This class is used to get all relevant information you would need when dealing with an antibody. More...

#include <AntibodyInfo.hh>

Inheritance diagram for protocols::antibody::AntibodyInfo:

Public Member Functions
	AntibodyInfo (core::pose::Pose const &pose, bool const cdr_pdb_numbered=true)
	Constructor that Loads default numbering scheme and cdr definition from options (Chothia/Aroop) More...

	AntibodyInfo (core::pose::Pose const &pose, AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const cdr_definition, bool const cdr_pdb_numbered=true)
	Constructor that uses the numbering scheme and cdr_definition given. More...

	AntibodyInfo (core::pose::Pose const &pose, CDRDefinitionEnum const cdr_definition, bool const cdr_pdb_numbered=true)
	Constructor using just the cdr definition. More...

	AntibodyInfo (AntibodyInfo const &src)
	Copy Constructor. More...

AntibodyInfoOP	clone () const
	Clone the pointer. More...

	~AntibodyInfo () override

std::string	get_current_AntibodyNumberingScheme () const
	: get the current numbering scheme being used More...

std::string	get_current_CDRDefinition () const

AntibodyEnumManagerCOP	get_antibody_enum_manager () const
	Get a const OP to the antibody enum manager. More...

clusters::CDRClusterEnumManagerCOP	get_cdr_cluster_enum_manager () const
	Get a const OP to the cluster enum manager. More...

core::Size	get_CDR_length (CDRNameEnum const cdr_name) const
	get the length of the cdr upon construction of AntibodyInfo More...

core::Size	get_CDR_length (CDRNameEnum const cdr_name, core::pose::Pose const &pose) const
	@breif On-the-fly CDR length. More...

core::Size	get_CDR_length (CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const transform) const

std::string	get_CDR_name (CDRNameEnum const cdr_name) const

CDRNameEnum	get_CDR_name_enum (std::string const &cdr_name) const

char	get_CDR_chain (CDRNameEnum const cdr_name) const

bool	is_camelid () const
	return this antibody is camelid or not More...

std::string	get_light_chain_type () const
	Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now. More...

LightChainTypeEnum	get_light_chain_type_enum () const
	Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now. More...

void	set_light_chain_type (LightChainTypeEnum light_chain)
	Set the light chain type via enum. More...

bool	antigen_present () const
	return whether this pose has antigen or not More...

core::Size	get_total_num_CDRs (bool include_proto_cdr4=false) const
	return whether a cdr contacts antigen. If no antigen is present, returns false. More...

utility::vector1< CDRNameEnum > const &	get_all_cdrs_present (bool include_proto_cdr4=false) const
	Get a vector of all the CDRs in this antibody. Easy to iterate on. More...

utility::vector1< CDRNameEnum > const &	get_all_cdrs (bool include_proto_cdr4=false) const
	Get a vector of all CDRs. Easy to iterate on. More...

bool	has_CDR (CDRNameEnum const cdr_name) const
	Does the antibody have this CDR? See also: is_camelid()) get_total_num_CDRs()) More...

core::Size	get_CDR_start_PDB_num (CDRNameEnum const cdr_name) const
	Return PDB residue number of CDR start residue. More...

core::Size	get_CDR_end_PDB_num (CDRNameEnum const cdr_name) const
	Return PDB residue number of CDR end residue. More...

core::Size	get_CDR_start (CDRNameEnum const cdr_name, core::pose::Pose const &pose) const
	Return pose number of CDR start residue. More...

core::Size	get_CDR_start (CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform) const

core::Size	get_CDR_end (CDRNameEnum const cdr_name, core::pose::Pose const &pose) const
	Return pose number of CDR end residue in the definition of the numbering scheme of transform. More...

core::Size	get_CDR_end (CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform) const

CDRNameEnum	get_CDRNameEnum_of_residue (core::pose::Pose const &pose, core::Size resnum, bool de_as_framework=true) const
	Get the CDRNameEnum for region, if not in a CDR throw exception – CDR can be id'ed with the "get_region_of_residue" function. More...

AntibodyRegionEnum	get_region_of_residue (core::pose::Pose const &pose, core::Size resnum, bool de_as_framework=true) const
	Get the region of the resnum - aka - antigen_region, cdr_region, or framework_region By default, count the DE region (CDR4) as framework. More...

utility::vector1< utility::vector1< FrameWork > >	get_AntibodyFrameworkInfo () const
	return the framework numbering information More...

H3BaseTypeEnum	get_H3_kink_type () const
	get H3 cterminal kink/extended conformation (predicted by constructor) More...

std::string	get_H3_kink_type_name () const

utility::vector1< core::Size >	get_PackingAngleResidues () const
	get residues used to calculate VL/VH packing angle More...

utility::vector1< char >	get_antigen_chains () const
	gets all non-LH chains. Empty vector if no antigen present. More...

utility::vector1< core::Size >	get_antigen_chain_ids (const core::pose::Pose &pose) const

std::string	get_antigen_chain_string () const
	Return the antigen chains as a string. More...

utility::vector1< char >	get_antibody_chains () const

utility::vector1< core::Size >	get_antibody_chain_ids (const core::pose::Pose &pose) const

std::string	get_antibody_chain_string () const
	Returns H or LH depeding on camelid. More...

core::Size	kink_begin (core::pose::Pose const &pose) const
	return pose residue number of the first residue of the H3 kink More...

core::Size	kink_end (core::pose::Pose const &pose) const
	return pose residue number of the last residue of the H3 kink More...

core::Size	kink_trp (core::pose::Pose const &pose) const
	return pose residue number of the last residue of the H3 kink More...

core::Size	kink_anion_residue (core::pose::Pose const &pose) const
	return pose residue number of the kink 'anion' (typically Asp/Glu) residue in the kink bulge HBond More...

core::Size	kink_cation_residue (core::pose::Pose const &pose) const
	return pose residue number of the kink 'cation' (typically Arg/Lys) residue in the kink bulge HBond More...

std::vector< core::Vector >	kink_anion_atoms (const core::pose::Pose &pose) const
	return side chain anion atoms (typically Asp/Glu oxygens) in the kink bulge HBond More...

std::vector< core::Vector >	kink_cation_atoms (const core::pose::Pose &pose) const
	return side chain cation atoms (typically Lys/His nitrogens) in the kink bulge HBond More...

core::Size	qq_light_residue (const core::pose::Pose &pose) const
	get pose number for light chain residue that is part of the qq constraint More...

core::Size	qq_heavy_residue (const core::pose::Pose &pose) const
	get pose number for heavy chain residue that is part of the qq constraint More...

core::Size	get_landmark_resnum (core::pose::Pose const &pose, AntibodyNumberingSchemeEnum const scheme, char const chain, core::Size const pdb_resnum, char const insertion_code=' ', bool fail_on_missing_resnum=true) const
	Used to get a residue number of a particular place in the framework or conserved residue in the CDR. Use this instead of PDBInfo!! More...

AntibodyNumbering const &	get_antibody_numbering_info () const
	Get the full antibody numbering struct for use in anything. More...

void	setup_CDR_clusters (core::pose::Pose const &pose, bool attempt_set_from_pose=false)
	setup the clustering information for each CDR to totalCDRLoops Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. More...

void	setup_CDR_clusters (core::pose::Pose const &pose, utility::vector1< bool > const &cdrs, bool attempt_set_from_pose=false)
	setup the clustering information for each CDR according to boolean vector. Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. More...

void	setup_CDR_cluster (core::pose::Pose const &pose, CDRNameEnum cdr, bool attempt_set_from_pose=false)
	setup the clustering information for a particular CDR. Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. More...

void	set_CDR_cluster (CDRNameEnum cdr, clusters::CDRClusterCOP cluster)
	Manually set the CDR cluster for a particular CDR. More...

clusters::CDRClusterCOP	get_CDR_cluster (CDRNameEnum const cdr_name) const
	get the cdr's cluster identity and distance to cluster using it's structure as a CDRCluster object. More...

clusters::CDRClusterSetOP	get_CDR_cluster_set () const

bool	has_cluster_for_cdr (CDRNameEnum const cdr_name) const
	Check to make sure AbInfo has a cluster object for this CDR. In that all 6 CDRs not nessessarily present for each antibody. More...

std::string	get_cluster_name (clusters::CDRClusterEnum const cluster) const

clusters::CDRClusterEnum	get_cluster_enum (std::string const &cluster) const

CDRNameEnum	get_cdr_enum_for_cluster (clusters::CDRClusterEnum const cluster) const

core::Size	get_cluster_length (clusters::CDRClusterEnum const cluster) const

std::string	get_CDR_sequence_with_stem (CDRNameEnum const cdr_name, core::Size left_stem=0, core::Size right_stem=0) const
	return the sequence of a particular CDR loop Deprecated in favor of on the fly sequence. More...

std::string	get_CDR_sequence_with_stem (CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size left_stem=0, core::Size right_stem=0) const
	On-The-Fly CDR sequence. More...

std::string	get_CDR_sequence_with_stem (CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size left_stem, core::Size right_stem, CDRDefinitionEnum const &transform) const
	On-The-Fly CDR sequence. More...

std::string	get_antibody_sequence () const
	return the antibody sequence of LH or just H for camelid More...

loops::Loop	get_CDR_loop (CDRNameEnum const cdr_name) const
	return the loop of a certain loop type More...

loops::Loop	get_CDR_loop (CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size overhang=0) const
	return the loop of a certain loop type on the fly More...

loops::Loop	get_CDR_loop (CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const transform, core::Size overhang=0) const
	return the loop of a certain loop type in definitions of the numbering scheme transform. More...

loops::LoopsOP	get_CDR_in_loopsop (CDRNameEnum const cdr_name) const
	return the loop of a certain loop type More...

loops::LoopsOP	get_AllCDRs_in_loopsop () const
	return a LoopsOP object, initialized upon class construction. More...

loops::LoopsOP	get_CDR_loops (core::pose::Pose const &pose, core::Size overhang=0) const
	On-the-fly CDR LoopsOP. More...

loops::LoopsOP	get_CDR_loops (core::pose::Pose const &pose, const utility::vector1< bool > &cdrs, core::Size overhang=0) const

core::kinematics::FoldTreeCOP	setup_simple_fold_tree (core::Size const &jumppoint1, core::Size const &cutpoint, core::Size const &jumppoint2, core::pose::Pose const &pose) const

core::kinematics::FoldTreeCOP	get_FoldTree_AllCDRs_LHDock (core::pose::Pose const &pose) const
	change to all CDR and VL-VH dock fold tree More...

core::kinematics::FoldTreeCOP	get_FoldTree_AllCDRs (core::pose::Pose const &pose) const

core::kinematics::FoldTree	get_FoldTree_LH_A (core::pose::Pose const &pose) const
	SnugDock foldtrees. More...

core::kinematics::FoldTree	get_FoldTree_L_HA (core::pose::Pose const &pose) const
	Fold tree for LH refinement in snugdock, docks L with H + antigen chains. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains. More...

core::kinematics::FoldTree	get_FoldTree_LA_H (core::pose::Pose const &pose) const
	Fold tree for LH refinement in snugdock, docks L + antigen chains with H. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains. More...

core::kinematics::MoveMap	get_MoveMap_for_Loops (core::pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const
	get a movemap for loops. More...

core::kinematics::MoveMap	get_MoveMap_for_AllCDRsSideChains_and_H3backbone (core::pose::Pose const &pose, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const

void	add_CDR_to_MoveMap (core::pose::Pose const &pose, core::kinematics::MoveMapOP movemap, CDRNameEnum const cdr_name, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const
	Add CDR flexibility to a movemap. Uses pose for numbering. More...

core::kinematics::MoveMap	get_MoveMap_for_LoopsandDock (core::pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const
	get a movemap for loops and set the first jump be true More...

core::pack::task::TaskFactoryOP	get_TaskFactory_AllCDRs (core::pose::Pose &pose) const
	TaskFactory. More...

core::pack::task::TaskFactoryOP	get_TaskFactory_OneCDR (core::pose::Pose &pose, CDRNameEnum const cdr_name) const

void	show (std::ostream &out=std::cout) const

Private Member Functions
void	set_default ()
	Setters for private AntibodyInfo variables /// //////////////////////////////////////////////////////////////////////////////////////. More...

void	identify_antibody (core::pose::Pose const &pose)
	check the input pose is nanobody, antibody or wrong. Sets sequence. Sets Antigen chains. More...

void	identify_light_chain (core::pose::Pose const &pose)
	place-holder for identification of light chain type: lambda/kappa/unknown. More...

void	init (core::pose::Pose const &pose)

void	setup_CDRsInfo (core::pose::Pose const &pose)
	setup the CDR loops objects based on the input numbering scheme More...

void	setup_FrameWorkInfo (core::pose::Pose const &pose)
	setup the framework information based on the input numbering scheme More...

void	setup_VL_VH_packing_angle (core::pose::Pose const &pose)
	setup the residues used to calculate VL/VH packing angle More...

void	predict_H3_base_type (core::pose::Pose const &pose)
	predict H3 cterminus base as Kinked or Extended More...

void	detect_and_set_camelid_CDR_H3_stem_type (core::pose::Pose const &pose)

void	detect_and_set_regular_CDR_H3_stem_type (core::pose::Pose const &pose)

void	detect_and_set_regular_CDR_H3_stem_type_new_rule (core::pose::Pose const &pose)

void	identify_CDR_from_a_sequence (std::string const &querychain)
	identify CDRs on L or H sequence More...

void	setup_numbering_info_for_scheme (AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const cdr_definition)
	Setup the Internal AntibodyNumbering variables. More...

utility::vector1< utility::vector1< PDBLandmarkOP > >	get_cdr_definition_transform (CDRDefinitionEnum const cdr_definition) const
	Gets transform for numbering scheme. Allows const qualification for other functions. More...

bool	cdr_definition_transform_present (CDRDefinitionEnum const cdr_definition) const
	Is the transform from our numbering scheme to cdr_definition defined? More...

utility::vector1< PDBLandmarkOP >	get_numbering_scheme_landmarks (AntibodyNumberingSchemeEnum const numbering_scheme) const

bool	numbering_scheme_transform_present (AntibodyNumberingSchemeEnum const numbering_scheme) const

void	check_cdr_quality (core::pose::Pose const &pose) const
	Make sure there are no large chainbreaks - aka missing residues - in the CDR loops or really bad peptide bonds Controlled via cmd-line flags. More...

Static Private Member Functions
static core::scoring::ScoreFunctionCOP	get_Pack_ScoreFxn (void)
	/// More...

static core::scoring::ScoreFunctionCOP	get_Dock_ScoreFxn (void)

static core::scoring::ScoreFunctionCOP	get_LoopCentral_ScoreFxn (void)

static core::scoring::ScoreFunctionCOP	get_LoopHighRes_ScoreFxn (void)

Private Attributes
bool	is_camelid_
	private data More...

bool	has_antigen_

bool	cdr_pdb_numbered_

utility::vector1< loops::LoopsOP >	vector1_loopsop_having_cdr_
	the CDR and Framework information More...

loops::LoopsOP	loopsop_having_allcdrs_

utility::vector1< utility::vector1< FrameWork > >	framework_info_

utility::vector1< char >	ab_sequence_

std::map< core::Size, char >	sequence_map_

utility::vector1< core::Size >	packing_angle_residues_

utility::vector1< utility::vector1< core::Size > >	packing_angle_numbering_

H3BaseTypeEnum	predicted_H3_base_type_
	Antibody properties. More...

CDRNameEnum	total_cdr_loops_

utility::vector1< char >	chains_for_cdrs_

utility::vector1< char >	chains_for_antigen_

core::Size	L_chain_

core::Size	H_chain_

LightChainTypeEnum	light_chain_type_

clusters::CDRClusterSetOP	cdr_cluster_set_

AntibodyNumbering	numbering_info_
	Internal Per-Scheme Numbering. More...

utility::vector1< utility::vector1< core::Size > >	current_transform_

AntibodyEnumManagerOP	enum_manager_

clusters::CDRClusterEnumManagerOP	cdr_cluster_manager_

AntibodyNumberingParserOP	numbering_parser_

utility::vector1< CDRNameEnum >	all_cdrs_present_

utility::vector1< CDRNameEnum >	all_cdrs_present_and_proto_

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

Detailed Description

This class is used to get all relevant information you would need when dealing with an antibody.

It mainly holds numbering information, but passes out a variety of Rosetta specific objects like movemaps, Loops, taskfactories, etc. as well as other information such as CDR cluster type, camelid, H3 types, etc.

Constructor & Destructor Documentation

◆ AntibodyInfo() [1/4]

protocols::antibody::AntibodyInfo::AntibodyInfo	(	core::pose::Pose const &	pose,
		bool const	cdr_pdb_numbered = `true`
	)

Constructor that Loads default numbering scheme and cdr definition from options (Chothia/Aroop)

References cdr_pdb_numbered_, enum_manager_, identify_antibody(), init(), and set_default().

◆ AntibodyInfo() [2/4]

protocols::antibody::AntibodyInfo::AntibodyInfo	(	core::pose::Pose const &	pose,
		AntibodyNumberingSchemeEnum const &	numbering_scheme,
		CDRDefinitionEnum const	cdr_definition,
		bool const	cdr_pdb_numbered = `true`
	)

Constructor that uses the numbering scheme and cdr_definition given.

References protocols::antibody::AntibodyNumbering::cdr_definition, cdr_pdb_numbered_, enum_manager_, identify_antibody(), init(), numbering_info_, protocols::antibody::AntibodyNumbering::numbering_scheme, and set_default().

◆ AntibodyInfo() [3/4]

protocols::antibody::AntibodyInfo::AntibodyInfo	(	core::pose::Pose const &	pose,
		CDRDefinitionEnum const	cdr_definition,
		bool const	cdr_pdb_numbered = `true`
	)

Constructor using just the cdr definition.

References protocols::antibody::AntibodyNumbering::cdr_definition, cdr_pdb_numbered_, enum_manager_, identify_antibody(), init(), numbering_info_, and set_default().

◆ AntibodyInfo() [4/4]

protocols::antibody::AntibodyInfo::AntibodyInfo ( AntibodyInfo const & src )

Copy Constructor.

References cdr_cluster_manager_, cdr_cluster_set_, enum_manager_, loopsop_having_allcdrs_, numbering_parser_, and vector1_loopsop_having_cdr_.

◆ ~AntibodyInfo()

protocols::antibody::AntibodyInfo::~AntibodyInfo ( )

overridedefault

Member Function Documentation

◆ add_CDR_to_MoveMap()

void protocols::antibody::AntibodyInfo::add_CDR_to_MoveMap	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP	movemap,
		CDRNameEnum const	cdr_name,
		bool const &	bb_only = `false`,
		bool const &	include_nb_sc = `false`,
		core::Real const &	nb_dist = `10.0`
	)		const

Add CDR flexibility to a movemap. Uses pose for numbering.

References get_CDR_end(), get_CDR_start(), protocols::loops::select_loop_residues(), core::pose::Pose::size(), protocols::loops::start, and protocols::loops::stop.

◆ antigen_present()

bool protocols::antibody::AntibodyInfo::antigen_present ( ) const

inline

return whether this pose has antigen or not

References has_antigen_.

◆ cdr_definition_transform_present()

bool protocols::antibody::AntibodyInfo::cdr_definition_transform_present ( CDRDefinitionEnum const cdr_definition ) const

private

Is the transform from our numbering scheme to cdr_definition defined?

References protocols::antibody::AntibodyNumbering::cdr_definition_transform, and numbering_info_.

Referenced by get_cdr_definition_transform().

◆ check_cdr_quality()

void protocols::antibody::AntibodyInfo::check_cdr_quality ( core::pose::Pose const & pose ) const

private

Make sure there are no large chainbreaks - aka missing residues - in the CDR loops or really bad peptide bonds Controlled via cmd-line flags.

References get_CDR_loop(), get_CDR_name(), protocols::loops::has_severe_pep_bond_geom_issues(), core::pose::Pose::pdb_info(), and total_cdr_loops_.

Referenced by init().

◆ clone()

AntibodyInfoOP protocols::antibody::AntibodyInfo::clone ( ) const

Clone the pointer.

Referenced by protocols::antibody::deep_copy().

◆ detect_and_set_camelid_CDR_H3_stem_type()

void protocols::antibody::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type ( core::pose::Pose const & pose )

private

References protocols::antibody::Aroop, enum_manager_, protocols::antibody::Extended, get_CDR_loop(), protocols::antibody::h3, protocols::antibody::Kinked, protocols::antibody::Neutral, predicted_H3_base_type_, core::pose::Pose::sequence(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, and protocols::antibody::TR().

Referenced by predict_H3_base_type().

◆ detect_and_set_regular_CDR_H3_stem_type()

void protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type ( core::pose::Pose const & pose )

private

References protocols::antibody::Aroop, protocols::antibody::Chothia_Scheme, enum_manager_, protocols::antibody::Extended, get_CDR_loop(), get_landmark_resnum(), protocols::antibody::h3, protocols::antibody::Kinked, core::conformation::Residue::name1(), protocols::antibody::Neutral, predicted_H3_base_type_, core::pose::Pose::residue(), core::pose::Pose::sequence(), protocols::loops::start, protocols::loops::Loop::stop(), and protocols::antibody::TR().

◆ detect_and_set_regular_CDR_H3_stem_type_new_rule()

void protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule ( core::pose::Pose const & pose )

private

References protocols::antibody::Aroop, protocols::antibody::Chothia_Scheme, enum_manager_, protocols::antibody::Extended, get_CDR_loop(), get_landmark_resnum(), protocols::antibody::h3, protocols::antibody::Kinked, core::conformation::Residue::name1(), protocols::antibody::Neutral, predicted_H3_base_type_, core::pose::Pose::residue(), core::pose::Pose::sequence(), protocols::loops::start, protocols::loops::Loop::stop(), core::id::to_string(), and protocols::antibody::TR().

Referenced by predict_H3_base_type().

◆ get_all_cdrs()

utility::vector1< CDRNameEnum > const & protocols::antibody::AntibodyInfo::get_all_cdrs ( bool include_proto_cdr4 = false ) const

Get a vector of all CDRs. Easy to iterate on.

References enum_manager_.

◆ get_all_cdrs_present()

utility::vector1< CDRNameEnum > const & protocols::antibody::AntibodyInfo::get_all_cdrs_present ( bool include_proto_cdr4 = false ) const

Get a vector of all the CDRs in this antibody. Easy to iterate on.

References all_cdrs_present_, and all_cdrs_present_and_proto_.

Referenced by get_CDRNameEnum_of_residue(), protocols::antibody::design::NativeAntibodySeq::get_native_sequence_matching_current_length(), get_region_of_residue(), protocols::antibody::paratope_charge(), protocols::antibody::paratope_sasa(), and protocols::antibody::design::NativeAntibodySeq::set_sequence().

◆ get_AllCDRs_in_loopsop()

loops::LoopsOP protocols::antibody::AntibodyInfo::get_AllCDRs_in_loopsop ( ) const

return a LoopsOP object, initialized upon class construction.

References loopsop_having_allcdrs_.

Referenced by get_FoldTree_AllCDRs(), get_FoldTree_AllCDRs_LHDock(), get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), and get_TaskFactory_AllCDRs().

◆ get_antibody_chain_ids()

vector1< core::Size > protocols::antibody::AntibodyInfo::get_antibody_chain_ids ( const core::pose::Pose & pose ) const

References core::pose::get_chain_id_from_chain(), and is_camelid_.

◆ get_antibody_chain_string()

std::string protocols::antibody::AntibodyInfo::get_antibody_chain_string ( ) const

Returns H or LH depeding on camelid.

References is_camelid_.

◆ get_antibody_chains()

vector1< char > protocols::antibody::AntibodyInfo::get_antibody_chains ( ) const

References is_camelid_.

◆ get_antibody_enum_manager()

AntibodyEnumManagerCOP protocols::antibody::AntibodyInfo::get_antibody_enum_manager ( ) const

Get a const OP to the antibody enum manager.

References enum_manager_.

◆ get_antibody_numbering_info()

AntibodyNumbering const& protocols::antibody::AntibodyInfo::get_antibody_numbering_info ( ) const

inline

Get the full antibody numbering struct for use in anything.

References numbering_info_.

◆ get_antibody_sequence()

std::string protocols::antibody::AntibodyInfo::get_antibody_sequence ( ) const

return the antibody sequence of LH or just H for camelid

References ab_sequence_.

◆ get_AntibodyFrameworkInfo()

vector1< vector1< FrameWork > > protocols::antibody::AntibodyInfo::get_AntibodyFrameworkInfo ( ) const

return the framework numbering information

References framework_info_.

◆ get_antigen_chain_ids()

vector1< core::Size > protocols::antibody::AntibodyInfo::get_antigen_chain_ids ( const core::pose::Pose & pose ) const

References chains_for_antigen_, and core::pose::get_chain_id_from_chain().

◆ get_antigen_chain_string()

std::string protocols::antibody::AntibodyInfo::get_antigen_chain_string ( ) const

Return the antigen chains as a string.

References chains_for_antigen_.

◆ get_antigen_chains()

utility::vector1< char > protocols::antibody::AntibodyInfo::get_antigen_chains ( ) const

inline

gets all non-LH chains. Empty vector if no antigen present.

References chains_for_antigen_.

◆ get_CDR_chain()

char protocols::antibody::AntibodyInfo::get_CDR_chain ( CDRNameEnum const cdr_name ) const

inline

References chains_for_cdrs_.

◆ get_CDR_cluster()

CDRClusterCOP protocols::antibody::AntibodyInfo::get_CDR_cluster ( CDRNameEnum const cdr_name ) const

get the cdr's cluster identity and distance to cluster using it's structure as a CDRCluster object.

See North, B., A. Lehmann, et al. (2011). JMB 406(2): 228-256. Must use setup_CDR_clusters first.

Note: If this AbInfo does not have all 6 chains, CDRClusterOP may be NULL if the CDR is not present to begin with.

References cdr_cluster_set_.

◆ get_cdr_cluster_enum_manager()

CDRClusterEnumManagerCOP protocols::antibody::AntibodyInfo::get_cdr_cluster_enum_manager ( ) const

Get a const OP to the cluster enum manager.

References cdr_cluster_manager_.

◆ get_CDR_cluster_set()

CDRClusterSetOP protocols::antibody::AntibodyInfo::get_CDR_cluster_set ( ) const

References cdr_cluster_set_.

◆ get_cdr_definition_transform()

vector1< vector1< PDBLandmarkOP > > protocols::antibody::AntibodyInfo::get_cdr_definition_transform ( CDRDefinitionEnum const cdr_definition ) const

private

Gets transform for numbering scheme. Allows const qualification for other functions.

References protocols::antibody::AntibodyNumbering::cdr_definition, protocols::antibody::AntibodyNumbering::cdr_definition_transform, cdr_definition_transform_present(), enum_manager_, and numbering_info_.

Referenced by get_CDR_end(), and get_CDR_start().

◆ get_CDR_end() [1/2]

Size protocols::antibody::AntibodyInfo::get_CDR_end	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose
	)		const

Return pose number of CDR end residue in the definition of the numbering scheme of transform.

References protocols::antibody::AHO_Scheme, protocols::antibody::cdr_end, protocols::antibody::AntibodyNumbering::cdr_numbering, chains_for_cdrs_, get_CDR_name(), get_landmark_resnum(), protocols::antibody::h4, protocols::antibody::PDBLandmark::insertion_code(), protocols::antibody::l4, numbering_info_, core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and core::id::to_string().

Referenced by add_CDR_to_MoveMap(), get_CDR_end(), get_CDR_loop(), get_CDR_sequence_with_stem(), get_CDRNameEnum_of_residue(), get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), get_region_of_residue(), protocols::antibody::paratope_charge(), and protocols::antibody::paratope_sasa().

◆ get_CDR_end() [2/2]

Size protocols::antibody::AntibodyInfo::get_CDR_end	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose,
		CDRDefinitionEnum const &	transform
	)		const

References protocols::antibody::AHO_Scheme, protocols::antibody::AntibodyNumbering::cdr_definition, protocols::antibody::cdr_end, chains_for_cdrs_, enum_manager_, get_cdr_definition_transform(), get_CDR_end(), get_CDR_name(), get_landmark_resnum(), protocols::antibody::h4, protocols::antibody::PDBLandmark::insertion_code(), protocols::antibody::l4, numbering_info_, core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and core::id::to_string().

◆ get_CDR_end_PDB_num()

core::Size protocols::antibody::AntibodyInfo::get_CDR_end_PDB_num ( CDRNameEnum const cdr_name ) const

inline

Return PDB residue number of CDR end residue.

References protocols::antibody::cdr_end, protocols::antibody::AntibodyNumbering::cdr_numbering, and numbering_info_.

◆ get_cdr_enum_for_cluster()

CDRNameEnum protocols::antibody::AntibodyInfo::get_cdr_enum_for_cluster ( clusters::CDRClusterEnum const cluster ) const

References cdr_cluster_manager_, and enum_manager_.

◆ get_CDR_in_loopsop()

loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_in_loopsop ( CDRNameEnum const cdr_name ) const

return the loop of a certain loop type

References vector1_loopsop_having_cdr_.

Referenced by get_TaskFactory_OneCDR().

◆ get_CDR_length() [1/3]

Size protocols::antibody::AntibodyInfo::get_CDR_length ( CDRNameEnum const cdr_name ) const

get the length of the cdr upon construction of AntibodyInfo

Does not work for proto CDR4 (DE loop)

References get_CDR_loop(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by get_CDR_length(), protocols::antibody::design::NativeAntibodySeq::get_native_sequence_matching_current_length(), and protocols::antibody::design::NativeAntibodySeq::set_from_cdr().

◆ get_CDR_length() [2/3]

Size protocols::antibody::AntibodyInfo::get_CDR_length	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose
	)		const

@breif On-the-fly CDR length.

References protocols::antibody::AntibodyNumbering::cdr_definition, get_CDR_length(), and numbering_info_.

◆ get_CDR_length() [3/3]

Size protocols::antibody::AntibodyInfo::get_CDR_length	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose,
		CDRDefinitionEnum const	transform
	)		const

References get_CDR_loop(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

◆ get_CDR_loop() [1/3]

loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop ( CDRNameEnum const cdr_name ) const

return the loop of a certain loop type

References vector1_loopsop_having_cdr_.

Referenced by check_cdr_quality(), detect_and_set_camelid_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type_new_rule(), get_CDR_length(), get_CDR_loop(), get_CDR_loops(), get_CDR_sequence_with_stem(), kink_anion_atoms(), kink_anion_residue(), kink_begin(), kink_cation_atoms(), kink_cation_residue(), kink_end(), and kink_trp().

◆ get_CDR_loop() [2/3]

loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose,
		CDRDefinitionEnum const	transform,
		core::Size	overhang = `0`
	)		const

return the loop of a certain loop type in definitions of the numbering scheme transform.

References protocols::antibody::AntibodyNumbering::cdr_definition, get_CDR_end(), get_CDR_loop(), get_CDR_start(), numbering_info_, protocols::loops::start, and protocols::loops::stop.

◆ get_CDR_loop() [3/3]

loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose,
		core::Size	overhang = `0`
	)		const

return the loop of a certain loop type on the fly

References get_CDR_end(), get_CDR_start(), protocols::loops::start, and protocols::loops::stop.

◆ get_CDR_loops() [1/2]

loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_loops	(	core::pose::Pose const &	pose,
		const utility::vector1< bool > &	cdrs,
		core::Size	overhang = `0`
	)		const

◆ get_CDR_loops() [2/2]

loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_loops	(	core::pose::Pose const &	pose,
		core::Size	overhang = `0`
	)		const

On-the-fly CDR LoopsOP.

References get_CDR_loop(), and total_cdr_loops_.

◆ get_CDR_name()

std::string protocols::antibody::AntibodyInfo::get_CDR_name ( CDRNameEnum const cdr_name ) const

References enum_manager_.

Referenced by check_cdr_quality(), get_CDR_end(), get_CDR_start(), protocols::antibody::paratope_charge(), protocols::antibody::paratope_sasa(), setup_CDR_cluster(), and setup_CDRsInfo().

◆ get_CDR_name_enum()

CDRNameEnum protocols::antibody::AntibodyInfo::get_CDR_name_enum ( std::string const & cdr_name ) const

References enum_manager_.

◆ get_CDR_sequence_with_stem() [1/3]

std::string protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose,
		core::Size	left_stem,
		core::Size	right_stem,
		CDRDefinitionEnum const &	transform
	)		const

On-The-Fly CDR sequence.

References get_CDR_end(), get_CDR_start(), and core::pose::Pose::sequence().

◆ get_CDR_sequence_with_stem() [2/3]

std::string protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose,
		core::Size	left_stem = `0`,
		core::Size	right_stem = `0`
	)		const

On-The-Fly CDR sequence.

References protocols::antibody::AntibodyNumbering::cdr_definition, get_CDR_sequence_with_stem(), and numbering_info_.

◆ get_CDR_sequence_with_stem() [3/3]

std::string protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem	(	CDRNameEnum const	cdr_name,
		core::Size	left_stem = `0`,
		core::Size	right_stem = `0`
	)		const

return the sequence of a particular CDR loop Deprecated in favor of on the fly sequence.

References get_CDR_loop(), sequence_map_, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by get_CDR_sequence_with_stem().

◆ get_CDR_start() [1/2]

Size protocols::antibody::AntibodyInfo::get_CDR_start	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose
	)		const

Return pose number of CDR start residue.

References protocols::antibody::AHO_Scheme, protocols::antibody::AntibodyNumbering::cdr_numbering, protocols::antibody::cdr_start, chains_for_cdrs_, get_CDR_name(), get_landmark_resnum(), protocols::antibody::h4, protocols::antibody::PDBLandmark::insertion_code(), protocols::antibody::l4, numbering_info_, core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and core::id::to_string().

Referenced by add_CDR_to_MoveMap(), get_CDR_loop(), get_CDR_sequence_with_stem(), get_CDR_start(), get_CDRNameEnum_of_residue(), get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::design::NativeAntibodySeq::get_native_sequence_matching_current_length(), get_region_of_residue(), protocols::antibody::paratope_charge(), protocols::antibody::paratope_sasa(), and protocols::antibody::design::NativeAntibodySeq::set_from_cdr().

◆ get_CDR_start() [2/2]

Size protocols::antibody::AntibodyInfo::get_CDR_start	(	CDRNameEnum const	cdr_name,
		core::pose::Pose const &	pose,
		CDRDefinitionEnum const &	transform
	)		const

References protocols::antibody::AHO_Scheme, protocols::antibody::AntibodyNumbering::cdr_definition, protocols::antibody::cdr_start, chains_for_cdrs_, enum_manager_, get_cdr_definition_transform(), get_CDR_name(), get_CDR_start(), get_landmark_resnum(), protocols::antibody::h4, protocols::antibody::PDBLandmark::insertion_code(), protocols::antibody::l4, numbering_info_, core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and core::id::to_string().

◆ get_CDR_start_PDB_num()

core::Size protocols::antibody::AntibodyInfo::get_CDR_start_PDB_num ( CDRNameEnum const cdr_name ) const

inline

Return PDB residue number of CDR start residue.

References protocols::antibody::AntibodyNumbering::cdr_numbering, protocols::antibody::cdr_start, and numbering_info_.

◆ get_CDRNameEnum_of_residue()

CDRNameEnum protocols::antibody::AntibodyInfo::get_CDRNameEnum_of_residue	(	core::pose::Pose const &	pose,
		core::Size	resnum,
		bool	de_as_framework = `true`
	)		const

Get the CDRNameEnum for region, if not in a CDR throw exception – CDR can be id'ed with the "get_region_of_residue" function.

References core::pose::Pose::chain(), core::sequence::end, get_all_cdrs_present(), get_CDR_end(), get_CDR_start(), core::pose::get_chain_from_chain_id(), and protocols::loops::start.

◆ get_cluster_enum()

CDRClusterEnum protocols::antibody::AntibodyInfo::get_cluster_enum ( std::string const & cluster ) const

References cdr_cluster_manager_.

◆ get_cluster_length()

core::Size protocols::antibody::AntibodyInfo::get_cluster_length ( clusters::CDRClusterEnum const cluster ) const

References cdr_cluster_manager_.

◆ get_cluster_name()

std::string protocols::antibody::AntibodyInfo::get_cluster_name ( clusters::CDRClusterEnum const cluster ) const

References cdr_cluster_manager_.

◆ get_current_AntibodyNumberingScheme()

std::string protocols::antibody::AntibodyInfo::get_current_AntibodyNumberingScheme ( ) const

: get the current numbering scheme being used

References enum_manager_, numbering_info_, and protocols::antibody::AntibodyNumbering::numbering_scheme.

◆ get_current_CDRDefinition()

std::string protocols::antibody::AntibodyInfo::get_current_CDRDefinition ( ) const

References protocols::antibody::AntibodyNumbering::cdr_definition, enum_manager_, and numbering_info_.

◆ get_Dock_ScoreFxn()

static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_Dock_ScoreFxn ( void )

staticprivate

◆ get_FoldTree_AllCDRs()

kinematics::FoldTreeCOP protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs ( core::pose::Pose const & pose ) const

References protocols::loops::fold_tree_from_loops(), and get_AllCDRs_in_loopsop().

Referenced by get_FoldTree_AllCDRs_LHDock().

◆ get_FoldTree_AllCDRs_LHDock()

kinematics::FoldTreeCOP protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock ( core::pose::Pose const & pose ) const

change to all CDR and VL-VH dock fold tree

Author: Aroop 07/13/2010; Brian D. Weitzner

References core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), get_AllCDRs_in_loopsop(), get_FoldTree_AllCDRs(), core::kinematics::Edge::label(), core::kinematics::Edge::PEPTIDE, core::pose::residue_center_of_mass(), core::pose::Pose::size(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

◆ get_FoldTree_L_HA()

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_L_HA ( core::pose::Pose const & pose ) const

Fold tree for LH refinement in snugdock, docks L with H + antigen chains. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains.

Author: Krishna Praneeth Kilambi 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::residue_center_of_mass(), core::kinematics::FoldTree::simple_tree(), and core::pose::Pose::size().

◆ get_FoldTree_LA_H()

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_LA_H ( core::pose::Pose const & pose ) const

Fold tree for LH refinement in snugdock, docks L + antigen chains with H. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains.

Author: Krishna Praneeth Kilambi 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::residue_center_of_mass(), core::kinematics::FoldTree::simple_tree(), and core::pose::Pose::size().

◆ get_FoldTree_LH_A()

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_LH_A ( core::pose::Pose const & pose ) const

SnugDock foldtrees.

Fold tree for snugdock, docks LH with the antigen chains. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains.

Author: Krishna Praneeth Kilambi 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::residue_center_of_mass(), core::kinematics::FoldTree::simple_tree(), and core::pose::Pose::size().

◆ get_H3_kink_type()

H3BaseTypeEnum protocols::antibody::AntibodyInfo::get_H3_kink_type ( ) const

get H3 cterminal kink/extended conformation (predicted by constructor)

References predicted_H3_base_type_.

◆ get_H3_kink_type_name()

std::string protocols::antibody::AntibodyInfo::get_H3_kink_type_name ( ) const

References enum_manager_, and predicted_H3_base_type_.

◆ get_landmark_resnum()

core::Size protocols::antibody::AntibodyInfo::get_landmark_resnum	(	core::pose::Pose const &	pose,
		AntibodyNumberingSchemeEnum const	scheme,
		char const	chain,
		core::Size const	pdb_resnum,
		char const	insertion_code = `' '`,
		bool	fail_on_missing_resnum = `true`
	)		const

Used to get a residue number of a particular place in the framework or conserved residue in the CDR. Use this instead of PDBInfo!!

If the current numbering scheme is not 'scheme', will return the equivalent position of the current numbering scheme using the transform scheme file in the database. Should not be used for residues within CDRs since numbering schemes vary greatly in their within cdr alignments and numbering. Use get_CDR_start/end/loop functions with relative positions for this purpose. Returns 0 if residue is not found in pose

References enum_manager_, get_numbering_scheme_landmarks(), numbering_info_, protocols::antibody::AntibodyNumbering::numbering_scheme, numbering_scheme_transform_present(), core::pose::Pose::pdb_info(), core::id::to_string(), and protocols::antibody::TR().

Referenced by detect_and_set_regular_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type_new_rule(), get_CDR_end(), get_CDR_start(), qq_heavy_residue(), qq_light_residue(), setup_FrameWorkInfo(), and setup_VL_VH_packing_angle().

◆ get_light_chain_type()

std::string protocols::antibody::AntibodyInfo::get_light_chain_type ( ) const

inline

Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now.

References enum_manager_, and light_chain_type_.

◆ get_light_chain_type_enum()

LightChainTypeEnum protocols::antibody::AntibodyInfo::get_light_chain_type_enum ( ) const

inline

Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now.

References light_chain_type_.

◆ get_LoopCentral_ScoreFxn()

static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_LoopCentral_ScoreFxn ( void )

staticprivate

◆ get_LoopHighRes_ScoreFxn()

static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_LoopHighRes_ScoreFxn ( void )

staticprivate

◆ get_MoveMap_for_AllCDRsSideChains_and_H3backbone()

kinematics::MoveMap protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone	(	core::pose::Pose const &	pose,
		bool const &	include_nb_sc = `false`,
		core::Real const &	nb_dist = `10.0`
	)		const

References core::kinematics::MoveMap::clear(), get_AllCDRs_in_loopsop(), get_CDR_end(), get_CDR_start(), protocols::antibody::h3, protocols::loops::select_loop_residues(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), and protocols::antibody::TR().

◆ get_MoveMap_for_Loops()

kinematics::MoveMap protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops	(	core::pose::Pose const &	pose,
		loops::Loops const &	the_loops,
		bool const &	bb_only = `false`,
		bool const &	include_nb_sc = `false`,
		core::Real const &	nb_dist = `10.0`
	)		const

get a movemap for loops.

TODO: this should be a standard utility for loops?

References core::kinematics::MoveMap::clear(), protocols::loops::Loops::num_loop(), protocols::loops::select_loop_residues(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), and core::pose::Pose::size().

Referenced by get_MoveMap_for_LoopsandDock().

◆ get_MoveMap_for_LoopsandDock()

kinematics::MoveMap protocols::antibody::AntibodyInfo::get_MoveMap_for_LoopsandDock	(	core::pose::Pose const &	pose,
		loops::Loops const &	the_loops,
		bool const &	bb_only = `false`,
		bool const &	include_nb_sc = `false`,
		core::Real const &	nb_dist = `10.0`
	)		const

get a movemap for loops and set the first jump be true

References get_MoveMap_for_Loops(), protocols::loops::Loops::num_loop(), and core::kinematics::MoveMap::set_jump().

◆ get_numbering_scheme_landmarks()

vector1< PDBLandmarkOP > protocols::antibody::AntibodyInfo::get_numbering_scheme_landmarks ( AntibodyNumberingSchemeEnum const numbering_scheme ) const

private

References enum_manager_, numbering_info_, protocols::antibody::AntibodyNumbering::numbering_scheme_transform, and numbering_scheme_transform_present().

Referenced by get_landmark_resnum().

◆ get_Pack_ScoreFxn()

static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_Pack_ScoreFxn ( void )

staticprivate

///

copy

all the static functions

◆ get_PackingAngleResidues()

utility::vector1< core::Size > protocols::antibody::AntibodyInfo::get_PackingAngleResidues ( ) const

inline

get residues used to calculate VL/VH packing angle

References packing_angle_residues_.

Referenced by protocols::antibody::vl_vh_orientation_coords().

◆ get_region_of_residue()

AntibodyRegionEnum protocols::antibody::AntibodyInfo::get_region_of_residue	(	core::pose::Pose const &	pose,
		core::Size	resnum,
		bool	de_as_framework = `true`
	)		const

Get the region of the resnum - aka - antigen_region, cdr_region, or framework_region By default, count the DE region (CDR4) as framework.

References protocols::antibody::antigen_region, protocols::antibody::cdr_region, core::pose::Pose::chain(), core::sequence::end, protocols::antibody::framework_region, get_all_cdrs_present(), get_CDR_end(), get_CDR_start(), core::pose::get_chain_from_chain_id(), and protocols::loops::start.

Referenced by protocols::antibody::design::NativeAntibodySeq::set_sequence().

◆ get_TaskFactory_AllCDRs()

pack::task::TaskFactoryOP protocols::antibody::AntibodyInfo::get_TaskFactory_AllCDRs ( core::pose::Pose & pose ) const

TaskFactory.

References get_AllCDRs_in_loopsop(), protocols::loops::select_loop_residues(), protocols::antibody::setup_packer_task(), and core::pose::Pose::size().

◆ get_TaskFactory_OneCDR()

pack::task::TaskFactoryOP protocols::antibody::AntibodyInfo::get_TaskFactory_OneCDR	(	core::pose::Pose &	pose,
		CDRNameEnum const	cdr_name
	)		const

References get_CDR_in_loopsop(), protocols::loops::select_loop_residues(), protocols::antibody::setup_packer_task(), and core::pose::Pose::size().

◆ get_total_num_CDRs()

core::Size protocols::antibody::AntibodyInfo::get_total_num_CDRs ( bool include_proto_cdr4 = false ) const

return whether a cdr contacts antigen. If no antigen is present, returns false.

Considered 'in_contact' if > 5 atoms of antigen are within 5 A of any atom of the CDR.

return num of cdr loops, 3 (nanobody) or 6 (regular antibody) Do not use for enum-based for loop if including cdr4. Use get_all_cdrs_present instead!

References all_cdrs_present_, and all_cdrs_present_and_proto_.

Referenced by protocols::antibody::paratope_charge(), and protocols::antibody::paratope_sasa().

◆ has_CDR()

bool protocols::antibody::AntibodyInfo::has_CDR ( CDRNameEnum const cdr_name ) const

Does the antibody have this CDR? See also: is_camelid()) get_total_num_CDRs())

References protocols::antibody::h4, is_camelid_, protocols::antibody::l4, and total_cdr_loops_.

Referenced by setup_CDR_cluster().

◆ has_cluster_for_cdr()

bool protocols::antibody::AntibodyInfo::has_cluster_for_cdr ( CDRNameEnum const cdr_name ) const

Check to make sure AbInfo has a cluster object for this CDR. In that all 6 CDRs not nessessarily present for each antibody.

References cdr_cluster_set_.

◆ identify_antibody()

void protocols::antibody::AntibodyInfo::identify_antibody ( core::pose::Pose const & pose )

private

check the input pose is nanobody, antibody or wrong. Sets sequence. Sets Antigen chains.

References ab_sequence_, core::conformation::Residue::chain(), chains_for_antigen_, core::pose::Pose::conformation(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_id_from_chain(), H_chain_, has_antigen_, core::pose::has_chain(), is_camelid_, L_chain_, core::conformation::Residue::name1(), core::conformation::Conformation::num_chains(), core::pose::Pose::residue(), sequence_map_, and core::pose::Pose::size().

Referenced by AntibodyInfo().

◆ identify_CDR_from_a_sequence()

void protocols::antibody::AntibodyInfo::identify_CDR_from_a_sequence ( std::string const & querychain )

private

identify CDRs on L or H sequence

TODO:

Author: : Daisuke Kuroda (dkuro.nosp@m.da19.nosp@m.81@gm.nosp@m.ail..nosp@m.com) 06/18/2012

: Identify 3 CDRs from a sequence. Automatically judge heavy or light chains (I hope!). The input can be either a light chain, a heavy chain or another sequence.

References protocols::antibody::TR().

◆ identify_light_chain()

void protocols::antibody::AntibodyInfo::identify_light_chain ( core::pose::Pose const & pose )

private

place-holder for identification of light chain type: lambda/kappa/unknown.

References enum_manager_, is_camelid(), light_chain_type_, and protocols::antibody::unknown.

Referenced by init().

◆ init()

void protocols::antibody::AntibodyInfo::init ( core::pose::Pose const & pose )

private

◆ is_camelid()

bool protocols::antibody::AntibodyInfo::is_camelid ( ) const

inline

return this antibody is camelid or not

References is_camelid_.

Referenced by identify_light_chain(), init(), set_light_chain_type(), setup_FrameWorkInfo(), and protocols::antibody::vl_vh_orientation_coords().

◆ kink_anion_atoms()

std::vector< Vector > protocols::antibody::AntibodyInfo::kink_anion_atoms ( const core::pose::Pose & pose ) const

return side chain anion atoms (typically Asp/Glu oxygens) in the kink bulge HBond

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, core::conformation::Residue::name1(), core::pose::Pose::residue(), protocols::loops::Loop::stop(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody::kink_RD_Hbond().

◆ kink_anion_residue()

core::Size protocols::antibody::AntibodyInfo::kink_anion_residue ( core::pose::Pose const & pose ) const

inline

return pose residue number of the kink 'anion' (typically Asp/Glu) residue in the kink bulge HBond

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::stop().

Referenced by protocols::antibody::kink_bb_Hbond().

◆ kink_begin()

core::Size protocols::antibody::AntibodyInfo::kink_begin ( core::pose::Pose const & pose ) const

inline

return pose residue number of the first residue of the H3 kink

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::stop().

Referenced by protocols::antibody::kink_dihedral(), and protocols::antibody::kink_Trp_Hbond().

◆ kink_cation_atoms()

std::vector< Vector > protocols::antibody::AntibodyInfo::kink_cation_atoms ( const core::pose::Pose & pose ) const

return side chain cation atoms (typically Lys/His nitrogens) in the kink bulge HBond

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, core::conformation::Residue::name1(), core::pose::Pose::residue(), protocols::loops::Loop::start(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody::kink_RD_Hbond().

◆ kink_cation_residue()

core::Size protocols::antibody::AntibodyInfo::kink_cation_residue ( core::pose::Pose const & pose ) const

inline

return pose residue number of the kink 'cation' (typically Arg/Lys) residue in the kink bulge HBond

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::start().

Referenced by protocols::antibody::kink_bb_Hbond().

◆ kink_end()

core::Size protocols::antibody::AntibodyInfo::kink_end ( core::pose::Pose const & pose ) const

inline

return pose residue number of the last residue of the H3 kink

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::stop().

◆ kink_trp()

core::Size protocols::antibody::AntibodyInfo::kink_trp ( core::pose::Pose const & pose ) const

inline

return pose residue number of the last residue of the H3 kink

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::stop().

Referenced by protocols::antibody::kink_Trp_Hbond().

◆ numbering_scheme_transform_present()

bool protocols::antibody::AntibodyInfo::numbering_scheme_transform_present ( AntibodyNumberingSchemeEnum const numbering_scheme ) const

private

References numbering_info_, and protocols::antibody::AntibodyNumbering::numbering_scheme_transform.

Referenced by get_landmark_resnum(), and get_numbering_scheme_landmarks().

◆ predict_H3_base_type()

void protocols::antibody::AntibodyInfo::predict_H3_base_type ( core::pose::Pose const & pose )

private

predict H3 cterminus base as Kinked or Extended

///

predicit H3 cterminus base type (Kinked or Extended) based on sequence /// ///

References detect_and_set_camelid_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type_new_rule(), and is_camelid_.

Referenced by init().

◆ qq_heavy_residue()

core::Size protocols::antibody::AntibodyInfo::qq_heavy_residue ( const core::pose::Pose & pose ) const

get pose number for heavy chain residue that is part of the qq constraint

References protocols::antibody::Chothia_Scheme, get_landmark_resnum(), core::pose::Pose::residue(), and protocols::antibody::TR().

◆ qq_light_residue()

core::Size protocols::antibody::AntibodyInfo::qq_light_residue ( const core::pose::Pose & pose ) const

get pose number for light chain residue that is part of the qq constraint

References protocols::antibody::Chothia_Scheme, get_landmark_resnum(), core::pose::Pose::residue(), and protocols::antibody::TR().

◆ set_CDR_cluster()

void protocols::antibody::AntibodyInfo::set_CDR_cluster	(	CDRNameEnum	cdr,
		clusters::CDRClusterCOP	cluster
	)

Manually set the CDR cluster for a particular CDR.

References cdr_cluster_set_.

◆ set_default()

void protocols::antibody::AntibodyInfo::set_default ( )

private

Setters for private AntibodyInfo variables /// //////////////////////////////////////////////////////////////////////////////////////.

References protocols::antibody::AntibodyNumbering::cdr_definition, enum_manager_, has_antigen_, is_camelid_, protocols::antibody::Kinked, loopsop_having_allcdrs_, numbering_info_, protocols::antibody::AntibodyNumbering::numbering_scheme, predicted_H3_base_type_, core::id::to_string(), and protocols::antibody::TR().

Referenced by AntibodyInfo().

◆ set_light_chain_type()

void protocols::antibody::AntibodyInfo::set_light_chain_type ( LightChainTypeEnum light_chain )

Set the light chain type via enum.

References is_camelid(), light_chain_type_, protocols::antibody::TR(), and protocols::antibody::unknown.

◆ setup_CDR_cluster()

void protocols::antibody::AntibodyInfo::setup_CDR_cluster	(	core::pose::Pose const &	pose,
		CDRNameEnum	cdr,
		bool	attempt_set_from_pose = `false`
	)

setup the clustering information for a particular CDR. Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.

References core::pose::datacache::CacheableDataType::CDR_CLUSTER_INFO, cdr_cluster_set_, core::pose::Pose::data(), get_CDR_name(), protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(), protocols::antibody::h4, has_CDR(), protocols::antibody::l4, core::pose::Pose::pdb_info(), and protocols::antibody::TR().

Referenced by setup_CDR_clusters().

◆ setup_CDR_clusters() [1/2]

void protocols::antibody::AntibodyInfo::setup_CDR_clusters	(	core::pose::Pose const &	pose,
		bool	attempt_set_from_pose = `false`
	)

setup the clustering information for each CDR to totalCDRLoops Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.

References total_cdr_loops_.

Referenced by init().

◆ setup_CDR_clusters() [2/2]

void protocols::antibody::AntibodyInfo::setup_CDR_clusters	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	cdrs,
		bool	attempt_set_from_pose = `false`
	)

setup the clustering information for each CDR according to boolean vector. Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.

References protocols::antibody::CDRNameEnum_proto_total, and setup_CDR_cluster().

◆ setup_CDRsInfo()

void protocols::antibody::AntibodyInfo::setup_CDRsInfo ( core::pose::Pose const & pose )

private

setup the CDR loops objects based on the input numbering scheme

References protocols::antibody::cdr_end, protocols::antibody::AntibodyNumbering::cdr_numbering, protocols::antibody::cdr_start, chains_for_cdrs_, get_CDR_name(), protocols::antibody::h3, loopsop_having_allcdrs_, numbering_info_, core::pose::Pose::pdb_info(), protocols::antibody::start_cdr_loop, core::id::to_string(), total_cdr_loops_, protocols::antibody::TR(), and vector1_loopsop_having_cdr_.

Referenced by init().

◆ setup_FrameWorkInfo()

void protocols::antibody::AntibodyInfo::setup_FrameWorkInfo ( core::pose::Pose const & pose )

private

setup the framework information based on the input numbering scheme

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::antibody::FrameWork::chain_name, protocols::antibody::Chothia_Scheme, core::pose::Pose::conformation(), framework_info_, get_landmark_resnum(), H_chain_, is_camelid(), is_camelid_, L_chain_, protocols::antibody::FrameWork::start, and protocols::antibody::FrameWork::stop.

Referenced by init().

◆ setup_numbering_info_for_scheme()

void protocols::antibody::AntibodyInfo::setup_numbering_info_for_scheme	(	AntibodyNumberingSchemeEnum const &	numbering_scheme,
		CDRDefinitionEnum const	cdr_definition
	)

private

Setup the Internal AntibodyNumbering variables.

References numbering_info_, numbering_parser_, packing_angle_numbering_, protocols::antibody::PackingAngleEnum_total, protocols::antibody::VH_sheet_1, protocols::antibody::VH_sheet_2, protocols::antibody::VL_sheet_1, and protocols::antibody::VL_sheet_2.

Referenced by init().

◆ setup_simple_fold_tree()

kinematics::FoldTreeCOP protocols::antibody::AntibodyInfo::setup_simple_fold_tree	(	core::Size const &	jumppoint1,
		core::Size const &	cutpoint,
		core::Size const &	jumppoint2,
		core::pose::Pose const &	pose
	)		const

///

provide fold tree utilities for various purpose /// ///

References protocols::loops::Loops::add_loop(), and protocols::loops::fold_tree_from_loops().

◆ setup_VL_VH_packing_angle()

void protocols::antibody::AntibodyInfo::setup_VL_VH_packing_angle ( core::pose::Pose const & pose )

private

setup the residues used to calculate VL/VH packing angle

References protocols::antibody::Chothia_Scheme, get_landmark_resnum(), is_camelid_, packing_angle_numbering_, packing_angle_residues_, protocols::antibody::PackingAngleEnum_total, protocols::antibody::TR(), protocols::antibody::VH_sheet_1, protocols::antibody::VH_sheet_2, protocols::antibody::VL_sheet_1, and protocols::antibody::VL_sheet_2.

Referenced by init().

◆ show()

void protocols::antibody::AntibodyInfo::show ( std::ostream & out = std::cout ) const

Show the complete setup of the docking protocol

References core::conformation::membrane::out.

Friends And Related Function Documentation

◆ operator<<

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

friend

Member Data Documentation

◆ ab_sequence_

utility::vector1<char> protocols::antibody::AntibodyInfo::ab_sequence_

private

Referenced by get_antibody_sequence(), and identify_antibody().

◆ all_cdrs_present_

utility::vector1< CDRNameEnum > protocols::antibody::AntibodyInfo::all_cdrs_present_

private

Referenced by get_all_cdrs_present(), get_total_num_CDRs(), and init().

◆ all_cdrs_present_and_proto_

utility::vector1< CDRNameEnum > protocols::antibody::AntibodyInfo::all_cdrs_present_and_proto_

private

Referenced by get_all_cdrs_present(), get_total_num_CDRs(), and init().

◆ cdr_cluster_manager_

clusters::CDRClusterEnumManagerOP protocols::antibody::AntibodyInfo::cdr_cluster_manager_

private

Referenced by AntibodyInfo(), get_cdr_cluster_enum_manager(), get_cdr_enum_for_cluster(), get_cluster_enum(), get_cluster_length(), get_cluster_name(), and init().

◆ cdr_cluster_set_

clusters::CDRClusterSetOP protocols::antibody::AntibodyInfo::cdr_cluster_set_

private

Referenced by AntibodyInfo(), get_CDR_cluster(), get_CDR_cluster_set(), has_cluster_for_cdr(), init(), set_CDR_cluster(), and setup_CDR_cluster().

◆ cdr_pdb_numbered_

bool protocols::antibody::AntibodyInfo::cdr_pdb_numbered_

private

Referenced by AntibodyInfo().

◆ chains_for_antigen_

utility::vector1<char> protocols::antibody::AntibodyInfo::chains_for_antigen_

private

Referenced by get_antigen_chain_ids(), get_antigen_chain_string(), get_antigen_chains(), and identify_antibody().

◆ chains_for_cdrs_

utility::vector1<char> protocols::antibody::AntibodyInfo::chains_for_cdrs_

private

Referenced by get_CDR_chain(), get_CDR_end(), get_CDR_start(), and setup_CDRsInfo().

◆ current_transform_

utility::vector1< utility::vector1< core::Size> > protocols::antibody::AntibodyInfo::current_transform_

private

◆ enum_manager_

◆ framework_info_

utility::vector1< utility::vector1<FrameWork> > protocols::antibody::AntibodyInfo::framework_info_

private

Referenced by get_AntibodyFrameworkInfo(), and setup_FrameWorkInfo().

◆ H_chain_

core::Size protocols::antibody::AntibodyInfo::H_chain_

private

Referenced by identify_antibody(), and setup_FrameWorkInfo().

◆ has_antigen_

bool protocols::antibody::AntibodyInfo::has_antigen_

private

Referenced by antigen_present(), identify_antibody(), and set_default().

◆ is_camelid_

bool protocols::antibody::AntibodyInfo::is_camelid_

private

private data

the information of the antibody pose

Referenced by get_antibody_chain_ids(), get_antibody_chain_string(), get_antibody_chains(), has_CDR(), identify_antibody(), init(), is_camelid(), predict_H3_base_type(), set_default(), setup_FrameWorkInfo(), and setup_VL_VH_packing_angle().

◆ L_chain_

core::Size protocols::antibody::AntibodyInfo::L_chain_

private

Referenced by identify_antibody(), and setup_FrameWorkInfo().

◆ light_chain_type_

LightChainTypeEnum protocols::antibody::AntibodyInfo::light_chain_type_

private

Referenced by get_light_chain_type(), get_light_chain_type_enum(), identify_light_chain(), and set_light_chain_type().

◆ loopsop_having_allcdrs_

loops::LoopsOP protocols::antibody::AntibodyInfo::loopsop_having_allcdrs_

private

Referenced by AntibodyInfo(), get_AllCDRs_in_loopsop(), set_default(), and setup_CDRsInfo().

◆ numbering_info_

AntibodyNumbering protocols::antibody::AntibodyInfo::numbering_info_

private

◆ numbering_parser_

AntibodyNumberingParserOP protocols::antibody::AntibodyInfo::numbering_parser_

private

Referenced by AntibodyInfo(), init(), and setup_numbering_info_for_scheme().

◆ packing_angle_numbering_

utility::vector1<utility::vector1< core::Size > > protocols::antibody::AntibodyInfo::packing_angle_numbering_

private

Referenced by setup_numbering_info_for_scheme(), and setup_VL_VH_packing_angle().

◆ packing_angle_residues_

utility::vector1< core::Size > protocols::antibody::AntibodyInfo::packing_angle_residues_

private

Referenced by get_PackingAngleResidues(), and setup_VL_VH_packing_angle().

◆ predicted_H3_base_type_

H3BaseTypeEnum protocols::antibody::AntibodyInfo::predicted_H3_base_type_

private

Antibody properties.

Referenced by detect_and_set_camelid_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type_new_rule(), get_H3_kink_type(), get_H3_kink_type_name(), and set_default().

◆ sequence_map_

std::map<core::Size, char> protocols::antibody::AntibodyInfo::sequence_map_

private

Referenced by get_CDR_sequence_with_stem(), and identify_antibody().

◆ total_cdr_loops_

CDRNameEnum protocols::antibody::AntibodyInfo::total_cdr_loops_

private

Referenced by check_cdr_quality(), get_CDR_loops(), has_CDR(), init(), setup_CDR_clusters(), and setup_CDRsInfo().

◆ vector1_loopsop_having_cdr_

utility::vector1<loops::LoopsOP> protocols::antibody::AntibodyInfo::vector1_loopsop_having_cdr_

private

the CDR and Framework information

Referenced by AntibodyInfo(), get_CDR_in_loopsop(), get_CDR_loop(), and setup_CDRsInfo().

The documentation for this class was generated from the following files:

src/protocols/antibody/AntibodyInfo.hh
src/protocols/antibody/AntibodyInfo.cc

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ AntibodyInfo() [1/4]

◆ AntibodyInfo() [2/4]

◆ AntibodyInfo() [3/4]

◆ AntibodyInfo() [4/4]

◆ ~AntibodyInfo()

Member Function Documentation

◆ add_CDR_to_MoveMap()

◆ antigen_present()

◆ cdr_definition_transform_present()

◆ check_cdr_quality()

◆ clone()

◆ detect_and_set_camelid_CDR_H3_stem_type()

◆ detect_and_set_regular_CDR_H3_stem_type()

◆ detect_and_set_regular_CDR_H3_stem_type_new_rule()

◆ get_all_cdrs()

◆ get_all_cdrs_present()

◆ get_AllCDRs_in_loopsop()

◆ get_antibody_chain_ids()

◆ get_antibody_chain_string()

◆ get_antibody_chains()

◆ get_antibody_enum_manager()

◆ get_antibody_numbering_info()

◆ get_antibody_sequence()

◆ get_AntibodyFrameworkInfo()

◆ get_antigen_chain_ids()

◆ get_antigen_chain_string()

◆ get_antigen_chains()

◆ get_CDR_chain()

◆ get_CDR_cluster()

◆ get_cdr_cluster_enum_manager()

◆ get_CDR_cluster_set()

◆ get_cdr_definition_transform()

◆ get_CDR_end() [1/2]

◆ get_CDR_end() [2/2]

◆ get_CDR_end_PDB_num()

◆ get_cdr_enum_for_cluster()

◆ get_CDR_in_loopsop()

◆ get_CDR_length() [1/3]

◆ get_CDR_length() [2/3]

◆ get_CDR_length() [3/3]

◆ get_CDR_loop() [1/3]

◆ get_CDR_loop() [2/3]

◆ get_CDR_loop() [3/3]

◆ get_CDR_loops() [1/2]

◆ get_CDR_loops() [2/2]

◆ get_CDR_name()

◆ get_CDR_name_enum()

◆ get_CDR_sequence_with_stem() [1/3]

◆ get_CDR_sequence_with_stem() [2/3]

◆ get_CDR_sequence_with_stem() [3/3]

◆ get_CDR_start() [1/2]

◆ get_CDR_start() [2/2]

◆ get_CDR_start_PDB_num()

◆ get_CDRNameEnum_of_residue()

◆ get_cluster_enum()

◆ get_cluster_length()

◆ get_cluster_name()

◆ get_current_AntibodyNumberingScheme()

◆ get_current_CDRDefinition()

◆ get_Dock_ScoreFxn()

◆ get_FoldTree_AllCDRs()

◆ get_FoldTree_AllCDRs_LHDock()

◆ get_FoldTree_L_HA()

◆ get_FoldTree_LA_H()

◆ get_FoldTree_LH_A()

◆ get_H3_kink_type()

◆ get_H3_kink_type_name()

◆ get_landmark_resnum()

◆ get_light_chain_type()

◆ get_light_chain_type_enum()

◆ get_LoopCentral_ScoreFxn()

◆ get_LoopHighRes_ScoreFxn()

◆ get_MoveMap_for_AllCDRsSideChains_and_H3backbone()