start = antigen_region ,   AntibodyRegionEnum_total = framework_region , unknown_ab_region }
enum	CDRLandmarkEnum { cdr_start = 1 , cdr_end , CDRLandmarkEnum_total = cdr_end }
	Main enumerator for AntibodyNumbering. More...
enum	H3BaseTypeEnum {   Kinked = 1 , Extended , Neutral , Unknown ,   H3BaseTypeEnum_start = Kinked , H3BaseTypeEnum_total = Unknown }
enum	PackingAngleEnum {   VL_sheet_1 = 1 , VL_sheet_2 , VH_sheet_1 , VH_sheet_2 ,   PackingAngleEnum_start = VL_sheet_1 , PackingAngleEnum_total = VH_sheet_2 }
	These are used to determine the VL_VH packing angle. More...

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)
AntibodyInfoOP	deep_copy (AntibodyInfo const &source)
std::ostream &	operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m)
std::ostream &	operator<< (std::ostream &os, AntibodyNumberingConverterMover const &mover)
static basic::Tracer	TR ("protocols.antibody.AntibodyNumberingParser")
std::ostream &	operator<< (std::ostream &out, const CDRsMinPackMin &ab_m_2)
std::ostream &	operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2)
vector1< Real >	vl_vh_orientation_coords (const core::pose::Pose &pose_in, const AntibodyInfo &ab_info)
	calculate the VH_VL packing angle from 2 sheet definitions on each antibody chain More...
std::pair< core::Real, core::Real >	kink_dihedral (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info, bool debug)
core::Real	kink_bb_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
core::Real	kink_RD_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
core::Real	kink_Trp_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
std::pair< ParatopeMetric< core::Real >, ParatopeMetric< core::Real > >	paratope_sasa (const core::pose::Pose &pose, const AntibodyInfo &ab_info, bool include_de_loop=false)
	calculate the SASA of the antibody paratope. Returns all and hydrophobic components. More...
core::SSize	pose_charge (core::pose::Pose const &pose)
	calculate the net charge of the antibody More...
ParatopeMetric< core::SSize >	paratope_charge (core::pose::Pose const &pose, const protocols::antibody::AntibodyInfo &abinfo, bool include_de_loop=false)
	calculate the net charge of the paratope More...
core::Real	cdr_energy (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, core::scoring::ScoreFunctionCOP scorefxn, CDRNameEnum const &cdr)
	calculate dSASA of the paratope and antigen using result of InterfaceAnalyzerMover More...
core::Real	cdr_CN_anchor_distance (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, CDRNameEnum const &cdr)
	Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively. More...
vector1< Real >	cdr_backbone_rmsds (core::pose::Pose &p1, core::pose::Pose const &p2, AntibodyInfoOP const a1, AntibodyInfoOP const a2, core::Size aln_thresh=10)
	Align two sequence matching antibodies and calculate CDR rmsds (add OCD), then store in scores. More...
utility::vector1< bool >	get_cdr_bool_from_tag (utility::tag::TagCOP tag, std::string const &name, bool include_cdr4=false)
	Geta boolean vector of CDRs from a RosettaScripts tag. Companion function for XSD generation: attributes_for_get_cdr_bool_from_tag. More...
void	attributes_for_get_cdr_bool_from_tag (utility::tag::AttributeList &attlist, std::string const &tagname, std::string const &Description)
protocols::loops::LoopsOP	get_cdr_loops (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, utility::vector1< bool > const &cdrs, core::Size stem_size)
	Get a set of loops for a boolean vector of CDRNameEnums including any stem residues. More...
core::pack::task::TaskFactoryOP	setup_packer_task (core::pose::Pose &pose_in)
	Very specific packertask,. More...
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, core::Size cutpoint)
Real	global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop)
void	align_to_native (core::pose::Pose &pose, core::pose::Pose const &native_pose, AntibodyInfoOP const ab_info, AntibodyInfoOP const native_ab_info, std::string const &request_chain="LH")
	align current Fv to native.Fv More...
vector1< bool >	select_epitope_residues (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, core::Size const interface_distance=10.0)
	Get the epitope residues using the InterGroupNeighborsCalculator. More...
void	check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, CDRNameEnum cdr, core::pose::Pose &pose)
	Checks the length of the CDR, fixes AHO numbering for longer CDR loops that don't fit within the numbering scheme. More...
void	check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
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)
std::string	setup_LH_A_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Setup LH_A foldtree via docking. Return dock_chains string. More...
std::string	setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Setup A_LH foldtree via docking. Return dock_chains string. More...
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)
bool	is_H3_rama_kinked (std::string const &rama)
	Very basic kink function based on rama groups. Kink is defined as having AB + DB at the C-terminal stem. This is in the North/Dunbrack CDR definition. Avoid this definition if you can and talk to brain. This is currently used for a quick filtering for design. More...
void	kink_constrain_antibody_H3 (core::pose::Pose &pose, AntibodyInfoOP const antibody_info)
void	kink_constrain_antibody_H3 (core::pose::Pose &pose, core::Size kink_begin)
	Apply auto-generated kink constraint. More...
void	qq_constrain_antibody (core::pose::Pose &pose, core::Size VH_qq_resi, core::Size VL_qq_resi)
PDBLandmarkCOP	get_matching_landmark (AntibodyNumbering const &numbering, PDBLandmark const &landmark, AntibodyNumberingSchemeEnum const from_scheme, AntibodyNumberingSchemeEnum const to_scheme)
	get the equivalent landmark in a numbering scheme. Set the resnum to zero if not found. More...
vector1< Real >	get_conserved_residue_list (char chain)
	return vector of Chothia-nubmered, conserved residues for grafting and alignment More...

Typedef Documentation

AAProbabilities

typedef std::map< core::chemical::AA, core::Real > protocols::antibody::AAProbabilities

Ab_TemplateInfoCOP

typedef utility::pointer::shared_ptr< Ab_TemplateInfo const > protocols::antibody::Ab_TemplateInfoCOP

Ab_TemplateInfoOP

typedef utility::pointer::shared_ptr< Ab_TemplateInfo > protocols::antibody::Ab_TemplateInfoOP

AntibodyCDRGrafterCOP

typedef utility::pointer::shared_ptr< AntibodyCDRGrafter const > protocols::antibody::AntibodyCDRGrafterCOP

AntibodyCDRGrafterOP

typedef utility::pointer::shared_ptr< AntibodyCDRGrafter > protocols::antibody::AntibodyCDRGrafterOP

AntibodyCDRSetOptions

typedef utility::vector1<CDRSetOptionsOP> protocols::antibody::AntibodyCDRSetOptions

AntibodyDatabaseManagerCOP

typedef utility::pointer::shared_ptr< AntibodyDatabaseManager const > protocols::antibody::AntibodyDatabaseManagerCOP

AntibodyDatabaseManagerOP

typedef utility::pointer::shared_ptr< AntibodyDatabaseManager > protocols::antibody::AntibodyDatabaseManagerOP

AntibodyEnumManagerCOP

typedef utility::pointer::shared_ptr< AntibodyEnumManager const > protocols::antibody::AntibodyEnumManagerCOP

AntibodyEnumManagerOP

typedef utility::pointer::shared_ptr< AntibodyEnumManager > protocols::antibody::AntibodyEnumManagerOP

AntibodyFeaturesCOP

typedef utility::pointer::shared_ptr< AntibodyFeatures const > protocols::antibody::AntibodyFeaturesCOP

AntibodyFeaturesOP

typedef utility::pointer::shared_ptr< AntibodyFeatures > protocols::antibody::AntibodyFeaturesOP

AntibodyInfoAP

typedef utility::pointer::weak_ptr< AntibodyInfo > protocols::antibody::AntibodyInfoAP

AntibodyInfoCAP

typedef utility::pointer::weak_ptr< AntibodyInfo const > protocols::antibody::AntibodyInfoCAP

AntibodyInfoCOP

typedef utility::pointer::shared_ptr< AntibodyInfo const > protocols::antibody::AntibodyInfoCOP

AntibodyInfoOP

typedef utility::pointer::shared_ptr< AntibodyInfo > protocols::antibody::AntibodyInfoOP

AntibodyModelerProtocolCOP

typedef utility::pointer::shared_ptr< AntibodyModelerProtocol const > protocols::antibody::AntibodyModelerProtocolCOP

AntibodyModelerProtocolOP

typedef utility::pointer::shared_ptr< AntibodyModelerProtocol > protocols::antibody::AntibodyModelerProtocolOP

AntibodyNumberingConverterMoverCOP

typedef utility::pointer::shared_ptr< AntibodyNumberingConverterMover const > protocols::antibody::AntibodyNumberingConverterMoverCOP

AntibodyNumberingConverterMoverOP

typedef utility::pointer::shared_ptr< AntibodyNumberingConverterMover > protocols::antibody::AntibodyNumberingConverterMoverOP

AntibodyNumberingParserCOP

typedef utility::pointer::shared_ptr< AntibodyNumberingParser const > protocols::antibody::AntibodyNumberingParserCOP

AntibodyNumberingParserOP

typedef utility::pointer::shared_ptr< AntibodyNumberingParser > protocols::antibody::AntibodyNumberingParserOP

CDRDBPoseSet

typedef std::map< CDRNameEnum, utility::vector1< CDRDBPose > > protocols::antibody::CDRDBPoseSet

CDRDBSequenceSet

typedef std::map<CDRNameEnum, utility::vector1<CDRDBSequence> > protocols::antibody::CDRDBSequenceSet

CDRSetOptionsCOP

typedef utility::pointer::shared_ptr< CDRSetOptions const > protocols::antibody::CDRSetOptionsCOP

CDRSetOptionsOP

typedef utility::pointer::shared_ptr< CDRSetOptions > protocols::antibody::CDRSetOptionsOP

CDRSetOptionsParserCOP

typedef utility::pointer::shared_ptr< CDRSetOptionsParser const > protocols::antibody::CDRSetOptionsParserCOP

CDRSetOptionsParserOP

typedef utility::pointer::shared_ptr< CDRSetOptionsParser > protocols::antibody::CDRSetOptionsParserOP

CDRsMinPackMinCOP

typedef utility::pointer::shared_ptr< CDRsMinPackMin const > protocols::antibody::CDRsMinPackMinCOP

CDRsMinPackMinOP

typedef utility::pointer::shared_ptr< CDRsMinPackMin > protocols::antibody::CDRsMinPackMinOP

CloseOneCDRLoopCOP

typedef utility::pointer::shared_ptr< CloseOneCDRLoop const > protocols::antibody::CloseOneCDRLoopCOP

CloseOneCDRLoopOP

typedef utility::pointer::shared_ptr< CloseOneCDRLoop > protocols::antibody::CloseOneCDRLoopOP

GraftCDRLoopsProtocolCOP

typedef utility::pointer::shared_ptr< GraftCDRLoopsProtocol const > protocols::antibody::GraftCDRLoopsProtocolCOP

GraftCDRLoopsProtocolOP

typedef utility::pointer::shared_ptr< GraftCDRLoopsProtocol > protocols::antibody::GraftCDRLoopsProtocolOP

GraftedStemOptimizerCOP

typedef utility::pointer::shared_ptr<const GraftedStemOptimizer> protocols::antibody::GraftedStemOptimizerCOP

GraftedStemOptimizerOP

typedef utility::pointer::shared_ptr< GraftedStemOptimizer > protocols::antibody::GraftedStemOptimizerOP

GraftOneCDRLoopCOP

typedef utility::pointer::shared_ptr<const GraftOneCDRLoop> protocols::antibody::GraftOneCDRLoopCOP

GraftOneCDRLoopOP

typedef utility::pointer::shared_ptr< GraftOneCDRLoop > protocols::antibody::GraftOneCDRLoopOP

H3CterInsertCOP

typedef utility::pointer::shared_ptr< H3CterInsert const > protocols::antibody::H3CterInsertCOP

H3CterInsertOP

typedef utility::pointer::shared_ptr< H3CterInsert > protocols::antibody::H3CterInsertOP

H3PerturbCCDCOP

typedef utility::pointer::shared_ptr< H3PerturbCCD const > protocols::antibody::H3PerturbCCDCOP

H3PerturbCCDOP

typedef utility::pointer::shared_ptr< H3PerturbCCD > protocols::antibody::H3PerturbCCDOP

H3RefineCCDCOP

typedef utility::pointer::shared_ptr< H3RefineCCD const > protocols::antibody::H3RefineCCDCOP

H3RefineCCDOP

typedef utility::pointer::shared_ptr< H3RefineCCD > protocols::antibody::H3RefineCCDOP

LHRepulsiveRampCOP

typedef utility::pointer::shared_ptr< LHRepulsiveRamp const > protocols::antibody::LHRepulsiveRampCOP

LHRepulsiveRampLegacyCOP

typedef utility::pointer::shared_ptr< LHRepulsiveRampLegacy const > protocols::antibody::LHRepulsiveRampLegacyCOP

LHRepulsiveRampLegacyOP

typedef utility::pointer::shared_ptr< LHRepulsiveRampLegacy > protocols::antibody::LHRepulsiveRampLegacyOP

LHRepulsiveRampOP

typedef utility::pointer::shared_ptr< LHRepulsiveRamp > protocols::antibody::LHRepulsiveRampOP

LHSnugFitLegacyCOP

typedef utility::pointer::shared_ptr< LHSnugFitLegacy const > protocols::antibody::LHSnugFitLegacyCOP

LHSnugFitLegacyOP

typedef utility::pointer::shared_ptr< LHSnugFitLegacy > protocols::antibody::LHSnugFitLegacyOP

PDBLandmarkCOP

typedef utility::pointer::shared_ptr< PDBLandmark const > protocols::antibody::PDBLandmarkCOP

PDBLandmarkOP

typedef utility::pointer::shared_ptr< PDBLandmark > protocols::antibody::PDBLandmarkOP

RefineBetaBarrelCOP

typedef utility::pointer::shared_ptr< RefineBetaBarrel const > protocols::antibody::RefineBetaBarrelCOP

RefineBetaBarrelOP

typedef utility::pointer::shared_ptr< RefineBetaBarrel > protocols::antibody::RefineBetaBarrelOP

Vector2DSize

typedef utility::vector1< utility::vector1< core::Size > > protocols::antibody::Vector2DSize

Enumeration Type Documentation

AntibodyNumberingSchemeEnum

enum protocols::antibody::AntibodyNumberingSchemeEnum

Enumerator
Chothia_Scheme
Kabat_Scheme
Enhanced_Chothia_Scheme
IMGT_Scheme
AHO_Scheme
AntibodyNumberingSchemeEnum_start
AntibodyNumberingSchemeEnum_total
NONE

AntibodyRegionEnum

enum protocols::antibody::AntibodyRegionEnum

Enumerator
antigen_region
cdr_region
framework_region
AntibodyRegionEnum_start
AntibodyRegionEnum_total
unknown_ab_region

CDRDefinitionEnum

enum protocols::antibody::CDRDefinitionEnum

Enumerator
Chothia
Aroop
Kabat
Martin
North
CDRDefinitionEnum_start
CDRDefinitionEnum_total

CDRLandmarkEnum

enum protocols::antibody::CDRLandmarkEnum

Main enumerator for AntibodyNumbering.

Enumerator
cdr_start
cdr_end
CDRLandmarkEnum_total

CDRNameEnum

enum protocols::antibody::CDRNameEnum

Enumerator
h1
h2
h3
l1
l2
l3
proto_h4	Proto, not quite CDR loops for design and analysis /// Also known as the DE loop ///
proto_l4
start_cdr_loop
H_chain_last_loop
L_chain_last_loop
camelid_last_loop
num_cdr_loops
CDRNameEnum_start
CDRNameEnum_total
CDRNameEnum_proto_start
CDRNameEnum_proto_total
l4
h4
L1
L2
L3
H1
H2
H3
L4
H4

H3BaseTypeEnum

enum protocols::antibody::H3BaseTypeEnum

Enumerator
Kinked
Extended
Neutral
Unknown
H3BaseTypeEnum_start
H3BaseTypeEnum_total

LightChainTypeEnum

enum protocols::antibody::LightChainTypeEnum

Enumerator
lambda
kappa
lambda6
unknown
LightChainTypeEnum_start
LightChainTypeEnum_total

PackingAngleEnum

enum protocols::antibody::PackingAngleEnum

These are used to determine the VL_VH packing angle.

Enumerator
VL_sheet_1
VL_sheet_2
VH_sheet_1
VH_sheet_2
PackingAngleEnum_start
PackingAngleEnum_total

Function Documentation

align_to_native()

void protocols::antibody::align_to_native	(	core::pose::Pose &	pose,
		core::pose::Pose const &	native_pose,
		AntibodyInfoOP const	ab_info,
		AntibodyInfoOP const	native_ab_info,
		std::string const &	reqeust_chain
	)

align current Fv to native.Fv

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

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

attributes_for_get_cdr_bool_from_tag()

void protocols::antibody::attributes_for_get_cdr_bool_from_tag	(	utility::tag::AttributeList &	attlist,
		std::string const &	tagname,
		std::string const &	Description
	)

References protocols::antibody::AntibodyEnumManager::get_recognized_cdr_definitions().

Referenced by protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::provide_xml_schema(), protocols::antibody::constraints::ParatopeSiteConstraintMover::provide_xml_schema(), protocols::antibody::design::AntibodyDesignMover::provide_xml_schema(), protocols::antibody::task_operations::DisableCDRsOperation::provide_xml_schema(), and protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::provide_xml_schema().

cdr_backbone_rmsds()

utility::vector1< core::Real > protocols::antibody::cdr_backbone_rmsds	(	core::pose::Pose &	p1,
		core::pose::Pose const &	p2,
		AntibodyInfoOP const	a1,
		AntibodyInfoOP const	a2,
		core::Size	aln_thresh = 10
	)

Align two sequence matching antibodies and calculate CDR rmsds (add OCD), then store in scores.

vector is made up of: OCD FRH H1 RMS H2 RMS H3 RMS FRL L1 RMS L2 RMS L3 RMS

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), cdr_region, get_conserved_residue_list(), h1, h2, h3, core::pose::initialize_atomid_map(), l1, l2, l3, core::sequence::map_seq1_seq2(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::rms_at_corresponding_atoms_no_super(), core::pose::Pose::sequence(), core::pose::Pose::size(), core::scoring::superimpose_pose(), TR(), and vl_vh_orientation_coords().

cdr_CN_anchor_distance()

core::Real protocols::antibody::cdr_CN_anchor_distance	(	core::pose::Pose const &	pose,
		AntibodyInfoCOP	ab_info,
		CDRNameEnum const &	cdr
	)

Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively.

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

Referenced by protocols::antibody::AntibodyFeatures::report_cdr_metrics_features().

cdr_energy()

core::Real protocols::antibody::cdr_energy	(	core::pose::Pose const &	pose,
		AntibodyInfoCOP	ab_info,
		core::scoring::ScoreFunctionCOP	scorefxn,
		CDRNameEnum const &	cdr
	)

calculate dSASA of the paratope and antigen using result of InterfaceAnalyzerMover

calculate dSASA of the paratope using data held in PerResidueInterfaceData returned from InterfaceAnalyzerMover

calculate dSASA of a cdr and antigen using InterfaceAnalyzerMover. Returns all and hydrophobic components.

calculate dSASA of a cdr using data held in PerResidueInterfaceData returned from InterfaceAnalyzerMover.

Calculates energy of cdr by decomposing scorefxn into pair and then summing. This means it includes hbonding components, etc.

References cdr_end, cdr_start, core::pose::Pose::clone(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::pose::Pose::energies(), protocols::buns::energy, core::scoring::methods::EnergyMethodOptions::hbond_options(), and core::scoring::Energies::residue_total_energy().

Referenced by protocols::antibody::AntibodyFeatures::report_cdr_metrics_features().

CDR_H3_cter_filter()

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

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

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

CDR_H3_filter_legacy_code_with_old_rule()

bool protocols::antibody::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

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

Author

Aroop 02/04/2010

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, TR(), and core::conformation::Residue::xyz().

check_fix_aho_cdr_numbering() [1/2]

void protocols::antibody::check_fix_aho_cdr_numbering	(	AntibodyInfoCOP	ab_info,
		CDRNameEnum	cdr,
		core::pose::Pose &	pose
	)

Checks the length of the CDR, fixes AHO numbering for longer CDR loops that don't fit within the numbering scheme.

References core::pose::Pose::pdb_info(), and TR().

Referenced by protocols::antibody::AntibodyCDRGrafter::apply(), check_fix_aho_cdr_numbering(), and protocols::antibody::design::AntibodyDesignMover::finalize_pose().

check_fix_aho_cdr_numbering() [2/2]

void protocols::antibody::check_fix_aho_cdr_numbering	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose &	pose
	)

References check_fix_aho_cdr_numbering().

cutpoint_separation()

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

Compute the separation at the cutpoint. The N-C distance of the peptide bond which should be formed at the cutpoint. A closed loop is assumed to have a gap < 1.9 Ang

References core::chemical::element::C, core::chemical::element::N, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by cutpoints_separation().

cutpoints_separation()

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

return false if any cdr cutpoint is broken

References cutpoint_separation().

Referenced by protocols::antibody::H3RefineCCD::apply().

deep_copy()

AntibodyInfoOP protocols::antibody::deep_copy ( AntibodyInfo const &  source )

inline

References protocols::antibody::AntibodyInfo::clone().

get_cdr_bool_from_tag()

utility::vector1< bool > protocols::antibody::get_cdr_bool_from_tag	(	utility::tag::TagCOP	tag,
		std::string const &	name,
		bool	include_cdr4
	)

Geta boolean vector of CDRs from a RosettaScripts tag. Companion function for XSD generation: attributes_for_get_cdr_bool_from_tag.

References protocols::antibody::AntibodyEnumManager::cdr_name_string_to_enum(), CDRNameEnum_proto_total, and CDRNameEnum_total.

Referenced by protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::parse_my_tag(), protocols::antibody::constraints::ParatopeSiteConstraintMover::parse_my_tag(), protocols::antibody::design::AntibodyDesignMover::parse_my_tag(), protocols::antibody::design::MutateFrameworkForCluster::parse_my_tag(), protocols::antibody::AntibodyCDRGrafter::parse_my_tag(), protocols::antibody::residue_selector::CDRResidueSelector::parse_my_tag(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::parse_tag(), protocols::antibody::task_operations::AddCDRProfilesOperation::parse_tag(), protocols::antibody::task_operations::DisableCDRsOperation::parse_tag(), and protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::parse_tag().

get_cdr_loops()

protocols::loops::LoopsOP protocols::antibody::get_cdr_loops	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose const &	pose,
		utility::vector1< bool > const &	cdrs,
		core::Size	stem_size
	)

Get a set of loops for a boolean vector of CDRNameEnums including any stem residues.

References CDRNameEnum_proto_total.

Referenced by protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::apply(), and protocols::antibody::design::AntibodySeqDesignTFCreator::get_design_cdr_loops().

get_conserved_residue_list()

utility::vector1< core::Real > protocols::antibody::get_conserved_residue_list

(

char

chain

)

return vector of Chothia-nubmered, conserved residues for grafting and alignment

Referenced by cdr_backbone_rmsds().

get_Dock_ScoreFxn()

scoring::ScoreFunctionCOP protocols::antibody::get_Dock_ScoreFxn

(

void

)

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

get_LoopCentral_ScoreFxn()

scoring::ScoreFunctionCOP protocols::antibody::get_LoopCentral_ScoreFxn

(

void

)

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

get_LoopHighRes_ScoreFxn()

scoring::ScoreFunctionCOP protocols::antibody::get_LoopHighRes_ScoreFxn

(

void

)

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

get_matching_landmark()

PDBLandmarkCOP protocols::antibody::get_matching_landmark	(	AntibodyNumbering const &	numbering,
		PDBLandmark const &	query_landmark,
		AntibodyNumberingSchemeEnum const	from_scheme,
		AntibodyNumberingSchemeEnum const	to_scheme
	)

get the equivalent landmark in a numbering scheme. Set the resnum to zero if not found.

References protocols::antibody::AntibodyNumbering::numbering_scheme_transform.

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

get_Pack_ScoreFxn()

scoring::ScoreFunctionCOP protocols::antibody::get_Pack_ScoreFxn

(

void

)

References core::scoring::get_score_function_legacy(), and core::scoring::PRE_TALARIS_2013_STANDARD_WTS.

global_loop_rmsd()

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

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

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output().

is_H3_rama_kinked()

bool protocols::antibody::is_H3_rama_kinked

(

std::string const &

rama

)

Very basic kink function based on rama groups. Kink is defined as having AB + DB at the C-terminal stem. This is in the North/Dunbrack CDR definition. Avoid this definition if you can and talk to brain. This is currently used for a quick filtering for design.

References core::scoring::rama.

Referenced by protocols::antibody::AntibodyDatabaseManager::load_cdr_poses(), and protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences_for_cdr().

kink_bb_Hbond()

core::Real protocols::antibody::kink_bb_Hbond	(	const core::pose::Pose &	pose,
		const protocols::antibody::AntibodyInfo &	ab_info
	)

References core::id::D, protocols::antibody::AntibodyInfo::kink_anion_residue(), protocols::antibody::AntibodyInfo::kink_cation_residue(), core::pose::Pose::residue(), and TR().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().

kink_constrain_antibody_H3() [1/2]

void protocols::antibody::kink_constrain_antibody_H3	(	core::pose::Pose &	pose,
		AntibodyInfoOP const	antibody_info
	)

Referenced by protocols::antibody::AntibodyModelerProtocol::apply(), and protocols::antibody::snugdock::SnugDockProtocol::apply().

kink_constrain_antibody_H3() [2/2]

void protocols::antibody::kink_constrain_antibody_H3	(	core::pose::Pose &	pose,
		core::Size	kink_begin
	)

Apply auto-generated kink constraint.

References core::pose::Pose::add_constraint(), core::scoring::fiber_diffraction::alpha_func(), protocols::frag_picker::CA, and TR().

kink_dihedral()

std::pair< core::Real, core::Real > protocols::antibody::kink_dihedral	(	const core::pose::Pose &	pose,
		const protocols::antibody::AntibodyInfo &	ab_info,
		bool	debug
	)

References core::pack::interaction_graph::debug, protocols::antibody::AntibodyInfo::kink_begin(), core::conformation::Residue::name1(), core::chemical::rings::q, core::pose::Pose::residue(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().

kink_RD_Hbond()

core::Real protocols::antibody::kink_RD_Hbond	(	const core::pose::Pose &	pose,
		const protocols::antibody::AntibodyInfo &	ab_info
	)

References protocols::antibody::AntibodyInfo::kink_anion_atoms(), protocols::antibody::AntibodyInfo::kink_cation_atoms(), and protocols::mean_field::min().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().

kink_Trp_Hbond()

core::Real protocols::antibody::kink_Trp_Hbond	(	const core::pose::Pose &	pose,
		const protocols::antibody::AntibodyInfo &	ab_info
	)

References protocols::antibody::AntibodyInfo::kink_begin(), protocols::antibody::AntibodyInfo::kink_trp(), core::conformation::Residue::name3(), core::pose::Pose::residue(), TR(), core::chemical::element::W, and core::conformation::Residue::xyz().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().

operator<<() [1/6]

std::ostream & protocols::antibody::operator<<	(	std::ostream &	os,
		AntibodyNumberingConverterMover const &	mover
	)

References protocols::antibody::AntibodyNumberingConverterMover::show().

operator<<() [2/6]

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

operator<<() [3/6]

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

operator<<() [4/6]

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

operator<<() [5/6]

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

operator<<() [6/6]

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

paratope_charge()

ParatopeMetric< core::SSize > protocols::antibody::paratope_charge	(	core::pose::Pose const &	pose,
		const protocols::antibody::AntibodyInfo &	ab_info,
		bool	include_de_loop
	)

calculate the net charge of the paratope

References protocols::antibody::ParatopeMetric< T >::cdr, protocols::antibody::AntibodyInfo::get_all_cdrs_present(), protocols::antibody::AntibodyInfo::get_CDR_end(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_CDR_start(), protocols::antibody::AntibodyInfo::get_total_num_CDRs(), core::conformation::Residue::name3(), protocols::antibody::ParatopeMetric< T >::paratope, core::pose::Pose::residue(), and TR().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), protocols::antibody::AntibodyFeatures::report_features(), and protocols::antibody::AntibodyFeatures::write_ab_metrics_schema_to_db().

paratope_sasa()

std::pair< ParatopeMetric< core::Real >, ParatopeMetric< core::Real > > protocols::antibody::paratope_sasa	(	const core::pose::Pose &	pose,
		const protocols::antibody::AntibodyInfo &	ab_info,
		bool	include_de_loop
	)

calculate the SASA of the antibody paratope. Returns all and hydrophobic components.

References protocols::antibody::ParatopeMetric< T >::cdr, protocols::antibody::AntibodyInfo::get_all_cdrs_present(), protocols::antibody::AntibodyInfo::get_CDR_end(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_CDR_start(), protocols::antibody::AntibodyInfo::get_total_num_CDRs(), core::conformation::Residue::name3(), protocols::antibody::ParatopeMetric< T >::paratope, core::pose::Pose::residue(), and TR().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), and protocols::antibody::AntibodyFeatures::report_features().

pose_charge()

core::SSize protocols::antibody::pose_charge

(

core::pose::Pose const &

pose

)

calculate the net charge of the antibody

References core::conformation::Residue::name3(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::antibody::AntibodyFeatures::report_ab_metrics_features().

qq_constrain_antibody()

void protocols::antibody::qq_constrain_antibody	(	core::pose::Pose &	pose,
		core::Size	VH_qq_resi,
		core::Size	VL_qq_resi
	)

References core::pose::Pose::add_constraint(), and TR().

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

select_epitope_residues()

utility::vector1< bool > protocols::antibody::select_epitope_residues	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose const &	pose,
		core::Size const	interface_distance
	)

Get the epitope residues using the InterGroupNeighborsCalculator.

References core::pose::Pose::chain(), core::pose::get_chain_from_chain_id(), protocols::interface::select_interface_residues(), and core::pose::Pose::size().

Referenced by protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_epitope_residues(), and protocols::antibody::design::AntibodyDesignMover::setup_epitope_residues().

setup_A_LH_foldtree()

std::string protocols::antibody::setup_A_LH_foldtree	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose &	pose
	)

Setup A_LH foldtree via docking. Return dock_chains string.

References protocols::docking::setup_foldtree().

setup_LH_A_foldtree()

std::string protocols::antibody::setup_LH_A_foldtree	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose &	pose
	)

Setup LH_A foldtree via docking. Return dock_chains string.

References protocols::docking::setup_foldtree().

setup_packer_task()

core::pack::task::TaskFactoryOP protocols::antibody::setup_packer_task

(

core::pose::Pose &

pose_in

)

Very specific packertask,.

Ubound rotamer options, repack only, protein only, no disulfides.

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

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

simple_fold_tree()

void protocols::antibody::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 TR().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), and protocols::antibody::H3RefineCCD::finalize_setup().

simple_one_loop_fold_tree()

void protocols::antibody::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 TR().

Referenced by protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::CloseOneCDRLoop::apply(), and protocols::tcr::ind_remodel_tcr_cdr_loops().

TR()

static basic::Tracer protocols::antibody::TR ( "protocols.antibody.AntibodyNumberingParser"  )

static

Referenced by protocols::antibody::constraints::CDRDihedralConstraintMover::add_harmonic_cluster_constraint(), protocols::antibody::AntibodyDatabaseManager::AntibodyDatabaseManager(), protocols::antibody::AntibodyCDRGrafter::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::antibody::constraints::CDRDihedralConstraintMover::apply(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::apply(), protocols::antibody::constraints::ParatopeSiteConstraintMover::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::antibody::design::MutateFrameworkForCluster::apply(), protocols::antibody::GraftCDRLoopsProtocol::apply(), protocols::antibody::H3CterInsert::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::H3RefineCCD::apply(), protocols::antibody::LHRepulsiveRamp::apply(), protocols::antibody::LHRepulsiveRampLegacy::apply(), protocols::antibody::RefineBetaBarrel::apply(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply(), protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), protocols::antibody::snugdock::SnugDock::apply(), protocols::antibody::snugdock::SnugDockProtocol::apply(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::antibody::AntibodyCDRGrafter::apply_to_cdr(), protocols::antibody::design::GeneralAntibodyModeler::backrub_cdrs(), protocols::antibody::AntibodyFeatures::calculate_cdr_contacts_nres(), protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts(), CDR_H3_cter_filter(), CDR_H3_filter_legacy_code_with_old_rule(), check_fix_aho_cdr_numbering(), protocols::antibody::AntibodyDatabaseManager::create_database_session(), protocols::antibody::AntibodyNumberingParser::debug_print(), protocols::antibody::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_disallowed_aa(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody::design::GeneralAntibodyModeler::dock_high_res(), protocols::antibody::design::GeneralAntibodyModeler::dock_low_res(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::design::AntibodyDesignMover::finalize_setup(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::AntibodyNumberingParser::get_antibody_numbering(), protocols::antibody::design::get_cdr_set_options(), protocols::antibody::design::AntibodySeqDesignTFCreator::get_design_cdr_loops(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), protocols::antibody::design::AntibodySeqDesignTFCreator::get_framework_conservative_op(), protocols::antibody::design::get_graft_design_options(), protocols::antibody::constraints::CDRDihedralConstraintMover::get_harmonic_cluster_constraint_filename(), protocols::antibody::AntibodyInfo::get_landmark_resnum(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::design::get_pdb_numbering_from_single_string(), protocols::antibody::design::get_resnums_from_strings_with_ranges(), protocols::antibody::design::get_seq_design_options(), protocols::antibody::AntibodyInfo::identify_CDR_from_a_sequence(), protocols::antibody::AntibodyModelerProtocol::init_from_options(), protocols::antibody::GraftCDRLoopsProtocol::init_from_options(), kink_constrain_antibody_H3(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data_for_cdrs(), protocols::antibody::AntibodyDatabaseManager::load_cdr_pose(), protocols::antibody::AntibodyDatabaseManager::load_cdr_poses(), protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences(), protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences_for_cdr(), protocols::antibody::AntibodyDatabaseManager::load_structure_loading_info(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::minimize_interface(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::parse_my_tag(), protocols::antibody::constraints::ParatopeSiteConstraintMover::parse_my_tag(), protocols::antibody::AntibodyCDRGrafter::parse_my_tag(), protocols::antibody::AntibodyFeatures::parse_my_tag(), protocols::antibody::residue_selector::AntibodyRegionSelector::parse_my_tag(), protocols::antibody::residue_selector::CDRResidueSelector::parse_my_tag(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::parse_tag(), protocols::antibody::task_operations::AddCDRProfilesOperation::parse_tag(), protocols::antibody::task_operations::DisableAntibodyRegionOperation::parse_tag(), protocols::antibody::task_operations::DisableCDRsOperation::parse_tag(), protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::parse_tag(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_load_data(), protocols::antibody::task_operations::AddCDRProfilesOperation::pre_load_data(), qq_constrain_antibody(), protocols::antibody::AntibodyInfo::qq_heavy_residue(), protocols::antibody::AntibodyInfo::qq_light_residue(), protocols::antibody::H3PerturbCCD::read_and_store_fragments(), protocols::antibody::AntibodyNumberingParser::read_cdr_definition_file(), protocols::antibody::design::AntibodyDesignMover::read_command_line_options(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::AntibodyNumberingParser::read_numbering_scheme_file(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::repack_antibody_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_ab_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_cdrs(), protocols::antibody::AntibodyFeatures::report_features(), protocols::antibody::design::AntibodyDesignMover::run_basic_mc_algorithm(), protocols::antibody::design::AntibodyDesignMover::run_deterministic_graft_algorithm(), protocols::antibody::design::AntibodyDesignMover::run_graft(), protocols::antibody::design::AntibodyDesignMover::run_optimization_cycle(), protocols::antibody::CDRSetOptionsParser::set_cdr_set_include_options(), protocols::antibody::AntibodyInfo::set_default(), protocols::antibody::AntibodyModelerProtocol::set_default(), protocols::antibody::GraftCDRLoopsProtocol::set_default(), protocols::antibody::AntibodyInfo::set_light_chain_type(), protocols::antibody::design::set_native_cdr_sequence(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::antibody::AntibodyInfo::setup_CDR_cluster(), protocols::antibody::AntibodyInfo::setup_CDRsInfo(), protocols::antibody::AntibodyModelerProtocol::setup_objects(), protocols::antibody::snugdock::SnugDockProtocol::setup_objects(), protocols::antibody::snugdock::SnugDock::setup_objects(), setup_packer_task(), protocols::antibody::design::AntibodyDesignMover::setup_random_start_pose(), protocols::antibody::AntibodyInfo::setup_VL_VH_packing_angle(), simple_fold_tree(), and simple_one_loop_fold_tree().

vl_vh_orientation_coords()

utility::vector1< core::Real > protocols::antibody::vl_vh_orientation_coords	(	const core::pose::Pose &	pose_in,
		const AntibodyInfo &	ab_info
	)

calculate the VH_VL packing angle from 2 sheet definitions on each antibody chain

vector is made up of: vl_vh_distance opening_angle opposite_angle packing_angle

References protocols::antibody::AntibodyInfo::get_PackingAngleResidues(), protocols::antibody::AntibodyInfo::is_camelid(), core::pose::Pose::residue(), TR(), and core::conformation::Residue::xyz().

Referenced by cdr_backbone_rmsds(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), and protocols::antibody::AntibodyFeatures::report_ab_metrics_features().