util.hh File Reference

Utility functions for the Antibody namespace. More...

#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/antibody/AntibodyInfo.hh>
#include <protocols/antibody/AntibodyEnumManager.hh>
#include <protocols/antibody/clusters/CDRClusterEnumManager.hh>
#include <utility/vector1.hh>

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

Functions
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. Return dock_chains string. More...
std::string	protocols::antibody::setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Setup A_LH foldtree. 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)
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)
std::map< CDRNameEnum, bool >	protocols::antibody::add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose)
	Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo. More...
std::map< CDRNameEnum, bool >	protocols::antibody::add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
	Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
bool	protocols::antibody::add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster)
	Adds a harmonic constraint to a Pose CDR based on cluster type. More...
bool	protocols::antibody::add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
	Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
std::string	protocols::antibody::get_harmonic_cluster_constraint_filename (AntibodyInfoCOP ab_info, CDRClusterEnum const cluster)
	Gets the cluster constraint name. Returns NA if not found. 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)