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protocols::match Namespace Reference

Namespaces

 downstream
 
 output
 
 upstream
 

Classes

class  AddAllPositionsMPM
 MPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere. More...
 
class  BfactorMPM
 removes positions at which the bfactors for c-alpha atoms are above a desired cutoff. bfactors stored in the pose pdbinfo are taken. if relative bfactors are used, all bfactors are divided by the largest observed bfactor More...
 
class  Bool3DGrid
 
class  Bool3DGridKinemageWriter
 
class  BumpGrid
 
class  downstream_hit
 
class  Hit
 
class  HitHasher
 This object hashes hits into 6D voxels. This hash can then be traversed to retrieve the hits that hash to the same voxel (matches!). There are 64 hashes representing the 2^6 ways to perturb the bins in 6D by 1/2 of their bin width. More...
 
class  HitNeighborFinder
 
struct  match_dspos1
 Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position) More...
 
struct  match_lite_equals
 
struct  match_lite_hasher
 
class  MatchCounter
 Class for counting the number of matches given a particular discretization level. More...
 
class  Matcher
 
class  MatcherMover
 
class  MatcherMoverCreator
 
class  MatcherOutputStats
 
class  MatcherTask
 
class  MatchOutputTracker
 
class  MatchPositionModifier
 base class for objects that modify the match positions based on some criterion More...
 
class  NumNeighborsMPM
 removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won't be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward More...
 
class  OccupiedSpaceHash
 This class keeps track of the active voxels "up until now" with 64 hashes. More...
 
class  RemoveNorCTermMPM
 added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching More...
 
class  SecondaryStructureMPM
 removes positions at which the pose does not have the desired secondary structure More...
 
class  TaskOperationMPM
 mpm that will get a task operation as specified in the tag from the TaskOperationFactory, apply the task operation to the pose and every residue that is then set to designing in the task will be a match position More...
 
class  upstream_hit
 
class  VoxelSetIterator
 Helper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< Bool3DGrid
Bool3DGridOP
 
typedef
utility::pointer::shared_ptr
< Bool3DGrid const > 
Bool3DGridCOP
 
typedef
utility::pointer::shared_ptr
< BumpGrid
BumpGridOP
 
typedef
utility::pointer::shared_ptr
< BumpGrid const > 
BumpGridCOP
 
typedef
numeric::geometry::hashing::Size3 
Size3
 
typedef
numeric::geometry::hashing::Size4 
Size4
 
typedef
numeric::geometry::hashing::Real6 
Real6
 
typedef utility::vector1< Hitmatch
 
typedef
numeric::kdtree::WrappedPrimitive
< std::list< Hit const * > > 
HitPtrList
 
typedef
utility::pointer::shared_ptr
< HitPtrList
HitPtrListOP
 
typedef
utility::pointer::shared_ptr
< HitPtrList const > 
HitPtrListCOP
 
typedef
utility::pointer::shared_ptr
< Matcher
MatcherOP
 
typedef
utility::pointer::shared_ptr
< Matcher const > 
MatcherCOP
 
typedef
utility::pointer::shared_ptr
< MatcherMover
MatcherMoverOP
 
typedef
utility::pointer::shared_ptr
< MatcherMover const > 
MatcherMoverCOP
 
typedef
utility::pointer::shared_ptr
< MatcherTask
MatcherTaskOP
 
typedef
utility::pointer::shared_ptr
< MatcherTask const > 
MatcherTaskCOP
 
typedef
utility::pointer::shared_ptr
< MatchPositionModifier
MatchPositionModifierOP
 
typedef
utility::pointer::shared_ptr
< MatchPositionModifier const > 
MatchPositionModifierCOP
 
typedef
utility::pointer::shared_ptr
< HitHasher
HitHasherOP
 
typedef
utility::pointer::shared_ptr
< HitHasher const > 
HitHasherCOP
 
typedef utility::vector1< Hit
const * > 
match_lite
 
typedef
utility::pointer::shared_ptr
< OccupiedSpaceHash
OccupiedSpaceHashOP
 
typedef
utility::pointer::shared_ptr
< OccupiedSpaceHash const > 
OccupiedSpaceHashCOP
 

Enumerations

enum  ProbeRadius {
  ZERO = 0, H_ARO, H_ALA, OXY,
  NIT, C_CAR, C_ALA, SULPH,
  n_probe_radii = SULPH
}
 

Functions

static basic::Tracer TR ("protocols.BumpGrid")
 
utility::vector1< ProbeRadiusinitialize_atomtype_2_probe_radius_map ()
 
ProbeRadius probe_radius_for_atom_type (core::Size atomtype)
 
BumpGridOP bump_grid_to_enclose_pose (core::pose::Pose const &pose)
 
BumpGridOP bump_grid_to_enclose_residue_backbone (core::conformation::Residue const &residue, BumpGrid const &original_grid)
 Construct a BumpGrid that encloses the backbone atoms for a single residue. Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together. More...
 
BumpGridOP bump_grid_to_enclose_residue (core::conformation::Residue const &residue, BumpGrid const &original_grid)
 Construct a BumpGrid that encloses a single residue. Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together. More...
 
void fill_grid_with_residue_spheres (core::conformation::Residue const &residue, BumpGrid &grid)
 
void fill_grid_with_residue_heavyatom_spheres (core::conformation::Residue const &residue, BumpGrid &grid)
 
void fill_grid_with_backbone_heavyatom_spheres (core::conformation::Residue const &residue, BumpGrid &grid)
 
Hit fake_hit (upstream_hit const &)
 Create a fake hit from an upstream_hit where hit.first()[4] and hit.second() are 0's. More...
 
Hit fake_hit (downstream_hit const &)
 Create a fake hit from a downstream_hit where hit.first()[1-3] are 0's. More...
 
Hit full_hit (match_dspos1 const &m)
 Create a hit with the full data from a given match_dspos1 representing the upstream conformation from the originating_geom_cst and its description of the downstream position. More...
 
static basic::Tracer TR ("protocols.match.Matcher")
 
static basic::Tracer tr ("protocols.match.MatcherMover")
 
void set_ligpose_rotamer (core::pose::Pose &ligpose)
 
static basic::Tracer TR ("protocols.match.MatcherTask")
 
static basic::Tracer tr ("protocols.match.MatchPositionModifiers")
 
MatchPositionModifierCOP create_match_position_modifier (std::string const &mpm_name, core::Size geom_cst, utility::vector1< std::string > const &input_tokens)
 "factory" function to create the match position modifiers More...
 
core::Size advance_to_neighbor_bin (Real6 orig_point, Real6 steps, numeric::geometry::hashing::SixDCoordinateBinner const &binner, numeric::geometry::hashing::Bin6D &next_bin)
 Non-member function that handles the logic for finding a nearby bin in 6D when taking a step of a specified size from an existing bin. More...
 
numeric::geometry::hashing::Real3 advance_euler_angles (numeric::geometry::hashing::Real3 const &orig_angles, numeric::geometry::hashing::Real3 const &offsets)
 Increment the euler angles and then wrap them into their appropriate ranges. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< Bool3DGrid const > protocols::match::Bool3DGridCOP
typedef utility::pointer::shared_ptr< Bool3DGrid > protocols::match::Bool3DGridOP
typedef utility::pointer::shared_ptr< BumpGrid const > protocols::match::BumpGridCOP
typedef utility::pointer::shared_ptr< BumpGrid > protocols::match::BumpGridOP
typedef utility::pointer::shared_ptr< HitHasher const > protocols::match::HitHasherCOP
typedef utility::pointer::shared_ptr< HitHasher > protocols::match::HitHasherOP
typedef numeric::kdtree::WrappedPrimitive< std::list< Hit const * > > protocols::match::HitPtrList
typedef utility::pointer::shared_ptr< HitPtrList const > protocols::match::HitPtrListCOP
typedef utility::pointer::shared_ptr< HitPtrList > protocols::match::HitPtrListOP
typedef utility::vector1< Hit > protocols::match::match
typedef utility::vector1< Hit const * > protocols::match::match_lite
typedef utility::pointer::shared_ptr< Matcher const > protocols::match::MatcherCOP
typedef utility::pointer::shared_ptr< MatcherMover const > protocols::match::MatcherMoverCOP
typedef utility::pointer::shared_ptr< MatcherMover > protocols::match::MatcherMoverOP
typedef utility::pointer::shared_ptr< Matcher > protocols::match::MatcherOP
typedef utility::pointer::shared_ptr< MatcherTask const > protocols::match::MatcherTaskCOP
typedef utility::pointer::shared_ptr< MatcherTask > protocols::match::MatcherTaskOP
typedef utility::pointer::shared_ptr< MatchPositionModifier const > protocols::match::MatchPositionModifierCOP
typedef utility::pointer::shared_ptr< MatchPositionModifier > protocols::match::MatchPositionModifierOP
typedef utility::pointer::shared_ptr< OccupiedSpaceHash const > protocols::match::OccupiedSpaceHashCOP
typedef utility::pointer::shared_ptr< OccupiedSpaceHash > protocols::match::OccupiedSpaceHashOP
typedef numeric::geometry::hashing::Real6 protocols::match::Real6
typedef numeric::geometry::hashing::Size3 protocols::match::Size3
typedef numeric::geometry::hashing::Size4 protocols::match::Size4

Enumeration Type Documentation

The different radii types used in collision detection. These values are taken from Probe / Reduce from the Richardson lab. Code inside BumpGrid.cc assumes the radii listed here being in non-decreasing order, and that ZERO is the 0th element of this enumeration.

Enumerator
ZERO 
H_ARO 
H_ALA 
OXY 
NIT 
C_CAR 
C_ALA 
SULPH 
n_probe_radii 

Function Documentation

numeric::geometry::hashing::Real3 protocols::match::advance_euler_angles ( numeric::geometry::hashing::Real3 const &  orig_angles,
numeric::geometry::hashing::Real3 const &  offsets 
)

Increment the euler angles and then wrap them into their appropriate ranges.

"Advance" the euler angles by a given offset (postive or negative), and wrap them back into their appropriate ranges ([0,360) for phi/psi, [0..180] for theta) as necessary. Requirements: orig_angles[ i ] + offsets[ i ] < 520 (360) && > -360 (-180) for phi/psi (theta).

Referenced by advance_to_neighbor_bin().

core::Size protocols::match::advance_to_neighbor_bin ( Real6  orig_point,
Real6  steps,
numeric::geometry::hashing::SixDCoordinateBinner const &  binner,
numeric::geometry::hashing::Bin6D &  next_bin 
)

Non-member function that handles the logic for finding a nearby bin in 6D when taking a step of a specified size from an existing bin.

References advance_euler_angles().

Referenced by protocols::match::HitNeighborFinder::find_next_bin().

BumpGridOP protocols::match::bump_grid_to_enclose_pose ( core::pose::Pose const &  pose)
BumpGridOP protocols::match::bump_grid_to_enclose_residue ( core::conformation::Residue const &  residue,
BumpGrid const &  original_grid 
)

Construct a BumpGrid that encloses a single residue. Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together.

References core::conformation::Residue::atom(), protocols::match::BumpGrid::create_new_bump_grid_for_bb(), core::conformation::Residue::natoms(), protocols::match::BumpGrid::probe_radius(), probe_radius_for_atom_type(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

BumpGridOP protocols::match::bump_grid_to_enclose_residue_backbone ( core::conformation::Residue const &  residue,
BumpGrid const &  original_grid 
)
MatchPositionModifierCOP protocols::match::create_match_position_modifier ( std::string const &  mpm_name,
core::Size  geom_cst,
utility::vector1< std::string > const &  input_tokens 
)

"factory" function to create the match position modifiers

Referenced by protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input().

Hit protocols::match::fake_hit ( upstream_hit const &  uhit)
Hit protocols::match::fake_hit ( downstream_hit const &  dhit)
void protocols::match::fill_grid_with_backbone_heavyatom_spheres ( core::conformation::Residue const &  residue,
BumpGrid &  grid 
)
void protocols::match::fill_grid_with_residue_heavyatom_spheres ( core::conformation::Residue const &  residue,
BumpGrid &  grid 
)
void protocols::match::fill_grid_with_residue_spheres ( core::conformation::Residue const &  residue,
BumpGrid &  grid 
)
Hit protocols::match::full_hit ( match_dspos1 const &  m)
utility::vector1< ProbeRadius > protocols::match::initialize_atomtype_2_probe_radius_map ( )
ProbeRadius protocols::match::probe_radius_for_atom_type ( core::Size  atomtype)
void protocols::match::set_ligpose_rotamer ( core::pose::Pose ligpose)
static basic::Tracer protocols::match::TR ( "protocols.BumpGrid"  )
static
static basic::Tracer protocols::match::tr ( "protocols.match.MatchPositionModifiers"  )
static
static basic::Tracer protocols::match::TR ( "protocols.match.MatcherTask"  )
static
static basic::Tracer protocols::match::tr ( "protocols.match.MatcherMover"  )
static
static basic::Tracer protocols::match::TR ( "protocols.match.Matcher"  )
static