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- builtins.object
-
- VallFragmentEval
-
- ABEGOEval
- EnergyEval
- IdentityEval
class ABEGOEval(VallFragmentEval) |
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scores a fragment based on sum of secondary structure identity and sequence identity
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- Method resolution order:
- ABEGOEval
- VallFragmentEval
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.utility.vector1_std_string) -> NoneType
doc
3. __init__(handle, rosetta.utility.vector1_std_string, float) -> NoneType
doc
4. __init__(self : handle, input : rosetta.utility.vector1_std_string, penalty : float, randomize : bool) -> NoneType
5. __init__(handle, rosetta.core.fragment.picking_old.vall.eval.ABEGOEval) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- abego_str(...) from builtins.PyCapsule
- abego_str(*args, **kwargs)
Overloaded function.
1. abego_str(rosetta.core.fragment.picking_old.vall.eval.ABEGOEval) -> rosetta.utility.vector1_std_string
get secondary structure string
2. abego_str(self : rosetta.core.fragment.picking_old.vall.eval.ABEGOEval, abego : rosetta.utility.vector1_std_string) -> NoneType
set abego vector of string
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.fragment.picking_old.vall.eval.ABEGOEval, rval : rosetta.core.fragment.picking_old.vall.eval.ABEGOEval) -> rosetta.core.fragment.picking_old.vall.eval.ABEGOEval
copy assignment
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.fragment.picking_old.vall.eval.ABEGOEval) -> rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval
clone this object
- eval_impl(...) from builtins.PyCapsule
- eval_impl(self : rosetta.core.fragment.picking_old.vall.eval.ABEGOEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
for a fragment extent, evaluate and store results in a VallFragmentScore
true, so score is always stored during VallLibrarian::catalog()
- penalty(...) from builtins.PyCapsule
- penalty(rosetta.core.fragment.picking_old.vall.eval.ABEGOEval) -> float
get secondary structure penalty
- pre_catalog_op(...) from builtins.PyCapsule
- pre_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.ABEGOEval, : rosetta.core.fragment.picking_old.vall.VallLibrary) -> NoneType
operation to be perform before catalog() starts
- randomize(...) from builtins.PyCapsule
- randomize(rosetta.core.fragment.picking_old.vall.eval.ABEGOEval) -> bool
adding random noise to score?
Methods inherited from VallFragmentEval:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
called by VallLibrarian: for a fragment extent, evaluate and store
results in a VallFragmentScore
true if score should be stored, false otherwise
- post_catalog_op(...) from builtins.PyCapsule
- post_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, : core::fragment::picking_old::vall::VallLibrary) -> NoneType
operation to be performed after catalog() finished
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class EnergyEval(VallFragmentEval) |
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scores a fragment by inserting its backbone angles into a Pose and
evaluating its energy using a given ScoreFunction
Useful for e.g. evaluating a chainbreak score, constraint score, etc.
Class currently assumes insertion of backbone angles into protein
residues.
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- Method resolution order:
- EnergyEval
- VallFragmentEval
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.pose.Pose, int, rosetta.core.scoring.ScoreFunction) -> NoneType
doc
3. __init__(self : handle, pose : rosetta.core.pose.Pose, insert_position : int, score_function : rosetta.core.scoring.ScoreFunction, randomize : bool) -> NoneType
4. __init__(handle, rosetta.core.fragment.picking_old.vall.eval.EnergyEval) -> 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.core.fragment.picking_old.vall.eval.EnergyEval, rval : rosetta.core.fragment.picking_old.vall.eval.EnergyEval) -> rosetta.core.fragment.picking_old.vall.eval.EnergyEval
copy assignment
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.fragment.picking_old.vall.eval.EnergyEval) -> rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval
clone this object
- eval_impl(...) from builtins.PyCapsule
- eval_impl(self : rosetta.core.fragment.picking_old.vall.eval.EnergyEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
for a fragment extent, evaluate and store results in a VallFragmentScore
true, so score is always stored during VallLibrarian::catalog()
- insert_position(...) from builtins.PyCapsule
- insert_position(*args, **kwargs)
Overloaded function.
1. insert_position(rosetta.core.fragment.picking_old.vall.eval.EnergyEval) -> int
insert angles into the Pose starting from this position
2. insert_position(self : rosetta.core.fragment.picking_old.vall.eval.EnergyEval, position : int) -> NoneType
insert angles into the Pose starting from this position
- pose(...) from builtins.PyCapsule
- pose(*args, **kwargs)
Overloaded function.
1. pose(rosetta.core.fragment.picking_old.vall.eval.EnergyEval) -> rosetta.core.pose.Pose
the Pose to evaluate
2. pose(self : rosetta.core.fragment.picking_old.vall.eval.EnergyEval, p : rosetta.core.pose.Pose) -> NoneType
the Pose to evaluate
- pre_catalog_op(...) from builtins.PyCapsule
- pre_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.EnergyEval, : rosetta.core.fragment.picking_old.vall.VallLibrary) -> NoneType
operation to be perform before catalog() starts
- randomize(...) from builtins.PyCapsule
- randomize(*args, **kwargs)
Overloaded function.
1. randomize(rosetta.core.fragment.picking_old.vall.eval.EnergyEval) -> bool
adding random noise between [0, 0.000001) to the energy?
2. randomize(self : rosetta.core.fragment.picking_old.vall.eval.EnergyEval, flag : bool) -> NoneType
set flag to add random noise between [0, 0.000001) to the energy
- score_function(...) from builtins.PyCapsule
- score_function(*args, **kwargs)
Overloaded function.
1. score_function(rosetta.core.fragment.picking_old.vall.eval.EnergyEval) -> rosetta.core.scoring.ScoreFunction
the ScoreFunction used to evaluate the pose
2. score_function(self : rosetta.core.fragment.picking_old.vall.eval.EnergyEval, fx : rosetta.core.scoring.ScoreFunction) -> NoneType
the ScoreFunction used to evaluate the pose
Methods inherited from VallFragmentEval:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
called by VallLibrarian: for a fragment extent, evaluate and store
results in a VallFragmentScore
true if score should be stored, false otherwise
- post_catalog_op(...) from builtins.PyCapsule
- post_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, : core::fragment::picking_old::vall::VallLibrary) -> NoneType
operation to be performed after catalog() finished
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class IdentityEval(VallFragmentEval) |
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scores a fragment based on sum of secondary structure identity and sequence identity
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- Method resolution order:
- IdentityEval
- VallFragmentEval
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, str, str) -> NoneType
doc
3. __init__(handle, str, str, float) -> NoneType
doc
4. __init__(handle, str, str, float, float) -> NoneType
doc
5. __init__(self : handle, ss : str, aa : str, ss_penalty : float, aa_penalty : float, randomize : bool) -> NoneType
6. __init__(handle, str) -> NoneType
doc
7. __init__(handle, str, float) -> NoneType
doc
8. __init__(self : handle, ss : str, ss_penalty : float, randomize : bool) -> NoneType
9. __init__(handle, rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- aa_penalty(...) from builtins.PyCapsule
- aa_penalty(*args, **kwargs)
Overloaded function.
1. aa_penalty(rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> float
get amino acid penalty
2. aa_penalty(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, penalty : float) -> NoneType
set amino acid penalty
- aa_str(...) from builtins.PyCapsule
- aa_str(*args, **kwargs)
Overloaded function.
1. aa_str(rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> str
get amino acid string
2. aa_str(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, aa : str) -> NoneType
set amino acid string
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, rval : rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> rosetta.core.fragment.picking_old.vall.eval.IdentityEval
copy assignment
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval
clone this object
- eval_impl(...) from builtins.PyCapsule
- eval_impl(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
for a fragment extent, evaluate and store results in a VallFragmentScore
true, so score is always stored during VallLibrarian::catalog()
- pre_catalog_op(...) from builtins.PyCapsule
- pre_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, : rosetta.core.fragment.picking_old.vall.VallLibrary) -> NoneType
operation to be perform before catalog() starts
- randomize(...) from builtins.PyCapsule
- randomize(*args, **kwargs)
Overloaded function.
1. randomize(rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> bool
adding random noise to score?
2. randomize(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, flag : bool) -> NoneType
set flag to add random noise between [0, 0.001) to score
- ss_penalty(...) from builtins.PyCapsule
- ss_penalty(*args, **kwargs)
Overloaded function.
1. ss_penalty(rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> float
get secondary structure penalty
2. ss_penalty(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, penalty : float) -> NoneType
set secondary structure penalty
- ss_str(...) from builtins.PyCapsule
- ss_str(*args, **kwargs)
Overloaded function.
1. ss_str(rosetta.core.fragment.picking_old.vall.eval.IdentityEval) -> str
get secondary structure string
2. ss_str(self : rosetta.core.fragment.picking_old.vall.eval.IdentityEval, ss : str) -> NoneType
set secondary structure string
Methods inherited from VallFragmentEval:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
called by VallLibrarian: for a fragment extent, evaluate and store
results in a VallFragmentScore
true if score should be stored, false otherwise
- post_catalog_op(...) from builtins.PyCapsule
- post_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, : core::fragment::picking_old::vall::VallLibrary) -> NoneType
operation to be performed after catalog() finished
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class VallFragmentEval(builtins.object) |
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base class for Vall ExtentEvaluator
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Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
called by VallLibrarian: for a fragment extent, evaluate and store
results in a VallFragmentScore
true if score should be stored, false otherwise
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval) -> NoneType
2. __init__(rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval) -> 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.core.fragment.picking_old.vall.eval.VallFragmentEval, rval : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval) -> rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval
copy assignment
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval) -> rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval
clone this object
- eval_impl(...) from builtins.PyCapsule
- eval_impl(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, extent : rosetta.core.fragment.picking_old.concepts.Extent___gnu_cxx___normal_iterator_const_core_fragment_picking_old_vall_VallResidue_*_std_vector_core_fragment_picking_old_vall_VallResidue_std_allocator_core_fragment_picking_old_vall_VallResidue_t, fs : rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore) -> bool
do the actual work of fragment evaluation
true if score should be stored, false otherwise
- post_catalog_op(...) from builtins.PyCapsule
- post_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, : core::fragment::picking_old::vall::VallLibrary) -> NoneType
operation to be performed after catalog() finished
- pre_catalog_op(...) from builtins.PyCapsule
- pre_catalog_op(self : rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval, : core::fragment::picking_old::vall::VallLibrary) -> NoneType
operation to be perform before catalog() starts
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