Classes
class	AntibodyDesignEnumManager

class	AntibodyDesignMover
	This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase. Up-to-date versions can be downloaded from. More...

class	AntibodyDesignMoverCreator

class	AntibodySeqDesignTFCreator
	Create a TaskFactory or individual TaskOperations based on a set of options These options are mainly for per-CDR and per-framework control of sequence design. More...

class	CDRGraftDesignOptions
	Class that holds CDRGraftDesign Options. Now that GraftDesign is not a separate 'thing', this should be split into CDRGraftOptions and CDRMinOptions eventually. More...

class	CDRGraftDesignOptionsParser

class	CDRSeqDesignOptions

class	CDRSeqDesignOptionsParser

class	GeneralAntibodyModeler
	Basic Class that can run modeling for various protocols. Does not do any design. Setup design TF via AntibodySeqDesignTFCreator. More...

struct	MutantPosition

class	MutateFrameworkForCluster
	Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations. More...

class	MutateFrameworkForClusterCreator

class	NativeAntibodySeq
	Class that keeps track of the 'native' sequence during design. Native means that no design has occured. Used for conservative base design to keep it from hopping around residue types. More...

class	ResnumFromStringsWithRangesSelector
	A selector which uses the protocols::antibody::design::get_resnums_from_strings_with_ranges() approach. More...

struct	PDBNumbering
	Super-basic numbering struct. More...

Typedefs
typedef utility::pointer::shared_ptr< AntibodyDesignEnumManager >	AntibodyDesignEnumManagerOP

typedef utility::pointer::shared_ptr< AntibodyDesignEnumManager const >	AntibodyDesignEnumManagerCOP

typedef utility::pointer::shared_ptr< AntibodyDesignMover >	AntibodyDesignMoverOP

typedef utility::pointer::shared_ptr< AntibodyDesignMover const >	AntibodyDesignMoverCOP

typedef utility::pointer::shared_ptr< AntibodySeqDesignTFCreator >	AntibodySeqDesignTFCreatorOP

typedef utility::pointer::shared_ptr< AntibodySeqDesignTFCreator const >	AntibodySeqDesignTFCreatorCOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptions >	CDRGraftDesignOptionsOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptions const >	CDRGraftDesignOptionsCOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptionsParser >	CDRGraftDesignOptionsParserOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptionsParser const >	CDRGraftDesignOptionsParserCOP

typedef utility::vector1< CDRGraftDesignOptionsOP >	AntibodyCDRGraftDesignOptions

typedef utility::pointer::shared_ptr< CDRSeqDesignOptions >	CDRSeqDesignOptionsOP

typedef utility::pointer::shared_ptr< CDRSeqDesignOptions const >	CDRSeqDesignOptionsCOP

typedef utility::pointer::shared_ptr< CDRSeqDesignOptionsParser >	CDRSeqDesignOptionsParserOP

typedef utility::pointer::shared_ptr< CDRSeqDesignOptionsParser const >	CDRSeqDesignOptionsParserCOP

typedef utility::vector1< CDRSeqDesignOptionsOP >	AntibodyCDRSeqDesignOptions

typedef utility::pointer::shared_ptr< GeneralAntibodyModeler >	GeneralAntibodyModelerOP

typedef utility::pointer::shared_ptr< GeneralAntibodyModeler const >	GeneralAntibodyModelerCOP

typedef utility::pointer::shared_ptr< MutateFrameworkForCluster >	MutateFrameworkForClusterOP

typedef utility::pointer::shared_ptr< MutateFrameworkForCluster const >	MutateFrameworkForClusterCOP

typedef utility::pointer::shared_ptr< NativeAntibodySeq >	NativeAntibodySeqOP

typedef utility::pointer::shared_ptr< NativeAntibodySeq const >	NativeAntibodySeqCOP

Enumerations
enum	MinTypeEnum { relax = 1 , centroid_relax , minimize , minimize_cartesian , dualspace , repack , backrub_protocol , no_min , MinTypeEnum_total = no_min }

enum	SeqDesignStrategyEnum { seq_design_profiles = 1 , seq_design_conservative , seq_design_profile_sets , seq_design_profile_sets_combined , seq_design_basic , seq_design_none , SeqDesignStrategyEnum_total = seq_design_none }

enum	AntibodyDesignProtocolEnum { generalized_monte_carlo = 1 , even_cluster_monte_carlo , even_length_cluster_monte_carlo , deterministic_graft , DesignProtocolEnum_total = deterministic_graft }

Functions
CDRSeqDesignOptionsOP	deep_copy (CDRSeqDesignOptions const &)

ScoreFunctionOP	get_ab_design_global_scorefxn ()

ScoreFunctionOP	get_ab_design_global_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Get Global Scorefxn from RS; XSD companion function: attributes_for_get_ab_design_global_scorefxn. More...

void	attributes_for_get_ab_design_global_scorefxn (utility::tag::AttributeList &attlist)
	adds the required attribute to the AttributeList for XMLSchema generation More...

ScoreFunctionOP	get_ab_design_dock_high_scorefxn ()

ScoreFunctionOP	get_ab_design_dock_low_scorefxn ()

ScoreFunctionOP	get_ab_design_min_scorefxn ()
	XSD companion function: attributes_for_get_ab_design_min_scorefxn. More...

ScoreFunctionOP	get_ab_design_min_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)

void	attributes_for_get_ab_design_min_scorefxn (utility::tag::AttributeList &attlist)
	adds the required attribute to the AttributeList for XMLSchema generation More...

void	insert_cdr_into_antibody (AntibodyInfoCOP ab_info, CDRNameEnum const cdr, core::pose::Pose &pose, core::pose::Pose &cdr_piece, core::Size overhang=3)
	Use insert_pose_into_pose to replace the cdr_piece with the current antibody's CDR. No modeling or superposition. For that, use protocols/grafting. More...

vector1< vector1< core::Size > >	get_all_graft_permutations (vector1< vector1< core::Size > > permutations, vector1< core::Size > totals, core::Size const n)

AntibodyDesignProtocolEnum	design_protocol_to_enum (std::string const &design_type)

std::string	design_protocol_to_string (AntibodyDesignProtocolEnum const design_type)

SeqDesignStrategyEnum	seq_design_strategy_to_enum (std::string const &strategy)

std::string	seq_design_strategy_to_string (SeqDesignStrategyEnum strategy)

std::string	get_dock_chains_from_ab_dock_chains (AntibodyInfoCOP ab_info, std::string const &ab_dock_chains)
	Convert an ab_dock_chain (L_H/ LH_A, etc. to the full dock chain string) More...

PDBNumbering	get_pdb_numbering_from_single_string (std::string const &pdb_residue)
	These all need better names and they need to be moved to a general place. Make the ResidueKey of PDBInfo a public class: More...

core::Size	get_resnum_from_single_string (core::pose::Pose const &pose, std::string const &pdb_residue)
	Get a resnum from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...

core::Size	get_resnum_from_single_string_w_landmark (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, std::string const &pdb_residue, AntibodyNumberingSchemeEnum const &scheme)
	Get a resnum using the PDBLandmark from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...

vector1< PDBNumbering >	get_pdb_numbering_from_strings (vector1< std::string > const &pdb_residues)

vector1< bool >	get_resnums_from_strings_with_ranges (core::pose::Pose const &pose, vector1< std::string > const &pdb_residues)

vector1< bool >	get_resnum_from_pdb_numbering (core::pose::Pose const &pose, vector1< PDBNumbering > const &pdb_residues)

vector1< bool >	get_resnum_from_strings (core::pose::Pose const &pose, utility::vector1< std::string > const &pdb_residues)
	get a boolean vector from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...

void	add_loops_from_bool_vector (loops::Loops &loops, utility::vector1< bool > residues, bool add_cutpoints=false)
	Add this across protocol... More...

std::pair< bool, core::Size >	check_cb (core::pose::Pose const &pose, utility::vector1< bool > const &residues)
	Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond. More...

std::pair< bool, core::Size >	check_cb (core::pose::Pose const &pose, protocols::loops::Loops const &loops)
	Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond. More...

core::pack::task::operation::RestrictResidueToRepackingOP	disable_design_region (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, AntibodyRegionEnum region, bool cdr4_as_framework=true)
	Disable design of any particular region of the antibody complex. More...

core::pack::task::operation::RestrictResidueToRepackingOP	disable_design_antigen (AntibodyInfoCOP ab_info, const core::pose::Pose &pose)
	Disable design of the antigen residues. More...

core::pack::task::operation::RestrictResidueToRepackingOP	disable_design_framework (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, bool cdr4_as_framework=true)
	Disable design of the framework residues. More...

core::pack::task::operation::RestrictResidueToRepackingOP	disable_design_cdrs (AntibodyInfoCOP ab_info, const core::pose::Pose &pose)
	Get a Restrict operation to turn OFF design for all CDRs. More...

core::pack::task::operation::RestrictResidueToRepackingOP	disable_design_cdr (AntibodyInfoCOP ab_info, CDRNameEnum cdr, const core::pose::Pose &pose)
	Get a Restrict operation to turn OFF design for particular CDRs. More...

core::pack::task::operation::RestrictResidueToRepackingOP	disable_conserved_framework_positions (AntibodyInfoCOP ab_info, const core::pose::Pose &pose)
	Disable design for conserved framework positions. TODO: Needs to be expanded to read positions from database. More...

core::pack::task::operation::RestrictResidueToRepackingOP	disable_h3_stem_positions (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, core::Size nter_stem=2, core::Size cter_stem=3)
	Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants) More...

AntibodyCDRSetOptions	get_cdr_set_options ()
	Get default options. More...

AntibodyCDRSetOptions	get_cdr_set_options (std::string instruction_file)
	Get options from an instruction file. More...

AntibodyCDRGraftDesignOptions	get_graft_design_options ()
	Get default options. More...

AntibodyCDRGraftDesignOptions	get_graft_design_options (std::string instruction_file)
	Get options from an instruction file. More...

AntibodyCDRSeqDesignOptions	get_seq_design_options ()
	Get default options. More...

AntibodyCDRSeqDesignOptions	get_seq_design_options (std::string instruction_file)
	Get options from an instruction file. More...

std::map< core::Size, std::map< core::chemical::AA, core::Real > >	get_cluster_profile_probability_data (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, utility::vector1< bool > const &cdrs, utility::vector1< bool > &no_data_cdrs, const core::Size prob_cutoff=10, const bool use_outliers=false, const bool force_north_db=false, const bool ignore_light_chain_=false)
	Get probability data for a given set of CDRs. Will fill in the no_data_cdrs;. More...

std::map< core::Size, std::map< core::chemical::AA, core::Real > >	get_cluster_profile_probability_data (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, AntibodyCDRSeqDesignOptions const &seq_design_options, utility::vector1< bool > &no_data_cdrs, const core::Size prob_cutoff, const bool use_outliers, const bool force_north_db, const bool ignore_light_chain)

std::map< core::Size, core::chemical::AA >	transform_sequence_to_mutation_set (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, CDRNameEnum const cdr, std::string const &sequence)
	Transforms a sequence to a mutation set used by the AddCDRProfileSetsOperation. Assumes that the sequence is the same length as the CDR. Forces use of North CDR definitions. More...

void	set_native_cdr_sequence (AntibodyInfoCOP ab_info, CDRNameEnum cdr, core::pose::Pose &pose)
	Set the native CDR sequence into the pose datacache If none is set in the pose, will add it. More...

std::string	get_native_sequence (core::pose::Pose const &pose, AntibodyInfo const &ab_info)

bool	has_native_sequence (core::pose::Pose const &pose)

utility::vector1< utility::vector1< core::Size > >	get_all_graft_permutations (utility::vector1< utility::vector1< core::Size > > permutations, utility::vector1< core::Size > totals, core::Size const n)
	Gets all possible graft permutations. More...

utility::vector1< bool >	get_resnums_from_strings_with_ranges (core::pose::Pose const &pose, utility::vector1< std::string > const &pdb_residues)
	Get a boolean vector of resnums with ranges, where a - indicates range. Parses strings for PDB resnums such as 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. Example: 1A-10A or 1A-10A:I. More...

utility::vector1< PDBNumbering >	get_pdb_numbering_from_strings (utility::vector1< std::string > const &pdb_residues)
	Get PDBNumbering from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...

utility::vector1< bool >	get_resnum_from_pdb_numbering (core::pose::Pose const &pose, utility::vector1< PDBNumbering >const &pdb_residues)
	Get a boolean vector from a string of PDBNumbering. No error checking. Use with caution. More...

Typedef Documentation

◆ AntibodyCDRGraftDesignOptions

typedef utility::vector1<CDRGraftDesignOptionsOP> protocols::antibody::design::AntibodyCDRGraftDesignOptions

◆ AntibodyCDRSeqDesignOptions

typedef utility::vector1< CDRSeqDesignOptionsOP > protocols::antibody::design::AntibodyCDRSeqDesignOptions

◆ AntibodyDesignEnumManagerCOP

typedef utility::pointer::shared_ptr<AntibodyDesignEnumManager const> protocols::antibody::design::AntibodyDesignEnumManagerCOP

◆ AntibodyDesignEnumManagerOP

typedef utility::pointer::shared_ptr<AntibodyDesignEnumManager> protocols::antibody::design::AntibodyDesignEnumManagerOP

◆ AntibodyDesignMoverCOP

typedef utility::pointer::shared_ptr< AntibodyDesignMover const > protocols::antibody::design::AntibodyDesignMoverCOP

◆ AntibodyDesignMoverOP

typedef utility::pointer::shared_ptr< AntibodyDesignMover > protocols::antibody::design::AntibodyDesignMoverOP

◆ AntibodySeqDesignTFCreatorCOP

typedef utility::pointer::shared_ptr< AntibodySeqDesignTFCreator const > protocols::antibody::design::AntibodySeqDesignTFCreatorCOP

◆ AntibodySeqDesignTFCreatorOP

typedef utility::pointer::shared_ptr< AntibodySeqDesignTFCreator > protocols::antibody::design::AntibodySeqDesignTFCreatorOP

◆ CDRGraftDesignOptionsCOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptions const > protocols::antibody::design::CDRGraftDesignOptionsCOP

◆ CDRGraftDesignOptionsOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptions > protocols::antibody::design::CDRGraftDesignOptionsOP

◆ CDRGraftDesignOptionsParserCOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptionsParser const > protocols::antibody::design::CDRGraftDesignOptionsParserCOP

◆ CDRGraftDesignOptionsParserOP

typedef utility::pointer::shared_ptr< CDRGraftDesignOptionsParser > protocols::antibody::design::CDRGraftDesignOptionsParserOP

◆ CDRSeqDesignOptionsCOP

typedef utility::pointer::shared_ptr< CDRSeqDesignOptions const > protocols::antibody::design::CDRSeqDesignOptionsCOP

◆ CDRSeqDesignOptionsOP

typedef utility::pointer::shared_ptr< CDRSeqDesignOptions > protocols::antibody::design::CDRSeqDesignOptionsOP

◆ CDRSeqDesignOptionsParserCOP

typedef utility::pointer::shared_ptr< CDRSeqDesignOptionsParser const > protocols::antibody::design::CDRSeqDesignOptionsParserCOP

◆ CDRSeqDesignOptionsParserOP

typedef utility::pointer::shared_ptr< CDRSeqDesignOptionsParser > protocols::antibody::design::CDRSeqDesignOptionsParserOP

◆ GeneralAntibodyModelerCOP

typedef utility::pointer::shared_ptr< GeneralAntibodyModeler const > protocols::antibody::design::GeneralAntibodyModelerCOP

◆ GeneralAntibodyModelerOP

typedef utility::pointer::shared_ptr< GeneralAntibodyModeler > protocols::antibody::design::GeneralAntibodyModelerOP

◆ MutateFrameworkForClusterCOP

typedef utility::pointer::shared_ptr< MutateFrameworkForCluster const > protocols::antibody::design::MutateFrameworkForClusterCOP

◆ MutateFrameworkForClusterOP

typedef utility::pointer::shared_ptr< MutateFrameworkForCluster > protocols::antibody::design::MutateFrameworkForClusterOP

◆ NativeAntibodySeqCOP

typedef utility::pointer::shared_ptr< NativeAntibodySeq const> protocols::antibody::design::NativeAntibodySeqCOP

◆ NativeAntibodySeqOP

typedef utility::pointer::shared_ptr< NativeAntibodySeq> protocols::antibody::design::NativeAntibodySeqOP

Enumeration Type Documentation

◆ AntibodyDesignProtocolEnum

enum protocols::antibody::design::AntibodyDesignProtocolEnum

Enumerator
generalized_monte_carlo
even_cluster_monte_carlo
even_length_cluster_monte_carlo
deterministic_graft
DesignProtocolEnum_total

◆ MinTypeEnum

enum protocols::antibody::design::MinTypeEnum

Enumerator
relax
centroid_relax
minimize
minimize_cartesian
dualspace
repack
backrub_protocol
no_min
MinTypeEnum_total

◆ SeqDesignStrategyEnum

enum protocols::antibody::design::SeqDesignStrategyEnum

Enumerator
seq_design_profiles
seq_design_conservative
seq_design_profile_sets
seq_design_profile_sets_combined
seq_design_basic
seq_design_none
SeqDesignStrategyEnum_total

Function Documentation

◆ add_loops_from_bool_vector()

void protocols::antibody::design::add_loops_from_bool_vector	(	loops::Loops &	loops,
		utility::vector1< bool >	residues,
		bool	add_cutpoints
	)

Add this across protocol...

References protocols::denovo_design::add_cutpoints(), protocols::loops::Loops::add_loop(), core::sequence::end, and protocols::loops::start.

Referenced by protocols::antibody::design::GeneralAntibodyModeler::backrub_cdrs().

◆ attributes_for_get_ab_design_global_scorefxn()

void protocols::antibody::design::attributes_for_get_ab_design_global_scorefxn ( utility::tag::AttributeList & attlist )

adds the required attribute to the AttributeList for XMLSchema generation

References core::scoring::attributes_for_parse_score_function().

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

◆ attributes_for_get_ab_design_min_scorefxn()

void protocols::antibody::design::attributes_for_get_ab_design_min_scorefxn ( utility::tag::AttributeList & attlist )

adds the required attribute to the AttributeList for XMLSchema generation

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

◆ check_cb() [1/2]

std::pair< bool, core::Size > protocols::antibody::design::check_cb	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	loops
	)

Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond.

References protocols::loops::has_severe_pep_bond_geom_issues().

◆ check_cb() [2/2]

std::pair< bool, core::Size > protocols::antibody::design::check_cb	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	residues
	)

Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond.

References protocols::loops::has_severe_pep_bond_geom_issues(), and core::pose::Pose::size().

Referenced by protocols::antibody::AntibodyCDRGrafter::apply_to_cdr(), and protocols::antibody::design::AntibodyDesignMover::run_graft().

◆ deep_copy()

CDRSeqDesignOptionsOP protocols::antibody::design::deep_copy ( CDRSeqDesignOptions const & source )

inline

References protocols::antibody::design::CDRSeqDesignOptions::clone().

◆ design_protocol_to_enum()

AntibodyDesignProtocolEnum protocols::antibody::design::design_protocol_to_enum ( std::string const & design_type )

References deterministic_graft, even_cluster_monte_carlo, and generalized_monte_carlo.

◆ design_protocol_to_string()

std::string protocols::antibody::design::design_protocol_to_string ( AntibodyDesignProtocolEnum const design_type )

References deterministic_graft, even_cluster_monte_carlo, and generalized_monte_carlo.

◆ disable_conserved_framework_positions()

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_conserved_framework_positions	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose
	)

Disable design for conserved framework positions. TODO: Needs to be expanded to read positions from database.

References protocols::antibody::AHO_Scheme, and core::pose::has_chain().

Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::add_extra_restrict_operations().

◆ disable_design_antigen()

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_antigen	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose
	)

Disable design of the antigen residues.

References protocols::antibody::antigen_region, and disable_design_region().

◆ disable_design_cdr()

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_cdr	(	AntibodyInfoCOP	ab_info,
		CDRNameEnum	cdr,
		const core::pose::Pose &	pose
	)

Get a Restrict operation to turn OFF design for particular CDRs.

References core::sequence::end, and protocols::loops::start.

Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::disable_design_for_non_designing_cdrs(), and protocols::antibody::design::AntibodySeqDesignTFCreator::generate_tf_seq_design_graft_design().

◆ disable_design_cdrs()

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_cdrs	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose
	)

Get a Restrict operation to turn OFF design for all CDRs.

References protocols::antibody::cdr_region, and disable_design_region().

◆ disable_design_framework()

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_framework	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose,
		bool	cdr4_as_framework
	)

Disable design of the framework residues.

References disable_design_region(), and protocols::antibody::framework_region.

◆ disable_design_region()

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_region	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose,
		AntibodyRegionEnum	region,
		bool	cdr4_as_framework
	)

Disable design of any particular region of the antibody complex.

References core::pose::Pose::size().

Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::add_extra_restrict_operations(), disable_design_antigen(), disable_design_cdrs(), and disable_design_framework().

◆ disable_h3_stem_positions()

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_h3_stem_positions	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose,
		core::Size	nter_stem,
		core::Size	cter_stem
	)

Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants)

References protocols::antibody::AHO_Scheme.

Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::add_extra_restrict_operations().

◆ get_ab_design_dock_high_scorefxn()

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_dock_high_scorefxn ( )

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

Referenced by protocols::antibody::design::GeneralAntibodyModeler::setup_scorefxns().

◆ get_ab_design_dock_low_scorefxn()

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_dock_low_scorefxn ( )

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

Referenced by protocols::antibody::design::GeneralAntibodyModeler::setup_scorefxns().

◆ get_ab_design_global_scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_global_scorefxn ( )

References core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, and core::scoring::get_score_function().

Referenced by protocols::antibody::design::AntibodyDesignMover::parse_my_tag(), protocols::antibody::design::AntibodyDesignMover::setup_scorefxn(), and protocols::antibody::design::GeneralAntibodyModeler::setup_scorefxns().

◆ get_ab_design_global_scorefxn() [2/2]

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_global_scorefxn	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

Get Global Scorefxn from RS; XSD companion function: attributes_for_get_ab_design_global_scorefxn.

References core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, core::scoring::get_score_function(), and core::scoring::parse_score_function().

◆ get_ab_design_min_scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_min_scorefxn ( )

XSD companion function: attributes_for_get_ab_design_min_scorefxn.

References core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, and core::scoring::get_score_function().

Referenced by protocols::antibody::design::AntibodyDesignMover::parse_my_tag(), protocols::antibody::design::AntibodyDesignMover::setup_scorefxn(), and protocols::antibody::design::GeneralAntibodyModeler::setup_scorefxns().

◆ get_ab_design_min_scorefxn() [2/2]

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_min_scorefxn	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

References core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, and core::scoring::get_score_function().

◆ get_all_graft_permutations() [1/2]

utility::vector1<utility::vector1< core::Size > > protocols::antibody::design::get_all_graft_permutations	(	utility::vector1< utility::vector1< core::Size > >	permutations,
		utility::vector1< core::Size >	totals,
		core::Size const	n
	)

Gets all possible graft permutations.

all_permutations is a list of vectors corresponding to cdrs_to_design vector. Essentially, each inner index describes a position in the cdr_set. Indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set. Example: <1, 0, 1, 1, 1, 1>. This is a possible combination to try graft, the second CDR, H2 is not part of the combination.

◆ get_all_graft_permutations() [2/2]

vector1< vector1< core::Size > > protocols::antibody::design::get_all_graft_permutations	(	vector1< vector1< core::Size > >	permutations,
		vector1< core::Size >	totals,
		core::Size const	n
	)

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

◆ get_cdr_set_options() [1/2]

AntibodyCDRSetOptions protocols::antibody::design::get_cdr_set_options ( )

Get default options.

References protocols::antibody::CDRNameEnum_proto_total, protocols::abinitio::filename(), protocols::antibody::CDRSetOptionsParser::parse_options(), and protocols::antibody::TR().

Referenced by get_cdr_set_options(), and protocols::antibody::design::AntibodyDesignMover::setup_options_classes().

◆ get_cdr_set_options() [2/2]

AntibodyCDRSetOptions protocols::antibody::design::get_cdr_set_options ( std::string filename )

Get options from an instruction file.

References protocols::antibody::CDRNameEnum_proto_total, protocols::abinitio::filename(), get_cdr_set_options(), protocols::antibody::CDRSetOptionsParser::parse_default_and_user_options(), and protocols::antibody::TR().

◆ get_cluster_profile_probability_data() [1/2]

std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::antibody::design::get_cluster_profile_probability_data	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose,
		AntibodyCDRSeqDesignOptions const &	seq_design_options,
		utility::vector1< bool > &	no_data_cdrs,
		const core::Size	prob_cutoff,
		const bool	use_outliers,
		const bool	force_north_db,
		const bool	ignore_light_chain
	)

References protocols::antibody::AntibodyDatabaseManager::ignore_light_chain(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data(), and protocols::antibody::AntibodyDatabaseManager::set_outlier_use().

◆ get_cluster_profile_probability_data() [2/2]

std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::antibody::design::get_cluster_profile_probability_data	(	AntibodyInfoCOP	ab_info,
		const core::pose::Pose &	pose,
		utility::vector1< bool > const &	cdrs,
		utility::vector1< bool > &	no_data_cdrs,
		const core::Size	prob_cutoff,
		const bool	use_outliers,
		const bool	force_north_db,
		const bool	ignore_light_chain
	)

Get probability data for a given set of CDRs. Will fill in the no_data_cdrs;.

References protocols::antibody::AntibodyDatabaseManager::ignore_light_chain(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data_for_cdrs(), and protocols::antibody::AntibodyDatabaseManager::set_outlier_use().

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), and protocols::antibody::task_operations::AddCDRProfilesOperation::pre_load_data().

◆ get_dock_chains_from_ab_dock_chains()

std::string protocols::antibody::design::get_dock_chains_from_ab_dock_chains	(	AntibodyInfoCOP	ab_info,
		std::string const &	ab_dock_chains
	)

Convert an ab_dock_chain (L_H/ LH_A, etc. to the full dock chain string)

References protocols::antibody::TR().

Referenced by protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::design::GeneralAntibodyModeler::dock_high_res(), protocols::antibody::design::GeneralAntibodyModeler::dock_low_res(), protocols::antibody::design::AntibodyDesignMover::finalize_pose(), protocols::antibody::design::GeneralAntibodyModeler::get_dock_chains(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::minimize_interface(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), and protocols::antibody::design::GeneralAntibodyModeler::relax_interface().

◆ get_graft_design_options() [1/2]

AntibodyCDRGraftDesignOptions protocols::antibody::design::get_graft_design_options ( )

Get default options.

References protocols::antibody::CDRNameEnum_proto_total, protocols::abinitio::filename(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options(), and protocols::antibody::TR().

Referenced by get_graft_design_options(), and protocols::antibody::design::AntibodyDesignMover::setup_options_classes().

◆ get_graft_design_options() [2/2]

AntibodyCDRGraftDesignOptions protocols::antibody::design::get_graft_design_options ( std::string filename )

Get options from an instruction file.

References protocols::antibody::CDRNameEnum_proto_total, protocols::abinitio::filename(), get_graft_design_options(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_default_and_user_options(), and protocols::antibody::TR().

◆ get_native_sequence()

std::string protocols::antibody::design::get_native_sequence	(	core::pose::Pose const &	pose,
		AntibodyInfo const &	ab_info
	)

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::NATIVE_ANTIBODY_SEQ.

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), and protocols::antibody::design::AntibodySeqDesignTFCreator::get_framework_conservative_op().

◆ get_pdb_numbering_from_single_string()

PDBNumbering protocols::antibody::design::get_pdb_numbering_from_single_string ( std::string const & pdb_residue )

These all need better names and they need to be moved to a general place. Make the ResidueKey of PDBInfo a public class:

Get the PDBNumbering from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

References protocols::antibody::design::PDBNumbering::chain, protocols::antibody::design::PDBNumbering::icode, protocols::antibody::design::PDBNumbering::resnum, and protocols::antibody::TR().

Referenced by get_pdb_numbering_from_strings(), get_resnum_from_single_string(), get_resnum_from_single_string_w_landmark(), and get_resnums_from_strings_with_ranges().

◆ get_pdb_numbering_from_strings() [1/2]

utility::vector1<PDBNumbering> protocols::antibody::design::get_pdb_numbering_from_strings ( utility::vector1< std::string > const & pdb_residues )

Get PDBNumbering from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

◆ get_pdb_numbering_from_strings() [2/2]

vector1<PDBNumbering> protocols::antibody::design::get_pdb_numbering_from_strings ( vector1< std::string > const & pdb_residues )

References get_pdb_numbering_from_single_string().

Referenced by get_resnum_from_strings(), protocols::antibody::design::AntibodyDesignMover::parse_my_tag(), and protocols::antibody::design::AntibodyDesignMover::read_command_line_options().

◆ get_resnum_from_pdb_numbering() [1/2]

utility::vector1<bool> protocols::antibody::design::get_resnum_from_pdb_numbering	(	core::pose::Pose const &	pose,
		utility::vector1< PDBNumbering >const &	pdb_residues
	)

Get a boolean vector from a string of PDBNumbering. No error checking. Use with caution.

◆ get_resnum_from_pdb_numbering() [2/2]

vector1<bool> protocols::antibody::design::get_resnum_from_pdb_numbering	(	core::pose::Pose const &	pose,
		vector1< PDBNumbering > const &	pdb_residues
	)

References protocols::antibody::design::PDBNumbering::chain, protocols::antibody::design::PDBNumbering::icode, core::pose::Pose::pdb_info(), protocols::antibody::design::PDBNumbering::resnum, and core::pose::Pose::size().

Referenced by get_resnum_from_strings().

◆ get_resnum_from_single_string()

core::Size protocols::antibody::design::get_resnum_from_single_string	(	core::pose::Pose const &	pose,
		std::string const &	pdb_residue
	)

Get a resnum from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

References protocols::antibody::design::PDBNumbering::chain, get_pdb_numbering_from_single_string(), protocols::antibody::design::PDBNumbering::icode, core::pose::Pose::pdb_info(), and protocols::antibody::design::PDBNumbering::resnum.

◆ get_resnum_from_single_string_w_landmark()

core::Size protocols::antibody::design::get_resnum_from_single_string_w_landmark	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose const &	pose,
		std::string const &	pdb_residue,
		AntibodyNumberingSchemeEnum const &	scheme
	)

Get a resnum using the PDBLandmark from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

References protocols::antibody::design::PDBNumbering::chain, get_pdb_numbering_from_single_string(), protocols::antibody::design::PDBNumbering::icode, and protocols::antibody::design::PDBNumbering::resnum.

Referenced by protocols::antibody::design::MutateFrameworkForCluster::apply(), protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_mutations(), and protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_positions().

◆ get_resnum_from_strings()

vector1<bool> protocols::antibody::design::get_resnum_from_strings	(	core::pose::Pose const &	pose,
		utility::vector1< std::string > const &	pdb_residues
	)

get a boolean vector from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

References get_pdb_numbering_from_strings(), and get_resnum_from_pdb_numbering().

◆ get_resnums_from_strings_with_ranges() [1/2]

utility::vector1<bool> protocols::antibody::design::get_resnums_from_strings_with_ranges	(	core::pose::Pose const &	pose,
		utility::vector1< std::string > const &	pdb_residues
	)

Get a boolean vector of resnums with ranges, where a - indicates range. Parses strings for PDB resnums such as 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. Example: 1A-10A or 1A-10A:I.

◆ get_resnums_from_strings_with_ranges() [2/2]

vector1<bool> protocols::antibody::design::get_resnums_from_strings_with_ranges	(	core::pose::Pose const &	pose,
		vector1< std::string > const &	pdb_residues
	)

References protocols::antibody::design::PDBNumbering::chain, get_pdb_numbering_from_single_string(), protocols::antibody::design::PDBNumbering::icode, core::io::rna::numbers, core::pose::Pose::pdb_info(), protocols::antibody::design::PDBNumbering::resnum, core::pose::Pose::size(), and protocols::antibody::TR().

Referenced by protocols::antibody::design::ResnumFromStringsWithRangesSelector::apply(), and protocols::antibody::design::GeneralAntibodyModeler::backrub_cdrs().

◆ get_seq_design_options() [1/2]

AntibodyCDRSeqDesignOptions protocols::antibody::design::get_seq_design_options ( )

Get default options.

References protocols::antibody::CDRNameEnum_proto_total, protocols::abinitio::filename(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options(), and protocols::antibody::TR().

Referenced by get_seq_design_options(), and protocols::antibody::design::AntibodyDesignMover::setup_options_classes().

◆ get_seq_design_options() [2/2]

AntibodyCDRSeqDesignOptions protocols::antibody::design::get_seq_design_options ( std::string filename )

Get options from an instruction file.

References protocols::antibody::CDRNameEnum_proto_total, protocols::abinitio::filename(), get_seq_design_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_default_and_user_options(), and protocols::antibody::TR().

◆ has_native_sequence()

bool protocols::antibody::design::has_native_sequence ( core::pose::Pose const & pose )

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::NATIVE_ANTIBODY_SEQ.

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), and protocols::antibody::design::AntibodySeqDesignTFCreator::get_framework_conservative_op().

◆ insert_cdr_into_antibody()

void protocols::antibody::design::insert_cdr_into_antibody	(	AntibodyInfoCOP	ab_info,
		CDRNameEnum const	cdr,
		core::pose::Pose &	pose,
		core::pose::Pose &	cdr_piece,
		core::Size	overhang
	)

Use insert_pose_into_pose to replace the cdr_piece with the current antibody's CDR. No modeling or superposition. For that, use protocols/grafting.

References protocols::antibody::cdr_end, protocols::antibody::cdr_start, protocols::grafting::delete_region(), protocols::grafting::insert_pose_into_pose(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

◆ seq_design_strategy_to_enum()

SeqDesignStrategyEnum protocols::antibody::design::seq_design_strategy_to_enum ( std::string const & strategy )

References seq_design_basic, seq_design_conservative, seq_design_none, seq_design_profile_sets, seq_design_profile_sets_combined, and seq_design_profiles.

◆ seq_design_strategy_to_string()

std::string protocols::antibody::design::seq_design_strategy_to_string ( SeqDesignStrategyEnum strategy )

References seq_design_basic, seq_design_conservative, seq_design_none, and seq_design_profiles.

◆ set_native_cdr_sequence()

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

Set the native CDR sequence into the pose datacache If none is set in the pose, will add it.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::NATIVE_ANTIBODY_SEQ, and protocols::antibody::TR().

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

◆ transform_sequence_to_mutation_set()

std::map< core::Size, core::chemical::AA > protocols::antibody::design::transform_sequence_to_mutation_set	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose const &	pose,
		CDRNameEnum const	cdr,
		std::string const &	sequence
	)

Transforms a sequence to a mutation set used by the AddCDRProfileSetsOperation. Assumes that the sequence is the same length as the CDR. Forces use of North CDR definitions.

References core::chemical::aa_from_oneletter_code(), protocols::antibody::North, protocols::loops::start, and core::id::to_string().

Referenced by protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply().

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ AntibodyCDRGraftDesignOptions

◆ AntibodyCDRSeqDesignOptions

◆ AntibodyDesignEnumManagerCOP

◆ AntibodyDesignEnumManagerOP

◆ AntibodyDesignMoverCOP

◆ AntibodyDesignMoverOP

◆ AntibodySeqDesignTFCreatorCOP

◆ AntibodySeqDesignTFCreatorOP

◆ CDRGraftDesignOptionsCOP

◆ CDRGraftDesignOptionsOP

◆ CDRGraftDesignOptionsParserCOP

◆ CDRGraftDesignOptionsParserOP

◆ CDRSeqDesignOptionsCOP

◆ CDRSeqDesignOptionsOP

◆ CDRSeqDesignOptionsParserCOP

◆ CDRSeqDesignOptionsParserOP

◆ GeneralAntibodyModelerCOP

◆ GeneralAntibodyModelerOP

◆ MutateFrameworkForClusterCOP

◆ MutateFrameworkForClusterOP

◆ NativeAntibodySeqCOP

◆ NativeAntibodySeqOP

Enumeration Type Documentation

◆ AntibodyDesignProtocolEnum

◆ MinTypeEnum

◆ SeqDesignStrategyEnum

Function Documentation

◆ add_loops_from_bool_vector()

◆ attributes_for_get_ab_design_global_scorefxn()

◆ attributes_for_get_ab_design_min_scorefxn()

◆ check_cb() [1/2]

◆ check_cb() [2/2]

◆ deep_copy()

◆ design_protocol_to_enum()

◆ design_protocol_to_string()

◆ disable_conserved_framework_positions()

◆ disable_design_antigen()

◆ disable_design_cdr()

◆ disable_design_cdrs()

◆ disable_design_framework()

◆ disable_design_region()

◆ disable_h3_stem_positions()

◆ get_ab_design_dock_high_scorefxn()

◆ get_ab_design_dock_low_scorefxn()

◆ get_ab_design_global_scorefxn() [1/2]

◆ get_ab_design_global_scorefxn() [2/2]

◆ get_ab_design_min_scorefxn() [1/2]

◆ get_ab_design_min_scorefxn() [2/2]

◆ get_all_graft_permutations() [1/2]

◆ get_all_graft_permutations() [2/2]

◆ get_cdr_set_options() [1/2]

◆ get_cdr_set_options() [2/2]

◆ get_cluster_profile_probability_data() [1/2]

◆ get_cluster_profile_probability_data() [2/2]

◆ get_dock_chains_from_ab_dock_chains()

◆ get_graft_design_options() [1/2]

◆ get_graft_design_options() [2/2]

◆ get_native_sequence()

◆ get_pdb_numbering_from_single_string()

◆ get_pdb_numbering_from_strings() [1/2]

◆ get_pdb_numbering_from_strings() [2/2]

◆ get_resnum_from_pdb_numbering() [1/2]

◆ get_resnum_from_pdb_numbering() [2/2]

◆ get_resnum_from_single_string()

◆ get_resnum_from_single_string_w_landmark()

◆ get_resnum_from_strings()

◆ get_resnums_from_strings_with_ranges() [1/2]

◆ get_resnums_from_strings_with_ranges() [2/2]

◆ get_seq_design_options() [1/2]

◆ get_seq_design_options() [2/2]

◆ has_native_sequence()

◆ insert_cdr_into_antibody()

◆ seq_design_strategy_to_enum()

◆ seq_design_strategy_to_string()

◆ set_native_cdr_sequence()