| | |
- builtins.object
-
- ActiveSiteGrid
- DownstreamAlgorithm
-
- ClassicMatchAlgorithm
- SecondaryMatcherToDownstreamResidue
- SecondaryMatcherToUpstreamResidue
- DownstreamBuilder
-
- LigandConformerBuilder
- RigidLigandBuilder
- SecMatchEvaluatorFactory
- SecMatchResiduePairEvaluator
-
- AtomGeometrySecMatchRPE
-
- AtomAngleSecMatchRPE
- AtomDihedralSecMatchRPE
- AtomDistanceSecMatchRPE
- GeometrySecMatchRPE
- ScoringSecMatchRPE
- TargetRotamerCoords
- us_secmatch_hit_compare
- rosetta.protocols.match.upstream.UpstreamResidueProcessor(builtins.object)
-
- SecondaryMatchUpstreamResProcessor
class ActiveSiteGrid(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
2. __init__(self : rosetta.protocols.match.downstream.ActiveSiteGrid, : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.ActiveSiteGrid, rhs : rosetta.protocols.match.downstream.ActiveSiteGrid) -> rosetta.protocols.match.downstream.ActiveSiteGrid
- bounding_box(...) from builtins.PyCapsule
- bounding_box(rosetta.protocols.match.downstream.ActiveSiteGrid) -> rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t
Accessor for the bounding box
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
Reset all the voxels to false
- enlargen_to_capture_volume_within_radius_of_backbone(...) from builtins.PyCapsule
- enlargen_to_capture_volume_within_radius_of_backbone(self : rosetta.protocols.match.downstream.ActiveSiteGrid, res : rosetta.core.conformation.Residue, radius : float) -> NoneType
Set the bounding box to be large enough to hold the volume within the
radius of any backbone atom in the given residue. This function has the side-effect of
clearing the grid.
- enlargen_to_capture_volume_within_radius_of_residue(...) from builtins.PyCapsule
- enlargen_to_capture_volume_within_radius_of_residue(self : rosetta.protocols.match.downstream.ActiveSiteGrid, res : rosetta.core.conformation.Residue, radius : float) -> NoneType
Set the bounding box to be large enough to hold the volume within the
radius of any atom in the given residue. This function has the side-effect of
clearing the grid.
- enlargen_to_capture_volume_within_radius_of_sidechain(...) from builtins.PyCapsule
- enlargen_to_capture_volume_within_radius_of_sidechain(self : rosetta.protocols.match.downstream.ActiveSiteGrid, res : rosetta.core.conformation.Residue, radius : float) -> NoneType
Set the bounding box to be large enough to hold the volume within the
radius of any sidechain atom in the given residue. This function has the side-effect of
clearing the grid.
- grid(...) from builtins.PyCapsule
- grid(rosetta.protocols.match.downstream.ActiveSiteGrid) -> rosetta.protocols.match.Bool3DGrid
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
Ensures the grid is up-to-date after any calls to enlargen_*.
- initialize_from_gridlig_file(...) from builtins.PyCapsule
- initialize_from_gridlig_file(self : rosetta.protocols.match.downstream.ActiveSiteGrid, fname : str) -> NoneType
- occupied(...) from builtins.PyCapsule
- occupied(self : rosetta.protocols.match.downstream.ActiveSiteGrid, p : rosetta.numeric.xyzVector_double_t) -> bool
Is a point in this grid active? False for a point outside the bounding box.
- or_within_radius_of_backbone(...) from builtins.PyCapsule
- or_within_radius_of_backbone(self : rosetta.protocols.match.downstream.ActiveSiteGrid, res : rosetta.core.conformation.Residue, radius : float) -> NoneType
Set all the voxels within a certain radius of the backbone atoms to true.
- or_within_radius_of_residue(...) from builtins.PyCapsule
- or_within_radius_of_residue(self : rosetta.protocols.match.downstream.ActiveSiteGrid, res : rosetta.core.conformation.Residue, radius : float) -> NoneType
Set all the voxels within a certain radius of the residue atoms to true.
- or_within_radius_of_sidechain(...) from builtins.PyCapsule
- or_within_radius_of_sidechain(self : rosetta.protocols.match.downstream.ActiveSiteGrid, res : rosetta.core.conformation.Residue, radius : float) -> NoneType
Set all the voxels within a certain radius of the sidechain atoms to true.
- set_bin_width(...) from builtins.PyCapsule
- set_bin_width(self : rosetta.protocols.match.downstream.ActiveSiteGrid, width : float) -> NoneType
- set_bounding_box(...) from builtins.PyCapsule
- set_bounding_box(self : rosetta.protocols.match.downstream.ActiveSiteGrid, bb : rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t) -> NoneType
Set the bounding box for this grid
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class AtomAngleSecMatchRPE(AtomGeometrySecMatchRPE) |
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RPE to figure out if three atoms are within a given angle
atoms need to be set through the parent class add_at_ind function
|
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- Method resolution order:
- AtomAngleSecMatchRPE
- AtomGeometrySecMatchRPE
- SecMatchResiduePairEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, gsi : protocols::toolbox::match_enzdes_util::GeomSampleInfo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.AtomAngleSecMatchRPE, : rosetta.protocols.match.downstream.AtomAngleSecMatchRPE) -> rosetta.protocols.match.downstream.AtomAngleSecMatchRPE
- evaluate_residues(...) from builtins.PyCapsule
- evaluate_residues(self : rosetta.protocols.match.downstream.AtomAngleSecMatchRPE, candidate_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
- print(...) from builtins.PyCapsule
- print(self : rosetta.protocols.match.downstream.AtomAngleSecMatchRPE, candidate_restype : rosetta.core.chemical.ResidueType, target_restype : rosetta.core.chemical.ResidueType) -> str
Methods inherited from AtomGeometrySecMatchRPE:
- add_at_ind(...) from builtins.PyCapsule
- add_at_ind(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, which_cst_res : int, atom_ind_in_res : int) -> NoneType
- at_inds(...) from builtins.PyCapsule
- at_inds(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
- check_value(...) from builtins.PyCapsule
- check_value(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, value : float) -> bool
determines if the passed in value is between lowval and highval
- highval(...) from builtins.PyCapsule
- highval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- lowval(...) from builtins.PyCapsule
- lowval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- require_all_target_residue_atom_coordinates(...) from builtins.PyCapsule
- require_all_target_residue_atom_coordinates(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> bool
- require_target_atom_coordinate(...) from builtins.PyCapsule
- require_target_atom_coordinate(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, target_atom_id : int) -> bool
Methods inherited from SecMatchResiduePairEvaluator:
- candidate_res_atoms_reqd_near_target_atom(...) from builtins.PyCapsule
- candidate_res_atoms_reqd_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> rosetta.utility.vector1_unsigned_long
Return a list of atom indices on the candidate residue; if all atoms
in this list are further than max_separation_dist_to_target_atom() away
from the target_atom_id atom for a given pair of conformations of the
target_residue and the candidate_residue, then this evaluator will return false
in the call to evaluate( candidate_residue, target_residue ).
This list will allow the SecondaryMatcher to (conservatively!) prune
conformations of the candidate_residue from consideration. The base class implements
a noop -- it returns an empty list.
- max_separation_dist_to_target_atom(...) from builtins.PyCapsule
- max_separation_dist_to_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> float
Return the maximum separation distance that any of the match-residue
atoms identified by the function match_atoms_reqd_near_target_atom
may be from a particular atom on the target residue. Returns a negative value
if there is no requirement that any atom be within a certain radius of the
target atom. The base class implementation returns -1.0.
- require_candidate_residue_atoms_to_lie_near_target_atom(...) from builtins.PyCapsule
- require_candidate_residue_atoms_to_lie_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> bool
Are there atoms of the candidate residue that must be within
some cutoff distance of a given atom on the target residue? Base
class implementation returns false.
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class AtomDihedralSecMatchRPE(AtomGeometrySecMatchRPE) |
| |
RPE to figure out if four atoms are within a given dihedral angle
atoms need to be set through the parent class add_at_ind function
also checks whether a dihedral is periodic, i.e. multiple minima
|
| |
- Method resolution order:
- AtomDihedralSecMatchRPE
- AtomGeometrySecMatchRPE
- SecMatchResiduePairEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, gsi : protocols::toolbox::match_enzdes_util::GeomSampleInfo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE, : rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE) -> rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE
- evaluate_residues(...) from builtins.PyCapsule
- evaluate_residues(self : rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE, candidate_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
- print(...) from builtins.PyCapsule
- print(self : rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE, candidate_restype : rosetta.core.chemical.ResidueType, target_restype : rosetta.core.chemical.ResidueType) -> str
Methods inherited from AtomGeometrySecMatchRPE:
- add_at_ind(...) from builtins.PyCapsule
- add_at_ind(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, which_cst_res : int, atom_ind_in_res : int) -> NoneType
- at_inds(...) from builtins.PyCapsule
- at_inds(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
- check_value(...) from builtins.PyCapsule
- check_value(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, value : float) -> bool
determines if the passed in value is between lowval and highval
- highval(...) from builtins.PyCapsule
- highval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- lowval(...) from builtins.PyCapsule
- lowval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- require_all_target_residue_atom_coordinates(...) from builtins.PyCapsule
- require_all_target_residue_atom_coordinates(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> bool
- require_target_atom_coordinate(...) from builtins.PyCapsule
- require_target_atom_coordinate(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, target_atom_id : int) -> bool
Methods inherited from SecMatchResiduePairEvaluator:
- candidate_res_atoms_reqd_near_target_atom(...) from builtins.PyCapsule
- candidate_res_atoms_reqd_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> rosetta.utility.vector1_unsigned_long
Return a list of atom indices on the candidate residue; if all atoms
in this list are further than max_separation_dist_to_target_atom() away
from the target_atom_id atom for a given pair of conformations of the
target_residue and the candidate_residue, then this evaluator will return false
in the call to evaluate( candidate_residue, target_residue ).
This list will allow the SecondaryMatcher to (conservatively!) prune
conformations of the candidate_residue from consideration. The base class implements
a noop -- it returns an empty list.
- max_separation_dist_to_target_atom(...) from builtins.PyCapsule
- max_separation_dist_to_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> float
Return the maximum separation distance that any of the match-residue
atoms identified by the function match_atoms_reqd_near_target_atom
may be from a particular atom on the target residue. Returns a negative value
if there is no requirement that any atom be within a certain radius of the
target atom. The base class implementation returns -1.0.
- require_candidate_residue_atoms_to_lie_near_target_atom(...) from builtins.PyCapsule
- require_candidate_residue_atoms_to_lie_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> bool
Are there atoms of the candidate residue that must be within
some cutoff distance of a given atom on the target residue? Base
class implementation returns false.
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class AtomDistanceSecMatchRPE(AtomGeometrySecMatchRPE) |
| |
RPE to figure out if two atoms are within a given distance
atoms need to be set through the parent class add_at_ind function
|
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- Method resolution order:
- AtomDistanceSecMatchRPE
- AtomGeometrySecMatchRPE
- SecMatchResiduePairEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, gsi : protocols::toolbox::match_enzdes_util::GeomSampleInfo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE, : rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE) -> rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE
- candidate_res_atoms_reqd_near_target_atom(...) from builtins.PyCapsule
- candidate_res_atoms_reqd_near_target_atom(self : rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE, target_atom_id : int) -> rosetta.utility.vector1_unsigned_long
- evaluate_residues(...) from builtins.PyCapsule
- evaluate_residues(self : rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE, candidate_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
- max_separation_dist_to_target_atom(...) from builtins.PyCapsule
- max_separation_dist_to_target_atom(self : rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE, target_atom_id : int) -> float
- print(...) from builtins.PyCapsule
- print(self : rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE, candidate_restype : rosetta.core.chemical.ResidueType, target_restype : rosetta.core.chemical.ResidueType) -> str
- require_candidate_residue_atoms_to_lie_near_target_atom(...) from builtins.PyCapsule
- require_candidate_residue_atoms_to_lie_near_target_atom(self : rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE, target_atom_id : int) -> bool
Methods inherited from AtomGeometrySecMatchRPE:
- add_at_ind(...) from builtins.PyCapsule
- add_at_ind(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, which_cst_res : int, atom_ind_in_res : int) -> NoneType
- at_inds(...) from builtins.PyCapsule
- at_inds(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
- check_value(...) from builtins.PyCapsule
- check_value(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, value : float) -> bool
determines if the passed in value is between lowval and highval
- highval(...) from builtins.PyCapsule
- highval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- lowval(...) from builtins.PyCapsule
- lowval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- require_all_target_residue_atom_coordinates(...) from builtins.PyCapsule
- require_all_target_residue_atom_coordinates(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> bool
- require_target_atom_coordinate(...) from builtins.PyCapsule
- require_target_atom_coordinate(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, target_atom_id : int) -> bool
|
class AtomGeometrySecMatchRPE(SecMatchResiduePairEvaluator) |
| |
helper class for GeometrySec
abstract base class for distance, angle, and dihedral derived classes
|
| |
- Method resolution order:
- AtomGeometrySecMatchRPE
- SecMatchResiduePairEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, gsi : protocols::toolbox::match_enzdes_util::GeomSampleInfo) -> NoneType
2. __init__(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_at_ind(...) from builtins.PyCapsule
- add_at_ind(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, which_cst_res : int, atom_ind_in_res : int) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE
- at_inds(...) from builtins.PyCapsule
- at_inds(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
- check_value(...) from builtins.PyCapsule
- check_value(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, value : float) -> bool
determines if the passed in value is between lowval and highval
- evaluate_residues(...) from builtins.PyCapsule
- evaluate_residues(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, candidate_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
- highval(...) from builtins.PyCapsule
- highval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- lowval(...) from builtins.PyCapsule
- lowval(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> float
- print(...) from builtins.PyCapsule
- print(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, candidate_restype : rosetta.core.chemical.ResidueType, target_restype : rosetta.core.chemical.ResidueType) -> str
- require_all_target_residue_atom_coordinates(...) from builtins.PyCapsule
- require_all_target_residue_atom_coordinates(rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> bool
- require_target_atom_coordinate(...) from builtins.PyCapsule
- require_target_atom_coordinate(self : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE, target_atom_id : int) -> bool
Methods inherited from SecMatchResiduePairEvaluator:
- candidate_res_atoms_reqd_near_target_atom(...) from builtins.PyCapsule
- candidate_res_atoms_reqd_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> rosetta.utility.vector1_unsigned_long
Return a list of atom indices on the candidate residue; if all atoms
in this list are further than max_separation_dist_to_target_atom() away
from the target_atom_id atom for a given pair of conformations of the
target_residue and the candidate_residue, then this evaluator will return false
in the call to evaluate( candidate_residue, target_residue ).
This list will allow the SecondaryMatcher to (conservatively!) prune
conformations of the candidate_residue from consideration. The base class implements
a noop -- it returns an empty list.
- max_separation_dist_to_target_atom(...) from builtins.PyCapsule
- max_separation_dist_to_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> float
Return the maximum separation distance that any of the match-residue
atoms identified by the function match_atoms_reqd_near_target_atom
may be from a particular atom on the target residue. Returns a negative value
if there is no requirement that any atom be within a certain radius of the
target atom. The base class implementation returns -1.0.
- require_candidate_residue_atoms_to_lie_near_target_atom(...) from builtins.PyCapsule
- require_candidate_residue_atoms_to_lie_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> bool
Are there atoms of the candidate residue that must be within
some cutoff distance of a given atom on the target residue? Base
class implementation returns false.
|
class ClassicMatchAlgorithm(DownstreamAlgorithm) |
| |
Produce hits by hashing building the coordinates of the downstream partner
The downstream partner is responsible for building itself from the coordinate frame of
three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream
partner given the coordinates of the upstream partner.
|
| |
- Method resolution order:
- ClassicMatchAlgorithm
- DownstreamAlgorithm
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, geom_cst_id : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_external_geom_sampler(...) from builtins.PyCapsule
- add_external_geom_sampler(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, sampler : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, exgeom_id : int, atom1 : str, atom2 : str, atom3 : str, downstream_builder : protocols::match::downstream::DownstreamBuilder) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, : rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> rosetta.protocols.match.downstream.ClassicMatchAlgorithm
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, scaffold_build_point_id : int, upstream_conf_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Iterate across the external geom samplers that describe the rigid body orientations
of the downstream partner from the coordinates of the upstream partner.
- build_and_discard_first_round_hits_at_all_positions(...) from builtins.PyCapsule
- build_and_discard_first_round_hits_at_all_positions(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, matcher : rosetta.protocols.match.Matcher) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
- build_from_three_coords(...) from builtins.PyCapsule
- build_from_three_coords(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, which_external_sampler : int, scaffold_build_point_id : int, upstream_conf_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
This function completes the building of the downstream conformation
once the coordinates of the upstream conformation are known (and deemed
non-colliding or, generally, pass any filter the upstream builder would use).
- build_hits_at_all_positions(...) from builtins.PyCapsule
- build_hits_at_all_positions(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, matcher : rosetta.protocols.match.Matcher) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
- clear_external_geom_samplers(...) from builtins.PyCapsule
- clear_external_geom_samplers(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- external_sampler(...) from builtins.PyCapsule
- external_sampler(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, external_geom_id : int) -> rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler
- generates_primary_hits(...) from builtins.PyCapsule
- generates_primary_hits(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> bool
This method returns 'true' since the classic matcher builds the
downstream coordinates from scratch.
- launch_atom(...) from builtins.PyCapsule
- launch_atom(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, external_geom_id : int, which_point : int) -> int
- n_external_samplers(...) from builtins.PyCapsule
- n_external_samplers(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> int
- n_possible_hits_per_upstream_conformation(...) from builtins.PyCapsule
- n_possible_hits_per_upstream_conformation(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> int
- respond_to_peripheral_hitlist_change(...) from builtins.PyCapsule
- respond_to_peripheral_hitlist_change(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, matcher : rosetta.protocols.match.Matcher) -> NoneType
Delete hits for this geometric constraint if they fall into
now-empty regions of 6D. This step can be avoided if the occupied-space-grid's
revision ID has not changed since the last time this function was invoked.
- respond_to_primary_hitlist_change(...) from builtins.PyCapsule
- respond_to_primary_hitlist_change(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, matcher : rosetta.protocols.match.Matcher, round_just_completed : int) -> NoneType
Reset the occupied space grid for the matcher so that only those
regions which contain hits from this geometric constraint are marked as occupied.
- restype(...) from builtins.PyCapsule
- restype(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> rosetta.core.chemical.ResidueType
Accessors
- set_build_round1_hits_twice(...) from builtins.PyCapsule
- set_build_round1_hits_twice(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> NoneType
Enable a strategy where the first round hits are discarded after they are generated
and then, after the second round completes, they are regenerated but respecting the occ-space
hash, thereby decreasing the memory use dramatically. That is, the hits for the first
geometric constraint (round 1 hits) are discarded, but their presence in the occupied space
hash is recorded. Then the hits for the second round are collected, but only the ones that
fall into the regions of 6D where the hits from the first round fell. At the end of round 2,
the occ-space hash is updated to reflect the regions of 6D where both rounds produced hits. Then
the round 1 hits are generated a second time, and this time saved.
- set_residue_type(...) from builtins.PyCapsule
- set_residue_type(self : rosetta.protocols.match.downstream.ClassicMatchAlgorithm, restype : rosetta.core.chemical.ResidueType) -> NoneType
- upstream_only(...) from builtins.PyCapsule
- upstream_only(rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> bool
This method returns 'false' since the classic match algorithm
builds coordinates of the downstream partner and its hits should
be hashed in 6D to generate matches
Methods inherited from DownstreamAlgorithm:
- are_colliding(...) from builtins.PyCapsule
- are_colliding(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, us_res : rosetta.core.conformation.Residue, ds_res : rosetta.core.conformation.Residue, ds_atoms : rosetta.utility.vector1_core_id_AtomID, catalytic_atoms : rosetta.utility.vector1_unsigned_long) -> bool
- geom_cst_id(...) from builtins.PyCapsule
- geom_cst_id(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> int
- get_dsbuilder(...) from builtins.PyCapsule
- get_dsbuilder(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> protocols::match::downstream::DownstreamBuilder
- prepare_for_match_enumeration(...) from builtins.PyCapsule
- prepare_for_match_enumeration(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, : rosetta.protocols.match.Matcher) -> NoneType
Called at the conclusion of matching, the Matcher signals
to the downstream algorithm that it's time to prepare for
match generation; if the downstream algorithm needs to enumerate
compatible hits in response to the invokation of its
hits_to_include_with_partial_match method, then now is the time
to prepare for those calls. Base class has a noop implementation.
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
- set_dsbuilder(...) from builtins.PyCapsule
- set_dsbuilder(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, dsbuilder : protocols::match::downstream::DownstreamBuilder) -> NoneType
|
class DownstreamAlgorithm(builtins.object) |
| |
A class for an algorithm. Given a conformation of the upstream partner,
the algorithm is responsible for producing a set of hits.
|
| |
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- are_colliding(...) from builtins.PyCapsule
- are_colliding(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, us_res : rosetta.core.conformation.Residue, ds_res : rosetta.core.conformation.Residue, ds_atoms : rosetta.utility.vector1_core_id_AtomID, catalytic_atoms : rosetta.utility.vector1_unsigned_long) -> bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, : rosetta.protocols.match.downstream.DownstreamAlgorithm) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, scaffold_build_point_id : int, upstream_conf_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Return a set of hits given a conformation of an upstream residue.
This method must be bit-wise constant and parallelizable in derived classes.
- build_hits_at_all_positions(...) from builtins.PyCapsule
- build_hits_at_all_positions(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher : rosetta.protocols.match.Matcher) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Main driver function for hit generation. The algorithm
is responsible for generating hits at all scaffold build points that
are valid for this geometric constraint. The base class provides an
iterate-across-all-positions-and-splice-together-hit-lists implementation,
however, derived classes may overload this function. The base class
function is parallelizable with OpenMP. The returned hit list must be in sorted
order by 1) hit.scaffold_build_id() and then by 2) hit.upstream_conf_id().
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- generates_primary_hits(...) from builtins.PyCapsule
- generates_primary_hits(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> bool
This method returns 'true' if the Real6 portion of the returned
hits are "original" descriptions of the downstream coordinates,
and not merely duplicates of the downstream coordinates from previous
rounds. This method returns 'false' if the downstream portion
of the returned hits are duplications of previous-round geometries or
if the hits returned by this class do not describe the geometry of
the downstream coordinates
- geom_cst_id(...) from builtins.PyCapsule
- geom_cst_id(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> int
- get_dsbuilder(...) from builtins.PyCapsule
- get_dsbuilder(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> protocols::match::downstream::DownstreamBuilder
- n_possible_hits_per_upstream_conformation(...) from builtins.PyCapsule
- n_possible_hits_per_upstream_conformation(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> int
- prepare_for_match_enumeration(...) from builtins.PyCapsule
- prepare_for_match_enumeration(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, : rosetta.protocols.match.Matcher) -> NoneType
Called at the conclusion of matching, the Matcher signals
to the downstream algorithm that it's time to prepare for
match generation; if the downstream algorithm needs to enumerate
compatible hits in response to the invokation of its
hits_to_include_with_partial_match method, then now is the time
to prepare for those calls. Base class has a noop implementation.
- respond_to_peripheral_hitlist_change(...) from builtins.PyCapsule
- respond_to_peripheral_hitlist_change(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher : rosetta.protocols.match.Matcher) -> NoneType
Following the change in the number of hits of some other round -- either
from the conclusion of that round in which a new set of hits has been generated,
or from the cascading change to the hits from round A which were deleted after the
conclusion of round B.
- respond_to_primary_hitlist_change(...) from builtins.PyCapsule
- respond_to_primary_hitlist_change(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher : rosetta.protocols.match.Matcher, round_just_completed : int) -> NoneType
Reset appropriate Matcher data to spawn the deletion of hits from other rounds
following either hit generation by this geometric constraint, or
following hit generation by another geometric constraint which caused the deletion
of hits from this geometric constraint. The classic match algorithm, for example,
resets the occupied-space hash so that other classic-match algorithms can delete their
non-viable hits in subsequent calls to respond_to_peripheral_hitlist_change.
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
- set_dsbuilder(...) from builtins.PyCapsule
- set_dsbuilder(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, dsbuilder : protocols::match::downstream::DownstreamBuilder) -> NoneType
- upstream_only(...) from builtins.PyCapsule
- upstream_only(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> bool
This method returns 'false' if the hits generated by this
DownstreamAlgorithm store the 6-dimensional coordinate
of the downstream partner in hit.second(), and therefore
intend for the Matcher to find matches for this algorithm's hits by
hashing the 6-dimensional coordinate. This method returns 'true'
if the DownstreamAlgorithm does not use hit.second to store a
point in 6D and instead intends the Matcher to find matches
by querying this DownstreamAlgorithm's hits_to_include_with_partial_match
method.
|
class DownstreamBuilder(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
2. __init__(rosetta.protocols.match.downstream.DownstreamBuilder, rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.DownstreamBuilder, : rosetta.protocols.match.downstream.DownstreamBuilder) -> rosetta.protocols.match.downstream.DownstreamBuilder
- atom1_atom2_atom3_angle(...) from builtins.PyCapsule
- atom1_atom2_atom3_angle(rosetta.protocols.match.downstream.DownstreamBuilder) -> float
Returns an angle in degrees between the three downstream atoms.
- atom1_atom2_distance(...) from builtins.PyCapsule
- atom1_atom2_distance(rosetta.protocols.match.downstream.DownstreamBuilder) -> float
- atom1_belongs_in_active_site(...) from builtins.PyCapsule
- atom1_belongs_in_active_site(rosetta.protocols.match.downstream.DownstreamBuilder) -> bool
- atom1_radius(...) from builtins.PyCapsule
- atom1_radius(rosetta.protocols.match.downstream.DownstreamBuilder) -> rosetta.protocols.match.ProbeRadius
- atom2_atom3_distance(...) from builtins.PyCapsule
- atom2_atom3_distance(rosetta.protocols.match.downstream.DownstreamBuilder) -> float
- atom2_belongs_in_active_site(...) from builtins.PyCapsule
- atom2_belongs_in_active_site(rosetta.protocols.match.downstream.DownstreamBuilder) -> bool
- atom2_radius(...) from builtins.PyCapsule
- atom2_radius(rosetta.protocols.match.downstream.DownstreamBuilder) -> rosetta.protocols.match.ProbeRadius
- atom3_belongs_in_active_site(...) from builtins.PyCapsule
- atom3_belongs_in_active_site(rosetta.protocols.match.downstream.DownstreamBuilder) -> bool
- atom3_radius(...) from builtins.PyCapsule
- atom3_radius(rosetta.protocols.match.downstream.DownstreamBuilder) -> rosetta.protocols.match.ProbeRadius
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.downstream.DownstreamBuilder, atom6_frame : rosetta.numeric.HomogeneousTransform_double_t, scaffold_build_point_id : int, upstream_conf_id : int, external_geometry_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.downstream.DownstreamBuilder) -> rosetta.protocols.match.downstream.DownstreamBuilder
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.downstream.DownstreamBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.DownstreamBuilder, other_hit : rosetta.protocols.match.Hit) -> bool
2. compatible(self : rosetta.protocols.match.downstream.DownstreamBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.DownstreamBuilder, other_hit : rosetta.protocols.match.Hit, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.downstream.DownstreamBuilder, my_hit : rosetta.protocols.match.Hit, other : protocols::match::downstream::RigidLigandBuilder, other_hit : rosetta.protocols.match.Hit) -> bool
4. compatible(self : rosetta.protocols.match.downstream.DownstreamBuilder, my_hit : rosetta.protocols.match.Hit, other : protocols::match::downstream::RigidLigandBuilder, other_hit : rosetta.protocols.match.Hit, first_dispatch : bool) -> bool
5. compatible(self : rosetta.protocols.match.downstream.DownstreamBuilder, my_hit : rosetta.protocols.match.Hit, other : protocols::match::downstream::LigandConformerBuilder, other_hit : rosetta.protocols.match.Hit) -> bool
6. compatible(self : rosetta.protocols.match.downstream.DownstreamBuilder, my_hit : rosetta.protocols.match.Hit, other : protocols::match::downstream::LigandConformerBuilder, other_hit : rosetta.protocols.match.Hit, first_dispatch : bool) -> bool
- coordinates_from_hit(...) from builtins.PyCapsule
- coordinates_from_hit(self : rosetta.protocols.match.downstream.DownstreamBuilder, hit : rosetta.protocols.match.Hit, atom_indices : rosetta.utility.vector1_core_id_AtomID, atom_coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- downstream_pose_from_hit(...) from builtins.PyCapsule
- downstream_pose_from_hit(self : rosetta.protocols.match.downstream.DownstreamBuilder, hit : rosetta.protocols.match.Hit) -> rosetta.core.pose.Pose
- get_lig_conformers(...) from builtins.PyCapsule
- get_lig_conformers(self : rosetta.protocols.match.downstream.DownstreamBuilder, conf_id : int) -> protocols::toolbox::match_enzdes_util::LigandConformer
- get_upstream_restype(...) from builtins.PyCapsule
- get_upstream_restype(rosetta.protocols.match.downstream.DownstreamBuilder) -> rosetta.core.chemical.ResidueType
- hits_potentially_incompatible(...) from builtins.PyCapsule
- hits_potentially_incompatible(rosetta.protocols.match.downstream.DownstreamBuilder) -> bool
In case downstream builders can return hits that
are incompatible with each other (e.g. different ligand
conformations ) the matcher needs to know about this to
allow for speedy match enumeration
- n_possible_hits_per_at3frame(...) from builtins.PyCapsule
- n_possible_hits_per_at3frame(rosetta.protocols.match.downstream.DownstreamBuilder) -> int
- require_atom_to_reside_in_active_site(...) from builtins.PyCapsule
- require_atom_to_reside_in_active_site(self : rosetta.protocols.match.downstream.DownstreamBuilder, id : rosetta.core.id.AtomID) -> NoneType
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamBuilder, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.DownstreamBuilder, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
- set_occupied_space_hash(...) from builtins.PyCapsule
- set_occupied_space_hash(self : rosetta.protocols.match.downstream.DownstreamBuilder, occ_space : rosetta.protocols.match.OccupiedSpaceHash) -> NoneType
|
class GeometrySecMatchRPE(SecMatchResiduePairEvaluator) |
| |
holds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence
when an instance of this class is asked to evaluate two residues.
|
| |
- Method resolution order:
- GeometrySecMatchRPE
- SecMatchResiduePairEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, mcfi : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo, downstream_inds : rosetta.utility.vector1_unsigned_long, upstream_inds : rosetta.utility.vector1_unsigned_long) -> NoneType
2. __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_atomgeom_evaluator(...) from builtins.PyCapsule
- add_atomgeom_evaluator(self : rosetta.protocols.match.downstream.GeometrySecMatchRPE, evaluator : rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.GeometrySecMatchRPE, : rosetta.protocols.match.downstream.GeometrySecMatchRPE) -> rosetta.protocols.match.downstream.GeometrySecMatchRPE
- atom_geom_rpes(...) from builtins.PyCapsule
- atom_geom_rpes(rosetta.protocols.match.downstream.GeometrySecMatchRPE) -> rosetta.utility.vector1_std_shared_ptr_const_protocols_match_downstream_AtomGeometrySecMatchRPE_t
- candidate_res_atoms_reqd_near_target_atom(...) from builtins.PyCapsule
- candidate_res_atoms_reqd_near_target_atom(self : rosetta.protocols.match.downstream.GeometrySecMatchRPE, target_atom_id : int) -> rosetta.utility.vector1_unsigned_long
- evaluate_residues(...) from builtins.PyCapsule
- evaluate_residues(self : rosetta.protocols.match.downstream.GeometrySecMatchRPE, candidate_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
performs a logical AND for all of the AtomGeometry evaluators.
- max_separation_dist_to_target_atom(...) from builtins.PyCapsule
- max_separation_dist_to_target_atom(self : rosetta.protocols.match.downstream.GeometrySecMatchRPE, target_atom_id : int) -> float
- require_all_target_residue_atom_coordinates(...) from builtins.PyCapsule
- require_all_target_residue_atom_coordinates(rosetta.protocols.match.downstream.GeometrySecMatchRPE) -> bool
- require_candidate_residue_atoms_to_lie_near_target_atom(...) from builtins.PyCapsule
- require_candidate_residue_atoms_to_lie_near_target_atom(self : rosetta.protocols.match.downstream.GeometrySecMatchRPE, target_atom_id : int) -> bool
- require_target_atom_coordinate(...) from builtins.PyCapsule
- require_target_atom_coordinate(self : rosetta.protocols.match.downstream.GeometrySecMatchRPE, target_atom_id : int) -> bool
|
class LigandConformerBuilder(DownstreamBuilder) |
| | |
- Method resolution order:
- LigandConformerBuilder
- DownstreamBuilder
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.match.downstream.LigandConformerBuilder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.LigandConformerBuilder, : rosetta.protocols.match.downstream.LigandConformerBuilder) -> rosetta.protocols.match.downstream.LigandConformerBuilder
- assign_conformer_group_to_residue(...) from builtins.PyCapsule
- assign_conformer_group_to_residue(self : rosetta.protocols.match.downstream.LigandConformerBuilder, residue : rosetta.core.conformation.Residue, relevant_atom_indices : rosetta.utility.vector1_unsigned_long) -> int
- atom1_atom2_atom3_angle(...) from builtins.PyCapsule
- atom1_atom2_atom3_angle(rosetta.protocols.match.downstream.LigandConformerBuilder) -> float
Returns an angle in degrees between the three downstream atoms.
- atom1_atom2_distance(...) from builtins.PyCapsule
- atom1_atom2_distance(rosetta.protocols.match.downstream.LigandConformerBuilder) -> float
- atom1_belongs_in_active_site(...) from builtins.PyCapsule
- atom1_belongs_in_active_site(rosetta.protocols.match.downstream.LigandConformerBuilder) -> bool
- atom1_radius(...) from builtins.PyCapsule
- atom1_radius(rosetta.protocols.match.downstream.LigandConformerBuilder) -> rosetta.protocols.match.ProbeRadius
- atom2_atom3_distance(...) from builtins.PyCapsule
- atom2_atom3_distance(rosetta.protocols.match.downstream.LigandConformerBuilder) -> float
- atom2_belongs_in_active_site(...) from builtins.PyCapsule
- atom2_belongs_in_active_site(rosetta.protocols.match.downstream.LigandConformerBuilder) -> bool
- atom2_radius(...) from builtins.PyCapsule
- atom2_radius(rosetta.protocols.match.downstream.LigandConformerBuilder) -> rosetta.protocols.match.ProbeRadius
- atom3_belongs_in_active_site(...) from builtins.PyCapsule
- atom3_belongs_in_active_site(rosetta.protocols.match.downstream.LigandConformerBuilder) -> bool
- atom3_radius(...) from builtins.PyCapsule
- atom3_radius(rosetta.protocols.match.downstream.LigandConformerBuilder) -> rosetta.protocols.match.ProbeRadius
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.downstream.LigandConformerBuilder, atom3_frame : rosetta.numeric.HomogeneousTransform_double_t, scaffold_build_point_id : int, upstream_conf_id : int, external_geometry_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.downstream.LigandConformerBuilder) -> rosetta.protocols.match.downstream.DownstreamBuilder
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.downstream.LigandConformerBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.DownstreamBuilder, other_hit : rosetta.protocols.match.Hit) -> bool
2. compatible(self : rosetta.protocols.match.downstream.LigandConformerBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.DownstreamBuilder, other_hit : rosetta.protocols.match.Hit, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.downstream.LigandConformerBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.LigandConformerBuilder, other_hit : rosetta.protocols.match.Hit) -> bool
4. compatible(self : rosetta.protocols.match.downstream.LigandConformerBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.LigandConformerBuilder, other_hit : rosetta.protocols.match.Hit, first_dispatch : bool) -> bool
- coordinates_from_hit(...) from builtins.PyCapsule
- coordinates_from_hit(self : rosetta.protocols.match.downstream.LigandConformerBuilder, hit : rosetta.protocols.match.Hit, atom_indices : rosetta.utility.vector1_core_id_AtomID, atom_coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- determine_redundant_conformer_groups(...) from builtins.PyCapsule
- determine_redundant_conformer_groups(self : rosetta.protocols.match.downstream.LigandConformerBuilder, relevant_atom_indices : rosetta.utility.vector1_unsigned_long) -> NoneType
goes through the list of conformers and does rms calculations (overlaid
on the relevant_atom_indices) between them. any conformers that have an rms
< rmsd_unique_cutoff_ will be grouped together in a conformer_group
- downstream_pose_from_hit(...) from builtins.PyCapsule
- downstream_pose_from_hit(self : rosetta.protocols.match.downstream.LigandConformerBuilder, hit : rosetta.protocols.match.Hit) -> rosetta.core.pose.Pose
- get_lig_conformers(...) from builtins.PyCapsule
- get_lig_conformers(self : rosetta.protocols.match.downstream.LigandConformerBuilder, conf_id : int) -> protocols::toolbox::match_enzdes_util::LigandConformer
- get_upstream_restype(...) from builtins.PyCapsule
- get_upstream_restype(rosetta.protocols.match.downstream.LigandConformerBuilder) -> rosetta.core.chemical.ResidueType
- hits_potentially_incompatible(...) from builtins.PyCapsule
- hits_potentially_incompatible(rosetta.protocols.match.downstream.LigandConformerBuilder) -> bool
- ignore_h_collisions(...) from builtins.PyCapsule
- ignore_h_collisions(self : rosetta.protocols.match.downstream.LigandConformerBuilder, setting : bool) -> NoneType
- initialize_from_residue(...) from builtins.PyCapsule
- initialize_from_residue(self : rosetta.protocols.match.downstream.LigandConformerBuilder, atom1 : int, atom2 : int, atom3 : int, orientation_atom1 : int, orientation_atom2 : int, orientation_atom3 : int, residue : rosetta.core.conformation.Residue) -> NoneType
Specify the residue, with coordinates, that's being used as the downstream
partner. This class is meant to be used in conjuction with the ClassicMatchAglrotihm,
and therefore the initialization routines are specific for that algorithm. In this
initialization function, one must list atoms "D1, D2 and D3" in the convention of
describing the rigid-body orientation between three atoms of the upstream partner
(atoms U3, U2 & U1) and three atoms of the downstream partner (atoms D1, D2 & D3) in terms
of 2 angles, 1 distance, and 3 dihedrals. The user must also list the 3 atoms used to
define the orientation frame of the downstream ligand. It is essential to the
matching algorithm that the same three orientation atoms are used for all LigandConformerBuilders.
- initialize_upstream_residue(...) from builtins.PyCapsule
- initialize_upstream_residue(*args, **kwargs)
Overloaded function.
1. initialize_upstream_residue(self : rosetta.protocols.match.downstream.LigandConformerBuilder, upstream_res : rosetta.core.chemical.ResidueType) -> NoneType
2. initialize_upstream_residue(self : rosetta.protocols.match.downstream.LigandConformerBuilder, upstream_res : rosetta.core.chemical.ResidueType, count_pair : rosetta.core.scoring.etable.count_pair.CountPairFunction) -> NoneType
- n_possible_hits_per_at3frame(...) from builtins.PyCapsule
- n_possible_hits_per_at3frame(rosetta.protocols.match.downstream.LigandConformerBuilder) -> int
- require_atom_to_reside_in_active_site(...) from builtins.PyCapsule
- require_atom_to_reside_in_active_site(self : rosetta.protocols.match.downstream.LigandConformerBuilder, id : rosetta.core.id.AtomID) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.LigandConformerBuilder, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
- set_idealize_conformers(...) from builtins.PyCapsule
- set_idealize_conformers(self : rosetta.protocols.match.downstream.LigandConformerBuilder, setting : bool) -> NoneType
- set_rmsd_unique_cutoff(...) from builtins.PyCapsule
- set_rmsd_unique_cutoff(self : rosetta.protocols.match.downstream.LigandConformerBuilder, setting : float) -> NoneType
Methods inherited from DownstreamBuilder:
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamBuilder, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_occupied_space_hash(...) from builtins.PyCapsule
- set_occupied_space_hash(self : rosetta.protocols.match.downstream.DownstreamBuilder, occ_space : rosetta.protocols.match.OccupiedSpaceHash) -> NoneType
|
class RigidLigandBuilder(DownstreamBuilder) |
| | |
- Method resolution order:
- RigidLigandBuilder
- DownstreamBuilder
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.match.downstream.RigidLigandBuilder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.RigidLigandBuilder, : rosetta.protocols.match.downstream.RigidLigandBuilder) -> rosetta.protocols.match.downstream.RigidLigandBuilder
- atom1_atom2_atom3_angle(...) from builtins.PyCapsule
- atom1_atom2_atom3_angle(rosetta.protocols.match.downstream.RigidLigandBuilder) -> float
Returns an angle in degrees between the three downstream atoms.
- atom1_atom2_distance(...) from builtins.PyCapsule
- atom1_atom2_distance(rosetta.protocols.match.downstream.RigidLigandBuilder) -> float
- atom1_belongs_in_active_site(...) from builtins.PyCapsule
- atom1_belongs_in_active_site(rosetta.protocols.match.downstream.RigidLigandBuilder) -> bool
- atom1_radius(...) from builtins.PyCapsule
- atom1_radius(rosetta.protocols.match.downstream.RigidLigandBuilder) -> rosetta.protocols.match.ProbeRadius
- atom2_atom3_distance(...) from builtins.PyCapsule
- atom2_atom3_distance(rosetta.protocols.match.downstream.RigidLigandBuilder) -> float
- atom2_belongs_in_active_site(...) from builtins.PyCapsule
- atom2_belongs_in_active_site(rosetta.protocols.match.downstream.RigidLigandBuilder) -> bool
- atom2_radius(...) from builtins.PyCapsule
- atom2_radius(rosetta.protocols.match.downstream.RigidLigandBuilder) -> rosetta.protocols.match.ProbeRadius
- atom3_belongs_in_active_site(...) from builtins.PyCapsule
- atom3_belongs_in_active_site(rosetta.protocols.match.downstream.RigidLigandBuilder) -> bool
- atom3_radius(...) from builtins.PyCapsule
- atom3_radius(rosetta.protocols.match.downstream.RigidLigandBuilder) -> rosetta.protocols.match.ProbeRadius
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.downstream.RigidLigandBuilder, atom3_frame : rosetta.numeric.HomogeneousTransform_double_t, scaffold_build_point_id : int, upstream_conf_id : int, external_geometry_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.downstream.RigidLigandBuilder) -> rosetta.protocols.match.downstream.DownstreamBuilder
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.downstream.RigidLigandBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.DownstreamBuilder, other_hit : rosetta.protocols.match.Hit) -> bool
2. compatible(self : rosetta.protocols.match.downstream.RigidLigandBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.DownstreamBuilder, other_hit : rosetta.protocols.match.Hit, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.downstream.RigidLigandBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.RigidLigandBuilder, other_hit : rosetta.protocols.match.Hit) -> bool
4. compatible(self : rosetta.protocols.match.downstream.RigidLigandBuilder, my_hit : rosetta.protocols.match.Hit, other : rosetta.protocols.match.downstream.RigidLigandBuilder, other_hit : rosetta.protocols.match.Hit, first_dispatch : bool) -> bool
- coordinates_from_hit(...) from builtins.PyCapsule
- coordinates_from_hit(self : rosetta.protocols.match.downstream.RigidLigandBuilder, hit : rosetta.protocols.match.Hit, atom_indices : rosetta.utility.vector1_core_id_AtomID, atom_coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- downstream_pose_from_hit(...) from builtins.PyCapsule
- downstream_pose_from_hit(self : rosetta.protocols.match.downstream.RigidLigandBuilder, hit : rosetta.protocols.match.Hit) -> rosetta.core.pose.Pose
- get_lig_conformers(...) from builtins.PyCapsule
- get_lig_conformers(self : rosetta.protocols.match.downstream.RigidLigandBuilder, conf_id : int) -> protocols::toolbox::match_enzdes_util::LigandConformer
- get_upstream_restype(...) from builtins.PyCapsule
- get_upstream_restype(rosetta.protocols.match.downstream.RigidLigandBuilder) -> rosetta.core.chemical.ResidueType
- hits_potentially_incompatible(...) from builtins.PyCapsule
- hits_potentially_incompatible(rosetta.protocols.match.downstream.RigidLigandBuilder) -> bool
- ignore_h_collisions(...) from builtins.PyCapsule
- ignore_h_collisions(self : rosetta.protocols.match.downstream.RigidLigandBuilder, setting : bool) -> NoneType
- initialize_from_residue(...) from builtins.PyCapsule
- initialize_from_residue(self : rosetta.protocols.match.downstream.RigidLigandBuilder, atom1 : int, atom2 : int, atom3 : int, orientation_atom1 : int, orientation_atom2 : int, orientation_atom3 : int, residue : rosetta.core.conformation.Residue) -> NoneType
Specify the residue, with coordinates, that's being used as the downstream
partner. This class is meant to be used in conjuction with the ClassicMatchAglrotihm,
and therefore the initialization routines are specific for that algorithm. In this
initialization function, one must list atoms "D1, D2 and D3" in the convention of
describing the rigid-body orientation between three atoms of the upstream partner
(atoms U3, U2 & U1) and three atoms of the downstream partner (atoms D1, D2 & D3) in terms
of 2 angles, 1 distance, and 3 dihedrals. The user must also list the 3 atoms used to
define the orientation frame of the downstream ligand. It is essential to the
matching algorithm that the same three orientation atoms are used for all RigidLigandBuilders.
- initialize_upstream_residue(...) from builtins.PyCapsule
- initialize_upstream_residue(*args, **kwargs)
Overloaded function.
1. initialize_upstream_residue(self : rosetta.protocols.match.downstream.RigidLigandBuilder, upstream_res : rosetta.core.chemical.ResidueType) -> NoneType
2. initialize_upstream_residue(self : rosetta.protocols.match.downstream.RigidLigandBuilder, upstream_res : rosetta.core.chemical.ResidueType, count_pair : rosetta.core.scoring.etable.count_pair.CountPairFunction) -> NoneType
- n_possible_hits_per_at3frame(...) from builtins.PyCapsule
- n_possible_hits_per_at3frame(rosetta.protocols.match.downstream.RigidLigandBuilder) -> int
- require_atom_to_reside_in_active_site(...) from builtins.PyCapsule
- require_atom_to_reside_in_active_site(self : rosetta.protocols.match.downstream.RigidLigandBuilder, id : rosetta.core.id.AtomID) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.RigidLigandBuilder, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
Methods inherited from DownstreamBuilder:
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamBuilder, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_occupied_space_hash(...) from builtins.PyCapsule
- set_occupied_space_hash(self : rosetta.protocols.match.downstream.DownstreamBuilder, occ_space : rosetta.protocols.match.OccupiedSpaceHash) -> NoneType
|
class ScoringSecMatchRPE(SecMatchResiduePairEvaluator) |
| | |
- Method resolution order:
- ScoringSecMatchRPE
- SecMatchResiduePairEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, s_in : str, ref_pose : rosetta.core.pose.Pose) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.ScoringSecMatchRPE, : rosetta.protocols.match.downstream.ScoringSecMatchRPE) -> rosetta.protocols.match.downstream.ScoringSecMatchRPE
- check2bsc(...) from builtins.PyCapsule
- check2bsc(self : rosetta.protocols.match.downstream.ScoringSecMatchRPE, sType : rosetta.core.scoring.ScoreType, wts : float) -> bool
- eval_cd_2b_residues(...) from builtins.PyCapsule
- eval_cd_2b_residues(self : rosetta.protocols.match.downstream.ScoringSecMatchRPE, match_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
- eval_longRange_2b_residue(...) from builtins.PyCapsule
- eval_longRange_2b_residue(self : rosetta.protocols.match.downstream.ScoringSecMatchRPE, match_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
- evaluate_residues(...) from builtins.PyCapsule
- evaluate_residues(self : rosetta.protocols.match.downstream.ScoringSecMatchRPE, match_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
- getCutoff(...) from builtins.PyCapsule
- getCutoff(rosetta.protocols.match.downstream.ScoringSecMatchRPE) -> float
- get_score_function(...) from builtins.PyCapsule
- get_score_function(*args, **kwargs)
Overloaded function.
1. get_score_function(rosetta.protocols.match.downstream.ScoringSecMatchRPE) -> rosetta.core.scoring.ScoreFunction
2. get_score_function(rosetta.protocols.match.downstream.ScoringSecMatchRPE) -> rosetta.core.scoring.ScoreFunction
- require_all_target_residue_atom_coordinates(...) from builtins.PyCapsule
- require_all_target_residue_atom_coordinates(rosetta.protocols.match.downstream.ScoringSecMatchRPE) -> bool
- require_target_atom_coordinate(...) from builtins.PyCapsule
- require_target_atom_coordinate(self : rosetta.protocols.match.downstream.ScoringSecMatchRPE, target_atom_id : int) -> bool
- setPose(...) from builtins.PyCapsule
- setPose(self : rosetta.protocols.match.downstream.ScoringSecMatchRPE, ref_pose : rosetta.core.pose.Pose) -> NoneType
Data descriptors defined here:
- scoringEval_counter
Methods inherited from SecMatchResiduePairEvaluator:
- candidate_res_atoms_reqd_near_target_atom(...) from builtins.PyCapsule
- candidate_res_atoms_reqd_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> rosetta.utility.vector1_unsigned_long
Return a list of atom indices on the candidate residue; if all atoms
in this list are further than max_separation_dist_to_target_atom() away
from the target_atom_id atom for a given pair of conformations of the
target_residue and the candidate_residue, then this evaluator will return false
in the call to evaluate( candidate_residue, target_residue ).
This list will allow the SecondaryMatcher to (conservatively!) prune
conformations of the candidate_residue from consideration. The base class implements
a noop -- it returns an empty list.
- max_separation_dist_to_target_atom(...) from builtins.PyCapsule
- max_separation_dist_to_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> float
Return the maximum separation distance that any of the match-residue
atoms identified by the function match_atoms_reqd_near_target_atom
may be from a particular atom on the target residue. Returns a negative value
if there is no requirement that any atom be within a certain radius of the
target atom. The base class implementation returns -1.0.
- require_candidate_residue_atoms_to_lie_near_target_atom(...) from builtins.PyCapsule
- require_candidate_residue_atoms_to_lie_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> bool
Are there atoms of the candidate residue that must be within
some cutoff distance of a given atom on the target residue? Base
class implementation returns false.
|
class SecMatchResiduePairEvaluator(builtins.object) |
| |
base for class used by secondary matcher
to determine whether a given residue to be matched
interacts satisfactorily with a target residue
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator) -> NoneType
2. __init__(rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator) -> rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator
- candidate_res_atoms_reqd_near_target_atom(...) from builtins.PyCapsule
- candidate_res_atoms_reqd_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> rosetta.utility.vector1_unsigned_long
Return a list of atom indices on the candidate residue; if all atoms
in this list are further than max_separation_dist_to_target_atom() away
from the target_atom_id atom for a given pair of conformations of the
target_residue and the candidate_residue, then this evaluator will return false
in the call to evaluate( candidate_residue, target_residue ).
This list will allow the SecondaryMatcher to (conservatively!) prune
conformations of the candidate_residue from consideration. The base class implements
a noop -- it returns an empty list.
- evaluate_residues(...) from builtins.PyCapsule
- evaluate_residues(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, candidate_res : rosetta.core.conformation.Residue, target_res : rosetta.core.conformation.Residue) -> bool
Returns true if the interaction between the two residues satisifies the
secondary match requirement.
candidate_res: the rotamer of the residue trying to be placed
target_res: the previously placed residue
- max_separation_dist_to_target_atom(...) from builtins.PyCapsule
- max_separation_dist_to_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> float
Return the maximum separation distance that any of the match-residue
atoms identified by the function match_atoms_reqd_near_target_atom
may be from a particular atom on the target residue. Returns a negative value
if there is no requirement that any atom be within a certain radius of the
target atom. The base class implementation returns -1.0.
- require_all_target_residue_atom_coordinates(...) from builtins.PyCapsule
- require_all_target_residue_atom_coordinates(rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator) -> bool
Returns true if all coordinates of the target residue are required
in order to evaluate the interaction between the candidate and the target residues.
- require_candidate_residue_atoms_to_lie_near_target_atom(...) from builtins.PyCapsule
- require_candidate_residue_atoms_to_lie_near_target_atom(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> bool
Are there atoms of the candidate residue that must be within
some cutoff distance of a given atom on the target residue? Base
class implementation returns false.
- require_target_atom_coordinate(...) from builtins.PyCapsule
- require_target_atom_coordinate(self : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, target_atom_id : int) -> bool
If require_all_target_residue_atom_coordinates() returns false, then
this method should return true for the atoms on the target residue that the
evaluator requires.
|
class SecondaryMatcherToDownstreamResidue(DownstreamAlgorithm) |
| |
A class for an algorithm. Given a conformation of the downstream partner,
the algorithm is responsible for producing a set of hits.
|
| |
- Method resolution order:
- SecondaryMatcherToDownstreamResidue
- DownstreamAlgorithm
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, upstream_pose : rosetta.core.pose.Pose, geom_cst_id : int) -> NoneType
2. __init__(handle, rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_evaluator(...) from builtins.PyCapsule
- add_evaluator(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, evaluator : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, mcfi_id : int) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue) -> rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, scaffold_build_point_id : int, upstream_conf_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Iterate across the conformations of the downstream residue coming from hits
generated in previous rounds, and add hits for each upstream residue that
(Also, see comments for the
build_at_all_positions method.)
- build_hits_at_all_positions(...) from builtins.PyCapsule
- build_hits_at_all_positions(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, matcher : rosetta.protocols.match.Matcher) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Main driver function for hit generation. This DownstreamAlgorithm
structures it's iteration over the hits from previous rounds as follows:
for i = 1:this->geom_cst_id() - 1
if ( ! matcher->representative_downstream_algorithm( i )->generates_primary_hits() ) continue;
for j = 1:n_build_points_for_geomcst( i )
recover_downstream_coordinates_from_previous_round( hit_subset_j );
initialize TaretRotamerCoords data for all downstream algorithms with the same geom_cst_id
#omp parallel for /// All class access below this point is const and parallelizable
for k = 1:n_build_positions
/// call this function to start l loop: matcher.upstream_builder[ geom_cst_id() ]->build( k )
for l = 1:n_rotamers_k
/// call to start m loop: downstream_algorithm->build( k, l, rotamer_l ) )
for m = 1:n_hits_in_block_j
if ( respair_evaluator_->evaluate_residues( rotamer_l, rotamer_m )
hit_list.append( Hit( k, l, i, 1, hit[ m ].second() ));
return hit_list
There are two important consequences to this hit-generation layout.
1. The coordinates for rotamer_l are computed sum( i, n_build_points_for_geomcst( i )) times.
2. The number of downstream target coordinates that live in memory at the same time is bound by some constant (10K).
This is a clear trade-off between performance and memory
NOTE: the most time consuming portion will likely be the m loop, and not the repeated construction
of coordinates in the j loop. Reguardless of how many times we rebuild coordinates for rotamer j, the expense
will primarily lie in the same place: the call to evaluate_residues( rotamer_l, rotamer_m ).
NOTE: if there are ways to iterate across the j loop differently, it likely possible to prune m/l combinations early
and thereby improve running time.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- generates_primary_hits(...) from builtins.PyCapsule
- generates_primary_hits(rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue) -> bool
This method returns 'false' since this matcher does not describe
the coordinates of the downstream partner at all.
- n_possible_hits_per_upstream_conformation(...) from builtins.PyCapsule
- n_possible_hits_per_upstream_conformation(rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue) -> int
- respond_to_peripheral_hitlist_change(...) from builtins.PyCapsule
- respond_to_peripheral_hitlist_change(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, matcher : rosetta.protocols.match.Matcher) -> NoneType
Remove my hits if they fall into a volume of the occupied space hash
that is no longer occupied.
- respond_to_primary_hitlist_change(...) from builtins.PyCapsule
- respond_to_primary_hitlist_change(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, matcher : rosetta.protocols.match.Matcher, round_just_completed : int) -> NoneType
mimic the classic matcher's reset of the Occupied space hash.
- set_catalytic_atoms(...) from builtins.PyCapsule
- set_catalytic_atoms(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, catalytic_atoms : rosetta.utility.vector1_unsigned_long) -> NoneType
- set_downstream_restype(...) from builtins.PyCapsule
- set_downstream_restype(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, downstream_restype : rosetta.core.chemical.ResidueType) -> NoneType
- set_focused_geomcst_id(...) from builtins.PyCapsule
- set_focused_geomcst_id(self : rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue, focused_geomcst_id : int) -> NoneType
- upstream_only(...) from builtins.PyCapsule
- upstream_only(rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue) -> bool
returns false; this secondary matcher describes the location
of the downstream partner even though it does not generate that location
itself. Matches may be found by hashing the 6D coordinate of the
downstream partner.
Methods inherited from DownstreamAlgorithm:
- are_colliding(...) from builtins.PyCapsule
- are_colliding(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, us_res : rosetta.core.conformation.Residue, ds_res : rosetta.core.conformation.Residue, ds_atoms : rosetta.utility.vector1_core_id_AtomID, catalytic_atoms : rosetta.utility.vector1_unsigned_long) -> bool
- geom_cst_id(...) from builtins.PyCapsule
- geom_cst_id(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> int
- get_dsbuilder(...) from builtins.PyCapsule
- get_dsbuilder(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> protocols::match::downstream::DownstreamBuilder
- prepare_for_match_enumeration(...) from builtins.PyCapsule
- prepare_for_match_enumeration(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, : rosetta.protocols.match.Matcher) -> NoneType
Called at the conclusion of matching, the Matcher signals
to the downstream algorithm that it's time to prepare for
match generation; if the downstream algorithm needs to enumerate
compatible hits in response to the invokation of its
hits_to_include_with_partial_match method, then now is the time
to prepare for those calls. Base class has a noop implementation.
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
- set_dsbuilder(...) from builtins.PyCapsule
- set_dsbuilder(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, dsbuilder : protocols::match::downstream::DownstreamBuilder) -> NoneType
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class SecondaryMatcherToUpstreamResidue(DownstreamAlgorithm) |
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A class for an algorithm. Given a conformation of the upstream partner,
the algorithm is responsible for producing a set of hits.
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- Method resolution order:
- SecondaryMatcherToUpstreamResidue
- DownstreamAlgorithm
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, geom_cst_id : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_evaluator_for_target_restype(...) from builtins.PyCapsule
- add_evaluator_for_target_restype(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, target_restype : rosetta.core.chemical.ResidueType, evaluator : rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator, mcfi_id_for_evaluator : int) -> NoneType
- add_target_restype(...) from builtins.PyCapsule
- add_target_restype(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, target_restype : rosetta.core.chemical.ResidueType) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue) -> rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, scaffold_build_point_id : int, upstream_conf_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Iterate across the hits from a particular upstream build point i
that were generated in a previous round, and see if the geometry of the
input upstream_residue has "satisfactory interactions" with the
hits from upstream-build-point i; if so, it appends a Hit to the hitlist
returned at the end of the method. (Also, see comments for the
build_at_all_positions method.)
- build_hits_at_all_positions(...) from builtins.PyCapsule
- build_hits_at_all_positions(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, matcher : rosetta.protocols.match.Matcher) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Main driver function for hit generation. This DownstreamAlgorithm
structures it's iteration over the hits from previous rounds as follows:
for i = 1:n_build_positions
recover_rotamer_coordinates_from_previous_round( hits_for_build_point_i );
initialize rotcoord data for all downstream algorithms with the same geom_cst_id
#omp parallel for /// All class access below this point is const and parallelizable
for j = 1:n_build_positions
/// call this function to start k loop: matcher.upstream_builder[ geom_cst_id() ]->build( j )
for k = 1:n_rotamers_j
/// call to start l loop: downstream_algorithm->build( j, k, rotamer_k ) )
for l = 1:n_rotamers_from_build_point_i
if ( respair_evaluator_->evaluate_residues( rotamer_k, rotamer_l )
hit_list.append( Hit( j, k, ... ));
return hit_list
There are two important consequences to this hit-generation layout.
1. The coordinates for rotamer_k are computed n_build_position times.
2. Only a single build-position i has it's hit coordinates in memory at any point in time.
This is a clear trade-off between performance and memory with a few caveats:
A. It is very easy to bound the volume of space where build-point i's rotamers lie,
so it should be easy to prune rotamer building, so rotamer k will be build many fewer than
n_build_position times.
B. By not trying to store all rotamers in memory at once, we do not impose any undue restrictions
on the number of rotamers that can be enumerated. This is especially important if we're
using backbone flexibility to search a wider region of conformation space.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- generates_primary_hits(...) from builtins.PyCapsule
- generates_primary_hits(rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue) -> bool
This method returns 'false' since this matcher does not describe
the coordinates of the downstream partner at all.
- n_possible_hits_per_upstream_conformation(...) from builtins.PyCapsule
- n_possible_hits_per_upstream_conformation(rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue) -> int
- prepare_for_match_enumeration(...) from builtins.PyCapsule
- prepare_for_match_enumeration(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, matcher : rosetta.protocols.match.Matcher) -> NoneType
Prepare a map between upstream hits of the target-geomcst and
a list of Hit const *'s of this geom_cst_id(). This map will be used
in the function hits_to_include_with_partial_match.
- process_hit(...) from builtins.PyCapsule
- process_hit(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, hit : rosetta.protocols.match.Hit, upstream_conformation : rosetta.core.conformation.Residue) -> NoneType
Invoked by SecondaryMatchUpstreamResProcessor; avoids multiple inherritance,
while letting the SecondaryMatcherToUpstreamResidue
- respond_to_peripheral_hitlist_change(...) from builtins.PyCapsule
- respond_to_peripheral_hitlist_change(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, matcher : rosetta.protocols.match.Matcher) -> NoneType
Remove my hits if my target_geomcst's hit list has been shortened. This
will not trigger a round of peripheral-hitlist-change responses.
- respond_to_primary_hitlist_change(...) from builtins.PyCapsule
- respond_to_primary_hitlist_change(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, matcher : rosetta.protocols.match.Matcher, round_just_completed : int) -> NoneType
Prune hits away from the target_geomcst's hit list following a change to the
hits for my geom_cst_id(). Pruning hits from the target_geomcst's hit list will
trigger a round of peripheral-hitlist-change responses.
- set_target_geomcst_id(...) from builtins.PyCapsule
- set_target_geomcst_id(self : rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue, target_geomcst_id : int) -> NoneType
- upstream_only(...) from builtins.PyCapsule
- upstream_only(rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue) -> bool
returns true; this secondary matcher does not describe the location
of the downstream partner
Methods inherited from DownstreamAlgorithm:
- are_colliding(...) from builtins.PyCapsule
- are_colliding(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, us_res : rosetta.core.conformation.Residue, ds_res : rosetta.core.conformation.Residue, ds_atoms : rosetta.utility.vector1_core_id_AtomID, catalytic_atoms : rosetta.utility.vector1_unsigned_long) -> bool
- geom_cst_id(...) from builtins.PyCapsule
- geom_cst_id(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> int
- get_dsbuilder(...) from builtins.PyCapsule
- get_dsbuilder(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> protocols::match::downstream::DownstreamBuilder
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
- set_dsbuilder(...) from builtins.PyCapsule
- set_dsbuilder(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, dsbuilder : protocols::match::downstream::DownstreamBuilder) -> NoneType
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class TargetRotamerCoords(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.match.downstream.TargetRotamerCoords) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.TargetRotamerCoords, : rosetta.protocols.match.downstream.TargetRotamerCoords) -> rosetta.protocols.match.downstream.TargetRotamerCoords
- coord(...) from builtins.PyCapsule
- coord(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_index : int, rotamer_index : int, which_atom : int) -> rosetta.numeric.xyzVector_double_t
- get_clash_checking(...) from builtins.PyCapsule
- get_clash_checking(self : rosetta.protocols.match.downstream.TargetRotamerCoords, rotamer_index : int) -> bool
- get_coords_for_clash_check(...) from builtins.PyCapsule
- get_coords_for_clash_check(self : rosetta.protocols.match.downstream.TargetRotamerCoords, rotamer_index : int) -> rosetta.utility.vector1_numeric_xyzVector_double_t
- get_ds_atom_ids_needed(...) from builtins.PyCapsule
- get_ds_atom_ids_needed(rosetta.protocols.match.downstream.TargetRotamerCoords) -> rosetta.utility.vector1_core_id_AtomID
- hit(...) from builtins.PyCapsule
- hit(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_index : int, rotamer_index : int) -> rosetta.protocols.match.Hit
- n_atoms_for_restype(...) from builtins.PyCapsule
- n_atoms_for_restype(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_id : int) -> int
- n_restypes(...) from builtins.PyCapsule
- n_restypes(rosetta.protocols.match.downstream.TargetRotamerCoords) -> int
- n_rotamers_for_restype(...) from builtins.PyCapsule
- n_rotamers_for_restype(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_id : int) -> int
- n_rots_total(...) from builtins.PyCapsule
- n_rots_total(rosetta.protocols.match.downstream.TargetRotamerCoords) -> int
- restype(...) from builtins.PyCapsule
- restype(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_index : int) -> rosetta.core.chemical.ResidueType
- restype_atomno(...) from builtins.PyCapsule
- restype_atomno(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_index : int, which_atom : int) -> int
- set_clash_check_types(...) from builtins.PyCapsule
- set_clash_check_types(self : rosetta.protocols.match.downstream.TargetRotamerCoords, n_rotamers : int) -> NoneType
- set_clash_checking(...) from builtins.PyCapsule
- set_clash_checking(self : rosetta.protocols.match.downstream.TargetRotamerCoords, rotamer_index : int) -> NoneType
- set_coordinates_for_rotamer(...) from builtins.PyCapsule
- set_coordinates_for_rotamer(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_index : int, rotamer_index : int, hit : rosetta.protocols.match.Hit, rescoords : rosetta.core.conformation.Residue) -> NoneType
- set_coords_for_clash_check(...) from builtins.PyCapsule
- set_coords_for_clash_check(self : rosetta.protocols.match.downstream.TargetRotamerCoords, rotamer_index : int, coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- set_ds_atom_ids_needed(...) from builtins.PyCapsule
- set_ds_atom_ids_needed(self : rosetta.protocols.match.downstream.TargetRotamerCoords, atom_ids : rosetta.utility.vector1_core_id_AtomID) -> NoneType
- set_num_restypes(...) from builtins.PyCapsule
- set_num_restypes(self : rosetta.protocols.match.downstream.TargetRotamerCoords, n_restypes : int) -> NoneType
- set_num_target_rotamers(...) from builtins.PyCapsule
- set_num_target_rotamers(*args, **kwargs)
Overloaded function.
1. set_num_target_rotamers(self : rosetta.protocols.match.downstream.TargetRotamerCoords, n_rotamers_per_target_restype : rosetta.utility.vector1_unsigned_long) -> NoneType
2. set_num_target_rotamers(self : rosetta.protocols.match.downstream.TargetRotamerCoords, target_restype_id : int, n_rotamers : int) -> NoneType
- set_required_atoms(...) from builtins.PyCapsule
- set_required_atoms(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_index : int, atom_required : rosetta.utility.vector1_bool) -> NoneType
- set_restype(...) from builtins.PyCapsule
- set_restype(self : rosetta.protocols.match.downstream.TargetRotamerCoords, restype_index : int, restype : rosetta.core.chemical.ResidueType) -> NoneType
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class us_secmatch_hit_compare(builtins.object) |
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A simple struct to use in list.sort() to ensure that the
hits returned by a secondary matcher which has possibly generated upstream
hits out-of-order, will return an ordered-hit-list in its
build_hits_at_all_positions() method.
This struct compares the upstream portion of the hits it's returning
ensuring that the rotamer indices (the upstream_conf_ids()) are in ascending
order for each scaffold build point.
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Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.match.downstream.us_secmatch_hit_compare, lhs : rosetta.protocols.match.Hit, rhs : rosetta.protocols.match.Hit) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.match.downstream.us_secmatch_hit_compare) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
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