symmetry

Bindings for core::optimization::symmetry namespace

class pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer

Bases: pyrosetta.rosetta.core.optimization.AtomTreeMinimizer

High-level atom tree minimizer class

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer, : pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer) → pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer

C++: core::optimization::symmetry::SymAtomTreeMinimizer::operator=(const class core::optimization::symmetry::SymAtomTreeMinimizer &) –> class core::optimization::symmetry::SymAtomTreeMinimizer &

check_setup(self: pyrosetta.rosetta.core.optimization.AtomTreeMinimizer, pose: pyrosetta.rosetta.core.pose.Pose, move_map: pyrosetta.rosetta.core.kinematics.MoveMap, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, options: core::optimization::MinimizerOptions) → None

Do consistency checks for minimizer setup.

C++: core::optimization::AtomTreeMinimizer::check_setup(const class core::pose::Pose &, const class core::kinematics::MoveMap &, const class core::scoring::ScoreFunction &, const class core::optimization::MinimizerOptions &) const –> void

deriv_check_result(self: pyrosetta.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;

C++: core::optimization::AtomTreeMinimizer::deriv_check_result() const –> class std::shared_ptr<class core::optimization::NumericalDerivCheckResult>

make_asymmetric_movemap(pose: pyrosetta.rosetta.core.pose.Pose, move_map_sym: pyrosetta.rosetta.core.kinematics.MoveMap, move_map_asym: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(class core::pose::Pose &, const class core::kinematics::MoveMap &, class core::kinematics::MoveMap &) –> void

make_semisymmetric_movemap(pose: pyrosetta.rosetta.core.pose.Pose, move_map_sym: pyrosetta.rosetta.core.kinematics.MoveMap, move_map_semisym: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(class core::pose::Pose &, const class core::kinematics::MoveMap &, class core::kinematics::MoveMap &) –> void

run(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer, pose: pyrosetta.rosetta.core.pose.Pose, move_map: pyrosetta.rosetta.core.kinematics.MoveMap, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, options: pyrosetta.rosetta.core.optimization.MinimizerOptions) → float

Override the base class implementation. Non-const.

C++: core::optimization::symmetry::SymAtomTreeMinimizer::run(class core::pose::Pose &, const class core::kinematics::MoveMap &, const class core::scoring::ScoreFunction &, const class core::optimization::MinimizerOptions &) –> double

class pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc

Bases: pyrosetta.rosetta.core.optimization.Multifunc

Atom tree multifunction class

__call__(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) → float

C++: core::optimization::symmetry::SymAtomTreeMultifunc::operator()(const class utility::vector1<double, class std::allocator<double> > &) const –> double

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: core::optimization::symmetry::SymMinimizerMap, arg2: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

doc

2. __init__(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: core::optimization::symmetry::SymMinimizerMap, arg2: pyrosetta.rosetta.core.scoring.ScoreFunction, arg3: bool) -> None

doc

3. __init__(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, pose_in: pyrosetta.rosetta.core.pose.Pose, symm_min_map: core::optimization::symmetry::SymMinimizerMap, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction, deriv_check_in: bool, deriv_check_verbose_in: bool) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.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!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::optimization::symmetry::SymAtomTreeMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, vars2: pyrosetta.rosetta.utility.vector1_double) → None

Error state reached; dump out current pdb.

C++: core::optimization::symmetry::SymAtomTreeMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap

Bases: pyrosetta.rosetta.core.kinematics.MinimizerMapBase

Atom tree multifunction class

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: pyrosetta.rosetta.core.kinematics.MoveMap, arg2: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> None

doc

2. __init__(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, symm_info: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, new_sym_min: bool) -> None
3. __init__(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, arg0: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_atom(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, atom_id: pyrosetta.rosetta.core.id.AtomID, dof_id: pyrosetta.rosetta.core.id.DOF_ID) → None

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.

C++: core::optimization::symmetry::SymMinimizerMap::add_atom(const class core::id::AtomID &, const class core::id::DOF_ID &) –> void

add_torsion(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, new_torsion: pyrosetta.rosetta.core.id.DOF_ID, parent: pyrosetta.rosetta.core.id.DOF_ID) → None

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.

C++: core::optimization::symmetry::SymMinimizerMap::add_torsion(const class core::id::DOF_ID &, const class core::id::DOF_ID &) –> void

assign(self: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, : pyrosetta.rosetta.core.kinematics.MinimizerMapBase) → pyrosetta.rosetta.core.kinematics.MinimizerMapBase

C++: core::kinematics::MinimizerMapBase::operator=(const class core::kinematics::MinimizerMapBase &) –> class core::kinematics::MinimizerMapBase &

asymmetric_dof(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, cloned_dof: pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.id.DOF_ID

Convert a cloned dof into its equivalent in the asymmetric unit

C++: core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(const class core::id::DOF_ID &) const –> class core::id::DOF_ID

atom_derivatives(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, resid: int) → pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair

Retrieve the per-atom derivatives that are accumulated in to

C++: core::optimization::symmetry::SymMinimizerMap::atom_derivatives(unsigned long) –> class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &

begin(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >

begin iterator for the independent dofs

C++: core::optimization::symmetry::SymMinimizerMap::begin() const –> struct std::_List_const_iterator<class std::shared_ptr<class core::optimization::DOF_Node> >

copy_dofs_from_pose(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, pose: pyrosetta.rosetta.core.pose.Pose, dofs: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::optimization::symmetry::SymMinimizerMap::copy_dofs_from_pose(const class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &) const –> void

copy_dofs_to_pose(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, pose: pyrosetta.rosetta.core.pose.Pose, dofs: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::optimization::symmetry::SymMinimizerMap::copy_dofs_to_pose(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

dependent_begin(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >

C++: core::optimization::symmetry::SymMinimizerMap::dependent_begin() const –> struct std::_List_const_iterator<class std::shared_ptr<class core::optimization::DOF_Node> >

dependent_end(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >

C++: core::optimization::symmetry::SymMinimizerMap::dependent_end() const –> struct std::_List_const_iterator<class std::shared_ptr<class core::optimization::DOF_Node> >

dof_node_from_id(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, id: pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.optimization.DOF_Node

C++: core::optimization::symmetry::SymMinimizerMap::dof_node_from_id(const class core::id::DOF_ID &) const –> class std::shared_ptr<class core::optimization::DOF_Node>

dof_nodes(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t

C++: core::optimization::symmetry::SymMinimizerMap::dof_nodes() const –> const class std::list<class std::shared_ptr<class core::optimization::DOF_Node>, class std::allocator<class std::shared_ptr<class core::optimization::DOF_Node> > > &

domain_map(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → ObjexxFCL::FArray1D<int>

C++: core::optimization::symmetry::SymMinimizerMap::domain_map() const –> const class ObjexxFCL::FArray1D<int> &

end(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → std::_List_const_iterator<std::shared_ptr<core::optimization::DOF_Node> >

End iterator for the independent dofs

C++: core::optimization::symmetry::SymMinimizerMap::end() const –> struct std::_List_const_iterator<class std::shared_ptr<class core::optimization::DOF_Node> >

link_torsion_vectors(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → None

C++: core::optimization::symmetry::SymMinimizerMap::link_torsion_vectors() –> void

nangles(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → int

C++: core::optimization::symmetry::SymMinimizerMap::nangles() const –> unsigned long

new_sym_min(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → bool

C++: core::optimization::symmetry::SymMinimizerMap::new_sym_min() const –> bool

reset_jump_rb_deltas(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, pose: pyrosetta.rosetta.core.pose.Pose, dofs: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas(class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &) const –> void

torsion_scale_factor(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, dof_node: pyrosetta.rosetta.core.optimization.DOF_Node) → float

C++: core::optimization::symmetry::SymMinimizerMap::torsion_scale_factor(const class core::optimization::DOF_Node &) const –> double

zero_torsion_vectors(self: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap) → None

C++: core::optimization::symmetry::SymMinimizerMap::zero_torsion_vectors() –> void

pyrosetta.rosetta.core.optimization.symmetry.atom_tree_dfunc(pose: pyrosetta.rosetta.core.pose.Pose, symm_min_map: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::optimization::symmetry::atom_tree_dfunc(class core::pose::Pose &, class core::optimization::symmetry::SymMinimizerMap &, const class core::scoring::ScoreFunction &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.optimization.symmetry.atom_tree_get_atompairE_deriv(pose: pyrosetta.rosetta.core.pose.Pose, symm_min_map: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::optimization::symmetry::atom_tree_get_atompairE_deriv(class core::pose::Pose &, class core::optimization::symmetry::SymMinimizerMap &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.optimization.symmetry.numerical_derivative_check(min_map: pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap, func: pyrosetta.rosetta.core.optimization.Multifunc, start_vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, verbose: bool) → None

C++: core::optimization::symmetry::numerical_derivative_check(const class core::optimization::symmetry::SymMinimizerMap &, const class core::optimization::Multifunc &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const bool) –> void