| | |
- builtins.object
-
- BuildSet
- ChiStrategy
- FullChiSampleSet
- ProteinSCSampler
-
- DunbrackSCSampler
- SampleStrategyData
- ScaffoldBuildPoint
-
- ProteinBackboneBuildPoint
-
- OriginalBackboneBuildPoint
- UpstreamBuilder
-
- ProteinUpstreamBuilder
- UpstreamResTypeGeometry
- UpstreamResidueProcessor
class BuildSet(builtins.object) |
| |
Still sketchy on this class. It holds all of the data needed
for describing the geometry of the downstream partner relative to the upstream
partner for a single residue type. This class holds the data for deciding which
base rotamers to consider, how each base rotamer should be expanded to produce a
full set of chi rotamers, and how to orient the downstream partner relative to
this rotamer. It also holds the UpstreamResTypeGeometry object for the
restype being built.
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.upstream.BuildSet) -> NoneType
2. __init__(self : rosetta.protocols.match.upstream.BuildSet, : rosetta.protocols.match.upstream.BuildSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- algorithm(...) from builtins.PyCapsule
- algorithm(*args, **kwargs)
Overloaded function.
1. algorithm(rosetta.protocols.match.upstream.BuildSet) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
2. algorithm(rosetta.protocols.match.upstream.BuildSet) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.upstream.BuildSet, rhs : rosetta.protocols.match.upstream.BuildSet) -> rosetta.protocols.match.upstream.BuildSet
- atom_radius(...) from builtins.PyCapsule
- atom_radius(self : rosetta.protocols.match.upstream.BuildSet, atomno : int) -> rosetta.protocols.match.ProbeRadius
- backbone_only(...) from builtins.PyCapsule
- backbone_only(rosetta.protocols.match.upstream.BuildSet) -> bool
- check_fa_dun(...) from builtins.PyCapsule
- check_fa_dun(rosetta.protocols.match.upstream.BuildSet) -> bool
- fa_dun_cutoff(...) from builtins.PyCapsule
- fa_dun_cutoff(rosetta.protocols.match.upstream.BuildSet) -> float
- has_algorithm(...) from builtins.PyCapsule
- has_algorithm(rosetta.protocols.match.upstream.BuildSet) -> bool
- has_restype(...) from builtins.PyCapsule
- has_restype(rosetta.protocols.match.upstream.BuildSet) -> bool
accessors
- nbonds_from_bb_atom(...) from builtins.PyCapsule
- nbonds_from_bb_atom(self : rosetta.protocols.match.upstream.BuildSet, atom_index : int) -> int
- probability_limit(...) from builtins.PyCapsule
- probability_limit(rosetta.protocols.match.upstream.BuildSet) -> float
- restype(...) from builtins.PyCapsule
- restype(rosetta.protocols.match.upstream.BuildSet) -> rosetta.core.chemical.ResidueType
- restype_geometry(...) from builtins.PyCapsule
- restype_geometry(rosetta.protocols.match.upstream.BuildSet) -> protocols::match::upstream::UpstreamResTypeGeometry
- sample_strategy_for_chi(...) from builtins.PyCapsule
- sample_strategy_for_chi(self : rosetta.protocols.match.upstream.BuildSet, chi : int) -> rosetta.protocols.match.upstream.SampleStrategyData
- set_downstream_algorithm(...) from builtins.PyCapsule
- set_downstream_algorithm(self : rosetta.protocols.match.upstream.BuildSet, : rosetta.protocols.match.downstream.DownstreamAlgorithm) -> NoneType
- set_fa_dun_cutoff(...) from builtins.PyCapsule
- set_fa_dun_cutoff(self : rosetta.protocols.match.upstream.BuildSet, cutoff : float) -> NoneType
- set_residue_type(...) from builtins.PyCapsule
- set_residue_type(*args, **kwargs)
Overloaded function.
1. set_residue_type(self : rosetta.protocols.match.upstream.BuildSet, restype : rosetta.core.chemical.ResidueType) -> NoneType
initialization
2. set_residue_type(self : rosetta.protocols.match.upstream.BuildSet, restype : rosetta.core.chemical.ResidueType, backbone_only : bool) -> NoneType
initialization
- set_sample_strategy_for_chi(...) from builtins.PyCapsule
- set_sample_strategy_for_chi(self : rosetta.protocols.match.upstream.BuildSet, chi : int, data : rosetta.protocols.match.upstream.SampleStrategyData) -> NoneType
Data descriptors defined here:
- algorithm_
- atom_radii_
- backbone_only_
- check_fa_dun_
- fa_dun_cutoff_
- nbonds_from_bb_atom_
- restype_
- restype_geom_
- rot_prob_accumulation_limit_
- sample_strategy_for_chi_
|
class ChiStrategy(builtins.object) |
| | |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.protocols.match.upstream.ChiStrategy, rosetta.protocols.match.upstream.ChiStrategy) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.protocols.match.upstream.ChiStrategy) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.upstream.ChiStrategy, int) -> NoneType
2. __init__(rosetta.protocols.match.upstream.ChiStrategy, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.protocols.match.upstream.ChiStrategy) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.protocols.match.upstream.ChiStrategy, rosetta.protocols.match.upstream.ChiStrategy) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.protocols.match.upstream.ChiStrategy) -> str
Data and other attributes defined here:
- follow_EX_flags = ChiStrategy.follow_EX_flags
- no_samples = ChiStrategy.no_samples
- nonrotameric_chi_sample_wi_nrchi_bin = ChiStrategy.nonrotameric_chi_sample_wi_nrchi_bin
- nonrotameric_chi_sample_wi_nrchi_bin_to_lower_boundary = ChiStrategy.nonrotameric_chi_sample_wi_nrchi_bin_to_lower_boundary
- rotameric_chi_mimic_EX_flags = ChiStrategy.rotameric_chi_mimic_EX_flags
- rotameric_chi_partition_sd_range = ChiStrategy.rotameric_chi_partition_sd_range
- rotameric_chi_step_by_value = ChiStrategy.rotameric_chi_step_by_value
- rotameric_chi_step_wi_sd_range = ChiStrategy.rotameric_chi_step_wi_sd_range
|
class DunbrackSCSampler(ProteinSCSampler) |
| |
Basic class for sidechain sampling that pulls data from the
Dunbrack rotamer library. The samples that are returned are the basic
rotamers and do not include any expansions by the "ex" flags.
|
| |
- Method resolution order:
- DunbrackSCSampler
- ProteinSCSampler
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> 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.upstream.DunbrackSCSampler, : rosetta.protocols.match.upstream.DunbrackSCSampler) -> rosetta.protocols.match.upstream.DunbrackSCSampler
- desymmeterize(...) from builtins.PyCapsule
- desymmeterize(rosetta.protocols.match.upstream.DunbrackSCSampler) -> bool
- samples(...) from builtins.PyCapsule
- samples(self : rosetta.protocols.match.upstream.DunbrackSCSampler, bb_conf : rosetta.protocols.match.upstream.ScaffoldBuildPoint, restype : rosetta.core.chemical.ResidueType) -> rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData
- set_desymmeterize(...) from builtins.PyCapsule
- set_desymmeterize(self : rosetta.protocols.match.upstream.DunbrackSCSampler, setting : bool) -> NoneType
Should amino acids that are symmetric about their final chi torsion
be treated as if they actually are not symmetric? This can be useful if you
want to set a constraint to one side of the amino acid and a second constraint
to the other side. E.g., let's say you want OD1 on ASP to contact one thing 1,
and OD2 to contact thing 2. If you were to specify the constraint to atom type
OOC, then you wouldn't be able to prevent the case where OD1 contacted both things.
This functionality can be activated in the matcher constraint file by adding
DESYMMETERIZE
to the ALGORITHM_INFO:: block in a matcher constraint file. E.g.
<APL NOTE: FILL IN THE REST OF THE COMMENTS HERE>
|
class OriginalBackboneBuildPoint(ProteinBackboneBuildPoint) |
| | |
- Method resolution order:
- OriginalBackboneBuildPoint
- ProteinBackboneBuildPoint
- ScaffoldBuildPoint
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, index : int) -> NoneType
2. __init__(self : handle, res : rosetta.core.conformation.Residue) -> NoneType
3. __init__(self : handle, res : rosetta.core.conformation.Residue, index : int) -> 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.upstream.OriginalBackboneBuildPoint, : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint) -> rosetta.protocols.match.upstream.OriginalBackboneBuildPoint
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint, other : rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> bool
2. compatible(self : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint, other : rosetta.protocols.match.upstream.ScaffoldBuildPoint, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint, other : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint) -> bool
4. compatible(self : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint, other : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint, first_dispatch : bool) -> bool
- initialize_from_residue(...) from builtins.PyCapsule
- initialize_from_residue(self : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint, res : rosetta.core.conformation.Residue) -> NoneType
- input_conformation(...) from builtins.PyCapsule
- input_conformation(rosetta.protocols.match.upstream.OriginalBackboneBuildPoint) -> rosetta.core.conformation.Residue
- insert(...) from builtins.PyCapsule
- insert(self : rosetta.protocols.match.upstream.OriginalBackboneBuildPoint, seqpos_to_insert_at : int, hit : rosetta.protocols.match.Hit, builder : rosetta.protocols.match.upstream.UpstreamBuilder, pose : rosetta.core.pose.Pose) -> NoneType
- original_insertion_point(...) from builtins.PyCapsule
- original_insertion_point(rosetta.protocols.match.upstream.OriginalBackboneBuildPoint) -> int
- original_resid(...) from builtins.PyCapsule
- original_resid(rosetta.protocols.match.upstream.OriginalBackboneBuildPoint) -> int
Methods inherited from ProteinBackboneBuildPoint:
- CA_pos(...) from builtins.PyCapsule
- CA_pos(*args, **kwargs)
Overloaded function.
1. CA_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. CA_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- C_pos(...) from builtins.PyCapsule
- C_pos(*args, **kwargs)
Overloaded function.
1. C_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. C_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- HA_pos(...) from builtins.PyCapsule
- HA_pos(*args, **kwargs)
Overloaded function.
1. HA_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. HA_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- H_pos(...) from builtins.PyCapsule
- H_pos(*args, **kwargs)
Overloaded function.
1. H_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. H_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- N_pos(...) from builtins.PyCapsule
- N_pos(*args, **kwargs)
Overloaded function.
1. N_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. N_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- O_pos(...) from builtins.PyCapsule
- O_pos(*args, **kwargs)
Overloaded function.
1. O_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. O_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- phi(...) from builtins.PyCapsule
- phi(*args, **kwargs)
Overloaded function.
1. phi(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> float
2. phi(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : float) -> NoneType
Setters
- psi(...) from builtins.PyCapsule
- psi(*args, **kwargs)
Overloaded function.
1. psi(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> float
2. psi(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : float) -> NoneType
Methods inherited from ScaffoldBuildPoint:
- index(...) from builtins.PyCapsule
- index(*args, **kwargs)
Overloaded function.
1. index(rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> int
2. index(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, setting : int) -> NoneType
|
class ProteinBackboneBuildPoint(ScaffoldBuildPoint) |
| | |
- Method resolution order:
- ProteinBackboneBuildPoint
- ScaffoldBuildPoint
- builtins.object
Methods defined here:
- CA_pos(...) from builtins.PyCapsule
- CA_pos(*args, **kwargs)
Overloaded function.
1. CA_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. CA_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- C_pos(...) from builtins.PyCapsule
- C_pos(*args, **kwargs)
Overloaded function.
1. C_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. C_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- HA_pos(...) from builtins.PyCapsule
- HA_pos(*args, **kwargs)
Overloaded function.
1. HA_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. HA_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- H_pos(...) from builtins.PyCapsule
- H_pos(*args, **kwargs)
Overloaded function.
1. H_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. H_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- N_pos(...) from builtins.PyCapsule
- N_pos(*args, **kwargs)
Overloaded function.
1. N_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. N_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- O_pos(...) from builtins.PyCapsule
- O_pos(*args, **kwargs)
Overloaded function.
1. O_pos(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.numeric.xyzVector_double_t
2. O_pos(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : rosetta.numeric.xyzVector_double_t) -> NoneType
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> NoneType
2. __init__(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, index : int) -> 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.upstream.ProteinBackboneBuildPoint, : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> rosetta.protocols.match.upstream.ProteinBackboneBuildPoint
- phi(...) from builtins.PyCapsule
- phi(*args, **kwargs)
Overloaded function.
1. phi(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> float
2. phi(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : float) -> NoneType
Setters
- psi(...) from builtins.PyCapsule
- psi(*args, **kwargs)
Overloaded function.
1. psi(rosetta.protocols.match.upstream.ProteinBackboneBuildPoint) -> float
2. psi(self : rosetta.protocols.match.upstream.ProteinBackboneBuildPoint, setting : float) -> NoneType
Methods inherited from ScaffoldBuildPoint:
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> bool
2. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : rosetta.protocols.match.upstream.ScaffoldBuildPoint, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : protocols::match::upstream::OriginalBackboneBuildPoint) -> bool
4. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : protocols::match::upstream::OriginalBackboneBuildPoint, first_dispatch : bool) -> bool
- index(...) from builtins.PyCapsule
- index(*args, **kwargs)
Overloaded function.
1. index(rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> int
2. index(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, setting : int) -> NoneType
- insert(...) from builtins.PyCapsule
- insert(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, seqpos_to_insert_at : int, hit : rosetta.protocols.match.Hit, builder : rosetta.protocols.match.upstream.UpstreamBuilder, pose : rosetta.core.pose.Pose) -> NoneType
- original_insertion_point(...) from builtins.PyCapsule
- original_insertion_point(rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> int
Inform the calling function where in the original scaffold
this build point should be inserted. If the output pose from a matching
has a different number of residues than the original scaffold, then
the calling function must determine where the hit from this build point
should be inserted.
|
class ProteinUpstreamBuilder(UpstreamBuilder) |
| | |
- Method resolution order:
- ProteinUpstreamBuilder
- UpstreamBuilder
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_build_set(...) from builtins.PyCapsule
- add_build_set(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, build_set : rosetta.protocols.match.upstream.BuildSet) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, : rosetta.protocols.match.upstream.ProteinUpstreamBuilder) -> rosetta.protocols.match.upstream.ProteinUpstreamBuilder
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, build_point : rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Iterate across possible conformations for the upstream
half of the hit, and for each (non-coliding) conformation,
sample all external geometries specified by the external_sampler
to construct the three coordinates of the downstream sampler.
Return a list of hits.
- build_set(...) from builtins.PyCapsule
- build_set(*args, **kwargs)
Overloaded function.
1. build_set(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, restype : rosetta.core.chemical.ResidueType) -> rosetta.protocols.match.upstream.BuildSet
2. build_set(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, restype : rosetta.core.chemical.ResidueType) -> rosetta.protocols.match.upstream.BuildSet
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.upstream.ProteinUpstreamBuilder) -> rosetta.protocols.match.upstream.UpstreamBuilder
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : rosetta.protocols.match.upstream.ScaffoldBuildPoint, other : rosetta.protocols.match.upstream.UpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> bool
2. compatible(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : rosetta.protocols.match.upstream.ScaffoldBuildPoint, other : rosetta.protocols.match.upstream.UpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : rosetta.protocols.match.upstream.ScaffoldBuildPoint, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : rosetta.protocols.match.upstream.ScaffoldBuildPoint, other : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> bool
4. compatible(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : rosetta.protocols.match.upstream.ScaffoldBuildPoint, other : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : rosetta.protocols.match.upstream.ScaffoldBuildPoint, first_dispatch : bool) -> bool
- n_build_sets(...) from builtins.PyCapsule
- n_build_sets(rosetta.protocols.match.upstream.ProteinUpstreamBuilder) -> int
- n_restypes_to_build(...) from builtins.PyCapsule
- n_restypes_to_build(rosetta.protocols.match.upstream.ProteinUpstreamBuilder) -> int
- recover_hit(...) from builtins.PyCapsule
- recover_hit(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, hit : rosetta.protocols.match.Hit, build_point : rosetta.protocols.match.upstream.ScaffoldBuildPoint, processor : rosetta.protocols.match.upstream.UpstreamResidueProcessor) -> NoneType
Regenerate the rotamer for a particular hit and give that rotamer
to the UpstreamResidueProcessor.
- recover_hits(...) from builtins.PyCapsule
- recover_hits(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, hits_begin : std::_List_const_iterator<protocols::match::Hit>, hits_end : std::_List_const_iterator<protocols::match::Hit>, build_point : rosetta.protocols.match.upstream.ScaffoldBuildPoint, processor : rosetta.protocols.match.upstream.UpstreamResidueProcessor) -> NoneType
Regenerate a set of rotamers for a subset of hits bound by the
two input hit-list iterators.
- restype(...) from builtins.PyCapsule
- restype(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, which_restype : int) -> rosetta.core.chemical.ResidueType
- set_native_flag(...) from builtins.PyCapsule
- set_native_flag(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, native : bool) -> NoneType
- set_sampler(...) from builtins.PyCapsule
- set_sampler(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, sampler : rosetta.protocols.match.upstream.ProteinSCSampler) -> NoneType
- set_use_input_sidechain(...) from builtins.PyCapsule
- set_use_input_sidechain(self : rosetta.protocols.match.upstream.ProteinUpstreamBuilder, setting : bool) -> NoneType
Methods inherited from UpstreamBuilder:
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.upstream.UpstreamBuilder, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
|
class ScaffoldBuildPoint(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> NoneType
2. __init__(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, index : int) -> 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.upstream.ScaffoldBuildPoint, : rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> rosetta.protocols.match.upstream.ScaffoldBuildPoint
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> bool
2. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : rosetta.protocols.match.upstream.ScaffoldBuildPoint, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : protocols::match::upstream::OriginalBackboneBuildPoint) -> bool
4. compatible(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, : protocols::match::upstream::OriginalBackboneBuildPoint, first_dispatch : bool) -> bool
- index(...) from builtins.PyCapsule
- index(*args, **kwargs)
Overloaded function.
1. index(rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> int
2. index(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, setting : int) -> NoneType
- insert(...) from builtins.PyCapsule
- insert(self : rosetta.protocols.match.upstream.ScaffoldBuildPoint, seqpos_to_insert_at : int, hit : rosetta.protocols.match.Hit, builder : rosetta.protocols.match.upstream.UpstreamBuilder, pose : rosetta.core.pose.Pose) -> NoneType
- original_insertion_point(...) from builtins.PyCapsule
- original_insertion_point(rosetta.protocols.match.upstream.ScaffoldBuildPoint) -> int
Inform the calling function where in the original scaffold
this build point should be inserted. If the output pose from a matching
has a different number of residues than the original scaffold, then
the calling function must determine where the hit from this build point
should be inserted.
|
class UpstreamBuilder(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.match.upstream.UpstreamBuilder) -> 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.upstream.UpstreamBuilder, : rosetta.protocols.match.upstream.UpstreamBuilder) -> rosetta.protocols.match.upstream.UpstreamBuilder
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.upstream.UpstreamBuilder, build_point : protocols::match::upstream::ScaffoldBuildPoint) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Iterate across possible conformations for the upstream
half of the hit, and for each (non-colliding) conformation,
invoke build on the downstream algorithm.
Return a list of hits.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.upstream.UpstreamBuilder) -> rosetta.protocols.match.upstream.UpstreamBuilder
- compatible(...) from builtins.PyCapsule
- compatible(*args, **kwargs)
Overloaded function.
1. compatible(self : rosetta.protocols.match.upstream.UpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : protocols::match::upstream::ScaffoldBuildPoint, other : rosetta.protocols.match.upstream.UpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : protocols::match::upstream::ScaffoldBuildPoint) -> bool
2. compatible(self : rosetta.protocols.match.upstream.UpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : protocols::match::upstream::ScaffoldBuildPoint, other : rosetta.protocols.match.upstream.UpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : protocols::match::upstream::ScaffoldBuildPoint, first_dispatch : bool) -> bool
3. compatible(self : rosetta.protocols.match.upstream.UpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : protocols::match::upstream::ScaffoldBuildPoint, other : protocols::match::upstream::ProteinUpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : protocols::match::upstream::ScaffoldBuildPoint) -> bool
4. compatible(self : rosetta.protocols.match.upstream.UpstreamBuilder, my_hit : rosetta.protocols.match.Hit, build_point_mine : protocols::match::upstream::ScaffoldBuildPoint, other : protocols::match::upstream::ProteinUpstreamBuilder, other_hit : rosetta.protocols.match.Hit, build_point_other : protocols::match::upstream::ScaffoldBuildPoint, first_dispatch : bool) -> bool
- n_restypes_to_build(...) from builtins.PyCapsule
- n_restypes_to_build(rosetta.protocols.match.upstream.UpstreamBuilder) -> int
- recover_hit(...) from builtins.PyCapsule
- recover_hit(self : rosetta.protocols.match.upstream.UpstreamBuilder, hit : rosetta.protocols.match.Hit, build_point : protocols::match::upstream::ScaffoldBuildPoint, processor : protocols::match::upstream::UpstreamResidueProcessor) -> NoneType
Reconstruct the upstream conformation for a hit and pass that conformation to
an upstream residue processor.
- recover_hits(...) from builtins.PyCapsule
- recover_hits(self : rosetta.protocols.match.upstream.UpstreamBuilder, hits_begin : std::_List_const_iterator<protocols::match::Hit>, hits_end : std::_List_const_iterator<protocols::match::Hit>, build_point : protocols::match::upstream::ScaffoldBuildPoint, processor : protocols::match::upstream::UpstreamResidueProcessor) -> NoneType
Reconstruct the upstream conformation for a set of hits and pass their conformations to
an upstream residue processor.
- restype(...) from builtins.PyCapsule
- restype(self : rosetta.protocols.match.upstream.UpstreamBuilder, which_restype : int) -> rosetta.core.chemical.ResidueType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.upstream.UpstreamBuilder, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
|
class UpstreamResTypeGeometry(builtins.object) |
| |
A simple class that describes the geometry for a particular
residue type. It describes the coordinate frame geometry for the
fourth atom defining each chi dihedral. The fourth atom is called
the "chi tip" atom, as it's at the tip of the growing kinematic chain
when building chi i. This class also describes the location
of the atoms controlled by each chi which are not the chi-tip atoms;
it measures their location in the coordinate frame of the chi-tip atom.
To generate the coordinate of the chi-tip atom, the
stored coordinate frame is multiplied
by the coordinate frame at the third atom after that coordinate frame
has been multipled by the chi-angle-z-axis rotation HT.
|
| |
Methods defined here:
- CA_atom_id(...) from builtins.PyCapsule
- CA_atom_id(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- CB_atom_id(...) from builtins.PyCapsule
- CB_atom_id(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- C_atom_id(...) from builtins.PyCapsule
- C_atom_id(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- HA_atom_id(...) from builtins.PyCapsule
- HA_atom_id(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- H_atom_id(...) from builtins.PyCapsule
- H_atom_id(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- N_atom_id(...) from builtins.PyCapsule
- N_atom_id(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- O_atom_id(...) from builtins.PyCapsule
- O_atom_id(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> NoneType
2. __init__(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, : rosetta.core.chemical.ResidueType) -> NoneType
3. __init__(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, : rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> 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.upstream.UpstreamResTypeGeometry, : rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> rosetta.protocols.match.upstream.UpstreamResTypeGeometry
- atom_controlled_by_any_chi(...) from builtins.PyCapsule
- atom_controlled_by_any_chi(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, atomno : int) -> bool
- atom_has_nonchi_coordinate(...) from builtins.PyCapsule
- atom_has_nonchi_coordinate(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, restype_atomid : int) -> bool
- atom_is_chitip(...) from builtins.PyCapsule
- atom_is_chitip(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, atomno : int) -> bool
- chitip_atom(...) from builtins.PyCapsule
- chitip_atom(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi : int) -> int
- chitip_atoms(...) from builtins.PyCapsule
- chitip_atoms(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> rosetta.utility.vector1_unsigned_long
- controlling_chi_for_atom(...) from builtins.PyCapsule
- controlling_chi_for_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> rosetta.utility.vector1_unsigned_long
- coordinate_for_nonchi_atom_in_ideal_frame(...) from builtins.PyCapsule
- coordinate_for_nonchi_atom_in_ideal_frame(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, restype_atomid : int) -> rosetta.numeric.xyzVector_double_t
- has_CA_atom(...) from builtins.PyCapsule
- has_CA_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> bool
- has_CB_atom(...) from builtins.PyCapsule
- has_CB_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> bool
- has_C_atom(...) from builtins.PyCapsule
- has_C_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> bool
- has_HA_atom(...) from builtins.PyCapsule
- has_HA_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> bool
- has_H_atom(...) from builtins.PyCapsule
- has_H_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> bool
- has_N_atom(...) from builtins.PyCapsule
- has_N_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> bool
- has_O_atom(...) from builtins.PyCapsule
- has_O_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> bool
- ht_for_chitip_atom(...) from builtins.PyCapsule
- ht_for_chitip_atom(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi : int) -> rosetta.numeric.HomogeneousTransform_double_t
- ht_for_chitip_atoms(...) from builtins.PyCapsule
- ht_for_chitip_atoms(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> rosetta.utility.vector1_numeric_HomogeneousTransform_double_t
- initialize_from_residue_type(...) from builtins.PyCapsule
- initialize_from_residue_type(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, : rosetta.core.chemical.ResidueType) -> NoneType
- n_nonchitip_atoms_for_chi(...) from builtins.PyCapsule
- n_nonchitip_atoms_for_chi(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi : int) -> int
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> str
the name of the residue type used to generate this geometry
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
the number of atoms in this residue type
- nchi(...) from builtins.PyCapsule
- nchi(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> int
- nonchitip_atom(...) from builtins.PyCapsule
- nonchitip_atom(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi : int, which_nonchitip_atom_for_chi : int) -> int
- nonchitip_atoms(...) from builtins.PyCapsule
- nonchitip_atoms(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
- point_for_nonchitip_atom(...) from builtins.PyCapsule
- point_for_nonchitip_atom(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, atom : int) -> rosetta.numeric.xyzVector_double_t
Convenience function: get the coordinate in the chitip frame
for a particular atom. The atom must be a non-chitip atom that is
not part of the backbone (it must be controlled by a chi angle).
- points_for_nonchitip_atoms(...) from builtins.PyCapsule
- points_for_nonchitip_atoms(*args, **kwargs)
Overloaded function.
1. points_for_nonchitip_atoms(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
2. points_for_nonchitip_atoms(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi : int) -> rosetta.utility.vector1_numeric_xyzVector_double_t
- pre_chitip_transform(...) from builtins.PyCapsule
- pre_chitip_transform(self : rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi : int) -> rosetta.numeric.HomogeneousTransform_double_t
- which_point_for_atom(...) from builtins.PyCapsule
- which_point_for_atom(rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> rosetta.utility.vector1_unsigned_long
|
|