util.cc File Reference

initialization protocols for relax and utility functions More...

#include <protocols/relax/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/scoring/MembraneTopology.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <protocols/relax/RelaxProtocolBase.hh>
#include <protocols/relax/ClassicRelax.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/relax/MiniRelax.hh>
#include <protocols/relax/CentroidRelax.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <utility/options/keys/OptionKeyList.hh>

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

Functions
static basic::Tracer	TR ("protocols.relax")
RelaxProtocolBaseOP	protocols::relax::generate_relax_from_cmd (bool NULL_if_no_cmd=false)
	Create a relax mover reading from the global options collection. More...
RelaxProtocolBaseOP	protocols::relax::generate_relax_from_cmd (utility::options::OptionCollection const &options, bool NULL_if_no_flag=false)
void	protocols::relax::options_for_generate_relax_from_cmd (utility::options::OptionKeyList &opts)
void	protocols::relax::setup_membrane_topology (core::pose::Pose &pose, std::string spanfile)
	(pba) read in membrane topology More...
void	protocols::relax::make_dna_rigid (core::pose::Pose &pose, core::kinematics::MoveMap &mm)
	Make DNA Rigid in movemap if found in pose. More...
void	protocols::relax::setup_for_dna (core::scoring::ScoreFunction &scorefxn)
	Set energy method options for DNA-DNA. Any other optimization for DNA relax should go here. More...
void	protocols::relax::relax_pose (pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, std::string const &tag)
void	protocols::relax::fixH (core::pose::Pose &pose)
	Rebuild all polymer bond-dependent atoms in the pose. More...
void	protocols::relax::cyclize_pose (core::pose::Pose &pose)
	Add terminal peptide bond and cyclic constraints to pose. More...
core::scoring::constraints::ConstraintCOPs	protocols::relax::add_coordinate_constraint_func_atoms (core::pose::Pose const &pose, core::Size const resnum, core::conformation::Residue const &rsd_i, core::scoring::func::HarmonicFuncOP coord_cst_func, core::id::AtomID const &anchor_atom)

Detailed Description

initialization protocols for relax and utility functions

Author

Mike Tyka, Monica Berrondo

Roland A. Pache

Function Documentation

TR()

static basic::Tracer TR ( "protocols.relax"  )

static

Referenced by protocols::relax::add_coordinate_constraint_func_atoms(), protocols::relax::generate_relax_from_cmd(), and protocols::relax::make_dna_rigid().