protocols::antibody Namespace Reference

Namespaces
	clusters
	design

Classes
class	Ab_TemplateInfo
	Specifically for AntibodyModeling protocol templates. Not for general use. More...
class	AntibodyEnumManager
	Interface to this class is in AntibodyInfo. More...
class	AntibodyInfo
	This class is used to get all relevant information you would need when dealing with an antibody. More...
class	AntibodyModelerProtocol
struct	AntibodyNumbering
class	AntibodyNumberingParser
	Class responsible for reading database Numbering Scheme definitions and their transforms from the database. More...
class	CDRsMinPackMin
class	CloseOneCDRLoop
	Closes only one CDR onto a framework. More...
struct	FrameWork
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
class	LHRepulsiveRampLegacy
class	LHSnugFitLegacy
class	ModelCDRH3
	Ab initio modeling of CDR H3 loop. More...
class	PDBLandmark
	Class that was once a struct; Used for matching pdb information between numbering schemes and cdr definitions. More...
class	RefineBetaBarrel
class	RefineOneCDRLoop
class	RefineOneCDRLoopCentroid
class	SnugDock
	MoveSet step of Snugdock as described in: More...
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 < AntibodyEnumManager >	AntibodyEnumManagerOP
typedef utility::pointer::owning_ptr < AntibodyEnumManager const >	AntibodyEnumManagerCOP
typedef utility::pointer::owning_ptr < AntibodyInfo >	AntibodyInfoOP
typedef utility::pointer::owning_ptr < AntibodyInfo const >	AntibodyInfoCOP
typedef utility::pointer::access_ptr < AntibodyInfo >	AntibodyInfoAP
typedef utility::pointer::access_ptr < AntibodyInfo const >	AntibodyInfoCAP
typedef utility::pointer::owning_ptr < AntibodyModelerProtocol >	AntibodyModelerProtocolOP
typedef utility::pointer::owning_ptr < AntibodyModelerProtocol const >	AntibodyModelerProtocolCOP
typedef utility::pointer::owning_ptr < AntibodyNumberingParser >	AntibodyNumberingParserOP
typedef utility::pointer::owning_ptr < AntibodyNumberingParser const >	AntibodyNumberingParserCOP
typedef utility::pointer::owning_ptr < PDBLandmark >	PDBLandmarkOP
typedef utility::pointer::owning_ptr < PDBLandmark const >	PDBLandmarkCOP
typedef vector1< vector1< Size > >	Vector2DSize
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 < GraftedStemOptimizer >	GraftedStemOptimizerOP
typedef utility::pointer::owning_ptr < const GraftedStemOptimizer >	GraftedStemOptimizerCOP
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 < 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
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

Enumerations
enum	CDRNameEnum {   h1 = 1, h2, h3, l1,   l2, l3, 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 }
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	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)
std::ostream &	operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m)
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 protocols::antibody::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< core::Real, core::Real >	paratope_sasa (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
	calculate the SASA of the antibody paratope More...
core::SSize	pose_charge (core::pose::Pose const &pose)
	calculate the net charge of the antibody More...
core::SSize	paratope_charge (core::pose::Pose const &pose, const protocols::antibody::AntibodyInfo &abinfo)
	calculate the net charge of the paratope More...
std::ostream &	operator<< (std::ostream &out, SnugDock const &)
std::ostream &	operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)
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)
std::string	setup_LH_A_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Setup LH_A foldtree. Return dock_chains string. More...
std::string	setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Setup A_LH foldtree. 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)
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, 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...
std::map< CDRNameEnum, bool >	add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose)
	Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo. More...
std::map< CDRNameEnum, bool >	add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
	Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
bool	add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster)
	Adds a harmonic constraint to a Pose CDR based on cluster type. More...
bool	add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
	Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
std::string	get_harmonic_cluster_constraint_filename (AntibodyInfoCOP ab_info, CDRClusterEnum const cluster)
	Gets the cluster constraint name. Returns NA if not found. More...

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

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::antibody::AntibodyNumberingSchemeEnum

Enumerator
Chothia_Scheme
Kabat_Scheme
Enhanced_Chothia_Scheme
IMGT_Scheme
AHO_Scheme
AntibodyNumberingSchemeEnum_start
AntibodyNumberingSchemeEnum_total
NONE

enum protocols::antibody::CDRDefinitionEnum

Enumerator
Chothia
Aroop
Kabat
Martin
North
CDRDefinitionEnum_start
CDRDefinitionEnum_total

enum protocols::antibody::CDRLandmarkEnum

Main enumerator for AntibodyNumbering.

Enumerator
cdr_start
cdr_end
CDRLandmarkEnum_total

enum protocols::antibody::CDRNameEnum

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

enum protocols::antibody::H3BaseTypeEnum

Enumerator
Kinked
Extended
Neutral
Unknown
H3BaseTypeEnum_start
H3BaseTypeEnum_total

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

bool protocols::antibody::add_harmonic_cluster_constraint	(	AntibodyInfoCOP	ab_info,
		pose::Pose &	pose,
		CDRClusterEnum const	cluster
	)

Adds a harmonic constraint to a Pose CDR based on cluster type.

Currently requires North_AHO numbering.

References core::pose::Pose::add_constraints(), cst, core::scoring::constraints::ConstraintSet::get_all_constraints(), get_harmonic_cluster_constraint_filename(), and TR.

Referenced by protocols::antibody::design::AntibodyGraftDesigner::graft_cdr(), and protocols::antibody::design::AntibodyCDRDesigner::setup_constraints().

bool protocols::antibody::add_harmonic_cluster_constraint	(	AntibodyInfoCOP	ab_info,
		pose::Pose &	pose,
		CDRClusterEnum const	cluster,
		utility::vector1< core::scoring::constraints::ConstraintCOP >	constraints
	)

Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed.

Returns true or false depending on success

References core::pose::Pose::add_constraints(), cst, core::scoring::constraints::ConstraintSet::get_all_constraints(), get_harmonic_cluster_constraint_filename(), and TR.

Referenced by add_harmonic_cluster_constraints().

std::map< CDRNameEnum, bool > protocols::antibody::add_harmonic_cluster_constraints	(	AntibodyInfoOP	ab_info,
		pose::Pose &	pose
	)

Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo.

Currently requires North_AHO numbering. Returns map of success/failure

References add_harmonic_cluster_constraint().

std::map< CDRNameEnum, bool > protocols::antibody::add_harmonic_cluster_constraints	(	AntibodyInfoOP	ab_info,
		pose::Pose &	pose,
		utility::vector1< core::scoring::constraints::ConstraintCOP >	constraints
	)

Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed.

Returns map of success/failure

References add_harmonic_cluster_constraint().

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::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_jd2().

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

References protocols::frag_picker::CA, numeric::dihedral_degrees(), 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(), protocols::antibody::RefineOneCDRLoop::apply(), and protocols::antibody::H3RefineCCD::apply().

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

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

References protocols::frag_picker::CA, numeric::dihedral_degrees(), 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().

core::Real protocols::antibody::cutpoint_separation	(	core::pose::Pose &	pose_in,
		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 protocols::forge::build::SegmentInsertConnectionScheme::N, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

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

scoring::ScoreFunctionCOP protocols::antibody::get_Dock_ScoreFxn

(

void

)

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

std::string protocols::antibody::get_harmonic_cluster_constraint_filename	(	AntibodyInfoCOP	ab_info,
		CDRClusterEnum const	cluster
	)

Gets the cluster constraint name. Returns NA if not found.

References utility::file::file_exists(), option, path, and TR.

Referenced by add_harmonic_cluster_constraint().

scoring::ScoreFunctionCOP protocols::antibody::get_LoopCentral_ScoreFxn

(

void

)

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

scoring::ScoreFunctionCOP protocols::antibody::get_LoopHighRes_ScoreFxn

(

void

)

References protocols::forge::methods::overlap_chainbreak().

scoring::ScoreFunctionCOP protocols::antibody::get_Pack_ScoreFxn

(

void

)

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

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

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

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

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

References D, protocols::antibody::AntibodyInfo::kink_anion_residue(), protocols::antibody::AntibodyInfo::kink_cation_residue(), core::conformation::Residue::name3(), norm(), core::pose::Pose::residue(), TR, and core::conformation::Residue::xyz().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

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

References dihedral(), protocols::antibody::AntibodyInfo::kink_begin(), core::conformation::Residue::name1(), q, core::pose::Pose::residue(), TR, and core::conformation::Residue::xyz().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

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 norm().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

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

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

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

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

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

References protocols::antibody::CDRsMinPackMin::rt_min_, and protocols::antibody::CDRsMinPackMin::sc_min_.

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

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

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

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

References protocols::antibody::GraftCDRLoopsProtocol::camelid_, protocols::antibody::GraftCDRLoopsProtocol::graft_h1_, protocols::antibody::GraftCDRLoopsProtocol::graft_h2_, protocols::antibody::GraftCDRLoopsProtocol::graft_h3_, protocols::antibody::GraftCDRLoopsProtocol::graft_l1_, protocols::antibody::GraftCDRLoopsProtocol::graft_l2_, and protocols::antibody::GraftCDRLoopsProtocol::graft_l3_.

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

References protocols::antibody::AntibodyModelerProtocol::camelid_, protocols::antibody::AntibodyModelerProtocol::cter_insert_, protocols::antibody::AntibodyModelerProtocol::h3_filter_, protocols::antibody::AntibodyModelerProtocol::h3_filter_tolerance_, protocols::antibody::AntibodyModelerProtocol::h3_perturb_type_, protocols::antibody::AntibodyModelerProtocol::h3_refine_type_, protocols::antibody::AntibodyModelerProtocol::LH_repulsive_ramp_, protocols::antibody::AntibodyModelerProtocol::model_h3_, protocols::antibody::AntibodyModelerProtocol::refine_h3_, and protocols::antibody::AntibodyModelerProtocol::snugfit_.

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

References protocols::antibody::AntibodyInfo::enum_manager_, protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem(), protocols::antibody::AntibodyEnumManager::h3_base_type_enum_to_string(), protocols::antibody::AntibodyInfo::is_camelid(), protocols::loops::Loop::length(), protocols::antibody::AntibodyInfo::predicted_H3_base_type_, start_cdr_loop, and protocols::antibody::AntibodyInfo::total_cdr_loops_.

core::SSize protocols::antibody::paratope_charge	(	core::pose::Pose const &	pose,
		const protocols::antibody::AntibodyInfo &	ab_info
	)

calculate the net charge of the paratope

References CDRNameEnum_total, protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_CDR_name(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and TR.

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

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

calculate the SASA of the antibody paratope

References core::scoring::calc_per_res_hydrophobic_sasa(), CDRNameEnum_total, protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_CDR_name(), core::pose::Pose::metric(), basic::options::option, probe_radius, core::pose::Pose::residue(), basic::options::OptionKeys::pose_metrics::sasa_calculator_probe_radius, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and TR.

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

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

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

Setup A_LH foldtree. Return dock_chains string.

References protocols::docking::setup_foldtree().

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

Setup LH_A foldtree. Return dock_chains string.

References protocols::docking::setup_foldtree().

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(), tf, TR, and unboundrot.

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

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

References core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), nres, core::pose::Pose::total_residue(), and TR.

Referenced by protocols::antibody::RefineOneCDRLoop::apply(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::antibody::H3RefineCCD::finalize_setup(), and protocols::stepwise::sampling::rna::setup_simple_fold_tree().

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

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

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

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

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

References numeric::angle_degrees(), numeric::dihedral_degrees(), numeric::xyzVector< class >::distance(), numeric::first_principal_component(), protocols::antibody::AntibodyInfo::get_PackingAngleResidues(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

Variable Documentation

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

static

Referenced by protocols::antibody::RefineBetaBarrel::apply(), protocols::antibody::SnugDockProtocol::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::GraftCDRLoopsProtocol::apply(), protocols::antibody::H3CterInsert::apply(), protocols::antibody::design::ResidueProbDesignOperation::apply(), protocols::antibody::ModelCDRH3::apply(), protocols::antibody::RefineOneCDRLoopCentroid::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::LHRepulsiveRamp::apply(), protocols::antibody::SnugDock::apply(), protocols::antibody::LHRepulsiveRampLegacy::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::antibody::H3RefineCCD::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::antibody::design::AntibodyGraftDesigner::apply(), protocols::antibody::design::AntibodyCDRDesigner::apply(), 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::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_H_L_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_H_L_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_L_H_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_L_H_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_low_res(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), protocols::antibody::design::AntibodyGraftDesigner::extend_native_cdrs(), protocols::antibody::RefineOneCDRLoopCentroid::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::antibody::design::AntibodyGraftDesigner::fix_pdb_info(), protocols::antibody::AntibodyInfo::get_landmark_resnum(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::design::AntibodyGraftDesigner::graft_cdr(), protocols::antibody::AntibodyInfo::identify_CDR_from_a_sequence(), protocols::antibody::GraftCDRLoopsProtocol::init_from_options(), protocols::antibody::AntibodyModelerProtocol::init_from_options(), protocols::antibody::design::AntibodyDatabaseManager::load_cdr_design_data(), protocols::antibody::design::AntibodyDatabaseManager::load_cdrs_for_grafting(), protocols::antibody::design::ConservativeDesignOperation::load_data_from_db(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs_and_neighbor_sc(), protocols::antibody::design::AntibodyDesignModeler::minimize_interface(), protocols::antibody::design::AntibodyDesignMover::model_post_graft(), protocols::antibody::design::AntibodyDesignMover::output_ensemble(), protocols::antibody::H3PerturbCCD::read_and_store_fragments(), protocols::antibody::AntibodyNumberingParser::read_cdr_definition_file(), protocols::antibody::design::DesignInstructionsParser::read_cdr_graft_instructions(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::AntibodyNumberingParser::read_numbering_scheme_file(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs_and_neighbor_sc(), protocols::antibody::design::AntibodyDesignModeler::relax_interface(), protocols::antibody::design::AntibodyCDRDesigner::remove_conservative_design_residues_from_prob_set(), protocols::antibody::design::AntibodyDesignModeler::repack_antibody_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_antigen_ab_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_antigen_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_CDRs(), protocols::antibody::design::AntibodyDesignModeler::repack_CDRs_and_neighbors(), protocols::antibody::design::AntibodyGraftDesigner::run_basic_mc_algorithm(), protocols::antibody::design::AntibodyGraftDesigner::run_deterministic_graft_algorithm(), protocols::antibody::AntibodyModelerProtocol::set_default(), protocols::antibody::GraftCDRLoopsProtocol::set_default(), protocols::antibody::RefineOneCDRLoopCentroid::set_default(), protocols::antibody::AntibodyInfo::set_default(), protocols::antibody::AntibodyInfo::setup_CDR_clusters(), protocols::antibody::AntibodyInfo::setup_CDRsInfo(), protocols::antibody::design::AntibodyCDRDesigner::setup_constraints(), protocols::antibody::SnugDockProtocol::setup_objects(), protocols::antibody::SnugDock::setup_objects(), and protocols::antibody::design::AntibodyCDRDesigner::setup_task_factory().