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util.cc File Reference
#include <protocols/antibody/design/util.hh>
#include <protocols/antibody/AntibodyInfo.hh>
#include <protocols/antibody/database/CDRSetOptions.hh>
#include <protocols/antibody/database/CDRSetOptionsParser.hh>
#include <protocols/antibody/design/CDRSeqDesignOptions.hh>
#include <protocols/antibody/design/CDRGraftDesignOptions.hh>
#include <protocols/antibody/database/AntibodyDatabaseManager.hh>
#include <protocols/antibody/design/NativeAntibodySeq.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/pose/chains_util.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <protocols/grafting/util.hh>
#include <protocols/loops/util.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/DataCache.hh>
#include <basic/datacache/CacheableData.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/antibody.OptionKeys.gen.hh>
#include <boost/algorithm/string.hpp>
#include <string>
#include <utility/exit.hh>
#include <iostream>
#include <basic/Tracer.hh>
#include <utility/string_util.hh>
#include <utility/tag/Tag.hh>
#include <utility/tag/XMLSchemaGeneration.hh>

Namespaces

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

Functions

static basic::Tracer TR ("protocols.antibody.design.util")
 
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; XSD companion function: attributes_for_get_ab_design_global_scorefxn. More...
 
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...
 
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 ()
 XSD companion function: attributes_for_get_ab_design_min_scorefxn. More...
 
ScoreFunctionOP protocols::antibody::design::get_ab_design_min_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
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...
 
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...
 
vector1< vector1< core::Size > > protocols::antibody::design::get_all_graft_permutations (vector1< vector1< core::Size > > permutations, vector1< core::Size > totals, core::Size const n)
 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 const &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 const &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< PDBNumbering > protocols::antibody::design::get_pdb_numbering_from_strings (vector1< std::string > const &pdb_residues)
 
vector1< boolprotocols::antibody::design::get_resnums_from_strings_with_ranges (core::pose::Pose const &pose, vector1< std::string > const &pdb_residues)
 
vector1< boolprotocols::antibody::design::get_resnum_from_pdb_numbering (core::pose::Pose const &pose, vector1< PDBNumbering > const &pdb_residues)
 Get a boolean vector from a string of PDBNumbering. No error checking. Use with caution. More...
 
vector1< boolprotocols::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...
 
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::pair< bool, core::Sizeprotocols::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...
 
std::pair< bool, core::Sizeprotocols::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...
 
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...
 
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, bool cdr4_as_framework=true)
 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...
 
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...
 
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...
 
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)
 
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...
 
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...
 
std::string protocols::antibody::design::get_native_sequence (core::pose::Pose const &pose, AntibodyInfo const &ab_info)
 
bool protocols::antibody::design::has_native_sequence (core::pose::Pose const &pose)
 

Detailed Description

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

Function Documentation

static basic::Tracer TR ( "protocols.antibody.design.util"  )
static