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- rosetta.core.kinematics.MinimizerMapBase(builtins.object)
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- SymMinimizerMap
- rosetta.core.optimization.AtomTreeMinimizer(builtins.object)
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- SymAtomTreeMinimizer
- rosetta.core.optimization.Multifunc(builtins.object)
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- SymAtomTreeMultifunc
class SymAtomTreeMinimizer(rosetta.core.optimization.AtomTreeMinimizer) |
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High-level atom tree minimizer class
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- Method resolution order:
- SymAtomTreeMinimizer
- rosetta.core.optimization.AtomTreeMinimizer
- 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.core.optimization.symmetry.SymAtomTreeMinimizer, : rosetta.core.optimization.symmetry.SymAtomTreeMinimizer) -> rosetta.core.optimization.symmetry.SymAtomTreeMinimizer
- check_and_correct_edge_weights_for_new_minimizer(...) from builtins.PyCapsule
- check_and_correct_edge_weights_for_new_minimizer(self : rosetta.core.optimization.symmetry.SymAtomTreeMinimizer, pose : rosetta.core.pose.Pose) -> NoneType
- make_asymmetric_movemap(...) from builtins.PyCapsule
- make_asymmetric_movemap(pose : rosetta.core.pose.Pose, move_map_sym : rosetta.core.kinematics.MoveMap, move_map_asym : rosetta.core.kinematics.MoveMap) -> NoneType
- make_semisymmetric_movemap(...) from builtins.PyCapsule
- make_semisymmetric_movemap(pose : rosetta.core.pose.Pose, move_map_sym : rosetta.core.kinematics.MoveMap, move_map_semisym : rosetta.core.kinematics.MoveMap) -> NoneType
- run(...) from builtins.PyCapsule
- run(self : rosetta.core.optimization.symmetry.SymAtomTreeMinimizer, pose : rosetta.core.pose.Pose, move_map : rosetta.core.kinematics.MoveMap, scorefxn : rosetta.core.scoring.ScoreFunction, options : rosetta.core.optimization.MinimizerOptions) -> float
Override the base class implementation. Non-const.
Methods inherited from rosetta.core.optimization.AtomTreeMinimizer:
- check_setup(...) from builtins.PyCapsule
- check_setup(self : rosetta.core.optimization.AtomTreeMinimizer, pose : rosetta.core.pose.Pose, move_map : rosetta.core.kinematics.MoveMap, scorefxn : rosetta.core.scoring.ScoreFunction, options : core::optimization::MinimizerOptions) -> NoneType
Do consistency checks for minimizer setup.
- deriv_check_result(...) from builtins.PyCapsule
- deriv_check_result(rosetta.core.optimization.AtomTreeMinimizer) -> core::optimization::NumericalDerivCheckResult
After minimization has concluded, the user may access the deriv-check result,
assuming that they have run the AtomTreeMinimizer with deriv_check = true;
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class SymAtomTreeMultifunc(rosetta.core.optimization.Multifunc) |
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Atom tree multifunction class
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- Method resolution order:
- SymAtomTreeMultifunc
- rosetta.core.optimization.Multifunc
- builtins.object
Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, vars : rosetta.utility.vector1_double) -> float
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.core.pose.Pose, core::optimization::symmetry::SymMinimizerMap, rosetta.core.scoring.ScoreFunction) -> NoneType
doc
2. __init__(handle, rosetta.core.pose.Pose, core::optimization::symmetry::SymMinimizerMap, rosetta.core.scoring.ScoreFunction, bool) -> NoneType
doc
3. __init__(self : handle, pose_in : rosetta.core.pose.Pose, symm_min_map : core::optimization::symmetry::SymMinimizerMap, scorefxn_in : rosetta.core.scoring.ScoreFunction, deriv_check_in : bool, deriv_check_verbose_in : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- dfunc(...) from builtins.PyCapsule
- dfunc(self : rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double) -> NoneType
- dump(...) from builtins.PyCapsule
- dump(self : rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, vars : rosetta.utility.vector1_double, vars2 : rosetta.utility.vector1_double) -> NoneType
Error state reached; dump out current pdb.
Methods inherited from rosetta.core.optimization.Multifunc:
- abort_min(...) from builtins.PyCapsule
- abort_min(self : rosetta.core.optimization.Multifunc, : rosetta.utility.vector1_double) -> bool
Christophe added the following to allow premature end of minimization
If you want to abort the minimizer under specific circonstances
overload this function and return true if you want to stop, false if you want to continue.
FOR THE MOMENT, ONLY IN DFPMIN!
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class SymMinimizerMap(rosetta.core.kinematics.MinimizerMapBase) |
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Atom tree multifunction class
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- Method resolution order:
- SymMinimizerMap
- rosetta.core.kinematics.MinimizerMapBase
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.core.pose.Pose, rosetta.core.kinematics.MoveMap, rosetta.core.conformation.symmetry.SymmetryInfo) -> NoneType
doc
2. __init__(self : handle, pose : rosetta.core.pose.Pose, mm : rosetta.core.kinematics.MoveMap, symm_info : rosetta.core.conformation.symmetry.SymmetryInfo, new_sym_min : bool) -> NoneType
3. __init__(handle, rosetta.core.optimization.symmetry.SymMinimizerMap) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_atom(...) from builtins.PyCapsule
- add_atom(self : rosetta.core.optimization.symmetry.SymMinimizerMap, atom_id : rosetta.core.id.AtomID, dof_id : rosetta.core.id.DOF_ID) -> NoneType
Add an atom to the list of atoms controlled by a given DOF. The SymMinimzierMap
will figure out, first, if the dof_id is a dependent or independent dof. If it's a dependent
DOF, then it will figure out if the given atom has any interactions with an independent residue.
If not, then the atom is ignored. If it does, then the SymMinimizerMap will figure out
what independent DOF the given dependent DOF is a a clone of, and add this atom as being controlled
by that dependent DOF.
- add_torsion(...) from builtins.PyCapsule
- add_torsion(self : rosetta.core.optimization.symmetry.SymMinimizerMap, new_torsion : rosetta.core.id.DOF_ID, parent : rosetta.core.id.DOF_ID) -> NoneType
The atom tree will report that a new torsion has been identified as free in the traversal of the atom tree.
If this is an independent torsion, then the SymMinimizerMap will add a new DOF_Node, but otherwise, will
ignore the DOF. The atom tree will traverse through dependent torsions in addition to independent torsions, and
it's the job of the SymMinimizerMap to weed out the dependent torsions.
- asymmetric_dof(...) from builtins.PyCapsule
- asymmetric_dof(self : rosetta.core.optimization.symmetry.SymMinimizerMap, cloned_dof : rosetta.core.id.DOF_ID) -> rosetta.core.id.DOF_ID
Convert a cloned dof into its equivalent in the asymmetric unit
- atom_derivatives(...) from builtins.PyCapsule
- atom_derivatives(self : rosetta.core.optimization.symmetry.SymMinimizerMap, resid : int) -> rosetta.utility.vector1_core_scoring_DerivVectorPair
Retrieve the per-atom derivatives that are accumulated in to
- begin(...) from builtins.PyCapsule
- begin(rosetta.core.optimization.symmetry.SymMinimizerMap) -> std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >
begin iterator for the independent dofs
- copy_dofs_from_pose(...) from builtins.PyCapsule
- copy_dofs_from_pose(self : rosetta.core.optimization.symmetry.SymMinimizerMap, pose : rosetta.core.pose.Pose, dofs : rosetta.utility.vector1_double) -> NoneType
- copy_dofs_to_pose(...) from builtins.PyCapsule
- copy_dofs_to_pose(self : rosetta.core.optimization.symmetry.SymMinimizerMap, pose : rosetta.core.pose.Pose, dofs : rosetta.utility.vector1_double) -> NoneType
- dependent_begin(...) from builtins.PyCapsule
- dependent_begin(rosetta.core.optimization.symmetry.SymMinimizerMap) -> std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >
- dependent_end(...) from builtins.PyCapsule
- dependent_end(rosetta.core.optimization.symmetry.SymMinimizerMap) -> std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >
- dof_node_from_id(...) from builtins.PyCapsule
- dof_node_from_id(self : rosetta.core.optimization.symmetry.SymMinimizerMap, id : rosetta.core.id.DOF_ID) -> rosetta.core.optimization.DOF_Node
- dof_nodes(...) from builtins.PyCapsule
- dof_nodes(rosetta.core.optimization.symmetry.SymMinimizerMap) -> rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t
- domain_map(...) from builtins.PyCapsule
- domain_map(rosetta.core.optimization.symmetry.SymMinimizerMap) -> ObjexxFCL::FArray1D<int>
- end(...) from builtins.PyCapsule
- end(rosetta.core.optimization.symmetry.SymMinimizerMap) -> std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >
End iterator for the independent dofs
- link_torsion_vectors(...) from builtins.PyCapsule
- link_torsion_vectors(rosetta.core.optimization.symmetry.SymMinimizerMap) -> NoneType
- nangles(...) from builtins.PyCapsule
- nangles(rosetta.core.optimization.symmetry.SymMinimizerMap) -> int
- new_sym_min(...) from builtins.PyCapsule
- new_sym_min(rosetta.core.optimization.symmetry.SymMinimizerMap) -> bool
- reset_jump_rb_deltas(...) from builtins.PyCapsule
- reset_jump_rb_deltas(self : rosetta.core.optimization.symmetry.SymMinimizerMap, pose : rosetta.core.pose.Pose, dofs : rosetta.utility.vector1_double) -> NoneType
- torsion_scale_factor(...) from builtins.PyCapsule
- torsion_scale_factor(self : rosetta.core.optimization.symmetry.SymMinimizerMap, dof_node : rosetta.core.optimization.DOF_Node) -> float
- zero_torsion_vectors(...) from builtins.PyCapsule
- zero_torsion_vectors(rosetta.core.optimization.symmetry.SymMinimizerMap) -> NoneType
Methods inherited from rosetta.core.kinematics.MinimizerMapBase:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.kinematics.MinimizerMapBase, : rosetta.core.kinematics.MinimizerMapBase) -> rosetta.core.kinematics.MinimizerMapBase
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