Rosetta Protocols  2014.35
Namespaces | Functions | Variables
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 <protocols/toolbox/task_operations/RestrictToInterface.hh>
#include <protocols/docking/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>

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...
 
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)
 
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...
 
std::map< CDRNameEnum, boolprotocols::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, boolprotocols::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...
 

Variables

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

Detailed Description

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

Variable Documentation

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