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HotspotStubSet.cc File Reference
#include <protocols/hotspot_hashing/HotspotStubSet.hh>
#include <protocols/hotspot_hashing/HotspotStub.hh>
#include <core/pose/Pose.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/id/AtomID_Map.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/chemical/AA.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <protocols/docking/DockingProtocol.hh>
#include <protocols/docking/DockingInitialPerturbation.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <protocols/cluster/APCluster.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/moves/Mover.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/BackboneStubConstraint.hh>
#include <core/scoring/constraints/BackboneStubLinearConstraint.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/rms_util.hh>
#include <protocols/filters/Filter.hh>
#include <protocols/filters/BasicFilters.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/io/ozstream.hh>
#include <core/types.hh>
#include <core/io/Remarks.hh>
#include <core/conformation/Atom.hh>
#include <numeric/random/random.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>
#include <sstream>
#include <map>
#include <set>
#include <utility/assert.hh>
#include <algorithm>
#include <cmath>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/hotspot.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/simple_ddg/DdgFilter.hh>
#include <utility/vector0.hh>
#include <basic/options/option.hh>
#include <numeric/random/random_permutation.hh>

Namespaces

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

Functions

static basic::Tracer protocols::hotspot_hashing::TR ("protocols.hotspot_hashing")
 
core::scoring::constraints::ConstraintCOPs protocols::hotspot_hashing::remove_hotspot_constraints_from_pose (core::pose::Pose &)
 utility function for deleting all backbone stub constraints from a pose. Returns the removed constraints (ambiguous). More...
 
core::Real protocols::hotspot_hashing::residue_sc_rmsd_no_super (core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2, bool const fxnal_group_only=false)
 utility function to calculate per-residue sidechain rmsd without superposition More...
 
core::Real protocols::hotspot_hashing::stub_tgt_angle (core::pose::Pose const &pose, core::conformation::ResidueCOP stub, core::Size const target_res)
 utility function to make sure stub's Cbeta is not pointed away from the target. Returns true if stub is pointed generally towards target's center of mass. Returns false otherwise. algorithm: get vector between CA and target center of mass, then CA-CB vector. Check alignment between the two. doesn't take into account hotspots at the end of the pose so might be a little off in CoM. But probably pretty OK More...