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

#include <AntibodyInfo.hh>

Public Member Functions
	AntibodyInfo (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 (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...

virtual	~AntibodyInfo ()

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

std::string	get_current_CDRDefinition () const

Size	get_CDR_length (CDRNameEnum const &cdr_name) const
	get the length of the cdr More...

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...

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

CDRNameEnum	get_total_num_CDRs () const
	return whether a cdr contacts antigen. If no antigen is present, returns false. More...

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

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

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

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

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

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

vector1< 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

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

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

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

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

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

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

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

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

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

core::Size	get_landmark_resnum (pose::Pose const &pose, AntibodyNumberingSchemeEnum const scheme, char const chain, 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...

void	setup_CDR_clusters (pose::Pose const &pose)
	setup the clustering information for each CDR to totalCDRLoops More...

CDRClusterOP	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...

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 (CDRClusterEnum const cluster) const

CDRClusterEnum	get_cluster_enum (std::string const cluster) const

CDRNameEnum	get_cdr_enum_for_cluster (CDRClusterEnum const cluster) const

core::Size	get_cluster_length (CDRClusterEnum const cluster) const

std::string	get_CDR_sequence_with_stem (CDRNameEnum const &cdr_name, Size left_stem=0, Size right_stem=0) const
	return the sequence of a particular CDR loop More...

std::string	get_CDR_sequence_with_stem (CDRNameEnum const &cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform, Size left_stem=0, Size right_stem=0) const

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, pose::Pose const &pose) const
	return the loop of a certain loop type on the fly More...

loops::Loop	get_CDR_loop (CDRNameEnum const cdr_name, pose::Pose const &pose, CDRDefinitionEnum const transform) 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 (pose::Pose const &pose) const
	On-the-fly CDR LoopsOP. More...

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

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

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

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

kinematics::FoldTree	get_FoldTree_L_HA (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...

kinematics::FoldTree	get_FoldTree_LA_H (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...

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

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

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

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

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

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

AntibodyEnumManagerOP	get_antibody_enum_manager () const
	use the H3 cterm coordinates in the pose to calculate the cterminal type More...

CDRClusterEnumManagerOP	get_cdr_cluster_enum_manager () const

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

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

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

void	init (pose::Pose const &pose)

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

vector1< 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...

vector1< PDBLandmarkOP >	get_numbering_scheme_landmarks (AntibodyNumberingSchemeEnum const numbering_scheme) const

bool	numbering_scheme_transform_present (AntibodyNumberingSchemeEnum const numbering_scheme) const

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

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

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

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

void	detect_and_set_camelid_CDR_H3_stem_type (pose::Pose const &pose)

void	detect_and_set_regular_CDR_H3_stem_type (pose::Pose const &pose)

void	detect_and_set_regular_CDR_H3_stem_type_new_rule (pose::Pose const &pose)

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

void	check_cdr_quality (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	InputPose_has_antigen_

bool	cdr_pdb_numbered_

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

loops::LoopsOP	loopsop_having_allcdrs_

vector1< vector1< FrameWork > >	framework_info_

vector1< char >	ab_sequence_

std::map< Size, char >	sequence_map_

vector1< Size >	packing_angle_residues_

vector1< vector1< Size > >	packing_angle_numbering_

H3BaseTypeEnum	predicted_H3_base_type_
	Antibody properties. More...

CDRNameEnum	total_cdr_loops_

vector1< char >	chains_for_cdrs_

vector1< char >	chains_for_antigen_

Size	L_chain_

Size	H_chain_

CDRClusterSetOP	cdr_cluster_set_

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

vector1< vector1< core::Size > >	current_transform_

AntibodyEnumManagerOP	enum_manager_

CDRClusterEnumManagerOP	cdr_cluster_manager_

AntibodyNumberingParserOP	numbering_parser_

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

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

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

References protocols::init::init().

protocols::antibody::AntibodyInfo::AntibodyInfo	(	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::init::init().

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

virtual

Member Function Documentation

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

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

References protocols::loops::select_loop_residues(), protocols::loops::start, protocols::loops::stop, and core::pose::Pose::total_residue().

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

inline

return whether this pose has antigen or not

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?

void protocols::antibody::AntibodyInfo::check_cdr_quality ( 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 protocols::loops::has_severe_pep_bond_geom_issues(), option, and core::pose::Pose::pdb_info().

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

private

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

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

private

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

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

private

References protocols::antibody::Aroop, protocols::antibody::Chothia_Scheme, protocols::antibody::Extended, protocols::antibody::h3, protocols::antibody::Kinked, core::conformation::Residue::name1(), protocols::antibody::Neutral, core::pose::Pose::residue(), seq, core::pose::Pose::sequence(), protocols::loops::start, utility::to_string(), and protocols::antibody::TR.

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

return a LoopsOP object, initialized upon class construction.

Referenced by protocols::antibody::LHSnugFitLegacy::apply(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy(), and protocols::antibody::LHSnugFitLegacy::LHSnugFitLegacy().

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

use the H3 cterm coordinates in the pose to calculate the cterminal type

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

return the antibody sequence of LH or just H for camelid

References seq.

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

return the framework numbering information

References utility_exit_with_message.

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

References core::pose::get_chain_id_from_chain().

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

inline

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

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr().

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

inline

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::fix_pdb_info(), and protocols::antibody::clusters::CDRClusterFeatures::report_features().

CDRClusterOP 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 utility_exit_with_message.

Referenced by protocols::antibody::design::AntibodyDesignMover::add_cluster_comments_to_pose(), protocols::antibody::operator<<(), protocols::antibody::clusters::CDRClusterFeatures::report_features(), and protocols::antibody::design::AntibodyGraftDesignMover::setup_native_clusters().

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

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 utility_exit_with_message.

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

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

References protocols::antibody::cdr_end, protocols::antibody::PDBLandmark::insertion_code(), core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and utility::to_string().

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::apply(), protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr(), and protocols::antibody::clusters::CDRClusterFeatures::report_features().

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

References protocols::antibody::cdr_end, protocols::antibody::PDBLandmark::insertion_code(), core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and utility::to_string().

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.

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

References utility::string_split().

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

return the loop of a certain loop type

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

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

get the length of the cdr

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

Referenced by protocols::antibody::clusters::CDRClusterFeatures::report_features().

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

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

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

return the loop of a certain loop type

loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop	(	CDRNameEnum const	cdr_name,
		pose::Pose const &	pose
	)		const

return the loop of a certain loop type on the fly

References protocols::loops::start, and protocols::loops::stop.

loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop	(	CDRNameEnum const	cdr_name,
		pose::Pose const &	pose,
		CDRDefinitionEnum const	transform
	)		const

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

References protocols::loops::start, and protocols::loops::stop.

loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_loops ( pose::Pose const & pose ) const

On-the-fly CDR LoopsOP.

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

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

Referenced by protocols::antibody::design::AntibodyDesignMover::read_command_line_design_options().

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

return the sequence of a particular CDR loop

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

Referenced by protocols::antibody::operator<<(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), and protocols::antibody::clusters::CDRClusterFeatures::report_features().

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

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

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

Return pose number of CDR start residue.

References protocols::antibody::cdr_start, protocols::antibody::PDBLandmark::insertion_code(), core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and utility::to_string().

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::apply(), protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr(), and protocols::antibody::clusters::CDRClusterFeatures::report_features().

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

References protocols::antibody::cdr_start, protocols::antibody::PDBLandmark::insertion_code(), core::pose::Pose::pdb_info(), protocols::antibody::PDBLandmark::resnum(), and utility::to_string().

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::cdr_start.

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

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

References utility::string2int(), and utility::string_split().

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::fix_pdb_info().

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

Referenced by protocols::antibody::design::AntibodyDesignMover::add_cluster_comments_to_pose(), protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr(), and protocols::antibody::clusters::CDRClusterFeatures::report_features().

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

: get the current numbering scheme being used

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::AntibodyGraftDesignMover(), and protocols::antibody::design::AntibodyDesignMover::apply().

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

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::AntibodyGraftDesignMover(), and protocols::antibody::design::AntibodyDesignMover::apply().

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

staticprivate

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

References protocols::loops::fold_tree_from_loops().

Referenced by protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::CDRsMinPackMin::finalize_setup(), and protocols::antibody::AntibodyModelerProtocol::finalize_setup().

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

change to all CDR and VL-VH dock fold tree

all_cdr_VL_VH_fold_tree

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

Last Modified: 06/25/2013

References begin, core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), end, core::kinematics::Edge::PEPTIDE, core::pose::residue_center_of_mass(), core::kinematics::Edge::stop(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody::RefineBetaBarrel::finalize_setup().

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_L_HA ( 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.

L_HA_foldtree

Authors: Krishna Praneeth Kilambi 08/14/2012

Last Modified: 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), nres, core::pose::Pose::pdb_info(), core::pose::residue_center_of_mass(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody::SnugDock::setup_objects().

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_LA_H ( 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.

LA_H_foldtree

Authors: Krishna Praneeth Kilambi 08/14/2012

Last Modified: 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), nres, core::pose::Pose::pdb_info(), core::pose::residue_center_of_mass(), and core::pose::Pose::total_residue().

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_LH_A ( 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.

LH_A_foldtree

Authors: Krishna Praneeth Kilambi 08/14/2012

Last Modified: 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), nres, core::pose::Pose::pdb_info(), core::pose::residue_center_of_mass(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody::SnugDockProtocol::apply(), protocols::antibody::SnugDock::apply(), and protocols::antibody::SnugDock::setup_objects().

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

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

Referenced by protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody::ModelCDRH3::init(), and protocols::antibody::H3CterInsert::read_H3_cter_fragment().

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

core::Size protocols::antibody::AntibodyInfo::get_landmark_resnum	(	pose::Pose const &	pose,
		AntibodyNumberingSchemeEnum const	scheme,
		char const	chain,
		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 core::pose::Pose::pdb_info(), utility::to_string(), protocols::antibody::TR, and utility_exit_with_message.

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

staticprivate

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

staticprivate

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

References core::kinematics::MoveMap::clear(), 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::total_residue(), and protocols::antibody::TR.

kinematics::MoveMap protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops	(	pose::Pose const &	pose,
		loops::Loops const &	the_loops,
		bool const &	bb_only = `false`,
		bool const &	include_nb_sc = `false`,
		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::total_residue().

Referenced by protocols::antibody::CDRsMinPackMin::finalize_setup().

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

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

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

Referenced by protocols::antibody::LHSnugFitLegacy::apply(), and protocols::antibody::RefineBetaBarrel::finalize_setup().

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

private

References utility_exit_with_message.

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

staticprivate

///

copy all the static functions

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

inline

get residues used to calculate VL/VH packing angle

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

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

TaskFactory.

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

Referenced by protocols::antibody::CDRsMinPackMin::finalize_setup().

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

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

CDRNameEnum protocols::antibody::AntibodyInfo::get_total_num_CDRs ( ) const

inline

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)

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

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.

Referenced by protocols::antibody::clusters::CDRClusterFeatures::report_features().

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

private

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

References core::conformation::Residue::chain(), chain, core::pose::Pose::conformation(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_id_from_chain(), core::pose::has_chain(), core::conformation::Residue::name1(), core::conformation::Conformation::num_chains(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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.

Last Modified: 08/28/2012 by DK

References l, and protocols::antibody::TR.

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

private

References protocols::antibody::camelid_last_loop, and protocols::antibody::num_cdr_loops.

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

inline

return this antibody is camelid or not

Referenced by protocols::antibody::operator<<(), and protocols::antibody::H3CterInsert::read_H3_cter_fragment().

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

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

References protocols::antibody::Aroop, protocols::antibody::h3, core::conformation::Residue::name1(), resi, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

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

Size protocols::antibody::AntibodyInfo::kink_anion_residue ( 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, and protocols::antibody::h3.

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

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

inline

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

References protocols::antibody::Aroop, and protocols::antibody::h3.

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

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

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

References protocols::antibody::Aroop, protocols::antibody::h3, core::conformation::Residue::name1(), resi, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

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

Size protocols::antibody::AntibodyInfo::kink_cation_residue ( 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, and protocols::antibody::h3.

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

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

inline

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

References protocols::antibody::Aroop, and protocols::antibody::h3.

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

inline

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

References protocols::antibody::Aroop, and protocols::antibody::h3.

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

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

private

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

private

predict H3 cterminus base as Kinked or Extended

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

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

private

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

References cdr_definition, protocols::antibody::Kinked, numbering_scheme, option, protocols::antibody::TR, and utility_exit_with_message.

void protocols::antibody::AntibodyInfo::setup_CDR_clusters ( pose::Pose const & pose )

setup the clustering information for each CDR to totalCDRLoops

References protocols::antibody::TR.

Referenced by protocols::antibody::design::AntibodyDesignMover::apply(), and protocols::antibody::design::AntibodyGraftDesignMover::setup_native_clusters().

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

private

setup the CDR loops objects based on the input numbering scheme

References protocols::antibody::cdr_end, protocols::antibody::cdr_start, protocols::antibody::h3, core::pose::Pose::pdb_info(), protocols::antibody::start_cdr_loop, utility::to_string(), and protocols::antibody::TR.

void protocols::antibody::AntibodyInfo::setup_FrameWorkInfo ( 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(), protocols::antibody::FrameWork::start, and protocols::antibody::FrameWork::stop.

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

private

Setup the Internal AntibodyNumbering variables.

References 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.

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

Referenced by protocols::antibody::H3CterInsert::apply().

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

private

setup the residues used to calculate VL/VH packing angle

References protocols::antibody::Chothia_Scheme, 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.

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

Show the complete setup of the docking protocol

Referenced by protocols::antibody::design::AntibodyDesignMover::apply().

Friends And Related Function Documentation

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

friend

Member Data Documentation

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

private

CDRClusterEnumManagerOP protocols::antibody::AntibodyInfo::cdr_cluster_manager_

private

Referenced by protocols::antibody::operator<<().

CDRClusterSetOP protocols::antibody::AntibodyInfo::cdr_cluster_set_

private

bool protocols::antibody::AntibodyInfo::cdr_pdb_numbered_

private

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

private

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

private

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

private

AntibodyEnumManagerOP protocols::antibody::AntibodyInfo::enum_manager_

private

Referenced by protocols::antibody::operator<<().

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

private

Size protocols::antibody::AntibodyInfo::H_chain_

private

bool protocols::antibody::AntibodyInfo::InputPose_has_antigen_

private

bool protocols::antibody::AntibodyInfo::is_camelid_

private

private data

the information of the antibody pose

Size protocols::antibody::AntibodyInfo::L_chain_

private

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

private

AntibodyNumbering protocols::antibody::AntibodyInfo::numbering_info_

private

Internal Per-Scheme Numbering.

AntibodyNumberingParserOP protocols::antibody::AntibodyInfo::numbering_parser_

private

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

private

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

private

H3BaseTypeEnum protocols::antibody::AntibodyInfo::predicted_H3_base_type_

private

Antibody properties.

Referenced by protocols::antibody::operator<<().

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

private

CDRNameEnum protocols::antibody::AntibodyInfo::total_cdr_loops_

private

Referenced by protocols::antibody::operator<<().

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

private

the CDR and Framework information

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

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation