RigidChunkClaimer.cc File Reference

#include <protocols/topology_broker/RigidChunkClaimer.hh>
#include <protocols/topology_broker/claims/DofClaim.hh>
#include <protocols/topology_broker/claims/JumpClaim.hh>
#include <protocols/topology_broker/claims/CutClaim.hh>
#include <protocols/topology_broker/claims/BBClaim.hh>
#include <protocols/topology_broker/SequenceNumberResolver.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/variant_util.hh>
#include <core/id/DOF_ID.hh>
#include <core/sequence/SequenceAlignment.fwd.hh>
#include <protocols/comparative_modeling/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.tmpl.hh>
#include <protocols/loops/LoopsFileIO.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/comparative_modeling/ThreadingJob.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/VariantType.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/option.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/xyz.functions.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <vector>
#include <fstream>
#include <protocols/jd2/Job.hh>
#include <utility/vector1.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>

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

Functions
static basic::Tracer	tr ("protocols.topo_broker", basic::t_info)
protocols::loops::Loops	protocols::topology_broker::generate_rigid_from_alignment (pose::Pose query_pose, core::sequence::SequenceAlignment const &align, core::Size min_loop_size)
void	protocols::topology_broker::fix_internal_coords_of_siblings (pose::Pose &pose, pose::Pose const &ref_pose, id::AtomID atom, id::AtomID ref_atom)
void	protocols::topology_broker::fix_mainchain_connect (pose::Pose &pose, pose::Pose const &ref_pose, core::Size upper_residue)
void	protocols::topology_broker::copy_internal_coords (pose::Pose &pose, pose::Pose const &ref_pose, loops::Loops core)
bool	protocols::topology_broker::is_not_neighbor_to_rigid (loops::Loops const &rigid, core::Size pos1, core::Size pos2)
bool	protocols::topology_broker::connects_rigid_regions (loops::Loops const &rigid, core::Size pos1, core::Size pos2)

Function Documentation

tr()

static basic::Tracer tr ( "protocols.topo_broker"  , basic::t_info    )

static

Referenced by protocols::topology_broker::RigidChunkClaimer::accept_declined_claim(), protocols::topology_broker::copy_internal_coords(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::topology_broker::RigidChunkClaimer::generate_claims(), protocols::topology_broker::RigidChunkClaimer::init_after_reading(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::topology_broker::RigidChunkClaimer::JumpCalculator::irrelevant_jump(), protocols::topology_broker::RigidChunkClaimer::new_decoy(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::select_parts(), and protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom().