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core::scoring::atomic_depth Namespace Reference

Classes

class  AtomicDepth
 
struct  point3d
 
struct  volumepixel
 
struct  voxel
 
struct  voxel2
 

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::Realatomic_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::Realatomic_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. If atomic_depth is a nullptr, will create one and return it. Note that probe_radius is ignored if atomic_depth is not null. More...
 
core::id::AtomID_Map< core::Realatomic_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::Realatomic_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. If atomic_depth is a nullptr, will create one and return it. Note that probe_radius is ignored if atomic_depth is not null. More...
 
core::id::AtomID_Map< boolatoms_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

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

Function Documentation

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().

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. If atomic_depth is a nullptr, will create one and return it. Note that probe_radius is ignored if atomic_depth is not null.

Calculate depth of all atoms from edge of Sasa surface. If atomic_depth is a nullptr, will create one and return it. 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().

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().

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. If atomic_depth is a nullptr, will create one and return it. Note that probe_radius is ignored if atomic_depth is not null.

Calculate depth of all atoms from edge of Sasa surface. If atomic_depth is a nullptr, will create one and return it. 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().

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 
)

Variable Documentation

const int core::scoring::atomic_depth::fast_one_shell_cut[3] = {6, 12, 9}
const int core::scoring::atomic_depth::fast_one_shell_highb[3] = {6, 18, 26}
const int core::scoring::atomic_depth::fast_one_shell_lowb[3] = {0, 6, 18}
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::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_energy(), and core::scoring::atomic_depth::AtomicDepth::fastoneshell().