constraints_additional

Bindings for protocols::constraints_additional namespace

class pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint

Bases: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint

active_constraint(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::scoring::constraints::AmbiguousConstraint::active_constraint() const –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

add_individual_constraint(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, cst_in: pyrosetta.rosetta.core.scoring.constraints.Constraint) None

add individual constraint into MultiConstraint

C++: core::scoring::constraints::MultiConstraint::add_individual_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>) –> void

atom(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, n: int) pyrosetta.rosetta.core.id.AtomID

C++: core::scoring::constraints::MultiConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

calculate_total_cst_score(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) float

C++: core::scoring::constraints::AmbiguousConstraint::calculate_total_cst_score(const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> double

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : pyrosetta.rosetta.numeric.random.RandomGenerator) int

C++: core::scoring::constraints::MultiConstraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::AmbiguousMultiConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

  2. dist(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, : core::scoring::func::XYZ_Func) -> float

MultiConstraints don’t have a single distance

C++: core::scoring::constraints::MultiConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) int

C++: core::scoring::constraints::MultiConstraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

empty_clone(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint) pyrosetta.rosetta.core.scoring.constraints.MultiConstraint

C++: core::scoring::constraints::AmbiguousConstraint::empty_clone() const –> class std::shared_ptr<class core::scoring::constraints::MultiConstraint>

fill_f1_f2(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, weights: pyrosetta.rosetta.core.scoring.EMapVector) None

compute atom deriv

C++: protocols::constraints_additional::AmbiguousMultiConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

init_cst_score_types(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint) None

C++: core::scoring::constraints::AmbiguousConstraint::init_cst_score_types() –> void

member_constraints(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: core::scoring::constraints::MultiConstraint::member_constraints() const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &

natoms(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint) int

number of atoms involved in this MultiConstraint container

C++: core::scoring::constraints::MultiConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) None
This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) None
initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint, data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: core::scoring::func::FuncFactory) None

read in constraint defiinition

C++: core::scoring::constraints::AmbiguousConstraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::AmbiguousMultiConstraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(*args, **kwargs)

Overloaded function.

  1. remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

  2. remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::scoring::constraints::MultiConstraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::constraints::MultiConstraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

C++: protocols::constraints_additional::AmbiguousMultiConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

compute score

C++: protocols::constraints_additional::AmbiguousMultiConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

set_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, setting: int) None

C++: core::scoring::constraints::MultiConstraint::set_effective_sequence_separation(unsigned long) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::MultiConstraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, out: pyrosetta.rosetta.std.ostream) None

C++: protocols::constraints_additional::AmbiguousMultiConstraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::constraints::MultiConstraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int

  2. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int, threshold: float) -> int

C++: protocols::constraints_additional::AmbiguousMultiConstraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

size(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint) int

number of constraints that are held by this %MultiConstraint

C++: core::scoring::constraints::MultiConstraint::size() const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint) str

C++: protocols::constraints_additional::AmbiguousMultiConstraint::type() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint

Bases: pyrosetta.rosetta.core.scoring.constraints.Constraint

atom(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, n: int) pyrosetta.rosetta.core.id.AtomID

C++: protocols::constraints_additional::BindingSiteConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::BindingSiteConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

  2. dist(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, : pyrosetta.rosetta.core.scoring.func.XYZ_Func) -> float

BindingSiteConstraints don’t have a single distance

C++: protocols::constraints_additional::BindingSiteConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, weights: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint) int

C++: protocols::constraints_additional::BindingSiteConstraint::natoms() const –> unsigned long

pre_align(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, templ_atms: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, : pyrosetta.rosetta.utility.vector1_bool) None

C++: protocols::constraints_additional::BindingSiteConstraint::pre_align(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) None
This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) None
initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory) None

C++: protocols::constraints_additional::BindingSiteConstraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::BindingSiteConstraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.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.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.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.

C++: core::scoring::constraints::Constraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

C++: protocols::constraints_additional::BindingSiteConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

  2. score(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

  3. score(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: protocols::constraints_additional::BindingSiteConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

setup_for_derivatives(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::constraints_additional::BindingSiteConstraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, out: pyrosetta.rosetta.std.ostream) None

C++: protocols::constraints_additional::BindingSiteConstraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::constraints_additional::BindingSiteConstraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int

  2. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int, threshold: float) -> int

C++: protocols::constraints_additional::BindingSiteConstraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint) str

C++: protocols::constraints_additional::BindingSiteConstraint::type() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator

Bases: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator

Mover creator for the BindingSiteConstraint constraint

assign(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator, : pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator) pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator

C++: protocols::constraints_additional::BindingSiteConstraintCreator::operator=(const class protocols::constraints_additional::BindingSiteConstraintCreator &) –> class protocols::constraints_additional::BindingSiteConstraintCreator &

create_constraint(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::BindingSiteConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator) str

C++: protocols::constraints_additional::BindingSiteConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint

Bases: pyrosetta.rosetta.core.scoring.constraints.Constraint

atom(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, n: int) pyrosetta.rosetta.core.id.AtomID

C++: protocols::constraints_additional::COMCoordinateConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::COMCoordinateConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

  2. dist(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func) -> float

C++: protocols::constraints_additional::COMCoordinateConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, weights: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::constraints_additional::COMCoordinateConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint) int

C++: protocols::constraints_additional::COMCoordinateConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) None
This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) None
initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory) None

C++: protocols::constraints_additional::COMCoordinateConstraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, : pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::COMCoordinateConstraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::COMCoordinateConstraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.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.

C++: core::scoring::constraints::Constraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

C++: protocols::constraints_additional::COMCoordinateConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

  2. score(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

  3. score(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: protocols::constraints_additional::COMCoordinateConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

setup_for_derivatives(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::constraints_additional::COMCoordinateConstraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::constraints_additional::COMCoordinateConstraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, out: pyrosetta.rosetta.std.ostream) None

C++: protocols::constraints_additional::COMCoordinateConstraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::constraints_additional::COMCoordinateConstraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int

  2. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int, threshold: float) -> int

C++: protocols::constraints_additional::COMCoordinateConstraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint) str

C++: protocols::constraints_additional::COMCoordinateConstraint::type() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator

Bases: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator

applicable(self: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, : pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

  2. apply(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

C++: protocols::constraints_additional::CombinedConstraintEvaluator::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void

  1. apply(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, pose: pyrosetta.rosetta.core.pose.Pose) -> float

C++: protocols::constraints_additional::CombinedConstraintEvaluator::apply(class core::pose::Pose &) const –> double

assign(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, : pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator) pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator

C++: protocols::constraints_additional::CombinedConstraintEvaluator::operator=(const class protocols::constraints_additional::CombinedConstraintEvaluator &) –> class protocols::constraints_additional::CombinedConstraintEvaluator &

name(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, i: int) str

C++: protocols::constraints_additional::CombinedConstraintEvaluator::name(unsigned long) const –> std::string

size(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator) int

C++: protocols::constraints_additional::CombinedConstraintEvaluator::size() const –> unsigned long

class pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator

Bases: pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator

creator for the CombinedConstraintsEvaluatorCreator class

add_evaluators(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator, eval: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) None

C++: protocols::constraints_additional::CombinedConstraintEvaluatorCreator::add_evaluators(class protocols::evaluation::MetaPoseEvaluator &) const –> void

assign(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator, : pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator) pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator

C++: protocols::constraints_additional::CombinedConstraintEvaluatorCreator::operator=(const class protocols::constraints_additional::CombinedConstraintEvaluatorCreator &) –> class protocols::constraints_additional::CombinedConstraintEvaluatorCreator &

register_options(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator) None

C++: protocols::constraints_additional::CombinedConstraintEvaluatorCreator::register_options() –> void

type_name(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator) str

C++: protocols::constraints_additional::CombinedConstraintEvaluatorCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator

Bases: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator

applicable(self: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, : pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

  2. apply(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

C++: protocols::constraints_additional::ConstraintEvaluator::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void

  1. apply(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, pose: pyrosetta.rosetta.core.pose.Pose) -> float

C++: protocols::constraints_additional::ConstraintEvaluator::apply(class core::pose::Pose &) const –> double

assign(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, : pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator) pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator

C++: protocols::constraints_additional::ConstraintEvaluator::operator=(const class protocols::constraints_additional::ConstraintEvaluator &) –> class protocols::constraints_additional::ConstraintEvaluator &

name(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, i: int) str

C++: protocols::constraints_additional::ConstraintEvaluator::name(unsigned long) const –> std::string

set_combine_ratio(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, setting: int) None

C++: protocols::constraints_additional::ConstraintEvaluator::set_combine_ratio(unsigned long) –> void

set_cst_source(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, tag: str) None

C++: protocols::constraints_additional::ConstraintEvaluator::set_cst_source(const std::string &) –> void

size(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator) int

C++: protocols::constraints_additional::ConstraintEvaluator::size() const –> unsigned long

class pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator

Bases: pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator

creator for the ConstraintsEvaluatorCreator class

add_evaluators(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator, eval: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) None

C++: protocols::constraints_additional::ConstraintEvaluatorCreator::add_evaluators(class protocols::evaluation::MetaPoseEvaluator &) const –> void

assign(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator, : pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator) pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator

C++: protocols::constraints_additional::ConstraintEvaluatorCreator::operator=(const class protocols::constraints_additional::ConstraintEvaluatorCreator &) –> class protocols::constraints_additional::ConstraintEvaluatorCreator &

register_options(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator) None

C++: protocols::constraints_additional::ConstraintEvaluatorCreator::register_options() –> void

type_name(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator) str

C++: protocols::constraints_additional::ConstraintEvaluatorCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet

Bases: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

add_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst: pyrosetta.rosetta.core.scoring.constraints.Constraint) None

C++: core::scoring::constraints::ConstraintSet::add_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>) –> void

add_constraints(*args, **kwargs)

Overloaded function.

  1. add_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> None

C++: core::scoring::constraints::ConstraintSet::add_constraints(class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >) –> void

  1. add_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None

add another constraint set to this constraint set

C++: core::scoring::constraints::ConstraintSet::add_constraints(const class std::shared_ptr<const class core::scoring::constraints::ConstraintSet>) –> void

add_dof_constraint(*args, **kwargs)

Overloaded function.

  1. add_dof_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, id: pyrosetta.rosetta.core.id.DOF_ID, func: pyrosetta.rosetta.core.scoring.func.Func) -> None

  2. add_dof_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, id: pyrosetta.rosetta.core.id.DOF_ID, func: pyrosetta.rosetta.core.scoring.func.Func, t: pyrosetta.rosetta.core.scoring.ScoreType) -> None

Note – still hacky. Will not be included in packing, just scoring

and minimization

C++: core::scoring::constraints::ConstraintSet::add_dof_constraint(const class core::id::DOF_ID &, class std::shared_ptr<class core::scoring::func::Func>, const enum core::scoring::ScoreType &) –> void

assign(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, rhs: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::operator=(const class core::scoring::constraints::ConstraintSet &) –> class core::scoring::constraints::ConstraintSet &

  1. assign(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, : pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) -> pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::operator=(const class protocols::constraints_additional::MaxSeqSepConstraintSet &) –> class protocols::constraints_additional::MaxSeqSepConstraintSet &

attach_to_conformation(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, conformation: pyrosetta.rosetta.std.weak_ptr_const_core_conformation_Conformation_t) None

C++: core::scoring::constraints::ConstraintSet::attach_to_conformation(class std::weak_ptr<const class core::conformation::Conformation>) –> void

clear(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None

C++: core::scoring::constraints::ConstraintSet::clear() –> void

clear_sequence_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None

Discard any and all sequence constraints in the sequence_constraints_ list.

C++: core::scoring::constraints::ConstraintSet::clear_sequence_constraints() –> void

clone(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::clone() const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

deprecated_eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None
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

C++: core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

detach_from_conformation(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None

C++: core::scoring::constraints::ConstraintSet::detach_from_conformation() –> void

detached_clone(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::detached_clone() const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

detached_copy(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, src: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::detached_copy(const class core::scoring::constraints::ConstraintSet &) –> void

eval_intrares_energy(*args, **kwargs)

Overloaded function.

  1. eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::ConstraintSet::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

  1. eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::ConstraintSet::eval_intrares_energy(const class core::conformation::Residue &, class core::scoring::EMapVector &) const –> void

eval_multibody_atom_derivative(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None
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).

C++: core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_non_residue_pair_energy(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

get_all_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) pyrosetta.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.

C++: core::scoring::constraints::ConstraintSet::get_all_constraints() const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

has_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool

C++: core::scoring::constraints::ConstraintSet::has_constraints() const –> bool

has_dof_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool

C++: core::scoring::constraints::ConstraintSet::has_dof_constraints() const –> bool

has_intra_residue_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool

C++: core::scoring::constraints::ConstraintSet::has_intra_residue_constraints() const –> bool

has_non_residue_pair_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool

C++: core::scoring::constraints::ConstraintSet::has_non_residue_pair_constraints() const –> bool

has_residue_pair_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool

C++: core::scoring::constraints::ConstraintSet::has_residue_pair_constraints() const –> bool

is_empty(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool

C++: core::scoring::constraints::ConstraintSet::is_empty() const –> bool

largest_possible_sequence_sep(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::largest_possible_sequence_sep(const class core::pose::Pose &) const –> unsigned long

max_seq_sep(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) int

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep() const –> unsigned long

n_sequence_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) int

Get the number of sequence constraints.

C++: core::scoring::constraints::ConstraintSet::n_sequence_constraints() const –> unsigned long

on_connection_change(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, event: pyrosetta.rosetta.core.conformation.signals.ConnectionEvent) None

C++: core::scoring::constraints::ConstraintSet::on_connection_change(const struct core::conformation::signals::ConnectionEvent &) –> void

on_length_change(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, event: pyrosetta.rosetta.core.conformation.signals.LengthEvent) None

C++: core::scoring::constraints::ConstraintSet::on_length_change(const struct core::conformation::signals::LengthEvent &) –> void

remap_residue_positions(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, smap: pyrosetta.rosetta.core.id.SequenceMapping) None
remaps the constraints in this particular constraint set according

to brief the passed in sequence mapping — redundant with remapped_clone!!!

C++: core::scoring::constraints::ConstraintSet::remap_residue_positions(const class core::id::SequenceMapping &) –> void

remapped_clone(*args, **kwargs)

Overloaded function.

  1. remapped_clone(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

  2. remapped_clone(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

remove_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst: pyrosetta.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

C++: core::scoring::constraints::ConstraintSet::remove_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>, bool) –> bool

remove_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, object_comparison: bool) bool

C++: core::scoring::constraints::ConstraintSet::remove_constraints(class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >, bool) –> bool

residue_pair_constraint_exists(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pos1: int, pos2: int) bool

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_constraint_exists(const int, const int) const –> bool

residue_pair_constraints_exists(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pos: int) bool

C++: core::scoring::constraints::ConstraintSet::residue_pair_constraints_exists(const unsigned long) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

revision_id(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) int

C++: core::scoring::constraints::ConstraintSet::revision_id() const –> unsigned long

same_type_as_me(*args, **kwargs)

Overloaded function.

  1. same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> bool

  2. same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, recurse: bool) -> bool

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::same_type_as_me(const class core::scoring::constraints::ConstraintSet &, bool) const –> bool

sequence_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, index: int) pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint

Get the owning pointer to the Nth sequence constraint.

C++: core::scoring::constraints::ConstraintSet::sequence_constraint(const unsigned long) const –> class std::shared_ptr<const class core::scoring::aa_composition_energy::SequenceConstraint>

set_max_seq_sep(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, setting: int) None

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::set_max_seq_sep(unsigned long) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::ConstraintSet::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None
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.

C++: core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, respair_data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None
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.

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::ConstraintSet::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

shortest_path(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet) pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::shortest_path() const –> const class core::kinematics::ShortestPathInFoldTree &

show(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::constraints::ConstraintSet::show(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::constraints::ConstraintSet::show_definition(std::ostream &, const class core::pose::Pose &) const –> void

show_numbers(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::constraints::ConstraintSet::show_numbers(std::ostream &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int

  2. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int, threshold: float) -> int

  3. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int

  4. show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int, threshold: float) -> int

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::show_violations(std::ostream &, class core::pose::Pose &, unsigned long, double) –> unsigned long

steal_def_clone(*args, **kwargs)

Overloaded function.

  1. steal_def_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

  2. steal_def_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.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

C++: core::scoring::constraints::ConstraintSet::steal_def_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

too_far(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, pos1: int, pos2: int) bool

C++: protocols::constraints_additional::MaxSeqSepConstraintSet::too_far(const int, const int) const –> bool

class pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator

Bases: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator

This class can be used to replace the standard AtomPairConstraintsCreator; see BrokerMain.cc for an example

assign(self: pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator, : pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator) pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator

C++: protocols::constraints_additional::NamedAtomPairConstraintCreator::operator=(const class protocols::constraints_additional::NamedAtomPairConstraintCreator &) –> class protocols::constraints_additional::NamedAtomPairConstraintCreator &

create_constraint(self: pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::NamedAtomPairConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator) str

C++: protocols::constraints_additional::NamedAtomPairConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint

Bases: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint

atom(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, : int) pyrosetta.rosetta.core.id.AtomID

C++: core::scoring::constraints::SequenceProfileConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::SequenceCoupling1BDConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

  2. dist(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, aa: pyrosetta.rosetta.core.chemical.AA) -> float

C++: core::scoring::constraints::SequenceProfileConstraint::dist(enum core::chemical::AA) const –> double

  1. dist(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, xyz: core::scoring::func::XYZ_Func) -> float

C++: core::scoring::constraints::SequenceProfileConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, : pyrosetta.rosetta.core.id.AtomID, : pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::constraints_additional::SequenceCoupling1BDConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint) int

C++: core::scoring::constraints::SequenceProfileConstraint::natoms() const –> unsigned long

profile_mapping(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint) pyrosetta.rosetta.core.id.SequenceMapping

C++: core::scoring::constraints::SequenceProfileConstraint::profile_mapping() const –> class std::shared_ptr<const class core::id::SequenceMapping>

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) None
This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) None
initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.func.FuncFactory) None

used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)

C++: protocols::constraints_additional::SequenceCoupling1BDConstraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, : pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::scoring::constraints::SequenceProfileConstraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::scoring::constraints::SequenceProfileConstraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::constraints::SequenceProfileConstraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

C++: protocols::constraints_additional::SequenceCoupling1BDConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, : pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::constraints_additional::SequenceCoupling1BDConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

seqpos(*args, **kwargs)

Overloaded function.

  1. seqpos(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint) -> int

C++: core::scoring::constraints::SequenceProfileConstraint::seqpos() const –> unsigned long

  1. seqpos(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, seqpos: int) -> None

C++: core::scoring::constraints::SequenceProfileConstraint::seqpos(unsigned long) –> void

sequence_profile(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint) core::sequence::SequenceProfile

C++: core::scoring::constraints::SequenceProfileConstraint::sequence_profile() const –> class std::shared_ptr<const class core::sequence::SequenceProfile>

set_sequence_profile(*args, **kwargs)

Overloaded function.

  1. set_sequence_profile(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, profile: core::sequence::SequenceProfile) -> None

  2. set_sequence_profile(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, profile: core::sequence::SequenceProfile, mapping: pyrosetta.rosetta.core.id.SequenceMapping) -> None

C++: core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile(class std::shared_ptr<const class core::sequence::SequenceProfile>, class std::shared_ptr<const class core::id::SequenceMapping>) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint, out: pyrosetta.rosetta.std.ostream) None

C++: protocols::constraints_additional::SequenceCoupling1BDConstraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::constraints::SequenceProfileConstraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int

  2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int

Prints the violations of this constraint to the given

std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint) str

C++: protocols::constraints_additional::SequenceCoupling1BDConstraint::type() const –> std::string

weight(*args, **kwargs)

Overloaded function.

  1. weight(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, w: float) -> None

C++: core::scoring::constraints::SequenceProfileConstraint::weight(const double) –> void

  1. weight(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint) -> float

C++: core::scoring::constraints::SequenceProfileConstraint::weight() const –> double

class pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator

Bases: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator

Mover creator for the SequenceCoupling1BDconstraint

assign(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator, : pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator) pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator

C++: protocols::constraints_additional::SequenceCoupling1BDConstraintCreator::operator=(const class protocols::constraints_additional::SequenceCoupling1BDConstraintCreator &) –> class protocols::constraints_additional::SequenceCoupling1BDConstraintCreator &

create_constraint(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::SequenceCoupling1BDConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator) str

C++: protocols::constraints_additional::SequenceCoupling1BDConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint

Bases: pyrosetta.rosetta.core.scoring.constraints.Constraint

atom(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : int) pyrosetta.rosetta.core.id.AtomID

C++: protocols::constraints_additional::SequenceCouplingConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::SequenceCouplingConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

  2. dist(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.core.scoring.func.XYZ_Func) -> float

“Distance” for SequenceCouplingConstraint isn’t all that simple

C++: protocols::constraints_additional::SequenceCouplingConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.core.id.AtomID, : pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::constraints_additional::SequenceCouplingConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint) int

C++: protocols::constraints_additional::SequenceCouplingConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) None
This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) None
initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.func.FuncFactory) None

used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)

C++: protocols::constraints_additional::SequenceCouplingConstraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.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.

C++: core::scoring::constraints::Constraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.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.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::constraints_additional::SequenceCouplingConstraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

C++: protocols::constraints_additional::SequenceCouplingConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

  2. score(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

  3. score(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: protocols::constraints_additional::SequenceCouplingConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

seqpos1(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint) int

C++: protocols::constraints_additional::SequenceCouplingConstraint::seqpos1() const –> unsigned long

seqpos2(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint) int

C++: protocols::constraints_additional::SequenceCouplingConstraint::seqpos2() const –> unsigned long

sequence_coupling(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint) pyrosetta.rosetta.core.sequence.SequenceCoupling

C++: protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling() –> class std::shared_ptr<class core::sequence::SequenceCoupling>

set_sequence_coupling(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.core.sequence.SequenceCoupling) None

C++: protocols::constraints_additional::SequenceCouplingConstraint::set_sequence_coupling(class std::shared_ptr<class core::sequence::SequenceCoupling>) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, out: pyrosetta.rosetta.std.ostream) None

C++: protocols::constraints_additional::SequenceCouplingConstraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::constraints_additional::SequenceCouplingConstraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int

  2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int

Prints the violations of this constraint to the given

std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint) str

C++: protocols::constraints_additional::SequenceCouplingConstraint::type() const –> std::string

class pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator

Bases: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator

Mover creator for the SequenceCouplingconstraint

assign(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator, : pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator) pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator

C++: protocols::constraints_additional::SequenceCouplingConstraintCreator::operator=(const class protocols::constraints_additional::SequenceCouplingConstraintCreator &) –> class protocols::constraints_additional::SequenceCouplingConstraintCreator &

create_constraint(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::constraints_additional::SequenceCouplingConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator) str

C++: protocols::constraints_additional::SequenceCouplingConstraintCreator::keyname() const –> std::string