Module _protocols_antibody_design_

add_loops_from_bool_vector( (Loops)loops, (vector1_bool)residues [, (bool)add_cutpoints=False]) -> None :
    protocols/antibody/design/util.hh:233

    C++ signature :
        void add_loops_from_bool_vector(protocols::loops::Loops {lvalue},utility::vector1<bool, std::allocator<bool> > [,bool=False])

check_cb( (Pose)pose, (Loops)loops) -> object :
    protocols/antibody/design/util.hh:142

    C++ signature :
        std::pair<bool, unsigned long> check_cb(core::pose::Pose,protocols::loops::Loops)

check_cb( (Pose)pose, (vector1_bool)residues) -> object :
    protocols/antibody/design/util.hh:139

    C++ signature :
        std::pair<bool, unsigned long> check_cb(core::pose::Pose,utility::vector1<bool, std::allocator<bool> >)

design_protocol_to_enum( (str)design_type) -> AntibodyDesignProtocolEnum :
    protocols/antibody/design/util.hh:161

    C++ signature :
        protocols::antibody::design::AntibodyDesignProtocolEnum design_protocol_to_enum(std::string)

design_protocol_to_string( (AntibodyDesignProtocolEnum)design_type) -> str :
    protocols/antibody/design/util.hh:164

    C++ signature :
        std::string design_protocol_to_string(protocols::antibody::design::AntibodyDesignProtocolEnum)

disable_conserved_framework_positions( (AntibodyInfo)ab_info, (Pose)pose) -> RestrictResidueToRepacking :
    Disable design for conserved framework positions.
     TODO: Needs to be expanded to read positions from database.
    

    C++ signature :
        boost::shared_ptr<core::pack::task::operation::RestrictResidueToRepacking> disable_conserved_framework_positions(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose)

disable_design_antigen( (AntibodyInfo)ab_info, (Pose)pose) -> RestrictResidueToRepacking :
    Disable design of the antigen residues
    

    C++ signature :
        boost::shared_ptr<core::pack::task::operation::RestrictResidueToRepacking> disable_design_antigen(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose)

disable_design_cdr( (AntibodyInfo)ab_info, (CDRNameEnum)cdr, (Pose)pose) -> RestrictResidueToRepacking :
    Get a Restrict operation to turn OFF design for particular CDRs.
    

    C++ signature :
        boost::shared_ptr<core::pack::task::operation::RestrictResidueToRepacking> disable_design_cdr(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,protocols::antibody::CDRNameEnum,core::pose::Pose)

disable_design_cdrs( (AntibodyInfo)ab_info, (Pose)pose) -> RestrictResidueToRepacking :
    Get a Restrict operation to turn OFF design for all CDRs.
    

    C++ signature :
        boost::shared_ptr<core::pack::task::operation::RestrictResidueToRepacking> disable_design_cdrs(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose)

disable_design_framework( (AntibodyInfo)ab_info, (Pose)pose) -> RestrictResidueToRepacking :
    Disable design of the framework residues
    

    C++ signature :
        boost::shared_ptr<core::pack::task::operation::RestrictResidueToRepacking> disable_design_framework(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose)

disable_design_region( (AntibodyInfo)ab_info, (Pose)pose, (AntibodyRegionEnum)region) -> RestrictResidueToRepacking :
    Disable design of any particular region of the antibody complex.
    

    C++ signature :
        boost::shared_ptr<core::pack::task::operation::RestrictResidueToRepacking> disable_design_region(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose,protocols::antibody::AntibodyRegionEnum)

disable_h3_stem_positions( (AntibodyInfo)ab_info, (Pose)pose [, (int)nter_stem=2 [, (int)cter_stem=3]]) -> RestrictResidueToRepacking :
    Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants)
    

    C++ signature :
        boost::shared_ptr<core::pack::task::operation::RestrictResidueToRepacking> disable_h3_stem_positions(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose [,unsigned long=2 [,unsigned long=3]])

    protocols/antibody/design/util.hh:127

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_ab_design_dock_high_scorefxn()

Returns: ScoreFunction :

    protocols/antibody/design/util.hh:130

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_ab_design_dock_low_scorefxn()

Returns: ScoreFunction :

get_ab_design_global_scorefxn( (Tag)tag, (DataMap)data) -> ScoreFunction :
    Get Global Scorefxn from RS
    

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_ab_design_global_scorefxn(boost::shared_ptr<utility::tag::Tag const>,basic::datacache::DataMap {lvalue})

get_ab_design_global_scorefxn() -> ScoreFunction :
    protocols/antibody/design/util.hh:120

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_ab_design_global_scorefxn()

get_ab_design_min_scorefxn( (Tag)tag, (DataMap)data) -> ScoreFunction :
    protocols/antibody/design/util.hh:136

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_ab_design_min_scorefxn(boost::shared_ptr<utility::tag::Tag const>,basic::datacache::DataMap {lvalue})

get_ab_design_min_scorefxn() -> ScoreFunction :
    protocols/antibody/design/util.hh:133

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_ab_design_min_scorefxn()

get_all_graft_permutations( (vector1_Size)total_cdr_set, (vec1_vec1_Size)all_permutations, (vector1_Size)current_index, (int)cdr_num) -> None :
    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.
    

    C++ signature :
        void get_all_graft_permutations(utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >,unsigned long)

get_cdr_set_options( (str)instruction_file) -> object :
    Get options from an instruction file
    

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::antibody::CDRSetOptions>, std::allocator<boost::shared_ptr<protocols::antibody::CDRSetOptions> > > get_cdr_set_options(std::string)

get_cdr_set_options() -> object :
    Get default options
    

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::antibody::CDRSetOptions>, std::allocator<boost::shared_ptr<protocols::antibody::CDRSetOptions> > > get_cdr_set_options()

get_cluster_profile_probability_data( (AntibodyInfo)ab_info, (Pose)pose, (object)seq_design_options, (vector1_bool)no_data_cdrs [, (int)prob_cutoff=10 [, (bool)use_outliers=False [, (bool)force_north_db=False]]]) -> object :
    protocols/antibody/design/util.hh:257

    C++ signature :
        std::map<unsigned long, std::map<core::chemical::AA, double, std::less<core::chemical::AA>, std::allocator<std::pair<core::chemical::AA const, double> > >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::map<core::chemical::AA, double, std::less<core::chemical::AA>, std::allocator<std::pair<core::chemical::AA const, double> > > > > > get_cluster_profile_probability_data(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose,utility::vector1<boost::shared_ptr<protocols::antibody::design::CDRSeqDesignOptions>, std::allocator<boost::shared_ptr<protocols::antibody::design::CDRSeqDesignOptions> > >,utility::vector1<bool, std::allocator<bool> > {lvalue} [,unsigned long=10 [,bool=False [,bool=False]]])

get_cluster_profile_probability_data( (AntibodyInfo)ab_info, (Pose)pose, (vector1_bool)cdrs, (vector1_bool)no_data_cdrs [, (int)prob_cutoff=10 [, (bool)use_outliers=False [, (bool)force_north_db=False]]]) -> object :
    Get probability data for a given set of CDRs.  Will fill in the no_data_cdrs;
    

    C++ signature :
        std::map<unsigned long, std::map<core::chemical::AA, double, std::less<core::chemical::AA>, std::allocator<std::pair<core::chemical::AA const, double> > >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::map<core::chemical::AA, double, std::less<core::chemical::AA>, std::allocator<std::pair<core::chemical::AA const, double> > > > > > get_cluster_profile_probability_data(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose,utility::vector1<bool, std::allocator<bool> >,utility::vector1<bool, std::allocator<bool> > {lvalue} [,unsigned long=10 [,bool=False [,bool=False]]])

get_dock_chains_from_ab_dock_chains( (AntibodyInfo)ab_info, (str)ab_dock_chains) -> str :
    Convert an ab_dock_chain (L_H/ LH_A, etc. to the full dock chain string)
    

    C++ signature :
        std::string get_dock_chains_from_ab_dock_chains(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,std::string)

get_graft_design_options( (str)instruction_file) -> object :
    Get options from an instruction file
    

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::antibody::design::CDRGraftDesignOptions>, std::allocator<boost::shared_ptr<protocols::antibody::design::CDRGraftDesignOptions> > > get_graft_design_options(std::string)

get_graft_design_options() -> object :
    Get default options
    

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::antibody::design::CDRGraftDesignOptions>, std::allocator<boost::shared_ptr<protocols::antibody::design::CDRGraftDesignOptions> > > get_graft_design_options()

get_pdb_numbering_from_single_string( (str)pdb_residue) -> PDBNumbering :
    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.
    

    C++ signature :
        protocols::antibody::design::PDBNumbering get_pdb_numbering_from_single_string(std::string)

get_pdb_numbering_from_strings( (vector1_string)pdb_residues) -> object :
    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.
    
    

    C++ signature :
        utility::vector1<protocols::antibody::design::PDBNumbering, std::allocator<protocols::antibody::design::PDBNumbering> > get_pdb_numbering_from_strings(utility::vector1<std::string, std::allocator<std::string> >)

get_resnum_from_pdb_numbering( (Pose)pose, (object)pdb_residues) -> vector1_bool :
    Get a boolean vector from a string of PDBNumbering.  No error checking.  Use with caution.
    

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > get_resnum_from_pdb_numbering(core::pose::Pose,utility::vector1<protocols::antibody::design::PDBNumbering, std::allocator<protocols::antibody::design::PDBNumbering> >)

get_resnum_from_single_string( (Pose)pose, (str)pdb_residue) -> int :
    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.
    

    C++ signature :
        unsigned long get_resnum_from_single_string(core::pose::Pose,std::string)

get_resnum_from_single_string_w_landmark( (AntibodyInfo)ab_info, (Pose)pose, (str)pdb_residue, (AntibodyNumberingSchemeEnum)scheme) -> int :
    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.
    

    C++ signature :
        unsigned long get_resnum_from_single_string_w_landmark(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose,std::string,protocols::antibody::AntibodyNumberingSchemeEnum)

get_resnum_from_strings( (Pose)pose, (vector1_string)pdb_residues) -> vector1_bool :
    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.
    
    

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > get_resnum_from_strings(core::pose::Pose,utility::vector1<std::string, std::allocator<std::string> >)

get_resnums_from_strings_with_ranges( (Pose)pose, (vector1_string)pdb_residues) -> vector1_bool :
    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
    
    

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > get_resnums_from_strings_with_ranges(core::pose::Pose,utility::vector1<std::string, std::allocator<std::string> >)

get_seq_design_options( (str)instruction_file) -> object :
    Get options from an instruction file
    

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::antibody::design::CDRSeqDesignOptions>, std::allocator<boost::shared_ptr<protocols::antibody::design::CDRSeqDesignOptions> > > get_seq_design_options(std::string)

get_seq_design_options() -> object :
    Get default options
    

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::antibody::design::CDRSeqDesignOptions>, std::allocator<boost::shared_ptr<protocols::antibody::design::CDRSeqDesignOptions> > > get_seq_design_options()

insert_cdr_into_antibody( (AntibodyInfo)ab_info, (CDRNameEnum)cdr, (Pose)pose, (Pose)cdr_piece [, (int)overhang=3]) -> None :
    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
    

    C++ signature :
        void insert_cdr_into_antibody(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,protocols::antibody::CDRNameEnum,core::pose::Pose {lvalue},core::pose::Pose {lvalue} [,unsigned long=3])

seq_design_strategy_to_enum( (str)strategy) -> SeqDesignStrategyEnum :
    protocols/antibody/design/util.hh:167

    C++ signature :
        protocols::antibody::design::SeqDesignStrategyEnum seq_design_strategy_to_enum(std::string)

seq_design_strategy_to_string( (SeqDesignStrategyEnum)strategy) -> str :
    protocols/antibody/design/util.hh:170

    C++ signature :
        std::string seq_design_strategy_to_string(protocols::antibody::design::SeqDesignStrategyEnum)

transform_sequence_to_mutation_set( (AntibodyInfo)ab_info, (Pose)pose, (CDRNameEnum)cdr, (str)sequence) -> object :
    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.
    

    C++ signature :
        std::map<unsigned long, core::chemical::AA, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, core::chemical::AA> > > transform_sequence_to_mutation_set(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose,protocols::antibody::CDRNameEnum,std::string)

DesignProtocolEnum_total

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.Antibody DesignProtocolEnum.DesignProtocolEnum_total

MinTypeEnum_total

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.MinTypeEnum_total

SeqDesignStrategyEnum_total

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.SeqDesig nStrategyEnum.SeqDesignStrategyEnum_total

backrub_protocol

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.backrub_protocol

centroid_relax

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.centroid_relax

deterministic_graft

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.Antibody DesignProtocolEnum.deterministic_graft

dualspace

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.dualspace

generalized_monte_carlo

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.Antibody DesignProtocolEnum.generalized_monte_carlo

minimize

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.minimize

minimize_cartesian

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.minimize_cartesian

no_min

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.no_min

relax

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.relax

repack

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.MinTypeE num.repack

seq_design_basic

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.SeqDesig nStrategyEnum.seq_design_basic

seq_design_conservative

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.SeqDesig nStrategyEnum.seq_design_conservative

seq_design_none

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.SeqDesig nStrategyEnum.seq_design_none

seq_design_profile_sets

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.SeqDesig nStrategyEnum.seq_design_profile_sets

seq_design_profile_sets_combined

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.SeqDesig nStrategyEnum.seq_design_profile_sets_combined

seq_design_profiles

Value:

rosetta.protocols.antibody.design._protocols_antibody_design_.SeqDesig nStrategyEnum.seq_design_profiles