| | |
- rosetta.core.scoring.constraints.AmbiguousConstraint(rosetta.core.scoring.constraints.MultiConstraint)
-
- AmbiguousMultiConstraint
- rosetta.core.scoring.constraints.Constraint(builtins.object)
-
- BindingSiteConstraint
- COMCoordinateConstraint
- SequenceCouplingConstraint
- rosetta.core.scoring.constraints.ConstraintCreator(builtins.object)
-
- BindingSiteConstraintCreator
- NamedAtomPairConstraintCreator
- SequenceCoupling1BDConstraintCreator
- SequenceCouplingConstraintCreator
- rosetta.core.scoring.constraints.ConstraintSet(builtins.object)
-
- MaxSeqSepConstraintSet
- rosetta.core.scoring.constraints.SequenceProfileConstraint(rosetta.core.scoring.constraints.Constraint)
-
- SequenceCoupling1BDConstraint
- rosetta.protocols.evaluation.EvaluatorCreator(builtins.object)
-
- CombinedConstraintEvaluatorCreator
- ConstraintEvaluatorCreator
- rosetta.protocols.evaluation.PoseEvaluator(builtins.object)
-
- CombinedConstraintEvaluator
- ConstraintEvaluator
class AmbiguousMultiConstraint(rosetta.core.scoring.constraints.AmbiguousConstraint) |
| | |
- Method resolution order:
- AmbiguousMultiConstraint
- rosetta.core.scoring.constraints.AmbiguousConstraint
- rosetta.core.scoring.constraints.MultiConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, num_act_csts : int) -> NoneType
2. __init__(self : handle, num_act_csts : int, cst_in : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> NoneType
3. __init__(handle, rosetta.protocols.constraints_additional.AmbiguousMultiConstraint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.constraints_additional.AmbiguousMultiConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, atom : rosetta.core.id.AtomID, xyz : rosetta.core.scoring.func.XYZ_Func, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t, weights : rosetta.core.scoring.EMapVector) -> NoneType
compute atom deriv
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, seqmap : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, xyz_func : rosetta.core.scoring.func.XYZ_Func, weights : rosetta.core.scoring.EMapVector, emap : rosetta.core.scoring.EMapVector) -> NoneType
compute score
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.constraints_additional.AmbiguousMultiConstraint) -> str
Methods inherited from rosetta.core.scoring.constraints.AmbiguousConstraint:
- active_constraint(...) from builtins.PyCapsule
- active_constraint(rosetta.core.scoring.constraints.AmbiguousConstraint) -> rosetta.core.scoring.constraints.Constraint
- calculate_total_cst_score(...) from builtins.PyCapsule
- calculate_total_cst_score(self : rosetta.core.scoring.constraints.AmbiguousConstraint, weights : rosetta.core.scoring.EMapVector, emap : rosetta.core.scoring.EMapVector) -> float
- empty_clone(...) from builtins.PyCapsule
- empty_clone(rosetta.core.scoring.constraints.AmbiguousConstraint) -> rosetta.core.scoring.constraints.MultiConstraint
- init_cst_score_types(...) from builtins.PyCapsule
- init_cst_score_types(rosetta.core.scoring.constraints.AmbiguousConstraint) -> NoneType
Methods inherited from rosetta.core.scoring.constraints.MultiConstraint:
- add_individual_constraint(...) from builtins.PyCapsule
- add_individual_constraint(self : rosetta.core.scoring.constraints.MultiConstraint, cst_in : rosetta.core.scoring.constraints.Constraint) -> NoneType
add individual constraint into MultiConstraint
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.core.scoring.constraints.MultiConstraint, n : int) -> rosetta.core.id.AtomID
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.MultiConstraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.MultiConstraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- member_constraints(...) from builtins.PyCapsule
- member_constraints(rosetta.core.scoring.constraints.MultiConstraint) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.scoring.constraints.MultiConstraint) -> int
number of atoms involved in this MultiConstraint container
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(*args, **kwargs)
Overloaded function.
1. remapped_clone(self : rosetta.core.scoring.constraints.MultiConstraint, : rosetta.core.pose.Pose, : rosetta.core.pose.Pose) -> rosetta.core.scoring.constraints.Constraint
2. remapped_clone(self : rosetta.core.scoring.constraints.MultiConstraint, : rosetta.core.pose.Pose, : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
- residues(...) from builtins.PyCapsule
- residues(rosetta.core.scoring.constraints.MultiConstraint) -> rosetta.utility.vector1_unsigned_long
- set_effective_sequence_separation(...) from builtins.PyCapsule
- set_effective_sequence_separation(self : rosetta.core.scoring.constraints.MultiConstraint, setting : int) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.MultiConstraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.core.scoring.constraints.MultiConstraint) -> int
number of constraints that are held by this %MultiConstraint
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
|
class BindingSiteConstraint(rosetta.core.scoring.constraints.Constraint) |
| | |
- Method resolution order:
- BindingSiteConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.utility.vector1_core_id_AtomID, rosetta.core.pose.Pose) -> NoneType
doc
3. __init__(self : handle, atms : rosetta.utility.vector1_core_id_AtomID, start_pose : rosetta.core.pose.Pose, scoretype : rosetta.core.scoring.ScoreType) -> NoneType
4. __init__(handle, rosetta.utility.vector1_core_id_AtomID, ObjexxFCL::FArray2D<double>, ObjexxFCL::FArray2D<double>) -> NoneType
doc
5. __init__(self : handle, atms : rosetta.utility.vector1_core_id_AtomID, tgt_pos : ObjexxFCL::FArray2D<double>, tgt_pos_centroid : ObjexxFCL::FArray2D<double>, scoretype : rosetta.core.scoring.ScoreType) -> NoneType
6. __init__(handle, rosetta.protocols.constraints_additional.BindingSiteConstraint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, n : int) -> rosetta.core.id.AtomID
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.constraints_additional.BindingSiteConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, atom : rosetta.core.id.AtomID, xyz : rosetta.core.scoring.func.XYZ_Func, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t, weights : rosetta.core.scoring.EMapVector) -> NoneType
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.protocols.constraints_additional.BindingSiteConstraint) -> int
- pre_align(...) from builtins.PyCapsule
- pre_align(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, templ_atms : rosetta.utility.vector1_numeric_xyzVector_double_t, : rosetta.utility.vector1_bool) -> NoneType
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, seqmap : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, xyz : rosetta.core.scoring.func.XYZ_Func, : rosetta.core.scoring.EMapVector, emap : rosetta.core.scoring.EMapVector) -> NoneType
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, xyz : rosetta.core.scoring.func.XYZ_Func, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.protocols.constraints_additional.BindingSiteConstraint, xyz : rosetta.core.scoring.func.XYZ_Func, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.constraints_additional.BindingSiteConstraint) -> str
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose, : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
Copies the data from this Constraint into a new object and returns
an OP atoms are mapped to atoms with the same name in dest pose ( e.g.
for switch from centroid to fullatom ) if a sequence_mapping is present
it is used to map residue numbers .. NULL = identity mapping to the new
object. Intended to be implemented by derived classes.
- residues(...) from builtins.PyCapsule
- residues(rosetta.core.scoring.constraints.Constraint) -> rosetta.utility.vector1_unsigned_long
Returns the pose numbers of the residues involved in this constraint, in no particular order.
Used in determining one-body/two-body/multi-body status.
For historical reasons, the default uses a simple protocol based on natoms()/atom() -
feel free to reimplement more efficiently.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
|
class COMCoordinateConstraint(rosetta.core.scoring.constraints.Constraint) |
| | |
- Method resolution order:
- COMCoordinateConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.utility.vector1_core_id_AtomID, rosetta.numeric.xyzVector_double_t, float, float) -> NoneType
doc
3. __init__(self : handle, atms : rosetta.utility.vector1_core_id_AtomID, COM_target : rosetta.numeric.xyzVector_double_t, stdv : float, interval : float, scoretype : rosetta.core.scoring.ScoreType) -> NoneType
4. __init__(handle, rosetta.utility.vector1_core_id_AtomID, rosetta.numeric.xyzVector_double_t, float) -> NoneType
doc
5. __init__(self : handle, atms : rosetta.utility.vector1_core_id_AtomID, COM_target : rosetta.numeric.xyzVector_double_t, stdv : float, scoretype : rosetta.core.scoring.ScoreType) -> NoneType
6. __init__(handle, rosetta.utility.vector1_core_id_AtomID, rosetta.numeric.xyzVector_double_t) -> NoneType
doc
7. __init__(self : handle, atms : rosetta.utility.vector1_core_id_AtomID, COM_target : rosetta.numeric.xyzVector_double_t, scoretype : rosetta.core.scoring.ScoreType) -> NoneType
8. __init__(handle, rosetta.protocols.constraints_additional.COMCoordinateConstraint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, n : int) -> rosetta.core.id.AtomID
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.constraints_additional.COMCoordinateConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, atom : rosetta.core.id.AtomID, xyz : rosetta.core.scoring.func.XYZ_Func, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t, weights : rosetta.core.scoring.EMapVector) -> NoneType
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.protocols.constraints_additional.COMCoordinateConstraint) -> int
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, xyz : rosetta.core.scoring.func.XYZ_Func, : rosetta.core.scoring.EMapVector, emap : rosetta.core.scoring.EMapVector) -> NoneType
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, xyz : rosetta.core.scoring.func.XYZ_Func, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.protocols.constraints_additional.COMCoordinateConstraint, xyz : rosetta.core.scoring.func.XYZ_Func, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.constraints_additional.COMCoordinateConstraint) -> str
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- residues(...) from builtins.PyCapsule
- residues(rosetta.core.scoring.constraints.Constraint) -> rosetta.utility.vector1_unsigned_long
Returns the pose numbers of the residues involved in this constraint, in no particular order.
Used in determining one-body/two-body/multi-body status.
For historical reasons, the default uses a simple protocol based on natoms()/atom() -
feel free to reimplement more efficiently.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
|
class CombinedConstraintEvaluator(rosetta.protocols.evaluation.PoseEvaluator) |
| | |
- Method resolution order:
- CombinedConstraintEvaluator
- rosetta.protocols.evaluation.PoseEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, str, str) -> NoneType
doc
2. __init__(handle, str, str, int) -> NoneType
doc
3. __init__(self : handle, tag : str, filename : str, constraints_combine_ratio_ : int, repeat : int) -> NoneType
4. __init__(handle, rosetta.protocols.constraints_additional.CombinedConstraintEvaluator) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(*args, **kwargs)
Overloaded function.
1. apply(self : rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType
2. apply(self : rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, pose : rosetta.core.pose.Pose) -> float
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, : rosetta.protocols.constraints_additional.CombinedConstraintEvaluator) -> rosetta.protocols.constraints_additional.CombinedConstraintEvaluator
- name(...) from builtins.PyCapsule
- name(self : rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, i : int) -> str
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.constraints_additional.CombinedConstraintEvaluator) -> int
Methods inherited from rosetta.protocols.evaluation.PoseEvaluator:
- applicable(...) from builtins.PyCapsule
- applicable(self : rosetta.protocols.evaluation.PoseEvaluator, : rosetta.core.pose.Pose) -> bool
|
class ConstraintEvaluator(rosetta.protocols.evaluation.PoseEvaluator) |
| | |
- Method resolution order:
- ConstraintEvaluator
- rosetta.protocols.evaluation.PoseEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, str, rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
doc
2. __init__(handle, str, rosetta.core.scoring.constraints.ConstraintSet, int) -> NoneType
doc
3. __init__(handle, str, rosetta.core.scoring.constraints.ConstraintSet, int, float) -> NoneType
doc
4. __init__(self : handle, tag : str, : rosetta.core.scoring.constraints.ConstraintSet, viol_level : int, threshold : float, max_seq_sep : int) -> NoneType
5. __init__(handle, str, rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> NoneType
doc
6. __init__(handle, str, rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, int) -> NoneType
doc
7. __init__(handle, str, rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, int, float) -> NoneType
doc
8. __init__(self : handle, tag : str, : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, viol_level : int, threshold : float, max_seq_sep : int) -> NoneType
9. __init__(handle, str, str) -> NoneType
doc
10. __init__(handle, str, str, int) -> NoneType
doc
11. __init__(handle, str, str, int, float) -> NoneType
doc
12. __init__(self : handle, tag : str, filename : str, viol_level : int, threshold : float, max_seq_sep : int) -> NoneType
13. __init__(handle, rosetta.protocols.constraints_additional.ConstraintEvaluator) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(*args, **kwargs)
Overloaded function.
1. apply(self : rosetta.protocols.constraints_additional.ConstraintEvaluator, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType
2. apply(self : rosetta.protocols.constraints_additional.ConstraintEvaluator, pose : rosetta.core.pose.Pose) -> float
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.constraints_additional.ConstraintEvaluator, : rosetta.protocols.constraints_additional.ConstraintEvaluator) -> rosetta.protocols.constraints_additional.ConstraintEvaluator
- name(...) from builtins.PyCapsule
- name(self : rosetta.protocols.constraints_additional.ConstraintEvaluator, i : int) -> str
- set_combine_ratio(...) from builtins.PyCapsule
- set_combine_ratio(self : rosetta.protocols.constraints_additional.ConstraintEvaluator, setting : int) -> NoneType
- set_cst_source(...) from builtins.PyCapsule
- set_cst_source(self : rosetta.protocols.constraints_additional.ConstraintEvaluator, tag : str) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.constraints_additional.ConstraintEvaluator) -> int
Methods inherited from rosetta.protocols.evaluation.PoseEvaluator:
- applicable(...) from builtins.PyCapsule
- applicable(self : rosetta.protocols.evaluation.PoseEvaluator, : rosetta.core.pose.Pose) -> bool
|
class MaxSeqSepConstraintSet(rosetta.core.scoring.constraints.ConstraintSet) |
| | |
- Method resolution order:
- MaxSeqSepConstraintSet
- rosetta.core.scoring.constraints.ConstraintSet
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, other : rosetta.core.scoring.constraints.ConstraintSet, f : rosetta.core.kinematics.FoldTree) -> NoneType
2. __init__(handle, rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(*args, **kwargs)
Overloaded function.
1. assign(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, rhs : rosetta.core.scoring.constraints.ConstraintSet) -> rosetta.core.scoring.constraints.ConstraintSet
2. assign(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) -> rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) -> rosetta.core.scoring.constraints.ConstraintSet
- detached_clone(...) from builtins.PyCapsule
- detached_clone(rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) -> rosetta.core.scoring.constraints.ConstraintSet
- detached_copy(...) from builtins.PyCapsule
- detached_copy(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, src : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
- eval_non_residue_pair_energy(...) from builtins.PyCapsule
- eval_non_residue_pair_energy(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
- largest_possible_sequence_sep(...) from builtins.PyCapsule
- largest_possible_sequence_sep(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pose : rosetta.core.pose.Pose) -> int
- max_seq_sep(...) from builtins.PyCapsule
- max_seq_sep(rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) -> int
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(*args, **kwargs)
Overloaded function.
1. remapped_clone(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose) -> rosetta.core.scoring.constraints.ConstraintSet
2. remapped_clone(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.ConstraintSet
- residue_pair_constraint_exists(...) from builtins.PyCapsule
- residue_pair_constraint_exists(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pos1 : int, pos2 : int) -> bool
- residue_pair_energy(...) from builtins.PyCapsule
- residue_pair_energy(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(*args, **kwargs)
Overloaded function.
1. same_type_as_me(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, other : rosetta.core.scoring.constraints.ConstraintSet) -> bool
2. same_type_as_me(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, other : rosetta.core.scoring.constraints.ConstraintSet, recurse : bool) -> bool
- set_max_seq_sep(...) from builtins.PyCapsule
- set_max_seq_sep(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, setting : int) -> NoneType
- setup_for_minimizing_for_residue_pair(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue_pair(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, minmap : rosetta.core.kinematics.MinimizerMapBase, res1_data_cache : rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache : rosetta.core.scoring.ResSingleMinimizationData, respair_data_cache : rosetta.core.scoring.ResPairMinimizationData) -> NoneType
If a pair of residues are not too far, then let the
parent class implementation add the constraints for this
respair to the respair_data_cache. This is the only opportunity
the MaxSeqSepConstraint set has to influence how constraints
are evaluated during minimization.
- shortest_path(...) from builtins.PyCapsule
- shortest_path(rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) -> rosetta.core.kinematics.ShortestPathInFoldTree
- too_far(...) from builtins.PyCapsule
- too_far(self : rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pos1 : int, pos2 : int) -> bool
Methods inherited from rosetta.core.scoring.constraints.ConstraintSet:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.ConstraintSet) -> str
- add_constraint(...) from builtins.PyCapsule
- add_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, cst : rosetta.core.scoring.constraints.Constraint) -> NoneType
- add_constraints(...) from builtins.PyCapsule
- add_constraints(*args, **kwargs)
Overloaded function.
1. add_constraints(self : rosetta.core.scoring.constraints.ConstraintSet, cst_list : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> NoneType
2. add_constraints(self : rosetta.core.scoring.constraints.ConstraintSet, cst_set : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
add another constraint set to this constraint set
- add_dof_constraint(...) from builtins.PyCapsule
- add_dof_constraint(*args, **kwargs)
Overloaded function.
1. add_dof_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, id : rosetta.core.id.DOF_ID, func : rosetta.core.scoring.func.Func) -> NoneType
Note -- still hacky. Will not be included in packing, just scoring
and minimization
2. add_dof_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, id : rosetta.core.id.DOF_ID, func : rosetta.core.scoring.func.Func, t : rosetta.core.scoring.ScoreType) -> NoneType
Note -- still hacky. Will not be included in packing, just scoring
and minimization
- attach_to_conformation(...) from builtins.PyCapsule
- attach_to_conformation(self : rosetta.core.scoring.constraints.ConstraintSet, conformation : rosetta.std.weak_ptr_const_core_conformation_Conformation_t) -> NoneType
- clear(...) from builtins.PyCapsule
- clear(rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
- clear_sequence_constraints(...) from builtins.PyCapsule
- clear_sequence_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
Discard any and all sequence constraints in the sequence_constraints_ list.
- deprecated_eval_atom_derivative(...) from builtins.PyCapsule
- deprecated_eval_atom_derivative(self : rosetta.core.scoring.constraints.ConstraintSet, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
Switching over to a pairwise decomposable eval-atom-deriv system for
RTMin means deprecating the old "evaluate an atom's derivative wrt the entire structure"
This function is preserved (for now) for use by the RNA_TorsionEnergy
- detach_from_conformation(...) from builtins.PyCapsule
- detach_from_conformation(rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
- eval_intrares_energy(...) from builtins.PyCapsule
- eval_intrares_energy(*args, **kwargs)
Overloaded function.
1. eval_intrares_energy(self : rosetta.core.scoring.constraints.ConstraintSet, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
2. eval_intrares_energy(self : rosetta.core.scoring.constraints.ConstraintSet, rsd : rosetta.core.conformation.Residue, emap : rosetta.core.scoring.EMapVector) -> NoneType
- eval_multibody_atom_derivative(...) from builtins.PyCapsule
- eval_multibody_atom_derivative(self : rosetta.core.scoring.constraints.ConstraintSet, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
evaluate the derivatives for an atom that contains 3- or higher-body
constraints. Such derivatives cannot be evalauated in an extra-posal context
(e.g. such as in RTMin).
- get_all_constraints(...) from builtins.PyCapsule
- get_all_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t
Returns all constraints in the set as a flat list, regardless of
type.
- has_constraints(...) from builtins.PyCapsule
- has_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_dof_constraints(...) from builtins.PyCapsule
- has_dof_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_intra_residue_constraints(...) from builtins.PyCapsule
- has_intra_residue_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_non_residue_pair_constraints(...) from builtins.PyCapsule
- has_non_residue_pair_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_residue_pair_constraints(...) from builtins.PyCapsule
- has_residue_pair_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- is_empty(...) from builtins.PyCapsule
- is_empty(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- n_sequence_constraints(...) from builtins.PyCapsule
- n_sequence_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> int
Get the number of sequence constraints.
- on_connection_change(...) from builtins.PyCapsule
- on_connection_change(self : rosetta.core.scoring.constraints.ConstraintSet, event : rosetta.core.conformation.signals.ConnectionEvent) -> NoneType
- on_length_change(...) from builtins.PyCapsule
- on_length_change(self : rosetta.core.scoring.constraints.ConstraintSet, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType
- remap_residue_positions(...) from builtins.PyCapsule
- remap_residue_positions(self : rosetta.core.scoring.constraints.ConstraintSet, smap : rosetta.core.id.SequenceMapping) -> NoneType
remaps the constraints in this particular constraint set according
to brief the passed in sequence mapping --- redundant with
remapped_clone!!!
- remove_constraint(...) from builtins.PyCapsule
- remove_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, cst : rosetta.core.scoring.constraints.Constraint, object_comparison : bool) -> bool
Returns true if the constraint was successfully found and removed.
if object comparison is set to true, the constraint to be removed is found
through the Constraint::== operator and not through pointer comparison
- remove_constraints(...) from builtins.PyCapsule
- remove_constraints(self : rosetta.core.scoring.constraints.ConstraintSet, cst_list : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, object_comparison : bool) -> bool
- residue_pair_constraints_begin(...) from builtins.PyCapsule
- residue_pair_constraints_begin(self : rosetta.core.scoring.constraints.ConstraintSet, resid : int) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >
- residue_pair_constraints_end(...) from builtins.PyCapsule
- residue_pair_constraints_end(self : rosetta.core.scoring.constraints.ConstraintSet, resid : int) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >
- residue_pair_constraints_exists(...) from builtins.PyCapsule
- residue_pair_constraints_exists(self : rosetta.core.scoring.constraints.ConstraintSet, pos : int) -> bool
- revision_id(...) from builtins.PyCapsule
- revision_id(rosetta.core.scoring.constraints.ConstraintSet) -> int
- sequence_constraint(...) from builtins.PyCapsule
- sequence_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, index : int) -> rosetta.core.scoring.aa_composition_energy.SequenceConstraint
Get the owning pointer to the Nth sequence constraint.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_minimizing_for_residue(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue(self : rosetta.core.scoring.constraints.ConstraintSet, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, minmap : rosetta.core.kinematics.MinimizerMapBase, res_data_cache : rosetta.core.scoring.ResSingleMinimizationData) -> NoneType
Cache the ConstraintsCOP for a particular residue
in the res_data_cache, under the "cst_res_data" element of
the data-cache's CachableDataOP array. Derived ConstraintSet
classes should decide HERE whether any constraints should be evaluated
for this residue, since, once a ConstraintsOP is added
to the minimization graph, the derived class looses the chance to
veto the evaluation of that constraint.
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def_clone(...) from builtins.PyCapsule
- steal_def_clone(*args, **kwargs)
Overloaded function.
1. steal_def_clone(self : rosetta.core.scoring.constraints.ConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose) -> rosetta.core.scoring.constraints.ConstraintSet
like remapped_clone, but constraints also steal_def from src-pose
use, e.g., to get a new set of CoordinateConstraints for given xyz
coordinates in src-pose
2. steal_def_clone(self : rosetta.core.scoring.constraints.ConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.ConstraintSet
like remapped_clone, but constraints also steal_def from src-pose
use, e.g., to get a new set of CoordinateConstraints for given xyz
coordinates in src-pose
|
class SequenceCoupling1BDConstraint(rosetta.core.scoring.constraints.SequenceProfileConstraint) |
| | |
- Method resolution order:
- SequenceCoupling1BDConstraint
- rosetta.core.scoring.constraints.SequenceProfileConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, : rosetta.core.pose.Pose, : int, profile : rosetta.core.sequence.SequenceProfile) -> NoneType
3. __init__(self : handle, : int, profile : rosetta.core.sequence.SequenceProfile) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, : rosetta.core.id.AtomID, : rosetta.core.scoring.func.XYZ_Func, : rosetta.numeric.xyzVector_double_t, : rosetta.numeric.xyzVector_double_t, : rosetta.core.scoring.EMapVector) -> NoneType
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, : rosetta.core.scoring.func.XYZ_Func, : rosetta.core.scoring.EMapVector, : rosetta.core.scoring.EMapVector) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint) -> str
Methods inherited from rosetta.core.scoring.constraints.SequenceProfileConstraint:
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.core.scoring.constraints.SequenceProfileConstraint, : int) -> rosetta.core.id.AtomID
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.scoring.constraints.SequenceProfileConstraint) -> int
- profile_mapping(...) from builtins.PyCapsule
- profile_mapping(rosetta.core.scoring.constraints.SequenceProfileConstraint) -> rosetta.core.id.SequenceMapping
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.core.scoring.constraints.SequenceProfileConstraint, : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(self : rosetta.core.scoring.constraints.SequenceProfileConstraint, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
- residues(...) from builtins.PyCapsule
- residues(rosetta.core.scoring.constraints.SequenceProfileConstraint) -> rosetta.utility.vector1_unsigned_long
- seqpos(...) from builtins.PyCapsule
- seqpos(*args, **kwargs)
Overloaded function.
1. seqpos(rosetta.core.scoring.constraints.SequenceProfileConstraint) -> int
2. seqpos(self : rosetta.core.scoring.constraints.SequenceProfileConstraint, seqpos : int) -> NoneType
- sequence_profile(...) from builtins.PyCapsule
- sequence_profile(rosetta.core.scoring.constraints.SequenceProfileConstraint) -> core::sequence::SequenceProfile
- set_sequence_profile(...) from builtins.PyCapsule
- set_sequence_profile(*args, **kwargs)
Overloaded function.
1. set_sequence_profile(self : rosetta.core.scoring.constraints.SequenceProfileConstraint, profile : core::sequence::SequenceProfile) -> NoneType
2. set_sequence_profile(self : rosetta.core.scoring.constraints.SequenceProfileConstraint, profile : core::sequence::SequenceProfile, mapping : rosetta.core.id.SequenceMapping) -> NoneType
- weight(...) from builtins.PyCapsule
- weight(*args, **kwargs)
Overloaded function.
1. weight(self : rosetta.core.scoring.constraints.SequenceProfileConstraint, w : float) -> NoneType
2. weight(rosetta.core.scoring.constraints.SequenceProfileConstraint) -> float
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
|
class SequenceCouplingConstraint(rosetta.core.scoring.constraints.Constraint) |
| | |
- Method resolution order:
- SequenceCouplingConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.constraints_additional.SequenceCouplingConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.pose.Pose, int, int) -> NoneType
doc
3. __init__(self : handle, : rosetta.core.pose.Pose, : int, : int, profile : rosetta.core.sequence.SequenceCoupling) -> NoneType
4. __init__(handle, int, int) -> NoneType
doc
5. __init__(self : handle, : int, : int, profile : rosetta.core.sequence.SequenceCoupling) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : int) -> rosetta.core.id.AtomID
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : rosetta.core.id.AtomID, : rosetta.core.scoring.func.XYZ_Func, : rosetta.numeric.xyzVector_double_t, : rosetta.numeric.xyzVector_double_t, : rosetta.core.scoring.EMapVector) -> NoneType
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> int
- residues(...) from builtins.PyCapsule
- residues(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> rosetta.utility.vector1_unsigned_long
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.constraints_additional.SequenceCouplingConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : rosetta.core.scoring.func.XYZ_Func, : rosetta.core.scoring.EMapVector, : rosetta.core.scoring.EMapVector) -> NoneType
- seqpos1(...) from builtins.PyCapsule
- seqpos1(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> int
- seqpos2(...) from builtins.PyCapsule
- seqpos2(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> int
- sequence_coupling(...) from builtins.PyCapsule
- sequence_coupling(*args, **kwargs)
Overloaded function.
1. sequence_coupling(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> rosetta.core.sequence.SequenceCoupling
2. sequence_coupling(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> rosetta.core.sequence.SequenceCoupling
- set_sequence_coupling(...) from builtins.PyCapsule
- set_sequence_coupling(self : rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : rosetta.core.sequence.SequenceCoupling) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.constraints_additional.SequenceCouplingConstraint) -> str
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
apply a resid remapping to this constraint, returns the remapped
constraint Does this return an owning pointer to this constraint or a
copy? Documentation would be nice.
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose, : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
Copies the data from this Constraint into a new object and returns
an OP atoms are mapped to atoms with the same name in dest pose ( e.g.
for switch from centroid to fullatom ) if a sequence_mapping is present
it is used to map residue numbers .. NULL = identity mapping to the new
object. Intended to be implemented by derived classes.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
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