Package rosetta :: Package protocols :: Package match :: Module _protocols_match_
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Module _protocols_match_

Classes [hide private]
  AddAllPositionsMPM
MPM that returns a vector of all protein positions in the pose i.e.
  AddAllPositionsMPMAP
  AddAllPositionsMPMCAP
  BfactorMPM
removes positions at which the bfactors for c-alpha atoms are above a desired cutoff.
  BfactorMPMAP
  BfactorMPMCAP
  Bool3DGrid
protocols/match/BumpGrid.hh:49
  Bool3DGridAP
  Bool3DGridCAP
  Bool3DGridKinemageWriter
protocols/match/BumpGrid.hh:340
  Bool3DGridKinemageWriterAP
  Bool3DGridKinemageWriterCAP
  BumpGrid
protocols/match/BumpGrid.hh:200
  BumpGridAP
  BumpGridCAP
  Hit
protocols/match/Hit.hh:34
  HitAP
  HitCAP
  HitHasher
This object hashes hits into 6D voxels.
  HitHasherAP
  HitHasherCAP
  HitNeighborFinder
Class for finding hit neighbors in 6D considering all 64 origin definitions (but without forming all 64 hashes).
  HitNeighborFinderAP
  HitNeighborFinderCAP
  MatchCounter
Class for counting the number of matches given a particular discretization level.
  MatchCounterAP
  MatchCounterCAP
  MatchOutputTracker
protocols/match/MatchSet.hh:370
  MatchOutputTrackerAP
  MatchOutputTrackerCAP
  MatchPositionModifier
base class for objects that modify the match positions based on some criterion
  MatchPositionModifierAP
  MatchPositionModifierCAP
  Matcher
Overview: The matcher algorithm was originally concieved of within the domain of enzyme design.
  MatcherAP
  MatcherCAP
  MatcherMover
protocols/match/MatcherMover.hh:36
  MatcherMoverAP
  MatcherMoverCAP
  MatcherMoverCreator
protocols/match/MatcherMoverCreator.hh:22
  MatcherMoverCreatorAP
  MatcherMoverCreatorCAP
  MatcherOutputStats
protocols/match/Matcher.hh:572
  MatcherOutputStatsAP
  MatcherOutputStatsCAP
  MatcherTask
protocols/match/MatcherTask.hh:46
  MatcherTaskAP
  MatcherTaskCAP
  NumNeighborsMPM
removes positions whose numer of neighbors below a 10A cutoff is not within the desired range.
  NumNeighborsMPMAP
  NumNeighborsMPMCAP
  OccupiedSpaceHash
This class keeps track of the active voxels "up until now" with 64 hashes.
  OccupiedSpaceHashAP
  OccupiedSpaceHashCAP
  ProbeRadius
The different radii types used in collision detection.
  RemoveNorCTermMPM
added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching
  RemoveNorCTermMPMAP
  RemoveNorCTermMPMCAP
  SecondaryStructureMPM
removes positions at which the pose does not have the desired secondary structure
  SecondaryStructureMPMAP
  SecondaryStructureMPMCAP
  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
  TaskOperationMPMAP
  TaskOperationMPMCAP
  VoxelSetIterator
Helper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers.
  VoxelSetIteratorAP
  VoxelSetIteratorCAP
  __CPP_AddAllPositionsMPM__
  __CPP_BfactorMPM__
  __CPP_MatchPositionModifier__
  __CPP_MatcherMoverCreator__
  __CPP_MatcherMover__
  __CPP_NumNeighborsMPM__
  __CPP_RemoveNorCTermMPM__
  __CPP_SecondaryStructureMPM__
  __CPP_TaskOperationMPM__
  downstream_hit
protocols/match/Hit.hh:141
  downstream_hitAP
  downstream_hitCAP
  match_dspos1
Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position)
  match_dspos1AP
  match_dspos1CAP
  match_lite_equals
protocols/match/MatchSet.hh:338
  match_lite_equalsAP
  match_lite_equalsCAP
  match_lite_hasher
protocols/match/MatchSet.hh:353
  match_lite_hasherAP
  match_lite_hasherCAP
  upstream_hit
protocols/match/Hit.hh:81
  upstream_hitAP
  upstream_hitCAP
Functions [hide private]
 
advance_euler_angles(...)
advance_euler_angles( (object)orig_angles, (object)offsets) -> object : Increment the euler angles and then wrap them into their appropriate ranges
 
bump_grid_to_enclose_pose(...)
bump_grid_to_enclose_pose( (Pose)pose) -> BumpGrid : protocols/match/BumpGrid.hh:298
 
bump_grid_to_enclose_residue(...)
bump_grid_to_enclose_residue( (Residue)residue, (BumpGrid)original_grid) -> BumpGrid : Construct a BumpGrid that encloses a single residue.
 
bump_grid_to_enclose_residue_backbone(...)
bump_grid_to_enclose_residue_backbone( (Residue)residue, (BumpGrid)original_grid) -> BumpGrid : Construct a BumpGrid that encloses the backbone atoms for a single residue.
 
create_match_position_modifier(...)
create_match_position_modifier( (str)mpm_name, (int)geom_cst, (vector1_string)input_tokens) -> MatchPositionModifier : "factory" function to create the match position modifiers
 
fake_hit(...)
fake_hit( (downstream_hit)) -> Hit : Create a fake hit from a downstream_hit where hit.first()[1-3] are 0's.
 
fill_grid_with_backbone_heavyatom_spheres(...)
fill_grid_with_backbone_heavyatom_spheres( (Residue)residue, (BumpGrid)grid) -> None : protocols/match/BumpGrid.hh:336
 
fill_grid_with_residue_heavyatom_spheres(...)
fill_grid_with_residue_heavyatom_spheres( (Residue)residue, (BumpGrid)grid) -> None : protocols/match/BumpGrid.hh:330
 
fill_grid_with_residue_spheres(...)
fill_grid_with_residue_spheres( (Residue)residue, (BumpGrid)grid) -> None : protocols/match/BumpGrid.hh:324
 
full_hit(...)
full_hit( (match_dspos1)m) -> Hit : 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.
 
probe_radius_for_atom_type(...)
probe_radius_for_atom_type( (int)atomtype) -> ProbeRadius : protocols/match/BumpGrid.hh:295
Variables [hide private]
  C_ALA = rosetta.protocols.match._protocols_match_.ProbeRadius....
  C_CAR = rosetta.protocols.match._protocols_match_.ProbeRadius....
  H_ALA = rosetta.protocols.match._protocols_match_.ProbeRadius....
  H_ARO = rosetta.protocols.match._protocols_match_.ProbeRadius....
  NIT = rosetta.protocols.match._protocols_match_.ProbeRadius.NIT
  OXY = rosetta.protocols.match._protocols_match_.ProbeRadius.OXY
  SULPH = rosetta.protocols.match._protocols_match_.ProbeRadius....
  ZERO = rosetta.protocols.match._protocols_match_.ProbeRadius.ZERO
  __package__ = None
  n_probe_radii = rosetta.protocols.match._protocols_match_.Prob...
Function Details [hide private]

advance_euler_angles(...)

 

advance_euler_angles( (object)orig_angles, (object)offsets) -> object :
    Increment the euler angles and then wrap them into their appropriate ranges
    

    C++ signature :
        utility::fixedsizearray1<double, 3ul> advance_euler_angles(utility::fixedsizearray1<double, 3ul>,utility::fixedsizearray1<double, 3ul>)

bump_grid_to_enclose_pose(...)

 

bump_grid_to_enclose_pose( (Pose)pose) -> BumpGrid :
    protocols/match/BumpGrid.hh:298

    C++ signature :
        boost::shared_ptr<protocols::match::BumpGrid> bump_grid_to_enclose_pose(core::pose::Pose)

bump_grid_to_enclose_residue(...)

 

bump_grid_to_enclose_residue( (Residue)residue, (BumpGrid)original_grid) -> BumpGrid :
    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.
    

    C++ signature :
        boost::shared_ptr<protocols::match::BumpGrid> bump_grid_to_enclose_residue(core::conformation::Residue,protocols::match::BumpGrid)

bump_grid_to_enclose_residue_backbone(...)

 

bump_grid_to_enclose_residue_backbone( (Residue)residue, (BumpGrid)original_grid) -> BumpGrid :
    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.
    

    C++ signature :
        boost::shared_ptr<protocols::match::BumpGrid> bump_grid_to_enclose_residue_backbone(core::conformation::Residue,protocols::match::BumpGrid)

create_match_position_modifier(...)

 

create_match_position_modifier( (str)mpm_name, (int)geom_cst, (vector1_string)input_tokens) -> MatchPositionModifier :
    "factory" function to create the match position modifiers
    

    C++ signature :
        boost::shared_ptr<protocols::match::MatchPositionModifier const> create_match_position_modifier(std::string,unsigned long,utility::vector1<std::string, std::allocator<std::string> >)

fake_hit(...)

 

fake_hit( (downstream_hit)) -> Hit :
    Create a fake hit from a downstream_hit where hit.first()[1-3] are 0's.
    

    C++ signature :
        protocols::match::Hit fake_hit(protocols::match::downstream_hit)

fake_hit( (upstream_hit)) -> Hit :
    Create a fake hit from an upstream_hit where hit.first()[4] and hit.second() are 0's.
    

    C++ signature :
        protocols::match::Hit fake_hit(protocols::match::upstream_hit)

fill_grid_with_backbone_heavyatom_spheres(...)

 

fill_grid_with_backbone_heavyatom_spheres( (Residue)residue, (BumpGrid)grid) -> None :
    protocols/match/BumpGrid.hh:336

    C++ signature :
        void fill_grid_with_backbone_heavyatom_spheres(core::conformation::Residue,protocols::match::BumpGrid {lvalue})

fill_grid_with_residue_heavyatom_spheres(...)

 

fill_grid_with_residue_heavyatom_spheres( (Residue)residue, (BumpGrid)grid) -> None :
    protocols/match/BumpGrid.hh:330

    C++ signature :
        void fill_grid_with_residue_heavyatom_spheres(core::conformation::Residue,protocols::match::BumpGrid {lvalue})

fill_grid_with_residue_spheres(...)

 

fill_grid_with_residue_spheres( (Residue)residue, (BumpGrid)grid) -> None :
    protocols/match/BumpGrid.hh:324

    C++ signature :
        void fill_grid_with_residue_spheres(core::conformation::Residue,protocols::match::BumpGrid {lvalue})

full_hit(...)

 

full_hit( (match_dspos1)m) -> Hit :
    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.
    

    C++ signature :
        protocols::match::Hit full_hit(protocols::match::match_dspos1)

probe_radius_for_atom_type(...)

 

probe_radius_for_atom_type( (int)atomtype) -> ProbeRadius :
    protocols/match/BumpGrid.hh:295

    C++ signature :
        protocols::match::ProbeRadius probe_radius_for_atom_type(unsigned long)


Variables Details [hide private]

C_ALA

Value:
rosetta.protocols.match._protocols_match_.ProbeRadius.C_ALA

C_CAR

Value:
rosetta.protocols.match._protocols_match_.ProbeRadius.C_CAR

H_ALA

Value:
rosetta.protocols.match._protocols_match_.ProbeRadius.H_ALA

H_ARO

Value:
rosetta.protocols.match._protocols_match_.ProbeRadius.H_ARO

SULPH

Value:
rosetta.protocols.match._protocols_match_.ProbeRadius.SULPH

n_probe_radii

Value:
rosetta.protocols.match._protocols_match_.ProbeRadius.n_probe_radii