constraints_additional¶
Bindings for protocols::constraints_additional namespace
- class pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint¶
Bases:
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.
dist(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
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.
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
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.
show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int
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:
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.
dist(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
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.
score(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
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.
show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int
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:
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:
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.
dist(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
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.
score(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
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.
show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int
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:
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.
apply(self: pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None
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
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:
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:
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.
apply(self: pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None
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
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:
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:
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.
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
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.
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
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.
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 &
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.
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
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.
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
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.
same_type_as_me(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> bool
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.
show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int
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
show_violations(self: pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int
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.
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
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:
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:
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.
dist(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
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
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.
seqpos(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint) -> int
C++: core::scoring::constraints::SequenceProfileConstraint::seqpos() const –> unsigned long
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.
set_sequence_profile(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, profile: core::sequence::SequenceProfile) -> None
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.
show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int
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.
weight(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint, w: float) -> None
C++: core::scoring::constraints::SequenceProfileConstraint::weight(const double) –> void
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:
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:
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.
dist(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
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.
score(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
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.
show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int
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:
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