util.cc File Reference

#include <protocols/antibody/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <core/id/AtomID_Map.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/pack/rotamer_set/UnboundRotamersOperation.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <core/pack/task/operation/OperateOnCertainResidues.hh>
#include <core/pack/task/operation/OptH.hh>
#include <core/pack/task/operation/ResFilters.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/dunbrack/RotamerConstraint.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/pack/task/residue_selector/AndResidueSelector.hh>
#include <core/pack/task/residue_selector/NotResidueSelector.hh>
#include <core/pack/task/residue_selector/ChainSelector.hh>
#include <protocols/antibody/AntibodyInfo.hh>
#include <protocols/antibody/AntibodyEnumManager.hh>
#include <protocols/toolbox/task_operations/RestrictToInterface.hh>
#include <protocols/docking/util.hh>
#include <protocols/interface/util.hh>
#include <protocols/simple_moves/ConstraintSetMover.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/conversions.hh>
#include <numeric/PCA.hh>
#include <iostream>
#include <fstream>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/tag/Tag.hh>
#include <math.h>

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

Functions
static thread_local basic::Tracer	TR ("antibody.util")
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...
core::pack::task::TaskFactoryOP	protocols::antibody::setup_packer_task (core::pose::Pose &pose_in)
	Very specific packertask,. More...
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)
Real	protocols::antibody::global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop)
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...
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...
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

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)

Function Documentation

static thread_local basic::Tracer TR ( "antibody.util"  )

static