constraints¶

Bindings for core::scoring::constraints namespace

class pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint¶

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

Nested constraint where only the one with lowest energy is considered.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::AmbiguousConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint, cst_in: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

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.core.scoring.constraints.AmbiguousConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AmbiguousConstraint::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.core.scoring.constraints.AmbiguousConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::AmbiguousConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> 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(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AmbiguousConstraint::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.core.scoring.constraints.AmbiguousConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::AmbiguousConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint, xyz_func: core::scoring::func::XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None¶

compute score

C++: core::scoring::constraints::AmbiguousConstraint::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.core.scoring.constraints.AmbiguousConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::AmbiguousConstraint::show(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

C++: core::scoring::constraints::AmbiguousConstraint::show_violations(class std::basic_ostream<char> &, 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.core.scoring.constraints.AmbiguousConstraint) → str¶: C++: core::scoring::constraints::AmbiguousConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator¶

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

Mover creator for the AmbiguousConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator¶: C++: core::scoring::constraints::AmbiguousConstraintCreator::operator=(const class core::scoring::constraints::AmbiguousConstraintCreator &) –> class core::scoring::constraints::AmbiguousConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AmbiguousConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator) → str¶: C++: core::scoring::constraints::AmbiguousConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator¶

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

Mover creator for the AmbiguousNMRConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator¶: C++: core::scoring::constraints::AmbiguousNMRConstraintCreator::operator=(const class core::scoring::constraints::AmbiguousNMRConstraintCreator &) –> class core::scoring::constraints::AmbiguousNMRConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AmbiguousNMRConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator) → str¶: C++: core::scoring::constraints::AmbiguousNMRConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator¶

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

Mover creator for the AmbiguousNMRDistanceConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator¶: C++: core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator::operator=(const class core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator &) –> class core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator) → str¶: C++: core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.AngleConstraint¶

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

An Angular Constraint.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

possibility to compare constraint according to data: and not just pointers

C++: core::scoring::constraints::AngleConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, arg0: pyrosetta.rosetta.core.id.AtomID, arg1: pyrosetta.rosetta.core.id.AtomID, arg2: pyrosetta.rosetta.core.id.AtomID, arg3: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, a1: pyrosetta.rosetta.core.id.AtomID, a2: pyrosetta.rosetta.core.id.AtomID, a3: pyrosetta.rosetta.core.id.AtomID, func_in: pyrosetta.rosetta.core.scoring.func.Func, scotype: pyrosetta.rosetta.core.scoring.ScoreType) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, arg0: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, func_in: pyrosetta.rosetta.core.scoring.func.Func, scoretype: pyrosetta.rosetta.core.scoring.ScoreType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

angle(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, xyz1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz2: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz3: pyrosetta.rosetta.numeric.xyzVector_double_t) → float¶

compute

C++: core::scoring::constraints::AngleConstraint::angle(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

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

return AtomID for atom 1,2,3

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

atom1(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::AngleConstraint::atom1() const –> const class core::id::AtomID &

atom2(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::AngleConstraint::atom2() const –> const class core::id::AtomID &

atom3(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::AngleConstraint::atom3() const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : pyrosetta.rosetta.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.core.scoring.constraints.AngleConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AngleConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dfunc(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, theta: float) → float¶

evaluate dfunc at theta

C++: core::scoring::constraints::AngleConstraint::dfunc(const double) const –> double

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, xyz: core::scoring::func::XYZ_Func) -> float

C++: core::scoring::constraints::AngleConstraint::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.core.scoring.constraints.AngleConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::AngleConstraint::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

func(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, theta: float) → float¶

evaluate func at theta

C++: core::scoring::constraints::AngleConstraint::func(const double) const –> double

get_func(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::constraints::AngleConstraint::get_func() const –> const class core::scoring::func::Func &

helper(M: pyrosetta.rosetta.numeric.xyzVector_double_t, w: pyrosetta.rosetta.numeric.xyzVector_double_t, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::constraints::AngleConstraint::helper(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

natoms(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint) → int¶

number of atoms — always 3 for angles

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

p1_deriv(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, p1: pyrosetta.rosetta.numeric.xyzVector_double_t, p2: pyrosetta.rosetta.numeric.xyzVector_double_t, p3: pyrosetta.rosetta.numeric.xyzVector_double_t, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::constraints::AngleConstraint::p1_deriv(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

p1_theta_deriv(p1: pyrosetta.rosetta.numeric.xyzVector_double_t, p2: pyrosetta.rosetta.numeric.xyzVector_double_t, p3: pyrosetta.rosetta.numeric.xyzVector_double_t, f1: pyrosetta.rosetta.numeric.xyzVector_double_t, f2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::constraints::AngleConstraint::p1_theta_deriv(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

p2_deriv(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, p1: pyrosetta.rosetta.numeric.xyzVector_double_t, p2: pyrosetta.rosetta.numeric.xyzVector_double_t, p3: pyrosetta.rosetta.numeric.xyzVector_double_t, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::constraints::AngleConstraint::p2_deriv(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) 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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, 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::AngleConstraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AngleConstraint::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.AngleConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: 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::AngleConstraint::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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::AngleConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, xyz1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz2: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz3: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

compute score

C++: core::scoring::constraints::AngleConstraint::score(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

score(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, xyz: core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

compute score

C++: core::scoring::constraints::AngleConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, : pyrosetta.rosetta.core.conformation.Conformation) -> float

C++: core::scoring::constraints::AngleConstraint::score(const class core::conformation::Conformation &) const –> double

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.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.AngleConstraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: core::scoring::constraints::AngleConstraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::AngleConstraint::show(class std::basic_ostream<char> &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::constraints::AngleConstraint::show_def(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 )

C++: core::scoring::constraints::AngleConstraint::show_violations(class std::basic_ostream<char> &, 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.core.scoring.constraints.AngleConstraint) → str¶: C++: core::scoring::constraints::AngleConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator¶

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

Mover creator for the AngleConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator¶: C++: core::scoring::constraints::AngleConstraintCreator::operator=(const class core::scoring::constraints::AngleConstraintCreator &) –> class core::scoring::constraints::AngleConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AngleConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator) → str¶: C++: core::scoring::constraints::AngleConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator¶

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

Mover creator for the AtomPairConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator¶: C++: core::scoring::constraints::AtomPairConstraintCreator::operator=(const class core::scoring::constraints::AtomPairConstraintCreator &) –> class core::scoring::constraints::AtomPairConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::AtomPairConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator) → str¶: C++: core::scoring::constraints::AtomPairConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint¶

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

This constraint favors the backbone landing on a “stub” backbone, which puts the sidechain in a pre-determined desirable location

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

possibility to compare constraint according to data: and not just pointers

C++: core::scoring::constraints::BackboneStubConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, fixed_atom_id: pyrosetta.rosetta.core.id.AtomID, target_pose: pyrosetta.rosetta.core.pose.Pose, target_seqpos: int, superposition_bonus: float, force_constant: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, fixed_atom_id: pyrosetta.rosetta.core.id.AtomID, target_rsd: pyrosetta.rosetta.core.conformation.Residue, superposition_bonus: float, force_constant: float, sidechain_atom_name: str, primary_backbone_atom_name: str, backbone_atom1_name: str, backbone_atom2_name: str) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, fixed_atom_id: pyrosetta.rosetta.core.id.AtomID, target_rsd: pyrosetta.rosetta.core.conformation.Residue, superposition_bonus: float, force_constant: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, arg0: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, index: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::BackboneStubConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.BackboneStubConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::BackboneStubConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, : core::scoring::func::XYZ_Func) -> float

“Distance” for BackboneStubConstraint isn’t all that simple

C++: core::scoring::constraints::BackboneStubConstraint::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.core.scoring.constraints.BackboneStubConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::BackboneStubConstraint::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.BackboneStubConstraint) → int¶: C++: core::scoring::constraints::BackboneStubConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None¶

Reads the definition of a Constraint from the given std::istream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, 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(*args, **kwargs)¶

Overloaded function.

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: 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::BackboneStubConstraint::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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::BackboneStubConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint, xyz_func: core::scoring::func::XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::BackboneStubConstraint::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(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint) → int¶

returns the private member seqpos_

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

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.core.scoring.constraints.BackboneStubConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::BackboneStubConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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.core.scoring.constraints.BackboneStubConstraint) → str¶: C++: core::scoring::constraints::BackboneStubConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint¶

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

This constraint favors the backbone landing on a “stub” backbone, which puts the sidechain in a pre-determined desirable location

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

possibility to compare constraint according to data: and not just pointers

C++: core::scoring::constraints::BackboneStubLinearConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, fixed_atom_id: pyrosetta.rosetta.core.id.AtomID, target_rsd: pyrosetta.rosetta.core.conformation.Residue, superposition_bonus: float, CB_force_constant: float) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, index: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::BackboneStubLinearConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.BackboneStubLinearConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::BackboneStubLinearConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, : core::scoring::func::XYZ_Func) -> float

“Distance” for BackboneStubLinearConstraint isn’t all that simple

C++: core::scoring::constraints::BackboneStubLinearConstraint::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.core.scoring.constraints.BackboneStubLinearConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::BackboneStubLinearConstraint::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.BackboneStubLinearConstraint) → int¶: C++: core::scoring::constraints::BackboneStubLinearConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None¶

Reads the definition of a Constraint from the given std::istream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, 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(*args, **kwargs)¶

Overloaded function.

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: 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::BackboneStubLinearConstraint::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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::BackboneStubLinearConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint, xyz_func: core::scoring::func::XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::BackboneStubLinearConstraint::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(self: pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint) → int¶

returns the private member seqpos_

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

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.core.scoring.constraints.BackboneStubLinearConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::BackboneStubLinearConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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.core.scoring.constraints.BackboneStubLinearConstraint) → str¶: C++: core::scoring::constraints::BackboneStubLinearConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator¶

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

Mover creator for the BasePairConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator¶: C++: core::scoring::constraints::BasePairConstraintCreator::operator=(const class core::scoring::constraints::BasePairConstraintCreator &) –> class core::scoring::constraints::BasePairConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::BasePairConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator) → str¶: C++: core::scoring::constraints::BasePairConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint¶

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

constraint on dihedral angle formed by 4 points

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::BigBinConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, arg0: pyrosetta.rosetta.core.id.AtomID, arg1: pyrosetta.rosetta.core.id.AtomID, arg2: pyrosetta.rosetta.core.id.AtomID, arg3: pyrosetta.rosetta.core.id.AtomID, arg4: pyrosetta.rosetta.core.id.AtomID, arg5: pyrosetta.rosetta.core.id.AtomID, arg6: str) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, C0: pyrosetta.rosetta.core.id.AtomID, N1: pyrosetta.rosetta.core.id.AtomID, CA1: pyrosetta.rosetta.core.id.AtomID, C1: pyrosetta.rosetta.core.id.AtomID, N2: pyrosetta.rosetta.core.id.AtomID, CA2: pyrosetta.rosetta.core.id.AtomID, bin: str, scotype: pyrosetta.rosetta.core.scoring.ScoreType) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, res: int, bin: str, sdev: float) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, n: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::BigBinConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

bin(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint) → str¶: C++: core::scoring::constraints::BigBinConstraint::bin() const –> char

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : pyrosetta.rosetta.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.core.scoring.constraints.BigBinConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::BigBinConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, : core::scoring::func::XYZ_Func) -> float

BigBinConstraints don’t have a single distance

C++: core::scoring::constraints::BigBinConstraint::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.core.scoring.constraints.BigBinConstraint, : pyrosetta.rosetta.core.id.AtomID, xyz: core::scoring::func::XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) → None¶: C++: core::scoring::constraints::BigBinConstraint::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.BigBinConstraint) → int¶: C++: core::scoring::constraints::BigBinConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: core::scoring::func::FuncFactory) → None¶: C++: core::scoring::constraints::BigBinConstraint::read_def(class std::basic_istream<char> &, 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>

res(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint) → int¶: C++: core::scoring::constraints::BigBinConstraint::res() const –> unsigned long

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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::BigBinConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint, xyz: core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::BigBinConstraint::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 &

sdev(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint) → float¶: C++: core::scoring::constraints::BigBinConstraint::sdev() const –> double

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.core.scoring.constraints.BigBinConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::BigBinConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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.core.scoring.constraints.BigBinConstraint) → str¶: C++: core::scoring::constraints::BigBinConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator¶

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

Mover creator for the BigBinConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator¶: C++: core::scoring::constraints::BigBinConstraintCreator::operator=(const class core::scoring::constraints::BigBinConstraintCreator &) –> class core::scoring::constraints::BigBinConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::BigBinConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator) → str¶: C++: core::scoring::constraints::BigBinConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint¶

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

A Constant Constraint.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::ConstantConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, arg0: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, func_in: pyrosetta.rosetta.core.scoring.func.Func, scotype: pyrosetta.rosetta.core.scoring.ScoreType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, n: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::ConstantConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.ConstantConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::ConstantConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, xyz: core::scoring::func::XYZ_Func) -> float

C++: core::scoring::constraints::ConstantConstraint::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.core.scoring.constraints.ConstantConstraint, : pyrosetta.rosetta.core.id.AtomID, : core::scoring::func::XYZ_Func, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) → None¶

compute atom deriv

C++: core::scoring::constraints::ConstantConstraint::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.ConstantConstraint) → int¶

number of atoms — zero

C++: core::scoring::constraints::ConstantConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None¶

Reads the definition of a Constraint from the given std::istream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, 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.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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::ConstantConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint) -> float

compute score

C++: core::scoring::constraints::ConstantConstraint::score() const –> double

score(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

compute score

C++: core::scoring::constraints::ConstantConstraint::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.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.core.scoring.constraints.ConstantConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::ConstantConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(self: pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, : float) → int¶

output violation of constraint (none!)

C++: core::scoring::constraints::ConstantConstraint::show_violations(class std::basic_ostream<char> &, 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.core.scoring.constraints.ConstantConstraint) → str¶: C++: core::scoring::constraints::ConstantConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.Constraint¶

Bases: pybind11_builtins.pybind11_object

Actually a restraint, like a virtual rubber band between a pair of atoms.

All Constraints are expected to be immutable once created, meaning their internal data (state) should not change over their lifetime. This allows Constraints to be shared between copies of Poses (e.g. in Monte Carlo), and is important for both speed (with thousands of constraints) and correctness.

To “change” a constraint, remove the old one and add a new and different one. The steal() methods have been removed because it is incompatible with the idea of immutable constraints.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Equality operator to test whether two constraints are functionally

identical.

This operator should use floating point comparison and should not decide that two floats are identical if they are within some epsilon > 0. This method allows developes to remove specific constraints from Poses, even if the constraints have been cloned. Remapped constraints should not be considered identical – i.e., if cst1 is between residues i and j and cst2 is between residues i+1 and j+1. All subclasses of Constraint must implement this method.

C++: core::scoring::constraints::Constraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, t: pyrosetta.rosetta.core.scoring.ScoreType) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, arg0: pyrosetta.rosetta.core.scoring.constraints.Constraint) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, index: int) → pyrosetta.rosetta.core.id.AtomID¶

Returns the AtomID referred to by index.

C++: core::scoring::constraints::Constraint::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, : pyrosetta.rosetta.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(*args, **kwargs)¶

Overloaded function.

clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

Copies the data from this %Constraint into a new object and returns: an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint. This function must return a deep copy of itself – meaning that if this %Constraint holds pointers to other %Constraints that it must invoke clone on those %Constraints as well. If the %Constraint holds a FuncOP, then the Func should also be cloned.

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

clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::Func) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

Clone the constraint, but where a new Func object is to be used instead.

C++: core::scoring::constraints::Constraint::clone(class std::shared_ptr<class core::scoring::func::Func>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

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

return the raw “distance” before that distance is handed to the FUNC object

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

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

return the raw “distance” before that distance is handed to the FUNC object

C++: core::scoring::constraints::Constraint::dist(const class core::pose::Pose &) 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.core.scoring.constraints.Constraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz_func: 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¶

Fill the f1 and f2 vectors, necessary for considering the: derivative this constraint during minimization. (someone please reference Bill Wedermeyer’s paper here, as I’m in an airport and can’t fill it in myself!)

C++: core::scoring::constraints::Constraint::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.Constraint) → int¶

Returns the number of atoms involved in defining this constraint.

If the constraint doesn’t depend on particular atoms (e.g. a residue type constraint) this function can return zero

Note that this function isn’t actually used by the constraint scoring machenery. If you’re calling it on a generic Constraint (as opposed to specifically on a derived class) you’re probably doing something wrong.

C++: core::scoring::constraints::Constraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None¶

Reads the definition of a Constraint from the given std::istream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, 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.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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Determine if the calling class has the same type as the: input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it.

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

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, xyz_func: core::scoring::func::XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

Calculates a score for this constraint using XYZ_Func, and puts: the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself.

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

score(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

Returns the unweighted score of this constraint computed over the given pose.

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

score(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

Returns the weighted score of this constraint computed over the given pose.

C++: core::scoring::constraints::Constraint::score(const class core::pose::Pose &, const class core::scoring::EMapVector &) const –> double

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.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.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream) → None¶

This method is intended to show the value of the Constraint function: evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.

C++: core::scoring::constraints::Constraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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.core.scoring.constraints.Constraint) → str¶

Returns a unique string identified for this constraint. Used in several: places, including the ConstraintIO class.

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

class pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator¶

Bases: pybind11_builtins.pybind11_object

Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator¶: C++: core::scoring::constraints::ConstraintCreator::operator=(const class core::scoring::constraints::ConstraintCreator &) –> class core::scoring::constraints::ConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::ConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator) → str¶: C++: core::scoring::constraints::ConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.ConstraintIO¶

Bases: pyrosetta.rosetta.utility.SingletonBase_core_scoring_constraints_ConstraintIO_t

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

get_cst_factory() → pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory¶: C++: core::scoring::constraints::ConstraintIO::get_cst_factory() –> class core::scoring::constraints::ConstraintFactory &

get_func_factory() → pyrosetta.rosetta.core.scoring.func.FuncFactory¶: C++: core::scoring::constraints::ConstraintIO::get_func_factory() –> class core::scoring::func::FuncFactory &

get_instance() → core::scoring::constraints::ConstraintIO¶: C++: utility::SingletonBase<core::scoring::constraints::ConstraintIO>::get_instance() –> class core::scoring::constraints::ConstraintIO *

parse_atom_pair_constraint(*args, **kwargs)¶

Overloaded function.

parse_atom_pair_constraint(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
parse_atom_pair_constraint(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, force_pdb_info_mapping: bool) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint(class std::basic_istream<char> &, class core::pose::Pose, const bool) –> class std::shared_ptr<class core::scoring::constraints::Constraint>

parse_coordinate_constraint(*args, **kwargs)¶

Overloaded function.

parse_coordinate_constraint(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
parse_coordinate_constraint(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, force_pdb_info_mapping: bool) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::scoring::constraints::ConstraintIO::parse_coordinate_constraint(class std::basic_istream<char> &, class core::pose::Pose, const bool) –> class std::shared_ptr<class core::scoring::constraints::Constraint>

parse_residue(*args, **kwargs)¶

Overloaded function.

parse_residue(pose: pyrosetta.rosetta.core.pose.Pose, residue_string: str, residue_num: int) -> None
parse_residue(pose: pyrosetta.rosetta.core.pose.Pose, residue_string: str, residue_num: int, force_pdb_info_mapping: bool) -> None

C++: core::scoring::constraints::ConstraintIO::parse_residue(const class core::pose::Pose &, const class std::basic_string<char> &, unsigned long &, const bool) –> void

parse_residue(pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) -> int
parse_residue(pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, chain: str) -> int
parse_residue(pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, chain: str, force_pdb_info_numbering: bool) -> int

a value of 0 for the chain means to ignore PDBInfo settings,: and treat the resnum as Rosetta/Pose numbering.

C++: core::scoring::constraints::ConstraintIO::parse_residue(const class core::pose::Pose &, const int, const char, const bool) –> unsigned long

read_constraints(*args, **kwargs)¶

Overloaded function.

read_constraints(filename: str, cst_set: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose) -> core::scoring::constraints::ConstraintSet
read_constraints(filename: str, cst_set: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, force_pdb_info_mapping: bool) -> core::scoring::constraints::ConstraintSet

C++: core::scoring::constraints::ConstraintIO::read_constraints(const class std::basic_string<char> &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, const class core::pose::Pose &, const bool) –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

read_constraints(data: pyrosetta.rosetta.std.istream, cst_set: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose) -> core::scoring::constraints::ConstraintSet
read_constraints(data: pyrosetta.rosetta.std.istream, cst_set: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, force_pdb_info_mapping: bool) -> core::scoring::constraints::ConstraintSet

C++: core::scoring::constraints::ConstraintIO::read_constraints(class std::basic_istream<char> &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, const class core::pose::Pose &, const bool) –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

read_constraints_new(*args, **kwargs)¶

Overloaded function.

read_constraints_new(fname: str, cset: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose) -> core::scoring::constraints::ConstraintSet
read_constraints_new(fname: str, cset: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, force_pdb_info_mapping: bool) -> core::scoring::constraints::ConstraintSet

C++: core::scoring::constraints::ConstraintIO::read_constraints_new(const class std::basic_string<char> &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, const class core::pose::Pose &, const bool) –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

read_constraints_new(data: pyrosetta.rosetta.std.istream, cset: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose) -> core::scoring::constraints::ConstraintSet
read_constraints_new(data: pyrosetta.rosetta.std.istream, cset: core::scoring::constraints::ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, force_pdb_info_mapping: bool) -> core::scoring::constraints::ConstraintSet

C++: core::scoring::constraints::ConstraintIO::read_constraints_new(class std::basic_istream<char> &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, const class core::pose::Pose &, const bool) –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

read_individual_constraint_new(*args, **kwargs)¶

Overloaded function.

read_individual_constraint_new(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
read_individual_constraint_new(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory, force_pdb_info_mapping: bool) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

read one individual constraint defined.

C++: core::scoring::constraints::ConstraintIO::read_individual_constraint_new(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &, const bool) –> class std::shared_ptr<class core::scoring::constraints::Constraint>

read_individual_constraint_new(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory, type: str) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
read_individual_constraint_new(data: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory, type: str, force_pdb_info_mapping: bool) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

read one individual constraint defined.

C++: core::scoring::constraints::ConstraintIO::read_individual_constraint_new(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &, class std::basic_string<char>, const bool) –> class std::shared_ptr<class core::scoring::constraints::Constraint>

write_constraints(*args, **kwargs)¶

Overloaded function.

write_constraints(: pyrosetta.rosetta.std.ostream, cst_set: core::scoring::constraints::ConstraintSet, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::scoring::constraints::ConstraintIO::write_constraints(class std::basic_ostream<char> &, const class core::scoring::constraints::ConstraintSet &, const class core::pose::Pose &) –> void

write_constraints(filename: str, cst_set: core::scoring::constraints::ConstraintSet, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::scoring::constraints::ConstraintIO::write_constraints(const class std::basic_string<char> &, const class core::scoring::constraints::ConstraintSet &, const class core::pose::Pose &) –> void

class pyrosetta.rosetta.core.scoring.constraints.ConstraintSet¶

Bases: pybind11_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, arg0: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, start_residue: int, end_residue: int) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

add_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(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rhs: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → pyrosetta.rosetta.core.scoring.constraints.ConstraintSet¶

Assignment operator – requires that “same_type_as_me” has already: been called. This performs a shallow copy of all of the constraints held in the ConstraintSet, efficiently avoiding copy operations on ResidueConstraint objects that are already identical.

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

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.core.scoring.constraints.ConstraintSet) → pyrosetta.rosetta.core.scoring.constraints.ConstraintSet¶

Clone operator – performs a shallow copy of the contained: constraints.

C++: core::scoring::constraints::ConstraintSet::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.core.scoring.constraints.ConstraintSet) → pyrosetta.rosetta.core.scoring.constraints.ConstraintSet¶

Clone operator – performs a shallow copy of the contained: constraints.

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

detached_copy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → None¶

Perform a deep copy of the source %ConstraintSet into this %ConstraintSet: so that the two do not share any data in common – and can thus this %constraintSet can be safely handed to another thread; this function relies on the Constraint class’s clone() method, which is required to create a deep copy of itself.

C++: core::scoring::constraints::ConstraintSet::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.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None¶

Does NOT zero the emap values, just adds the additional contribution to the: existing emap energies (so can be called inside finalize_total_energies)

C++: core::scoring::constraints::ConstraintSet::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

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.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet
remapped_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

Copies the data from this ConstraintSet into a new object and: returns its 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. This will really clone all constraints since they have to change their atom-numbers and residue-numbers

C++: core::scoring::constraints::ConstraintSet::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.core.scoring.constraints.ConstraintSet, pos1: int, pos2: int) → bool¶: C++: core::scoring::constraints::ConstraintSet::residue_pair_constraint_exists(const int, const int) const –> bool

residue_pair_constraints_begin(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, resid: int) → std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >¶: C++: core::scoring::constraints::ConstraintSet::residue_pair_constraints_begin(unsigned long) const –> struct std::_Rb_tree_const_iterator<struct std::pair<const unsigned long, class std::shared_ptr<class core::scoring::constraints::Constraints> > >

residue_pair_constraints_end(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, resid: int) → std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >¶: C++: core::scoring::constraints::ConstraintSet::residue_pair_constraints_end(unsigned long) const –> struct std::_Rb_tree_const_iterator<struct std::pair<const unsigned long, class std::shared_ptr<class core::scoring::constraints::Constraints> > >

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.core.scoring.constraints.ConstraintSet, 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++: core::scoring::constraints::ConstraintSet::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.core.scoring.constraints.ConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> bool
same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, recurse: bool) -> bool

Does this ConstraintSet class have the same type as the other ConstraintSet: object? If so, then the assignment operator can be used to copy constraints from one ConstraintSet into the other. Always call this with recurse set to true or unspecified – derived classes should make sure that they set this variable to false in their implementations of this method to avoid infinite recursion.

C++: core::scoring::constraints::ConstraintSet::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>

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.core.scoring.constraints.ConstraintSet, 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¶

Cache the ConstraintsCOP for a particular residue pair: in the respair_data_cache, under the “cst_respair_data” element of the data-cache’s CachableDataOP array. Derived ConstraintSet classes should decide HERE whether any constraints should be evaluated between this pair of residues, 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_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

show(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::ConstraintSet::show(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

C++: core::scoring::constraints::ConstraintSet::show_violations(class std::basic_ostream<char> &, class core::pose::Pose &, unsigned long, double) const –> 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>

class pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint¶

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

CoordinateConstraint compares the coordinates of a given atom (AtomID atom_) to a fixed coordinate triplet (Vector xyz_target_). Its other argument, fixed_atom_, is somewhat nonobvious. CoordinateConstraints are meant to be used with a Pose that has a nonmoving virtual root residue. An AtomID in this virtual root residue should be passed as fixed_atom_. CoordinateConstraint does not use fixed_atom_, but the ScoreFunction code detects when fixed_atom_ and atom_ move relative to one another, and trigger re-scoring at that time. In other words, CoordinateConstraints are really context-independent one body energies, but we wish them to be evaluated as context-independent two-body energies. (Ideally, ScoreFunction would detect when atom_ moves relative to xyz_target_, but since ScoreFunction functions on atoms and not floating coordinate triplets, this is a good workaround.) – SML

Would be good to have something like StubCoordinateConstraint that allows definition of (x,y,z) of: moving atom to be defined in coordinate system defined by three “stub” atoms. Shows up when treating the effects of missing loops. Working out a sketch of this as a ‘standalone’ in rna::StubCoordinateHack, but should ideally integrate into Constraint machinery.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, other_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

possibility to do object comparison instead: of pointer comparison

C++: core::scoring::constraints::CoordinateConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, arg0: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, arg0: pyrosetta.rosetta.core.id.AtomID, arg1: pyrosetta.rosetta.core.id.AtomID, arg2: pyrosetta.rosetta.numeric.xyzVector_double_t, arg3: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, a1: pyrosetta.rosetta.core.id.AtomID, fixed_atom_in: pyrosetta.rosetta.core.id.AtomID, xyz_target_in: pyrosetta.rosetta.numeric.xyzVector_double_t, func: pyrosetta.rosetta.core.scoring.func.Func, scotype: pyrosetta.rosetta.core.scoring.ScoreType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, n: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::CoordinateConstraint::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, : pyrosetta.rosetta.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(*args, **kwargs)¶

Overloaded function.

clone(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

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

clone(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, : pyrosetta.rosetta.core.scoring.func.Func) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::scoring::constraints::CoordinateConstraint::clone(class std::shared_ptr<class core::scoring::func::Func>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, xyz: core::scoring::func::XYZ_Func) -> float

C++: core::scoring::constraints::CoordinateConstraint::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.core.scoring.constraints.CoordinateConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::CoordinateConstraint::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.CoordinateConstraint) → pyrosetta.rosetta.core.scoring.func.Func¶

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

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

natoms(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint) → int¶: C++: core::scoring::constraints::CoordinateConstraint::natoms() const –> unsigned long

non_virtual_score(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → float¶: C++: core::scoring::constraints::CoordinateConstraint::non_virtual_score(const class numeric::xyzVector<double> &) const –> double

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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.func.FuncFactory) → None¶: C++: core::scoring::constraints::CoordinateConstraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::CoordinateConstraint::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.CoordinateConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: 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::CoordinateConstraint::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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::CoordinateConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, xyz: core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::CoordinateConstraint::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.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.core.scoring.constraints.CoordinateConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::CoordinateConstraint::show(class std::basic_ostream<char> &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::constraints::CoordinateConstraint::show_def(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

C++: core::scoring::constraints::CoordinateConstraint::show_violations(class std::basic_ostream<char> &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::constraints::CoordinateConstraint::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.core.scoring.constraints.CoordinateConstraint) → str¶: C++: core::scoring::constraints::CoordinateConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator¶

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

Mover creator for the CoordinateConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator¶: C++: core::scoring::constraints::CoordinateConstraintCreator::operator=(const class core::scoring::constraints::CoordinateConstraintCreator &) –> class core::scoring::constraints::CoordinateConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::CoordinateConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator) → str¶: C++: core::scoring::constraints::CoordinateConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint¶

Bases: pybind11_builtins.pybind11_object

This isn’t quite a standard constraint since it acts on DOF’s directly: rather than on XYZ coordinates.

All DOF_Constraints are expected to be immutable once created, meaning their internal data (state) should not change over their lifetime. This allows DOF_Constraints to be shared between copies of Poses (e.g. in Monte Carlo), and is important for both speed (with thousands of contraints) and correctness.

DOF_Constraints are currently unsupported – they are never evaluated if you put them into a Pose.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint, arg0: pyrosetta.rosetta.core.id.DOF_ID, arg1: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

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

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

dfunc(self: pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint, val: float) → float¶

Returns the func::Function Derivative

C++: core::scoring::constraints::DOF_Constraint::dfunc(const double) const –> double

dof_id(self: pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint) → pyrosetta.rosetta.core.id.DOF_ID¶

Returns the ScoreType

C++: core::scoring::constraints::DOF_Constraint::dof_id() const –> const class core::id::DOF_ID &

func(self: pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint, val: float) → float¶

Returns the func::Function

C++: core::scoring::constraints::DOF_Constraint::func(const double) const –> double

score_type(self: pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint) → pyrosetta.rosetta.core.scoring.ScoreType¶

Returns the ScoreType

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

show(self: pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::DOF_Constraint::show(class std::basic_ostream<char> &) const –> void

class pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint¶

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

constraint on dihedral angle formed by 4 points

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

possibility to compare constraint according to data: and not just pointers

C++: core::scoring::constraints::DihedralConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, arg0: pyrosetta.rosetta.core.id.AtomID, arg1: pyrosetta.rosetta.core.id.AtomID, arg2: pyrosetta.rosetta.core.id.AtomID, arg3: pyrosetta.rosetta.core.id.AtomID, arg4: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, a1: pyrosetta.rosetta.core.id.AtomID, a2: pyrosetta.rosetta.core.id.AtomID, a3: pyrosetta.rosetta.core.id.AtomID, a4: pyrosetta.rosetta.core.id.AtomID, func: pyrosetta.rosetta.core.scoring.func.Func, scotype: pyrosetta.rosetta.core.scoring.ScoreType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, n: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::DihedralConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.DihedralConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶

Perform a deep clone by cloning the func_ pointer held by this %DihedralConstraint

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

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, xyz: core::scoring::func::XYZ_Func) -> float

C++: core::scoring::constraints::DihedralConstraint::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.core.scoring.constraints.DihedralConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::DihedralConstraint::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.DihedralConstraint) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::constraints::DihedralConstraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint) → int¶: C++: core::scoring::constraints::DihedralConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory) → None¶: C++: core::scoring::constraints::DihedralConstraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::DihedralConstraint::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.DihedralConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: 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::DihedralConstraint::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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::DihedralConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, xyz1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz2: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz3: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz4: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

C++: core::scoring::constraints::DihedralConstraint::score(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, xyz: core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::DihedralConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> float

C++: core::scoring::constraints::DihedralConstraint::score(const class core::conformation::Conformation &) const –> double

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.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.core.scoring.constraints.DihedralConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::DihedralConstraint::show(class std::basic_ostream<char> &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::constraints::DihedralConstraint::show_def(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

C++: core::scoring::constraints::DihedralConstraint::show_violations(class std::basic_ostream<char> &, 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.core.scoring.constraints.DihedralConstraint) → str¶: C++: core::scoring::constraints::DihedralConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator¶

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

Mover creator for the DihedralConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator¶: C++: core::scoring::constraints::DihedralConstraintCreator::operator=(const class core::scoring::constraints::DihedralConstraintCreator &) –> class core::scoring::constraints::DihedralConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::DihedralConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator) → str¶: C++: core::scoring::constraints::DihedralConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint¶

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

constraint on dihedral angle formed by 4 points

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, rhs: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::DihedralPairConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, arg0: pyrosetta.rosetta.core.id.AtomID, arg1: pyrosetta.rosetta.core.id.AtomID, arg2: pyrosetta.rosetta.core.id.AtomID, arg3: pyrosetta.rosetta.core.id.AtomID, arg4: pyrosetta.rosetta.core.id.AtomID, arg5: pyrosetta.rosetta.core.id.AtomID, arg6: pyrosetta.rosetta.core.id.AtomID, arg7: pyrosetta.rosetta.core.id.AtomID, arg8: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, a1: pyrosetta.rosetta.core.id.AtomID, a2: pyrosetta.rosetta.core.id.AtomID, a3: pyrosetta.rosetta.core.id.AtomID, a4: pyrosetta.rosetta.core.id.AtomID, b1: pyrosetta.rosetta.core.id.AtomID, b2: pyrosetta.rosetta.core.id.AtomID, b3: pyrosetta.rosetta.core.id.AtomID, b4: pyrosetta.rosetta.core.id.AtomID, func: pyrosetta.rosetta.core.scoring.func.Func, scotype: pyrosetta.rosetta.core.scoring.ScoreType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, n: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::DihedralPairConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.DihedralPairConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::DihedralPairConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dihedral_diff(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, X1: pyrosetta.rosetta.numeric.xyzVector_double_t, X2: pyrosetta.rosetta.numeric.xyzVector_double_t, X3: pyrosetta.rosetta.numeric.xyzVector_double_t, X4: pyrosetta.rosetta.numeric.xyzVector_double_t, Y1: pyrosetta.rosetta.numeric.xyzVector_double_t, Y2: pyrosetta.rosetta.numeric.xyzVector_double_t, Y3: pyrosetta.rosetta.numeric.xyzVector_double_t, Y4: pyrosetta.rosetta.numeric.xyzVector_double_t) → float¶: C++: core::scoring::constraints::DihedralPairConstraint::dihedral_diff(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, xyz: core::scoring::func::XYZ_Func) -> float

C++: core::scoring::constraints::DihedralPairConstraint::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.core.scoring.constraints.DihedralPairConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::DihedralPairConstraint::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.DihedralPairConstraint) → int¶: C++: core::scoring::constraints::DihedralPairConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory) → None¶: C++: core::scoring::constraints::DihedralPairConstraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::DihedralPairConstraint::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.DihedralPairConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: 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::DihedralPairConstraint::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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::DihedralPairConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, X1: pyrosetta.rosetta.numeric.xyzVector_double_t, X2: pyrosetta.rosetta.numeric.xyzVector_double_t, X3: pyrosetta.rosetta.numeric.xyzVector_double_t, X4: pyrosetta.rosetta.numeric.xyzVector_double_t, Y1: pyrosetta.rosetta.numeric.xyzVector_double_t, Y2: pyrosetta.rosetta.numeric.xyzVector_double_t, Y3: pyrosetta.rosetta.numeric.xyzVector_double_t, Y4: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

C++: core::scoring::constraints::DihedralPairConstraint::score(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, xyz: core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::DihedralPairConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> float

C++: core::scoring::constraints::DihedralPairConstraint::score(const class core::conformation::Conformation &) const –> double

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.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.core.scoring.constraints.DihedralPairConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::DihedralPairConstraint::show(class std::basic_ostream<char> &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::constraints::DihedralPairConstraint::show_def(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

C++: core::scoring::constraints::DihedralPairConstraint::show_violations(class std::basic_ostream<char> &, 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.core.scoring.constraints.DihedralPairConstraint) → str¶: C++: core::scoring::constraints::DihedralPairConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator¶

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

Constraint creator for DihedralPairConstraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator¶: C++: core::scoring::constraints::DihedralPairConstraintCreator::operator=(const class core::scoring::constraints::DihedralPairConstraintCreator &) –> class core::scoring::constraints::DihedralPairConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::DihedralPairConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator) → str¶: C++: core::scoring::constraints::DihedralPairConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint¶

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

constraint on CA distance

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, rhs: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::DistancePairConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, arg0: pyrosetta.rosetta.core.id.AtomID, arg1: pyrosetta.rosetta.core.id.AtomID, arg2: pyrosetta.rosetta.core.id.AtomID, arg3: pyrosetta.rosetta.core.id.AtomID, arg4: pyrosetta.rosetta.core.scoring.func.Func) -> None

doc

__init__(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, a1: pyrosetta.rosetta.core.id.AtomID, a2: pyrosetta.rosetta.core.id.AtomID, b1: pyrosetta.rosetta.core.id.AtomID, b2: pyrosetta.rosetta.core.id.AtomID, func: pyrosetta.rosetta.core.scoring.func.Func, scotype: pyrosetta.rosetta.core.scoring.ScoreType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, n: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::DistancePairConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.DistancePairConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::DistancePairConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, xyz: core::scoring::func::XYZ_Func) -> float

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

distance_diff(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, X1: pyrosetta.rosetta.numeric.xyzVector_double_t, X2: pyrosetta.rosetta.numeric.xyzVector_double_t, Y1: pyrosetta.rosetta.numeric.xyzVector_double_t, Y2: pyrosetta.rosetta.numeric.xyzVector_double_t) → float¶: C++: core::scoring::constraints::DistancePairConstraint::distance_diff(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) 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.core.scoring.constraints.DistancePairConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: 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++: core::scoring::constraints::DistancePairConstraint::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.DistancePairConstraint) → int¶: C++: core::scoring::constraints::DistancePairConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory) → None¶: C++: core::scoring::constraints::DistancePairConstraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::DistancePairConstraint::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.DistancePairConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: 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::DistancePairConstraint::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.

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

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::DistancePairConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, X1: pyrosetta.rosetta.numeric.xyzVector_double_t, X2: pyrosetta.rosetta.numeric.xyzVector_double_t, Y1: pyrosetta.rosetta.numeric.xyzVector_double_t, Y2: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

C++: core::scoring::constraints::DistancePairConstraint::score(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

score(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, xyz: core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::DistancePairConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score(self: pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> float

C++: core::scoring::constraints::DistancePairConstraint::score(const class core::conformation::Conformation &) const –> double

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.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.core.scoring.constraints.DistancePairConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::DistancePairConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

C++: core::scoring::constraints::DistancePairConstraint::show_violations(class std::basic_ostream<char> &, 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.core.scoring.constraints.DistancePairConstraint) → str¶: C++: core::scoring::constraints::DistancePairConstraint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator¶

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

Mover creator for the FabConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator¶: C++: core::scoring::constraints::FabConstraintCreator::operator=(const class core::scoring::constraints::FabConstraintCreator &) –> class core::scoring::constraints::FabConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::FabConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator) → str¶: C++: core::scoring::constraints::FabConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator¶

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

Mover creator for the KofNConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator¶: C++: core::scoring::constraints::KofNConstraintCreator::operator=(const class core::scoring::constraints::KofNConstraintCreator &) –> class core::scoring::constraints::KofNConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::KofNConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator) → str¶: C++: core::scoring::constraints::KofNConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator¶

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

Mover creator for the LocalCoordinateConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator¶: C++: core::scoring::constraints::LocalCoordinateConstraintCreator::operator=(const class core::scoring::constraints::LocalCoordinateConstraintCreator &) –> class core::scoring::constraints::LocalCoordinateConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::LocalCoordinateConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator) → str¶: C++: core::scoring::constraints::LocalCoordinateConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator¶

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

Mover creator for the MultiConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator¶: C++: core::scoring::constraints::MultiConstraintCreator::operator=(const class core::scoring::constraints::MultiConstraintCreator &) –> class core::scoring::constraints::MultiConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::MultiConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator) → str¶: C++: core::scoring::constraints::MultiConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator¶

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

Constraint creator for the NamedAngleConstraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator¶: C++: core::scoring::constraints::NamedAngleConstraintCreator::operator=(const class core::scoring::constraints::NamedAngleConstraintCreator &) –> class core::scoring::constraints::NamedAngleConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::NamedAngleConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator) → str¶: C++: core::scoring::constraints::NamedAngleConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint¶

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

This class favors a particular residue identity at a particular position by reducing its res_type energy.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, rhs: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::NonResidueTypeConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, non_native_residue_bonus: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, AAname: str, favor_non_native_bonus: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, seqpos: int, aa_in: str, name3_in: str, bonus_in: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, arg0: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, : int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::NonResidueTypeConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.NonResidueTypeConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::NonResidueTypeConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func) -> float

Return 1.0 if constraint will get a penalty, 0.0 if not

C++: core::scoring::constraints::NonResidueTypeConstraint::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.core.scoring.constraints.NonResidueTypeConstraint, 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++: core::scoring::constraints::NonResidueTypeConstraint::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.NonResidueTypeConstraint) → int¶: C++: core::scoring::constraints::NonResidueTypeConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None¶

Reads the definition of a Constraint from the given std::istream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::NonResidueTypeConstraint::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.NonResidueTypeConstraint) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::scoring::constraints::NonResidueTypeConstraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::NonResidueTypeConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::NonResidueTypeConstraint::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.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.core.scoring.constraints.NonResidueTypeConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::NonResidueTypeConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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.core.scoring.constraints.Constraint) → str¶

Returns a unique string identified for this constraint. Used in several: places, including the ConstraintIO class.

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

class pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc¶

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

a variant of the bound func that is periodic

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, rhs: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, lb: float, ub: float, sd: float, type: str, periodicity_in: float, offset_in: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, arg0: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.func.Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, : pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc) → pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::operator=(const class core::scoring::constraints::OffsetPeriodicBoundFunc &) –> class core::scoring::constraints::OffsetPeriodicBoundFunc &

clone(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, x: float) → float¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by: calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by: calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, x: float) → float¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::func(const double) const –> double

lb(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::lb() const –> double

read_data(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, : pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::read_data(class std::basic_istream<char> &) –> void

rswitch(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::rswitch() const –> double

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, rhs: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

sd(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::sd() const –> double

show(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None¶

Prints out space-delimited columns for r, func, dfunc and: dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

C++: core::scoring::func::Func::show(class std::basic_ostream<char> &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::OffsetPeriodicBoundFunc::show_definition(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::constraints::OffsetPeriodicBoundFunc::show_violations(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

type(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → str¶: C++: core::scoring::constraints::BoundFunc::type() const –> std::string

ub(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::ub() const –> double

class pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc¶

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

a variant of the bound func that is periodic

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, rhs: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::constraints::PeriodicBoundFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, lb: float, ub: float, sd: float, type: str, periodicity_in: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, arg0: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.func.Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, : pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc) → pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc¶: C++: core::scoring::constraints::PeriodicBoundFunc::operator=(const class core::scoring::constraints::PeriodicBoundFunc &) –> class core::scoring::constraints::PeriodicBoundFunc &

clone(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::constraints::PeriodicBoundFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, x: float) → float¶: C++: core::scoring::constraints::PeriodicBoundFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by: calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by: calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, x: float) → float¶: C++: core::scoring::constraints::PeriodicBoundFunc::func(const double) const –> double

lb(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::lb() const –> double

read_data(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, : pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::constraints::PeriodicBoundFunc::read_data(class std::basic_istream<char> &) –> void

rswitch(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::rswitch() const –> double

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, rhs: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::constraints::PeriodicBoundFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

sd(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::sd() const –> double

show(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None¶

Prints out space-delimited columns for r, func, dfunc and: dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

C++: core::scoring::func::Func::show(class std::basic_ostream<char> &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::PeriodicBoundFunc::show_definition(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::constraints::PeriodicBoundFunc::show_violations(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

type(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → str¶: C++: core::scoring::constraints::BoundFunc::type() const –> std::string

ub(self: pyrosetta.rosetta.core.scoring.constraints.BoundFunc) → float¶: C++: core::scoring::constraints::BoundFunc::ub() const –> double

class pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints¶

Bases: pybind11_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints, : pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints) → pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints¶: C++: core::scoring::constraints::ResidueConstraints::operator=(const class core::scoring::constraints::ResidueConstraints &) –> class core::scoring::constraints::ResidueConstraints &

begin(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints) → std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >¶: C++: core::scoring::constraints::ResidueConstraints::begin() const –> struct std::_Rb_tree_const_iterator<struct std::pair<const unsigned long, class std::shared_ptr<class core::scoring::constraints::Constraints> > >

clear(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints) → None¶: C++: core::scoring::constraints::ResidueConstraints::clear() –> void

end(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints) → std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >¶: C++: core::scoring::constraints::ResidueConstraints::end() const –> struct std::_Rb_tree_const_iterator<struct std::pair<const unsigned long, class std::shared_ptr<class core::scoring::constraints::Constraints> > >

erase(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints, seqpos: int) → None¶: C++: core::scoring::constraints::ResidueConstraints::erase(const unsigned long) –> void

has(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints, seqpos: int) → bool¶: C++: core::scoring::constraints::ResidueConstraints::has(const unsigned long) –> bool

insert(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints, seqpos: int, cst: pyrosetta.rosetta.core.scoring.constraints.Constraints) → None¶: C++: core::scoring::constraints::ResidueConstraints::insert(const unsigned long, class std::shared_ptr<class core::scoring::constraints::Constraints>) –> void

size(self: pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints) → int¶: C++: core::scoring::constraints::ResidueConstraints::size() const –> unsigned long

class pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint¶

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

This class favors a particular residue identity at a particular position by reducing its res_type energy.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::ResidueTypeConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, native_residue_bonus: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, AAname: str, favor_native_bonus: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, seqpos: int, aa_in: str, name3_in: str, bonus_in: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, arg0: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, : int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::ResidueTypeConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.ResidueTypeConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::ResidueTypeConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func) -> float

Return 1.0 if constraint will get a bonus, 0.0 if not

C++: core::scoring::constraints::ResidueTypeConstraint::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.core.scoring.constraints.ResidueTypeConstraint, 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++: core::scoring::constraints::ResidueTypeConstraint::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_favor_native_bonus(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint) → float¶: C++: core::scoring::constraints::ResidueTypeConstraint::get_favor_native_bonus() const –> double

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 &

get_rsd_type_name3(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint) → str¶: C++: core::scoring::constraints::ResidueTypeConstraint::get_rsd_type_name3() const –> std::string

natoms(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint) → int¶: C++: core::scoring::constraints::ResidueTypeConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None¶

Reads the definition of a Constraint from the given std::istream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::ResidueTypeConstraint::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.ResidueTypeConstraint, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, 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::ResidueTypeConstraint::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.ResidueTypeConstraint) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::scoring::constraints::ResidueTypeConstraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::ResidueTypeConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::ResidueTypeConstraint::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.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.core.scoring.constraints.ResidueTypeConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::ResidueTypeConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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.core.scoring.constraints.Constraint) → str¶

Returns a unique string identified for this constraint. Used in several: places, including the ConstraintIO class.

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

class pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint¶

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

This class favors a particular residue identity at a particular position by reducing its res_type energy.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

possibility to compare constraint according to data: and not just pointers

C++: core::scoring::constraints::ResidueTypeLinkingConstraint::operator==(const class core::scoring::constraints::Constraint &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos1: int, seqpos2: int, bonus: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, pose: pyrosetta.rosetta.core.pose.Pose, seqpos1: int, seqpos2: int, AA1name: str, AA2name: str, bonus: float) -> None
__init__(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, arg0: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶

Inequality operator to test whether two constraints are not functionally: identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

atom(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, : int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::scoring::constraints::ResidueTypeLinkingConstraint::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, : pyrosetta.rosetta.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.core.scoring.constraints.ResidueTypeLinkingConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::ResidueTypeLinkingConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, xyz: pyrosetta.rosetta.core.scoring.func.XYZ_Func) -> float

Return 1.0 if constraint will get a bonus/penalty, 0.0 if not

C++: core::scoring::constraints::ResidueTypeLinkingConstraint::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.core.scoring.constraints.ResidueTypeLinkingConstraint, 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++: core::scoring::constraints::ResidueTypeLinkingConstraint::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.ResidueTypeLinkingConstraint) → int¶: C++: core::scoring::constraints::ResidueTypeLinkingConstraint::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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None¶

Reads the definition of a Constraint from the given std::istream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, 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.core.scoring.constraints.ResidueTypeLinkingConstraint) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::scoring::constraints::ResidueTypeLinkingConstraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, : pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::constraints::ResidueTypeLinkingConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::ResidueTypeLinkingConstraint::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.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.core.scoring.constraints.ResidueTypeLinkingConstraint, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::constraints::ResidueTypeLinkingConstraint::show(class std::basic_ostream<char> &) const –> void

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

Prints the definition of a Constraint to the given std::ostream,: using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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.core.scoring.constraints.Constraint) → str¶

Returns a unique string identified for this constraint. Used in several: places, including the ConstraintIO class.

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

class pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator¶

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

Constraint creator for the SequenceProfileConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator¶: C++: core::scoring::constraints::SequenceProfileConstraintCreator::operator=(const class core::scoring::constraints::SequenceProfileConstraintCreator &) –> class core::scoring::constraints::SequenceProfileConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::SequenceProfileConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator) → str¶: C++: core::scoring::constraints::SequenceProfileConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator¶

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

Mover creator for the SiteConstraint constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator, : pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator¶: C++: core::scoring::constraints::SiteConstraintCreator::operator=(const class core::scoring::constraints::SiteConstraintCreator &) –> class core::scoring::constraints::SiteConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::SiteConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator) → str¶: C++: core::scoring::constraints::SiteConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator¶

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

Mover creator for the SiteConstraintResidues constraint

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator, : pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator) → pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator¶: C++: core::scoring::constraints::SiteConstraintResiduesCreator::operator=(const class core::scoring::constraints::SiteConstraintResiduesCreator &) –> class core::scoring::constraints::SiteConstraintResiduesCreator &

create_constraint(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: core::scoring::constraints::SiteConstraintResiduesCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator) → str¶: C++: core::scoring::constraints::SiteConstraintResiduesCreator::keyname() const –> std::string

pyrosetta.rosetta.core.scoring.constraints.add_constraints_from_cmdline(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

/: add constraints if specified by user.

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

pyrosetta.rosetta.core.scoring.constraints.add_constraints_from_cmdline_to_pose(pose: pyrosetta.rosetta.core.pose.Pose) → None¶

/: add constraints if specified by user.

C++: core::scoring::constraints::add_constraints_from_cmdline_to_pose(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.constraints.add_constraints_from_cmdline_to_scorefxn(scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

/: add constraints if specified by user.

C++: core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.scoring.constraints.add_coordinate_constraints(*args, **kwargs)¶

Overloaded function.

add_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose) -> None
add_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose, coord_sdev: float) -> None
add_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose, coord_sdev: float, include_sc: bool) -> None

handy function for tethering pose to starting coordinates.

C++: core::scoring::constraints::add_coordinate_constraints(class core::pose::Pose &, const double, bool) –> void

add_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int) -> None
add_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int, coord_sdev: float) -> None
add_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int, coord_sdev: float, include_sc: bool) -> None

Add coordinate constraints for starting coordinates, start:end residues, inclusive.

C++: core::scoring::constraints::add_coordinate_constraints(class core::pose::Pose &, const unsigned long, const unsigned long, const double, bool) –> void

pyrosetta.rosetta.core.scoring.constraints.add_fa_constraints_from_cmdline(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

add constraints if specified by user.

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

pyrosetta.rosetta.core.scoring.constraints.add_fa_constraints_from_cmdline_to_pose(pose: pyrosetta.rosetta.core.pose.Pose) → None¶

add constraints if specified by user.

C++: core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.constraints.add_fa_constraints_from_cmdline_to_scorefxn(scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

add constraints if specified by user.

C++: core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.scoring.constraints.choose_effective_sequence_separation(sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, in: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) → None¶

call this on your constraints if you have MultiConstraints before running Abinitio – already done by broker-type application

C++: core::scoring::constraints::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, 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

pyrosetta.rosetta.core.scoring.constraints.combine_constraints(in: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, combine_ratio: int, exclude_res: pyrosetta.rosetta.utility.vector1_bool, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) → None¶

combine constraints randomly into Ambiguous constraints…

C++: core::scoring::constraints::combine_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> > > &, unsigned long, class utility::vector1<bool, class std::allocator<bool> >, const class core::kinematics::ShortestPathInFoldTree &) –> void

pyrosetta.rosetta.core.scoring.constraints.cull_violators(*args, **kwargs)¶

Overloaded function.

cull_violators(target_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, culled_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, filter_pose: pyrosetta.rosetta.core.pose.Pose) -> None
cull_violators(target_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, culled_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, filter_pose: pyrosetta.rosetta.core.pose.Pose, threshold: float) -> None

C++: core::scoring::constraints::cull_violators(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> > > &, 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> > > &, const class core::pose::Pose &, double) –> void

pyrosetta.rosetta.core.scoring.constraints.dexponential(x: float, anchor: float, rate: float, weight: float) → float¶

Returns the weighted value of an Exponential distribution evaluated: with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10.

C++: core::scoring::constraints::dexponential(double, double, double, double) –> double

pyrosetta.rosetta.core.scoring.constraints.dgaussian(x: float, mean: float, sd: float, weight: float) → float¶: C++: core::scoring::constraints::dgaussian(double, double, double, double) –> double

pyrosetta.rosetta.core.scoring.constraints.drop_constraints(in: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, drop_rate: float) → None¶: C++: core::scoring::constraints::drop_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> > > &, double) –> void

pyrosetta.rosetta.core.scoring.constraints.exponential_deriv(x: float, anchor: float, rate: float, weight: float) → float¶

Returns the weighted derivative of an Exponential distribution: evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10.

C++: core::scoring::constraints::exponential_deriv(double, double, double, double) –> double

pyrosetta.rosetta.core.scoring.constraints.gaussian_deriv(x: float, mean: float, sd: float, weight: float) → float¶

Returns the weighted derivative of a Gaussian distribution: evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

C++: core::scoring::constraints::gaussian_deriv(double, double, double, double) –> double

pyrosetta.rosetta.core.scoring.constraints.get_cst_fa_file_option() → str¶

/////// FA constraints (add and replace)

C++: core::scoring::constraints::get_cst_fa_file_option() –> std::string

pyrosetta.rosetta.core.scoring.constraints.get_cst_file_option() → str¶

/////// Centroid constraints (add and replace)

C++: core::scoring::constraints::get_cst_file_option() –> std::string

pyrosetta.rosetta.core.scoring.constraints.linear_interpolate(x_val: float, x1: float, x2: float, y1: float, y2: float) → float¶

Estimates the y-value of the given x-value by interpolating between: the given points (x1,y1) and (x2,y2) by using linear interpolation between the two points.

C++: core::scoring::constraints::linear_interpolate(const double, const double, const double, const double, const double) –> double

pyrosetta.rosetta.core.scoring.constraints.logdgaussian(x: float, mean: float, sd: float, weight: float) → float¶

Returns the log of the weighted value of a Gaussian distribution: evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

C++: core::scoring::constraints::logdgaussian(double, double, double, double) –> double

pyrosetta.rosetta.core.scoring.constraints.logdgaussian_deriv(x: float, mean: float, sd: float, weight: float) → float¶

Returns the log of the weighted value of a Gaussian distribution: evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

C++: core::scoring::constraints::logdgaussian_deriv(double, double, double, double) –> double

pyrosetta.rosetta.core.scoring.constraints.map_constraints_from_original_pose(original_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

map constraints to new atom numbers after, e.g. variants change. requires pose to have same number of residues.

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

pyrosetta.rosetta.core.scoring.constraints.merge_constraints_from_cmdline(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

merge cmdline constraints to pre-existing constraints

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

pyrosetta.rosetta.core.scoring.constraints.merge_constraints_from_cmdline_to_pose(pose: pyrosetta.rosetta.core.pose.Pose) → None¶

merge cmdline constraints to pre-existing constraints

C++: core::scoring::constraints::merge_constraints_from_cmdline_to_pose(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.constraints.merge_constraints_from_cmdline_to_scorefxn(scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued

C++: core::scoring::constraints::merge_constraints_from_cmdline_to_scorefxn(class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.scoring.constraints.merge_fa_constraints_from_cmdline(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

merge cmdline constraints to pre-existing constraints

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

pyrosetta.rosetta.core.scoring.constraints.merge_fa_constraints_from_cmdline_to_pose(pose: pyrosetta.rosetta.core.pose.Pose) → None¶

/////// FA constraints (merge mode)

C++: core::scoring::constraints::merge_fa_constraints_from_cmdline_to_pose(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.constraints.merge_fa_constraints_from_cmdline_to_scorefxn(scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued

C++: core::scoring::constraints::merge_fa_constraints_from_cmdline_to_scorefxn(class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.scoring.constraints.parse_NMR_name(name: str, res: int, aa: pyrosetta.rosetta.core.chemical.AA, : pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) → None¶: C++: core::scoring::constraints::parse_NMR_name(class std::basic_string<char>, unsigned long, enum core::chemical::AA, class utility::vector1<class core::id::NamedAtomID, class std::allocator<class core::id::NamedAtomID> > &) –> void

pyrosetta.rosetta.core.scoring.constraints.print_atom_pair_constraints(*args, **kwargs)¶

Overloaded function.

print_atom_pair_constraints(pose: pyrosetta.rosetta.core.pose.Pose) -> None
print_atom_pair_constraints(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) -> None

example of how to go through a pose constraint set and print out stuff.

C++: core::scoring::constraints::print_atom_pair_constraints(const class core::pose::Pose &, class std::basic_ostream<char> &) –> void

pyrosetta.rosetta.core.scoring.constraints.remove_constraints_of_type(*args, **kwargs)¶

Overloaded function.

remove_constraints_of_type(pose: pyrosetta.rosetta.core.pose.Pose, type: str) -> None

Remove all constraints of a given type from a pose.

C++: core::scoring::constraints::remove_constraints_of_type(class core::pose::Pose &, const class std::basic_string<char> &) –> void

remove_constraints_of_type(pose: pyrosetta.rosetta.core.pose.Pose, type: str, start_res: int, end_res: int) -> None

Remove all constraints of a given type from a pose that involve start_res to end_res. Useful for coordinate/dihedral constraints

C++: core::scoring::constraints::remove_constraints_of_type(class core::pose::Pose &, const class std::basic_string<char> &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.core.scoring.constraints.remove_nonbb_constraints(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::constraints::remove_nonbb_constraints(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.constraints.skip_redundant_constraints(*args, **kwargs)¶

Overloaded function.

skip_redundant_constraints(in: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, total_residue: int) -> None
skip_redundant_constraints(in: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, total_residue: int, influence_width: int) -> None

have at most one constraint per residue pair…

C++: core::scoring::constraints::skip_redundant_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> > > &, unsigned long, unsigned long) –> void