core::scoring::cryst Namespace Reference

Classes
class	PhenixInterface
class	XtalMLEnergy
class	XtalMLEnergyCreator

Functions
static basic::Tracer	TR ("core.scoring.cryst.XtalMLEnergy")
static basic::Tracer	TR ("core.scoring.cryst.PhenixInterface")
PhenixInterface &	getPhenixInterface ()
	The EDM instance. More...
static basic::Tracer	TS ("core.scoring.cryst.util")
void	fix_bfactorsH (core::pose::Pose &)
	fix the hydrogen bfactors in the pose More...
void	fix_bfactorsMissing (core::pose::Pose &pose)

Function Documentation

void core::scoring::cryst::fix_bfactorsH

(

core::pose::Pose &

pose

)

fix the hydrogen bfactors in the pose

References core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::electron_density::BfactorFittingMover::apply(), core::scoring::cryst::PhenixInterface::fitBfactors(), fix_bfactorsMissing(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and core::scoring::cryst::PhenixInterface::stealBfactorsFromFile().

void core::scoring::cryst::fix_bfactorsMissing

(

core::pose::Pose &

pose

)

References core::conformation::Residue::first_sidechain_atom(), fix_bfactorsH(), core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by core::scoring::cryst::PhenixInterface::fitBfactors(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

PhenixInterface & core::scoring::cryst::getPhenixInterface

(

)

The EDM instance.

Referenced by protocols::cryst::RecomputeDensityMapMover::apply(), protocols::cryst::FitBfactorsMover::apply(), protocols::cryst::UpdateSolventMover::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::cryst::SetRefinementOptionsMover::apply(), core::scoring::cryst::XtalMLEnergy::finalize_total_energy(), core::scoring::cryst::XtalMLEnergy::setup_for_derivatives(), and core::scoring::cryst::XtalMLEnergy::setup_for_minimizing().

static basic::Tracer core::scoring::cryst::TR ( "core.scoring.cryst.XtalMLEnergy"  )

static

Referenced by core::scoring::cryst::PhenixInterface::fitBfactors(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), core::scoring::cryst::PhenixInterface::optimizeSolventMask(), core::scoring::cryst::PhenixInterface::optimizeSolvParams(), core::scoring::cryst::PhenixInterface::optimizeSolvParamsAndMask(), core::scoring::cryst::PhenixInterface::stealBfactorsFromFile(), and core::scoring::cryst::PhenixInterface::updateSolventMask().

static basic::Tracer core::scoring::cryst::TR ( "core.scoring.cryst.PhenixInterface"  )

static

static basic::Tracer core::scoring::cryst::TS ( "core.scoring.cryst.util"  )

static