protocols::antibody::design Namespace Reference

Classes
class	AntibodyDesignModeler
	Basic Class that can run modeling for various protocols. Does not do any design. Setup design TF via AntibodySeqDesignTFCreator. More...
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	AntibodyDesignProtocol
	Main AntibodyDesignProtocol, tieing together individual movers and classes. Main mover for application. More...
class	AntibodyDesignProtocolCreator
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	CDRClusterSequenceOperation
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
struct	MutantPosition
class	MutateFrameworkForCluster
	Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations. More...
class	MutateFrameworkForClusterCreator
struct	PDBNumbering
	Super-basic numbering struct. More...

Typedefs
typedef utility::pointer::shared_ptr < AntibodyDesignModeler >	AntibodyDesignModelerOP
typedef utility::pointer::shared_ptr < AntibodyDesignModeler const >	AntibodyDesignModelerCOP
typedef utility::pointer::shared_ptr < AntibodyDesignMover >	AntibodyDesignMoverOP
typedef utility::pointer::shared_ptr < AntibodyDesignMover const >	AntibodyDesignMoverCOP
typedef utility::pointer::shared_ptr < AntibodyDesignProtocol >	AntibodyDesignProtocolOP
typedef utility::pointer::shared_ptr < AntibodyDesignProtocol const >	AntibodyDesignProtocolCOP
typedef utility::pointer::shared_ptr < AntibodySeqDesignTFCreator >	AntibodySeqDesignTFCreatorOP
typedef utility::pointer::shared_ptr < AntibodySeqDesignTFCreator const >	AntibodySeqDesignTFCreatorCOP
typedef utility::pointer::shared_ptr < CDRClusterSequenceOperation >	CDRClusterSequenceOperationOP
typedef utility::pointer::shared_ptr < CDRClusterSequenceOperation const >	CDRClusterSequenceOperationCOP
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 < MutateFrameworkForCluster >	MutateFrameworkForClusterOP
typedef utility::pointer::shared_ptr < MutateFrameworkForCluster const >	MutateFrameworkForClusterCOP

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, deterministic_graft, DesignProtocolEnum_total = deterministic_graft }

Functions
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. More...
ScoreFunctionOP	get_ab_design_dock_high_scorefxn ()
ScoreFunctionOP	get_ab_design_dock_low_scorefxn ()
ScoreFunctionOP	get_ab_design_min_scorefxn ()
ScoreFunctionOP	get_ab_design_min_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
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...
void	get_all_graft_permutations (utility::vector1< core::Size > &total_cdr_set, utility::vector1< utility::vector1< core::Size > > &all_permutations, utility::vector1< core::Size >current_index, core::Size const cdr_num)
	Gets all possible graft permutations. More...
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 strategy)
std::string	seq_design_strategy_to_string (SeqDesignStrategyEnum strategy)
std::string	get_dock_chains_from_ab_dock_chains (AntibodyInfoCOP ab_info, std::string 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 (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...
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...
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...
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)
std::pair< bool, core::Size >	check_cb (core::pose::Pose const &pose, protocols::loops::Loops const &loops)
core::pack::task::operation::RestrictResidueToRepackingOP	disable_design_region (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, AntibodyRegionEnum region)
	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)
	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)
	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)
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...

Typedef Documentation

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

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

typedef utility::pointer::shared_ptr< AntibodyDesignModeler const > protocols::antibody::design::AntibodyDesignModelerCOP

typedef utility::pointer::shared_ptr< AntibodyDesignModeler > protocols::antibody::design::AntibodyDesignModelerOP

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

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

typedef utility::pointer::shared_ptr< AntibodyDesignProtocol const > protocols::antibody::design::AntibodyDesignProtocolCOP

typedef utility::pointer::shared_ptr< AntibodyDesignProtocol > protocols::antibody::design::AntibodyDesignProtocolOP

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

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

typedef utility::pointer::shared_ptr< CDRClusterSequenceOperation const > protocols::antibody::design::CDRClusterSequenceOperationCOP

typedef utility::pointer::shared_ptr< CDRClusterSequenceOperation > protocols::antibody::design::CDRClusterSequenceOperationOP

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::antibody::design::AntibodyDesignProtocolEnum

Enumerator
generalized_monte_carlo
deterministic_graft
DesignProtocolEnum_total

enum protocols::antibody::design::MinTypeEnum

Enumerator
relax
centroid_relax
minimize
minimize_cartesian
dualspace
repack
backrub_protocol
no_min
MinTypeEnum_total

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

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::loops::Loops::add_loop(), end, protocols::loops::start, and x().

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

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

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

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

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

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), and protocols::loops::has_severe_pep_bond_geom_issues().

AntibodyDesignProtocolEnum protocols::antibody::design::design_protocol_to_enum

(

std::string const

design_type

)

References deterministic_graft, generalized_monte_carlo, and utility_exit_with_message.

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

std::string protocols::antibody::design::design_protocol_to_string

(

AntibodyDesignProtocolEnum const

design_type

)

References deterministic_graft, generalized_monte_carlo, and utility_exit_with_message.

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

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().

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().

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 end, protocols::loops::start, and utility_exit_with_message.

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

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().

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

Disable design of the framework residues.

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

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

Disable design of any particular region of the antibody complex.

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

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

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().

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

(

)

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

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

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

(

)

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

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

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

(

)

References atom_pair_constraint, dihedral_constraint, get_score_function(), and option.

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

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

Get Global Scorefxn from RS.

References atom_pair_constraint, dihedral_constraint, get_score_function(), option, and protocols::rosetta_scripts::parse_score_function().

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

(

)

References atom_pair_constraint, dihedral_constraint, get_score_function(), and option.

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

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

References atom_pair_constraint, dihedral_constraint, basic::datacache::DataMap::get_ptr(), get_score_function(), and option.

void protocols::antibody::design::get_all_graft_permutations	(	utility::vector1< core::Size > &	total_cdr_set,
		utility::vector1< utility::vector1< core::Size > > &	all_permutations,
		utility::vector1< core::Size >	current_index,
		core::Size const	cdr_num
	)

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.

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

AntibodyCDRSetOptions protocols::antibody::design::get_cdr_set_options

(

)

Get default options.

References filename(), basic::options::option, protocols::antibody::CDRSetOptionsParser::parse_options(), and protocols::antibody::TR().

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

AntibodyCDRSetOptions protocols::antibody::design::get_cdr_set_options

(

std::string

filename

)

Get options from an instruction file.

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

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
	)

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

References 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().

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
	)

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

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

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

References protocols::antibody::TR(), utility_exit_with_message, and x().

Referenced by protocols::antibody::design::AntibodyDesignModeler::dock_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_low_res(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs(), protocols::antibody::design::AntibodyDesignModeler::minimize_interface(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs(), and protocols::antibody::design::AntibodyDesignModeler::relax_interface().

AntibodyCDRGraftDesignOptions protocols::antibody::design::get_graft_design_options

(

)

Get default options.

References filename(), basic::options::option, protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options(), and protocols::antibody::TR().

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

AntibodyCDRGraftDesignOptions protocols::antibody::design::get_graft_design_options

(

std::string

filename

)

Get options from an instruction file.

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

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, utility::from_string(), protocols::antibody::design::PDBNumbering::icode, protocols::antibody::design::PDBNumbering::resnum, utility::string_split(), protocols::antibody::TR(), and utility_exit_with_message.

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().

utility::vector1< PDBNumbering > protocols::antibody::design::get_pdb_numbering_from_strings

(

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.

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().

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

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

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::total_residue().

Referenced by protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_epitope_residues(), and get_resnum_from_strings().

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.

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().

utility::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().

utility::vector1< bool > protocols::antibody::design::get_resnums_from_strings_with_ranges	(	core::pose::Pose const &	pose,
		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.

References protocols::antibody::design::PDBNumbering::chain, get_pdb_numbering_from_single_string(), protocols::antibody::design::PDBNumbering::icode, numbers, core::pose::Pose::pdb_info(), protocols::antibody::design::PDBNumbering::resnum, utility::string_split(), core::pose::Pose::total_residue(), protocols::antibody::TR(), and utility_exit_with_message.

Referenced by protocols::antibody::design::AntibodyDesignModeler::backrub_cdrs(), protocols::antibody::constraints::ParatopeSiteConstraintMover::parse_my_tag(), and protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::parse_my_tag().

AntibodyCDRSeqDesignOptions protocols::antibody::design::get_seq_design_options

(

)

Get default options.

References filename(), basic::options::option, protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options(), and protocols::antibody::TR().

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

AntibodyCDRSeqDesignOptions protocols::antibody::design::get_seq_design_options

(

std::string

filename

)

Get options from an instruction file.

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

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::total_residue().

SeqDesignStrategyEnum protocols::antibody::design::seq_design_strategy_to_enum

(

std::string

strategy

)

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

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::parse_tag(), protocols::antibody::design::CDRSeqDesignOptionsParser::set_cdr_design_fallback_option(), and protocols::antibody::design::CDRSeqDesignOptionsParser::set_cdr_design_primary_option().

std::string protocols::antibody::design::seq_design_strategy_to_string

(

SeqDesignStrategyEnum

strategy

)

References seq_design_basic, seq_design_conservative, seq_design_none, seq_design_profiles, and utility_exit_with_message.

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, utility::to_string(), and utility_exit_with_message.

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