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| AntibodyCDRSetOptions | protocols::antibody::design::get_cdr_set_options () |
| | Get default options. More...
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| AntibodyCDRSetOptions | protocols::antibody::design::get_cdr_set_options (std::string instruction_file) |
| | Get options from an instruction file. More...
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| AntibodyCDRGraftDesignOptions | protocols::antibody::design::get_graft_design_options () |
| | Get default options. More...
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| AntibodyCDRGraftDesignOptions | protocols::antibody::design::get_graft_design_options (std::string instruction_file) |
| | Get options from an instruction file. More...
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| AntibodyCDRSeqDesignOptions | protocols::antibody::design::get_seq_design_options () |
| | Get default options. More...
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| AntibodyCDRSeqDesignOptions | protocols::antibody::design::get_seq_design_options (std::string instruction_file) |
| | Get options from an instruction file. More...
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| 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=true) |
| | Disable design of any particular region of the antibody complex. More...
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| 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. More...
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| core::pack::task::operation::RestrictResidueToRepackingOP | protocols::antibody::design::disable_design_framework (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, bool cdr4_as_framework=true) |
| | Disable design of the framework residues. More...
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| 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. More...
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| 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. More...
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| 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. More...
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| core::pack::task::operation::RestrictResidueToRepackingOP | protocols::antibody::design::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...
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| ScoreFunctionOP | protocols::antibody::design::get_ab_design_global_scorefxn () |
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| 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. More...
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| 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 More...
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| ScoreFunctionOP | protocols::antibody::design::get_ab_design_dock_high_scorefxn () |
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| ScoreFunctionOP | protocols::antibody::design::get_ab_design_dock_low_scorefxn () |
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| ScoreFunctionOP | protocols::antibody::design::get_ab_design_min_scorefxn () |
| | XSD companion function: attributes_for_get_ab_design_min_scorefxn. More...
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| 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 More...
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| ScoreFunctionOP | protocols::antibody::design::get_ab_design_min_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data) |
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| 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. More...
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| 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. More...
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| 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=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...
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| 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. More...
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| AntibodyDesignProtocolEnum | protocols::antibody::design::design_protocol_to_enum (std::string const &design_type) |
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| std::string | protocols::antibody::design::design_protocol_to_string (AntibodyDesignProtocolEnum const design_type) |
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| SeqDesignStrategyEnum | protocols::antibody::design::seq_design_strategy_to_enum (std::string const &strategy) |
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| std::string | protocols::antibody::design::seq_design_strategy_to_string (SeqDesignStrategyEnum strategy) |
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| 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) More...
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| 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: More...
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| 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. More...
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| 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. More...
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| 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. More...
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| 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. More...
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| 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. More...
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| 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. More...
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| void | protocols::antibody::design::add_loops_from_bool_vector (loops::Loops &loops, utility::vector1< bool > residues, bool add_cutpoints=false) |
| | Add this across protocol... More...
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| 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=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...
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| 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) |
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| 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. More...
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| 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. More...
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| std::string | protocols::antibody::design::get_native_sequence (core::pose::Pose const &pose, AntibodyInfo const &ab_info) |
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| bool | protocols::antibody::design::has_native_sequence (core::pose::Pose const &pose) |
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Utility functions for antibody design namespace.
- Author
- Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)
