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Rosetta Protocols
2014.35
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Rosetta Protocols
2014.35
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Classes | |
| class | AntibodyDatabaseManager |
| Class responsible for loading information from the AntibodyDatabase. More... | |
| class | AntibodyDesignModeler |
| Class that runs the modeling for AntibodyDesign protocols. Could be moved to antibody. More... | |
| class | AntibodyDesignMover |
| Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application. 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. The Antibody Database that this class uses will be available online (Too large for the rosetta_database) Till then, email me for access to the github repository. 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. More... | |
| struct | CDRDesignInstructions |
| struct | CDRGraftInstructions |
| This struct gives antibody designers complete control either through this classes interface or an instruction file. More... | |
| class | ConservativeDesignOperation |
| A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations. More... | |
| class | DesignInstructionsParser |
| Lightweight class for parsing design instructions. More... | |
| class | ResidueProbDesignOperation |
| A TaskOperation that allows amino acids at designable positions through a set of aa probabilities. More... | |
| struct | SamplingWeights |
Enumerations | |
| enum | MinTypeEnum { relax = 1, centroid_relax, minimize, repack, no_min, MinTypeEnum_total = no_min } |
| enum | DesignTypeEnum { relaxed_design = 1, docked_design, fixbb, flxbb, DesignTypeEnum_total = flxbb } |
Functions | |
| void | get_all_graft_permutations (vector1< core::Size > &total_cdr_set, vector1< vector1< core::Size > > &all_permutations, 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) |
| typedef utility::pointer::owning_ptr< AntibodyDatabaseManager const > protocols::antibody::design::AntibodyDatabaseManagerCOP |
| typedef utility::pointer::owning_ptr< AntibodyDatabaseManager > protocols::antibody::design::AntibodyDatabaseManagerOP |
| typedef utility::pointer::owning_ptr< AntibodyDesignModeler const > protocols::antibody::design::AntibodyDesignModelerCOP |
| typedef utility::pointer::owning_ptr< AntibodyDesignModeler > protocols::antibody::design::AntibodyDesignModelerOP |
| typedef utility::pointer::owning_ptr< AntibodyDesignMover const > protocols::antibody::design::AntibodyDesignMoverCOP |
| typedef utility::pointer::owning_ptr< AntibodyDesignMover > protocols::antibody::design::AntibodyDesignMoverOP |
| typedef utility::pointer::owning_ptr< AntibodyGraftDesignMover const > protocols::antibody::design::AntibodyGraftDesignMoverCOP |
| typedef utility::pointer::owning_ptr< AntibodyGraftDesignMover > protocols::antibody::design::AntibodyGraftDesignMoverOP |
| typedef utility::pointer::owning_ptr< AntibodySeqDesignMover const > protocols::antibody::design::AntibodySeqDesignMoverCOP |
| typedef utility::pointer::owning_ptr< AntibodySeqDesignMover > protocols::antibody::design::AntibodySeqDesignMoverOP |
| typedef utility::pointer::owning_ptr< ConservativeDesignOperation const > protocols::antibody::design::ConservativeDesignOperationCOP |
| typedef utility::pointer::owning_ptr< ConservativeDesignOperation > protocols::antibody::design::ConservativeDesignOperationOP |
| typedef std::map< CDRNameEnum, CDRDesignInstructions > protocols::antibody::design::DesignInstructions |
| typedef std::map< CDRNameEnum, CDRGraftInstructions > protocols::antibody::design::GraftInstructions |
| typedef std::map< CDRNameEnum, vector1< std::string > > protocols::antibody::design::PDBMap |
| typedef utility::pointer::owning_ptr< ResidueProbDesignOperation const > protocols::antibody::design::ResidueProbDesignOperationCOP |
| typedef utility::pointer::owning_ptr< ResidueProbDesignOperation > protocols::antibody::design::ResidueProbDesignOperationOP |
| DesignTypeEnum protocols::antibody::design::design_type_from_string | ( | std::string const | design_type | ) |
References fixbb, flxbb, relaxed_design, type, 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.
| void protocols::antibody::design::get_all_graft_permutations | ( | vector1< core::Size > & | total_cdr_set, |
| vector1< vector1< core::Size > > & | all_permutations, | ||
| 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().
1.8.7