util.hh File Reference

Utility functions for antibody design namespace. More...

#include <protocols/antibody/design/AntibodyDesignEnum.hh>
#include <protocols/antibody/AntibodyInfo.fwd.hh>
#include <protocols/antibody/AntibodyEnum.hh>
#include <protocols/antibody/database/CDRSetOptions.hh>
#include <protocols/antibody/design/CDRSeqDesignOptions.hh>
#include <protocols/antibody/design/CDRGraftDesignOptions.hh>
#include <protocols/loops/Loops.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pack/task/operation/TaskOperations.fwd.hh>
#include <basic/datacache/DataMap.hh>
#include <string>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.fwd.hh>
#include <map>

Classes
struct	protocols::antibody::design::PDBNumbering
	Super-basic numbering struct. More...

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::antibody
	protocols::antibody::design

Functions
AntibodyCDRSetOptions	protocols::antibody::design::get_cdr_set_options ()
	Get default options. More...
AntibodyCDRSetOptions	protocols::antibody::design::get_cdr_set_options (std::string instruction_file)
	Get options from an instruction file. More...
AntibodyCDRGraftDesignOptions	protocols::antibody::design::get_graft_design_options ()
	Get default options. More...
AntibodyCDRGraftDesignOptions	protocols::antibody::design::get_graft_design_options (std::string instruction_file)
	Get options from an instruction file. More...
AntibodyCDRSeqDesignOptions	protocols::antibody::design::get_seq_design_options ()
	Get default options. More...
AntibodyCDRSeqDesignOptions	protocols::antibody::design::get_seq_design_options (std::string instruction_file)
	Get options from an instruction file. More...
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. More...
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...
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. More...
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...
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...
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...
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...
ScoreFunctionOP	protocols::antibody::design::get_ab_design_global_scorefxn ()
ScoreFunctionOP	protocols::antibody::design::get_ab_design_global_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Get Global Scorefxn from RS. More...
ScoreFunctionOP	protocols::antibody::design::get_ab_design_dock_high_scorefxn ()
ScoreFunctionOP	protocols::antibody::design::get_ab_design_dock_low_scorefxn ()
ScoreFunctionOP	protocols::antibody::design::get_ab_design_min_scorefxn ()
ScoreFunctionOP	protocols::antibody::design::get_ab_design_min_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
std::pair< bool, core::Size >	protocols::antibody::design::check_cb (core::pose::Pose const &pose, utility::vector1< bool > const &residues)
std::pair< bool, core::Size >	protocols::antibody::design::check_cb (core::pose::Pose const &pose, protocols::loops::Loops const &loops)
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...
void	protocols::antibody::design::get_all_graft_permutations (utility::vector1< core::Size > &total_cdr_set, utility::vector1< utility::vector1< core::Size > > &all_permutations, utility::vector1< core::Size >current_index, core::Size const cdr_num)
	Gets all possible graft permutations. More...
AntibodyDesignProtocolEnum	protocols::antibody::design::design_protocol_to_enum (std::string const design_type)
std::string	protocols::antibody::design::design_protocol_to_string (AntibodyDesignProtocolEnum const design_type)
SeqDesignStrategyEnum	protocols::antibody::design::seq_design_strategy_to_enum (std::string strategy)
std::string	protocols::antibody::design::seq_design_strategy_to_string (SeqDesignStrategyEnum strategy)
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) More...
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...
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...
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...
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...
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...
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...
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...
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...
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)
	Get probability data for a given set of CDRs. Will fill in the no_data_cdrs;. More...
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)
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...

Detailed Description

Utility functions for antibody design namespace.

Author

Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)