core::scoring::atomic_depth Namespace Reference

Classes
struct	point3d
struct	volumepixel
struct	voxel
struct	voxel2
class	AtomicDepth

Typedefs
typedef utility::pointer::shared_ptr< AtomicDepth >	AtomicDepthOP
typedef utility::pointer::shared_ptr< AtomicDepth const >	AtomicDepthCOP
typedef struct core::scoring::atomic_depth::point3d	point3d
typedef struct core::scoring::atomic_depth::volumepixel	volumepixel
typedef struct core::scoring::atomic_depth::voxel	voxel
typedef struct core::scoring::atomic_depth::voxel2	voxel2

Functions
core::id::AtomID_Map< core::Real >	atomic_depth (pose::Pose const &pose, Real probe_radius, bool poly_leu_depth, Real resolution)
	Calculate depth of all atoms from edge of Sasa surface. More...
core::id::AtomID_Map< core::Real >	atomic_depth (pose::Pose const &pose, AtomicDepthOP &depth, Real probe_radius, bool poly_leu_depth, Real resolution)
	Calculate depth of all atoms from edge of Sasa surface. @detail If atomic_depth is a nullptr, will create one and return it. @detail Note that probe_radius is ignored if atomic_depth is not null. More...
core::id::AtomID_Map< core::Real >	atomic_depth (pose::Pose const &pose, core::id::AtomID_Map< bool > depth_atoms, Real probe_radius, bool poly_leu_depth, Real resolution)
	Calculate depth of certain atoms from edge of Sasa surface. More...
core::id::AtomID_Map< core::Real >	atomic_depth (pose::Pose const &pose, core::id::AtomID_Map< bool > depth_atoms, AtomicDepthOP &depth, Real probe_radius, bool poly_leu_depth, Real resolution)
	Calculate depth of certain atoms from edge of Sasa surface. @detail If atomic_depth is a nullptr, will create one and return it. @detail Note that probe_radius is ignored if atomic_depth is not null. More...
core::id::AtomID_Map< bool >	atoms_deeper_than (pose::Pose const &pose, Real threshold, bool invert, Real probe_radius, bool poly_leu_depth, Real resolution)
	Find all atoms deeper than threshold from the edge of the sasa surface. More...

Variables
static const signed char	nb [26][3]
const int	fast_one_shell_cut [3] = {6, 12, 9}
const int	fast_one_shell_lowb [3] = {0, 6, 18}
const int	fast_one_shell_highb [3] = {6, 18, 26}

Typedef Documentation

AtomicDepthCOP

typedef utility::pointer::shared_ptr< AtomicDepth const > core::scoring::atomic_depth::AtomicDepthCOP

AtomicDepthOP

typedef utility::pointer::shared_ptr< AtomicDepth > core::scoring::atomic_depth::AtomicDepthOP

point3d

typedef struct core::scoring::atomic_depth::point3d core::scoring::atomic_depth::point3d

volumepixel

typedef struct core::scoring::atomic_depth::volumepixel core::scoring::atomic_depth::volumepixel

voxel

typedef struct core::scoring::atomic_depth::voxel core::scoring::atomic_depth::voxel

voxel2

typedef struct core::scoring::atomic_depth::voxel2 core::scoring::atomic_depth::voxel2

Function Documentation

atomic_depth() [1/4]

core::id::AtomID_Map< core::Real > core::scoring::atomic_depth::atomic_depth	(	pose::Pose const &	pose,
		AtomicDepthOP &	depth,
		Real	probe_radius,
		bool	poly_leu_depth,
		Real	resolution
	)

Calculate depth of all atoms from edge of Sasa surface. @detail If atomic_depth is a nullptr, will create one and return it. @detail Note that probe_radius is ignored if atomic_depth is not null.

Calculate depth of all atoms from edge of Sasa surface. @detail If atomic_depth is a nullptr, will create one and return it. @detail Note that probe_radius and poly_leu_depth are ignored if atomic_depth is not null.

References atomic_depth(), core::pose::Pose::conformation(), and core::pose::initialize_atomid_map().

atomic_depth() [2/4]

core::id::AtomID_Map< core::Real > core::scoring::atomic_depth::atomic_depth	(	pose::Pose const &	pose,
		core::id::AtomID_Map< bool >	depth_atoms,
		AtomicDepthOP &	depth,
		Real	probe_radius,
		bool	poly_leu_depth,
		Real	resolution
	)

Calculate depth of certain atoms from edge of Sasa surface. @detail If atomic_depth is a nullptr, will create one and return it. @detail Note that probe_radius is ignored if atomic_depth is not null.

Calculate depth of all atoms from edge of Sasa surface. @detail If atomic_depth is a nullptr, will create one and return it. @detail Note that probe_radius and poly_leu_depth are ignored if atomic_depth is not null.

References core::conformation::Residue::atom(), core::chemical::ResidueTypeBase::atom_type_set(), core::pose::Pose::conformation(), core::pose::initialize_atomid_map(), core::id::AtomID_Map< T >::n_atom(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::size(), core::pose::Pose::size(), and core::conformation::Residue::type().

Referenced by core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation().

atomic_depth() [3/4]

core::id::AtomID_Map< core::Real > core::scoring::atomic_depth::atomic_depth	(	pose::Pose const &	pose,
		core::id::AtomID_Map< bool >	depth_atoms,
		Real	probe_radius,
		bool	poly_leu_depth,
		Real	resolution
	)

Calculate depth of certain atoms from edge of Sasa surface.

Calculate depth of all atoms from edge of Sasa surface.

References atomic_depth().

atomic_depth() [4/4]

core::id::AtomID_Map< core::Real > core::scoring::atomic_depth::atomic_depth	(	pose::Pose const &	pose,
		Real	probe_radius,
		bool	poly_leu_depth,
		Real	resolution
	)

Calculate depth of all atoms from edge of Sasa surface.

Referenced by protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), atomic_depth(), and atoms_deeper_than().

atoms_deeper_than()

core::id::AtomID_Map< bool > core::scoring::atomic_depth::atoms_deeper_than	(	pose::Pose const &	pose,
		Real	threshold,
		bool	invert,
		Real	probe_radius,
		bool	poly_leu_depth,
		Real	resolution
	)

Find all atoms deeper than threshold from the edge of the sasa surface.

References atomic_depth(), core::pose::Pose::conformation(), core::pose::initialize_atomid_map(), core::id::AtomID_Map< T >::n_atom(), and core::id::AtomID_Map< T >::size().

Referenced by protocols::simple_filters::BuriedUnsatHbondFilter::compute(), and protocols::simple_filters::BuriedUnsatHbondFilter::get_deep_apo_atoms().

Variable Documentation

fast_one_shell_cut

const int core::scoring::atomic_depth::fast_one_shell_cut[3] = {6, 12, 9}

Referenced by core::scoring::atomic_depth::AtomicDepth::fastoneshell().

fast_one_shell_highb

const int core::scoring::atomic_depth::fast_one_shell_highb[3] = {6, 18, 26}

Referenced by core::scoring::atomic_depth::AtomicDepth::fastoneshell().

fast_one_shell_lowb

const int core::scoring::atomic_depth::fast_one_shell_lowb[3] = {0, 6, 18}

Referenced by core::scoring::atomic_depth::AtomicDepth::fastoneshell().

nb

const signed char core::scoring::atomic_depth::nb[26][3]

static

Initial value:

={{1,0,0}, {-1,0,0}, {0,1,0}, {0,-1,0}, {0,0,1}, {0,0,-1},
{1,1,0}, {1,-1,0}, {-1,1,0}, {-1,-1,0}, {1,0,1}, {1,0,-1}, {-1,0,1}, {-1,0,-1}, {0,1,1}, {0,1,-1}, {0,-1,1}, {0,-1,-1},
{1,1,1}, {1,1,-1}, {1,-1,1}, {-1,1,1}, {1,-1,-1}, {-1,-1,1}, {-1,1,-1}, {-1,-1,-1}}

Referenced by core::scoring::atomic_depth::AtomicDepth::buildboundary(), core::energy_methods::FA_GrpElecEnergy::burial_deriv(), core::energy_methods::FA_GrpElecEnergy::burial_weight(), core::scoring::hbonds::burial_weight(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::energy_methods::FA_GrpElecEnergy::eval_intrares_energy(), and core::scoring::atomic_depth::AtomicDepth::fastoneshell().