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AddAllPositionsMPM MPM that returns a vector of all protein positions in the pose i.e. |
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AddAllPositionsMPMAP | |||
AddAllPositionsMPMCAP | |||
BfactorMPM removes positions at which the bfactors for c-alpha atoms are above a desired cutoff. |
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BfactorMPMAP | |||
BfactorMPMCAP | |||
Bool3DGrid protocols/match/BumpGrid.hh:49 |
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Bool3DGridAP | |||
Bool3DGridCAP | |||
Bool3DGridKinemageWriter protocols/match/BumpGrid.hh:340 |
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Bool3DGridKinemageWriterAP | |||
Bool3DGridKinemageWriterCAP | |||
BumpGrid protocols/match/BumpGrid.hh:200 |
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BumpGridAP | |||
BumpGridCAP | |||
Hit protocols/match/Hit.hh:34 |
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HitAP | |||
HitCAP | |||
HitHasher This object hashes hits into 6D voxels. |
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HitHasherAP | |||
HitHasherCAP | |||
HitNeighborFinder Class for finding hit neighbors in 6D considering all 64 origin definitions (but without forming all 64 hashes). |
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HitNeighborFinderAP | |||
HitNeighborFinderCAP | |||
MatchCounter Class for counting the number of matches given a particular discretization level. |
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MatchCounterAP | |||
MatchCounterCAP | |||
MatchOutputTracker protocols/match/MatchSet.hh:370 |
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MatchOutputTrackerAP | |||
MatchOutputTrackerCAP | |||
MatchPositionModifier base class for objects that modify the match positions based on some criterion |
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MatchPositionModifierAP | |||
MatchPositionModifierCAP | |||
Matcher Overview: The matcher algorithm was originally concieved of within the domain of enzyme design. |
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MatcherAP | |||
MatcherCAP | |||
MatcherMover protocols/match/MatcherMover.hh:36 |
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MatcherMoverAP | |||
MatcherMoverCAP | |||
MatcherMoverCreator protocols/match/MatcherMoverCreator.hh:22 |
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MatcherMoverCreatorAP | |||
MatcherMoverCreatorCAP | |||
MatcherOutputStats protocols/match/Matcher.hh:572 |
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MatcherOutputStatsAP | |||
MatcherOutputStatsCAP | |||
MatcherTask protocols/match/MatcherTask.hh:46 |
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MatcherTaskAP | |||
MatcherTaskCAP | |||
NumNeighborsMPM removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. |
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NumNeighborsMPMAP | |||
NumNeighborsMPMCAP | |||
OccupiedSpaceHash This class keeps track of the active voxels "up until now" with 64 hashes. |
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OccupiedSpaceHashAP | |||
OccupiedSpaceHashCAP | |||
ProbeRadius The different radii types used in collision detection. |
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RemoveNorCTermMPM added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching |
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RemoveNorCTermMPMAP | |||
RemoveNorCTermMPMCAP | |||
SecondaryStructureMPM removes positions at which the pose does not have the desired secondary structure |
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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 |
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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. |
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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 |
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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) |
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match_dspos1AP | |||
match_dspos1CAP | |||
match_lite_equals protocols/match/MatchSet.hh:338 |
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match_lite_equalsAP | |||
match_lite_equalsCAP | |||
match_lite_hasher protocols/match/MatchSet.hh:353 |
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match_lite_hasherAP | |||
match_lite_hasherCAP | |||
upstream_hit protocols/match/Hit.hh:81 |
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upstream_hitAP | |||
upstream_hitCAP |
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C_ALA = rosetta.protocols.match._protocols_match_.ProbeRadius.
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C_CAR = rosetta.protocols.match._protocols_match_.ProbeRadius.
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H_ALA = rosetta.protocols.match._protocols_match_.ProbeRadius.
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H_ARO = rosetta.protocols.match._protocols_match_.ProbeRadius.
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NIT = rosetta.protocols.match._protocols_match_.ProbeRadius.NIT
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OXY = rosetta.protocols.match._protocols_match_.ProbeRadius.OXY
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SULPH = rosetta.protocols.match._protocols_match_.ProbeRadius.
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ZERO = rosetta.protocols.match._protocols_match_.ProbeRadius.ZERO
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__package__ = None
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n_probe_radii = rosetta.protocols.match._protocols_match_.Prob
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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( (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( (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( (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( (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( (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( (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( (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( (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( (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( (int)atomtype) -> ProbeRadius : protocols/match/BumpGrid.hh:295 C++ signature : protocols::match::ProbeRadius probe_radius_for_atom_type(unsigned long) |
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C_ALA
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C_CAR
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H_ALA
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H_ARO
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SULPH
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n_probe_radii
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