protocols::loop_grower Namespace Reference

Classes
class	DensSkeleton
class	FragmentExtension
class	LoopComparator
class	FragmentExtensionCreator
struct	ResTorsions
struct	SheetPositions
class	LoopPartialSolution
struct	RMSComparator
class	LoopPartialSolutionStore
class	LoopGrower
class	SheetSampler

Typedefs
typedef utility::pointer::shared_ptr< DensSkeleton >	DensSkeletonOP
typedef utility::pointer::shared_ptr< DensSkeleton const >	DensSkeletonCOP
typedef utility::pointer::shared_ptr< FragmentExtension >	FragmentExtensionOP
typedef utility::pointer::shared_ptr< FragmentExtension const >	FragmentExtensionCOP
typedef utility::pointer::shared_ptr< LoopGrower >	LoopGrowerOP
typedef utility::pointer::shared_ptr< LoopGrower const >	LoopGrowerCOP
typedef utility::pointer::shared_ptr< SheetSampler >	SheetSamplerOP
typedef utility::pointer::shared_ptr< SheetSampler const >	SheetSamplerCOP

Functions
static basic::Tracer	TR ("protocols.loop_grower.FragmentExtension")
std::string	fragext_subelement_ct_name (std::string const &name)
static basic::Tracer	TR ("protocols.loop_grower.LoopGrower")
core::Real	gapdist (int n)
static basic::Tracer	TR ("protocols.loop_grower.SheetSampler")
void	printxyz (numeric::xyzVector< core::Real > printvec)
static basic::Tracer	TR ("protocols.loop_grower.util")
void	transform_res_to_subunit (core::pose::Pose &pose, core::conformation::ResidueOP xformed, core::Size symmcopy)
void	transform_to_closest_symmunit (core::pose::Pose &cen_pose, core::pose::Pose &fa_pose, core::Size lower_pose)

Typedef Documentation

DensSkeletonCOP

typedef utility::pointer::shared_ptr< DensSkeleton const > protocols::loop_grower::DensSkeletonCOP

DensSkeletonOP

typedef utility::pointer::shared_ptr< DensSkeleton > protocols::loop_grower::DensSkeletonOP

FragmentExtensionCOP

typedef utility::pointer::shared_ptr< FragmentExtension const > protocols::loop_grower::FragmentExtensionCOP

FragmentExtensionOP

typedef utility::pointer::shared_ptr< FragmentExtension > protocols::loop_grower::FragmentExtensionOP

LoopGrowerCOP

typedef utility::pointer::shared_ptr< LoopGrower const > protocols::loop_grower::LoopGrowerCOP

LoopGrowerOP

typedef utility::pointer::shared_ptr< LoopGrower > protocols::loop_grower::LoopGrowerOP

SheetSamplerCOP

typedef utility::pointer::shared_ptr< SheetSampler const > protocols::loop_grower::SheetSamplerCOP

SheetSamplerOP

typedef utility::pointer::shared_ptr< SheetSampler > protocols::loop_grower::SheetSamplerOP

Function Documentation

fragext_subelement_ct_name()

std::string protocols::loop_grower::fragext_subelement_ct_name

(

std::string const &

name

)

Referenced by protocols::loop_grower::FragmentExtension::provide_xml_schema().

gapdist()

core::Real protocols::loop_grower::gapdist

(

int

n

)

Referenced by protocols::loop_grower::LoopGrower::apply(), and protocols::loop_grower::LoopGrower::single_grow().

printxyz()

void protocols::loop_grower::printxyz

(

numeric::xyzVector< core::Real >

printvec

)

References TR().

TR() [1/4]

static basic::Tracer protocols::loop_grower::TR ( "protocols.loop_grower.FragmentExtension"  )

static

Referenced by protocols::loop_grower::LoopGrower::add_fragment_csts(), protocols::loop_grower::LoopGrower::add_user_csts(), protocols::loop_grower::LoopGrower::addnativesolution(), protocols::loop_grower::LoopComparator::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::loop_grower::LoopPartialSolution::apply(), protocols::loop_grower::DensSkeleton::breadth_first_connect(), protocols::loop_grower::LoopGrower::check_auto_stop(), protocols::loop_grower::LoopGrower::coordinate_filter(), protocols::loop_grower::LoopPartialSolutionStore::diversityfilter(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::loop_grower::LoopGrower::modifiedscore(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::loop_grower::FragmentExtension::parse_my_tag(), printxyz(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::loop_grower::LoopGrower::read_coordfile(), protocols::loop_grower::LoopGrower::read_from_disk(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::loop_grower::LoopGrower::RMStonative(), protocols::loop_grower::LoopComparator::set_scores(), protocols::loop_grower::LoopGrower::single_grow(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::loop_grower::LoopGrower::store_sheets(), and protocols::loop_grower::LoopPartialSolutionStore::zscoretransform().

TR() [2/4]

static basic::Tracer protocols::loop_grower::TR ( "protocols.loop_grower.LoopGrower"  )

static

TR() [3/4]

static basic::Tracer protocols::loop_grower::TR ( "protocols.loop_grower.SheetSampler"  )

static

TR() [4/4]

static basic::Tracer protocols::loop_grower::TR ( "protocols.loop_grower.util"  )

static

transform_res_to_subunit()

void protocols::loop_grower::transform_res_to_subunit	(	core::pose::Pose &	pose,
		core::conformation::ResidueOP	xformed,
		core::Size	symmcopy
	)

References core::pose::Pose::conformation(), and protocols::comparative_modeling::features::X.

Referenced by transform_to_closest_symmunit().

transform_to_closest_symmunit()

void protocols::loop_grower::transform_to_closest_symmunit	(	core::pose::Pose &	cen_pose,
		core::pose::Pose &	fa_pose,
		core::Size	lower_pose
	)

References core::conformation::Residue::atom(), core::pose::Pose::conformation(), protocols::mpi_refinement::distance(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Conformation::residue_cop(), core::pose::Pose::total_residue(), transform_res_to_subunit(), and core::conformation::Atom::xyz().

Referenced by protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::single_grow().