Module _protocols_antibody_

CDR_H3_cter_filter( (Pose)pose_in, (AntibodyInfo)ab_info) -> bool :
    protocols/antibody/util.hh:148

    C++ signature :
        bool CDR_H3_cter_filter(core::pose::Pose,boost::shared_ptr<protocols::antibody::AntibodyInfo>)

CDR_H3_filter_legacy_code_with_old_rule( (Pose)pose_in, (Loop)input_loop, (bool)is_camelid) -> bool :
    protocols/antibody/util.hh:143

    C++ signature :
        bool CDR_H3_filter_legacy_code_with_old_rule(core::pose::Pose,protocols::loops::Loop {lvalue},bool)

align_to_native( (Pose)pose, (Pose)native_pose, (AntibodyInfo)ab_info, (AntibodyInfo)native_ab_info [, (str)request_chain='LH']) -> None :
    align current Fv to native.Fv
    

    C++ signature :
        void align_to_native(core::pose::Pose {lvalue},core::pose::Pose,boost::shared_ptr<protocols::antibody::AntibodyInfo>,boost::shared_ptr<protocols::antibody::AntibodyInfo> [,std::string='LH'])

cdr_CN_anchor_distance( (Pose)pose, (AntibodyInfo)ab_info, (CDRNameEnum)cdr) -> float :
    Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively
    

    C++ signature :
        double cdr_CN_anchor_distance(core::pose::Pose,boost::shared_ptr<protocols::antibody::AntibodyInfo const>,protocols::antibody::CDRNameEnum)

cdr_energy( (Pose)pose, (AntibodyInfo)ab_info, (__CPP_ScoreFunction__)scorefxn, (CDRNameEnum)cdr) -> float :
    // CDR measures /////
     Calculates energy of cdr by decomposing scorefxn into pair and then summing.  This means it includes hbonding components, etc.
    

    C++ signature :
        double cdr_energy(core::pose::Pose,boost::shared_ptr<protocols::antibody::AntibodyInfo const>,boost::shared_ptr<core::scoring::ScoreFunction const>,protocols::antibody::CDRNameEnum)

check_fix_aho_cdr_numbering( (AntibodyInfo)ab_info, (Pose)pose) -> None :
    protocols/antibody/util.hh:95

    C++ signature :
        void check_fix_aho_cdr_numbering(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose {lvalue})

check_fix_aho_cdr_numbering( (AntibodyInfo)ab_info, (CDRNameEnum)cdr, (Pose)pose) -> None :
    /////////////////////////////// Numbering ///////////////////////////////////
    Checks the length of the CDR, fixes AHO numbering for longer CDR loops that don't
     fit within the numbering scheme
    

    C++ signature :
        void check_fix_aho_cdr_numbering(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,protocols::antibody::CDRNameEnum,core::pose::Pose {lvalue})

cutpoint_separation( (Pose)pose_in, (int)cutpoint) -> float :
    Compute the separation at the cutpoint. The N-C distance of the
      peptide bond which should be formed at the cutpoint. A closed loop is
      assumed to have a gap < 1.9 Ang
    

    C++ signature :
        double cutpoint_separation(core::pose::Pose {lvalue},unsigned long)

cutpoints_separation( (Pose)pose, (AntibodyInfo)antibody_info) -> bool :
    return false if any cdr cutpoint is broken
    

    C++ signature :
        bool cutpoints_separation(core::pose::Pose {lvalue},boost::shared_ptr<protocols::antibody::AntibodyInfo> {lvalue})

get_cdr_bool_from_tag( (Tag)tag, (str)name) -> vector1_bool :
    Geta boolean vector of CDRs from a RosettaScripts tag.
    

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > get_cdr_bool_from_tag(boost::shared_ptr<utility::tag::Tag const>,std::string)

get_cdr_loops( (AntibodyInfo)ab_info, (Pose)pose, (vector1_bool)cdrs [, (int)stem_size=0]) -> Loops :
    Get a set of loops for a boolean vector of CDRNameEnums including any stem residues.
    

    C++ signature :
        boost::shared_ptr<protocols::loops::Loops> get_cdr_loops(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose,utility::vector1<bool, std::allocator<bool> > [,unsigned long=0])

global_loop_rmsd( (Pose)pose_in, (Pose)native_pose, (Loops)current_loop) -> float :
    /////////////////////////////////////// things to compare to native //////////////////////////////////////////
    

    C++ signature :
        double global_loop_rmsd(core::pose::Pose,core::pose::Pose,boost::shared_ptr<protocols::loops::Loops>)

is_H3_rama_kinked( (str)rama) -> bool :
    Very basic kink function based on rama groups.  Kink is defined as having AB + DB at the C-terminal stem.
     This is in the North/Dunbrack CDR definition.
     Avoid this definition if you can and talk to brain.  This is currently used for a quick filtering for design.
    

    C++ signature :
        bool is_H3_rama_kinked(std::string)

kink_RD_Hbond( (Pose)pose, (AntibodyInfo)abinfo) -> float :
    // kink measures /////
    

    C++ signature :
        double kink_RD_Hbond(core::pose::Pose,protocols::antibody::AntibodyInfo)

kink_Trp_Hbond( (Pose)pose, (AntibodyInfo)abinfo) -> float :
    protocols/antibody/metrics.hh:52

    C++ signature :
        double kink_Trp_Hbond(core::pose::Pose,protocols::antibody::AntibodyInfo)

kink_bb_Hbond( (Pose)pose, (AntibodyInfo)abinfo) -> float :
    protocols/antibody/metrics.hh:47

    C++ signature :
        double kink_bb_Hbond(core::pose::Pose,protocols::antibody::AntibodyInfo)

kink_dihedral( (Pose)pose, (AntibodyInfo)abinfo [, (bool)debug=False]) -> pair_Real_Real :
    protocols/antibody/metrics.hh:56

    C++ signature :
        std::pair<double, double> kink_dihedral(core::pose::Pose,protocols::antibody::AntibodyInfo [,bool=False])

paratope_charge( (Pose)pose, (AntibodyInfo)abinfo) -> ParatopeMetric_T_long_int_T :
    calculate the net charge of the paratope
    

    C++ signature :
        protocols::antibody::ParatopeMetric<long> paratope_charge(core::pose::Pose,protocols::antibody::AntibodyInfo)

paratope_sasa( (Pose)pose, (AntibodyInfo)ab_info) -> object :
    calculate the SASA of the antibody paratope.  Returns all and hydrophobic components.
    

    C++ signature :
        std::pair<protocols::antibody::ParatopeMetric<double>, protocols::antibody::ParatopeMetric<double> > paratope_sasa(core::pose::Pose,protocols::antibody::AntibodyInfo)

pose_charge( (Pose)pose) -> int :
    calculate the net charge of the antibody
    

    C++ signature :
        long pose_charge(core::pose::Pose)

select_epitope_residues( (AntibodyInfo)ab_info, (Pose)pose [, (int)interface_distance=10.0]) -> vector1_bool :
    //////////////////////////////// Epitope + Paratope ////////////////////////////////////////////////////////////////////
    Get the epitope residues using the InterGroupNeighborsCalculator.
    

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > select_epitope_residues(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose [,unsigned long=10.0])

setup_A_LH_foldtree( (AntibodyInfo)ab_info, (Pose)pose) -> str :
    Setup A_LH foldtree via docking. Return dock_chains string.
    

    C++ signature :
        std::string setup_A_LH_foldtree(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose {lvalue})

setup_LH_A_foldtree( (AntibodyInfo)ab_info, (Pose)pose) -> str :
    Setup LH_A foldtree via docking.  Return dock_chains string.
    

    C++ signature :
        std::string setup_LH_A_foldtree(boost::shared_ptr<protocols::antibody::AntibodyInfo const>,core::pose::Pose {lvalue})

setup_packer_task( (Pose)pose_in) -> TaskFactory :
    Very specific packertask,
    Ubound rotamer options, repack only, protein only, no disulfides.
    

    C++ signature :
        boost::shared_ptr<core::pack::task::TaskFactory> setup_packer_task(core::pose::Pose {lvalue})

simple_fold_tree( (Pose)pose_in, (int)jumppoint1, (int)cutpoint, (int)jumppoint2) -> None :
    protocols/antibody/util.hh:114

    C++ signature :
        void simple_fold_tree(core::pose::Pose {lvalue},unsigned long,unsigned long,unsigned long)

simple_one_loop_fold_tree( (Pose)pose, (Loop)loop) -> None :
    ////////////////////////////// Etc. /////////////////////////////////////
    

    C++ signature :
        void simple_one_loop_fold_tree(core::pose::Pose {lvalue},protocols::loops::Loop)

vl_vh_orientation_coords( (Pose)pose_in, (AntibodyInfo)ab_info) -> vector1_Real :
    calculate the VH_VL packing angle from 2 sheet definitions on each antibody chain
    vector is made up of:
     vl_vh_distance
     opening_angle
     opposite_angle
     packing_angle
    

    C++ signature :
        utility::vector1<double, std::allocator<double> > vl_vh_orientation_coords(core::pose::Pose,protocols::antibody::AntibodyInfo)

AHO_Scheme

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.AHO_Scheme

AntibodyNumberingSchemeEnum_start

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.AntibodyNumberingSchemeEnum_start

AntibodyNumberingSchemeEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.AntibodyNumberingSchemeEnum_total

AntibodyRegionEnum_start

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyRegionEnum.Ant ibodyRegionEnum_start

AntibodyRegionEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyRegionEnum.Ant ibodyRegionEnum_total

Aroop

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRDefinitionEnum.Aroo p

CDRDefinitionEnum_start

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRDefinitionEnum.CDRD efinitionEnum_start

CDRDefinitionEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRDefinitionEnum.CDRD efinitionEnum_total

CDRLandmarkEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRLandmarkEnum.CDRLan dmarkEnum_total

CDRNameEnum_proto_start

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.CDRNameEnu m_proto_start

CDRNameEnum_proto_total

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.CDRNameEnu m_proto_total

CDRNameEnum_start

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.CDRNameEnu m_start

CDRNameEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.CDRNameEnu m_total

Chothia

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRDefinitionEnum.Chot hia

Chothia_Scheme

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.Chothia_Scheme

Enhanced_Chothia_Scheme

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.Enhanced_Chothia_Scheme

Extended

Value:

rosetta.protocols.antibody._protocols_antibody_.H3BaseTypeEnum.Extende d

H3BaseTypeEnum_start

Value:

rosetta.protocols.antibody._protocols_antibody_.H3BaseTypeEnum.H3BaseT ypeEnum_start

H3BaseTypeEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.H3BaseTypeEnum.H3BaseT ypeEnum_total

H_chain_last_loop

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.H_chain_la st_loop

IMGT_Scheme

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.IMGT_Scheme

Kabat

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRDefinitionEnum.Kaba t

Kabat_Scheme

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.Kabat_Scheme

Kinked

Value:

rosetta.protocols.antibody._protocols_antibody_.H3BaseTypeEnum.Kinked

L_chain_last_loop

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.L_chain_la st_loop

LightChainTypeEnum_start

Value:

rosetta.protocols.antibody._protocols_antibody_.LightChainTypeEnum.Lig htChainTypeEnum_start

LightChainTypeEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.LightChainTypeEnum.Lig htChainTypeEnum_total

Martin

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRDefinitionEnum.Mart in

NONE

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyNumberingSchem eEnum.NONE

Neutral

Value:

rosetta.protocols.antibody._protocols_antibody_.H3BaseTypeEnum.Neutral

North

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRDefinitionEnum.Nort h

PackingAngleEnum_start

Value:

rosetta.protocols.antibody._protocols_antibody_.PackingAngleEnum.Packi ngAngleEnum_start

PackingAngleEnum_total

Value:

rosetta.protocols.antibody._protocols_antibody_.PackingAngleEnum.Packi ngAngleEnum_total

Unknown

Value:

rosetta.protocols.antibody._protocols_antibody_.H3BaseTypeEnum.Unknown

VH_sheet_1

Value:

rosetta.protocols.antibody._protocols_antibody_.PackingAngleEnum.VH_sh eet_1

VH_sheet_2

Value:

rosetta.protocols.antibody._protocols_antibody_.PackingAngleEnum.VH_sh eet_2

VL_sheet_1

Value:

rosetta.protocols.antibody._protocols_antibody_.PackingAngleEnum.VL_sh eet_1

VL_sheet_2

Value:

rosetta.protocols.antibody._protocols_antibody_.PackingAngleEnum.VL_sh eet_2

antigen_region

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyRegionEnum.ant igen_region

camelid_last_loop

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.camelid_la st_loop

cdr_end

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRLandmarkEnum.cdr_en d

cdr_region

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyRegionEnum.cdr _region

cdr_start

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRLandmarkEnum.cdr_st art

framework_region

Value:

rosetta.protocols.antibody._protocols_antibody_.AntibodyRegionEnum.fra mework_region

h1

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.h1

h2

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.h2

h3

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.h3

h4

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.h4

kappa

Value:

rosetta.protocols.antibody._protocols_antibody_.LightChainTypeEnum.kap pa

l1

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.l1

l2

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.l2

l3

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.l3

l4

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.l4

lambda

Value:

rosetta.protocols.antibody._protocols_antibody_.LightChainTypeEnum.lam bda

lambda6

Value:

rosetta.protocols.antibody._protocols_antibody_.LightChainTypeEnum.lam bda6

num_cdr_loops

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.num_cdr_lo ops

proto_h4

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.proto_h4

proto_l4

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.proto_l4

start_cdr_loop

Value:

rosetta.protocols.antibody._protocols_antibody_.CDRNameEnum.start_cdr_ loop

unknown

Value:

rosetta.protocols.antibody._protocols_antibody_.LightChainTypeEnum.unk nown