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 <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/grafting/util.hh>
#include <protocols/loops/util.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>

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

Functions
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< vector1< core::Size > > &all_permutations, utility::vector1< core::Size >current_index, core::Size const cdr_num)
	Gets all possible graft permutations. More...
DesignTypeEnum	protocols::antibody::design::design_type_from_string (std::string const design_type)
std::string	protocols::antibody::design::design_type_to_string (DesignTypeEnum const design_type)
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...
vector1< PDBNumbering >	protocols::antibody::design::get_pdb_numbering_from_string (vector1< std::string > const &pdb_residues)
vector1< bool >	protocols::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...
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)
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...
AntibodyCDRSetOptions	protocols::antibody::design::get_cdr_set_options ()
	Application Options - Should be moved as part of parsers? More...
AntibodyCDRGraftDesignOptions	protocols::antibody::design::get_graft_design_options ()
	Get options set from default instructions file and any user overrides. More...
AntibodyCDRSeqDesignOptions	protocols::antibody::design::get_seq_design_options ()
	Get options set from default instructions file and any user overrides. More...

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

Detailed Description

Author

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

Variable Documentation

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

static