protocols::antibody::design Namespace Reference

Classes
class	AntibodyDesignModeler
	Basic Class that can run modeling for various protocols. Does not do any design. Mainly deprecated by AntibodyDesignMoverGenerator for the new class. More...
class	AntibodyDesignMover
	Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application. More...
class	AntibodyDesignMoverGenerator
	Generates pre-configured general MoverOPs for use in AntibodyDesign and modeling Helper functions for setting up FoldTrees. Can set the generated mover to apply, which will include the needed FoldTree and any changing of typeset. FoldTree stuff will eventually be refactored in favor of the TopologyBroker/Environment system. More...
class	AntibodyGraftDesignMover
	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	AntibodySeqDesignMover
	Designs antibody CDR structures using a variety of different methods. Main methods involve using cluster-based sequence probability statistics and conservative design strategies to limit unknown structural effects caused by aggressive design. Uses North_AHO numbering and cluster-based design. Part of Rosetta Antibody Designer. -> Will be replaced by SnugDesign Mover in the application, but still useful in it's own right. More...
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	CDRGraftDesignOptionsParser
class	CDRSeqDesignOptions
class	CDRSeqDesignOptionsParser
class	ConservativeDesignOperation
	A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations. More...
struct	PDBNumbering
	Super-basic numbering struct. More...
class	ResidueProbDesignOperation
	A TaskOperation that allows amino acids at designable positions through a set of aa probabilities. 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 < AntibodyDesignMoverGenerator >	AntibodyDesignMoverGeneratorOP
typedef utility::pointer::shared_ptr < AntibodyDesignMoverGenerator const >	AntibodyDesignMoverGeneratorCOP
typedef utility::pointer::shared_ptr < AntibodyGraftDesignMover >	AntibodyGraftDesignMoverOP
typedef utility::pointer::shared_ptr < AntibodyGraftDesignMover const >	AntibodyGraftDesignMoverCOP
typedef utility::pointer::shared_ptr < AntibodySeqDesignMover >	AntibodySeqDesignMoverOP
typedef utility::pointer::shared_ptr < AntibodySeqDesignMover const >	AntibodySeqDesignMoverCOP
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 < ConservativeDesignOperation >	ConservativeDesignOperationOP
typedef utility::pointer::shared_ptr < ConservativeDesignOperation const >	ConservativeDesignOperationCOP
typedef std::map < core::chemical::AA, Real >	AAProbabilities
typedef std::map< Size, AAProbabilities >	PerResidueAAProbSet
typedef utility::pointer::shared_ptr < ResidueProbDesignOperation >	ResidueProbDesignOperationOP
typedef utility::pointer::shared_ptr < ResidueProbDesignOperation const >	ResidueProbDesignOperationCOP

Enumerations
enum	MinTypeEnum {   relax = 1, centroid_relax, minimize, minimize_cartesian,   dualspace, repack, no_min, MinTypeEnum_total = no_min }
enum	DesignTypeEnum {   relaxed_design = 1, docked_design, fixbb, flxbb,   DesignTypeEnum_total = flxbb }
enum	SeqDesignStrategyEnum { seq_design_profiles = 1, seq_design_conservative, seq_design_basic, SeqDesignStrategyEnum_total = seq_design_basic }

Functions
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< vector1< core::Size > > &all_permutations, utility::vector1< core::Size >current_index, core::Size const cdr_num)
	Gets all possible graft permutations. More...
DesignTypeEnum	design_type_from_string (std::string const design_type)
std::string	design_type_to_string (DesignTypeEnum const design_type)
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...
vector1< PDBNumbering >	get_pdb_numbering_from_string (vector1< std::string > const &pdb_residues)
vector1< bool >	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. 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...
AntibodyCDRSetOptions	get_cdr_set_options ()
	Application Options - Should be moved as part of parsers? More...
AntibodyCDRGraftDesignOptions	get_graft_design_options ()
	Get options set from default instructions file and any user overrides. More...
AntibodyCDRSeqDesignOptions	get_seq_design_options ()
	Get options set from default instructions file and any user overrides. More...

Typedef Documentation

typedef std::map< core::chemical::AA, Real > protocols::antibody::design::AAProbabilities

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< AntibodyDesignMoverGenerator const > protocols::antibody::design::AntibodyDesignMoverGeneratorCOP

typedef utility::pointer::shared_ptr< AntibodyDesignMoverGenerator > protocols::antibody::design::AntibodyDesignMoverGeneratorOP

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

typedef utility::pointer::shared_ptr< AntibodyGraftDesignMover const > protocols::antibody::design::AntibodyGraftDesignMoverCOP

typedef utility::pointer::shared_ptr< AntibodyGraftDesignMover > protocols::antibody::design::AntibodyGraftDesignMoverOP

typedef utility::pointer::shared_ptr< AntibodySeqDesignMover const > protocols::antibody::design::AntibodySeqDesignMoverCOP

typedef utility::pointer::shared_ptr< AntibodySeqDesignMover > protocols::antibody::design::AntibodySeqDesignMoverOP

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< 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< ConservativeDesignOperation const > protocols::antibody::design::ConservativeDesignOperationCOP

typedef utility::pointer::shared_ptr< ConservativeDesignOperation > protocols::antibody::design::ConservativeDesignOperationOP

typedef std::map< Size, AAProbabilities > protocols::antibody::design::PerResidueAAProbSet

typedef utility::pointer::shared_ptr< ResidueProbDesignOperation const > protocols::antibody::design::ResidueProbDesignOperationCOP

typedef utility::pointer::shared_ptr< ResidueProbDesignOperation > protocols::antibody::design::ResidueProbDesignOperationOP

Enumeration Type Documentation

enum protocols::antibody::design::DesignTypeEnum

Enumerator
relaxed_design
docked_design
fixbb
flxbb
DesignTypeEnum_total

enum protocols::antibody::design::MinTypeEnum

Enumerator
relax
centroid_relax
minimize
minimize_cartesian
dualspace
repack
no_min
MinTypeEnum_total

enum protocols::antibody::design::SeqDesignStrategyEnum

Enumerator
seq_design_profiles
seq_design_conservative
seq_design_basic
SeqDesignStrategyEnum_total

Function Documentation

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::AntibodyGraftDesignMover::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().

DesignTypeEnum protocols::antibody::design::design_type_from_string

(

std::string const

design_type

)

References fixbb, flxbb, relaxed_design, and utility_exit_with_message.

Referenced by protocols::antibody::design::AntibodySeqDesignMover::read_command_line_options().

std::string protocols::antibody::design::design_type_to_string

(

DesignTypeEnum const

design_type

)

References fixbb, flxbb, relaxed_design, and utility_exit_with_message.

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::generate_tf_seq_design(), and protocols::antibody::design::AntibodySeqDesignTFCreator::generate_tf_seq_design_graft_design().

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, 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().

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 disable_design_antigen(), disable_design_cdrs(), disable_design_framework(), protocols::antibody::design::AntibodySeqDesignTFCreator::generate_tf_seq_design(), and protocols::antibody::design::AntibodySeqDesignTFCreator::generate_tf_seq_design_graft_design().

void protocols::antibody::design::get_all_graft_permutations	(	utility::vector1< core::Size > &	total_cdr_set,
		utility::vector1< 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::AntibodyGraftDesignMover::get_cdr_set_index_list().

AntibodyCDRSetOptions protocols::antibody::design::get_cdr_set_options

(

)

Application Options - Should be moved as part of parsers?

Get options set from default instructions file and any user overrides

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

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

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(), protocols::antibody::design::AntibodyDesignModeler::relax_interface(), protocols::antibody::design::AntibodyDesignMoverGenerator::setup_dock_foldtree(), and protocols::antibody::design::AntibodyDesignMoverGenerator::setup_general_min_foldtree().

AntibodyCDRGraftDesignOptions protocols::antibody::design::get_graft_design_options

(

)

Get options set from default instructions file and any user overrides.

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

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

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

(

vector1< std::string > const &

pdb_residues

)

References protocols::antibody::design::PDBNumbering::chain, protocols::antibody::design::PDBNumbering::icode, protocols::antibody::design::PDBNumbering::resnum, utility::string_split(), and utility_exit_with_message.

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

AntibodyCDRSeqDesignOptions protocols::antibody::design::get_seq_design_options

(

)

Get options set from default instructions file and any user overrides.

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

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

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().