util.hh File Reference

Utility functions for the Antibody namespace. More...

#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/antibody/AntibodyInfo.fwd.hh>
#include <protocols/antibody/AntibodyEnum.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.fwd.hh>

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

Functions
utility::vector1< bool >	protocols::antibody::get_cdr_bool_from_tag (utility::tag::TagCOP tag, std::string const &name)
	Geta boolean vector of CDRs from a RosettaScripts tag. More...
protocols::loops::LoopsOP	protocols::antibody::get_cdr_loops (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, utility::vector1< bool > cdrs, core::Size stem_size=0)
	Get a set of loops for a boolean vector of CDRNameEnums including any stem residues. More...
Real	protocols::antibody::global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop)
bool	protocols::antibody::cutpoints_separation (core::pose::Pose &pose, AntibodyInfoOP &antibody_info)
	return false if any cdr cutpoint is broken More...
Real	protocols::antibody::cutpoint_separation (pose::Pose &pose_in, Size cutpoint)
vector1< bool >	protocols::antibody::select_epitope_residues (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, core::Size const interface_distance=10.0)
	Get the epitope residues using the InterGroupNeighborsCalculator. More...
void	protocols::antibody::check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, CDRNameEnum cdr, core::pose::Pose &pose)
	Checks the length of the CDR, fixes AHO numbering for longer CDR loops that don't fit within the numbering scheme. More...
void	protocols::antibody::check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
void	protocols::antibody::simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop)
void	protocols::antibody::simple_fold_tree (pose::Pose &pose_in, Size jumppoint1, Size cutpoint, Size jumppoint2)
std::string	protocols::antibody::setup_LH_A_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Setup LH_A foldtree via docking. Return dock_chains string. More...
std::string	protocols::antibody::setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Setup A_LH foldtree via docking. Return dock_chains string. More...
core::pack::task::TaskFactoryOP	protocols::antibody::setup_packer_task (core::pose::Pose &pose_in)
	Very specific packertask,. More...
void	protocols::antibody::align_to_native (core::pose::Pose &pose, core::pose::Pose const &native_pose, AntibodyInfoOP const ab_info, AntibodyInfoOP const native_ab_info, std::string const &request_chain="LH")
	align current Fv to native.Fv More...
bool	protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule (const pose::Pose &pose_in, loops::Loop &input_loop, bool is_camelid)
	tests if a loop has H3 like base charachteristics More...
bool	protocols::antibody::CDR_H3_cter_filter (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
bool	protocols::antibody::is_H3_rama_kinked (std::string const rama)
	Very basic kink function based on rama groups. Kink is defined as having AB + DB at the C-terminal stem. This is in the North/Dunbrack CDR definition. Avoid this definition if you can and talk to brain. This is currently used for a quick filtering for design. More...

Detailed Description

Utility functions for the Antibody namespace.

Author

Jianqing Xu (xubes.nosp@m.t@gm.nosp@m.ail.c.nosp@m.om)

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