aa_composition_energy¶

Bindings for core::scoring::aa_composition_energy namespace

class pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint¶

Bases: SequenceConstraint

aa_composition_energy_setup(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup¶

Const access to the AACompositionEnergySetup object.

C++: core::scoring::aa_composition_energy::AACompositionConstraint::aa_composition_energy_setup() const –> class std::shared_ptr<const class core::scoring::aa_composition_energy::AACompositionEnergySetup>

atom(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : int) → pyrosetta.rosetta.core.id.AtomID¶

Implemented because the base class requires it; not used by a sequence constraint.

Always returns AtomID(0,0).

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

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) → int¶: C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶

Clone operator

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

dist(*args, **kwargs)¶

Overloaded function.

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

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::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.aa_composition_energy.SequenceConstraint, : pyrosetta.rosetta.core.id.AtomID, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) → None¶

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::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 &

initialize_from_file(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, filename: str) → None¶

Initialize the AACompositionEnergySetup object from a file.

C++: core::scoring::aa_composition_energy::AACompositionConstraint::initialize_from_file(const std::string &) –> void

initialize_from_file_contents(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, filecontents: str) → None¶

Initialize the AACompositionEnergySetup object from the contents of a file.

Allows external code to initialize a constriant object without having the object read directly from disk.

C++: core::scoring::aa_composition_energy::AACompositionConstraint::initialize_from_file_contents(const std::string &) –> void

natoms(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint) → int¶

Implemented because the base class requires it; not used by a sequence constraint.

Always returns zero.

C++: core::scoring::aa_composition_energy::SequenceConstraint::natoms() const –> unsigned long

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

This method is totally redundant with read_def YAY: DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

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

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) → None¶

initialize this Constraint from the given std::istream. It’s amazing: that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

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

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

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

apply a resid remapping to this constraint, returns the remapped: constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

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

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

Copies the data from this Constraint into a new object and returns: an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

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

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

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

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::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 &

selector(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Const access to the selector.

Returns a null pointer if no selector has been specified.

C++: core::scoring::aa_composition_energy::AACompositionConstraint::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_selector(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the selector to be used by this constraint.

Clones the input.

C++: core::scoring::aa_composition_energy::AACompositionConstraint::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

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

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

show(self: pyrosetta.rosetta.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(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, TO: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Print info on the constraint

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

show_violations(*args, **kwargs)¶

Overloaded function.

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

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

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

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

take coordinates, distances, angles, etc from given pose

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

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

Convenience function, returns the results of show() as a string.: Not to be overriden by derived classes.

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

type(self: pyrosetta.rosetta.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.aa_composition_energy.AACompositionEnergySetup¶

Bases: pybind11_object

AACompositionEnergySetup, a helper class for the AACompositionEnergy energy method that stores all of its setup data.

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

clone(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup¶

Clone: create a copy of this object, and return an owning pointer: to the copy.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::clone() const –> class std::shared_ptr<class core::scoring::aa_composition_energy::AACompositionEnergySetup>

expected_by_properties_absolute(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index: int) → int¶

Get the expected absolute number of residues for a given set of properties, by property set index.

Warning! For speed, there’s no check that the index is in range!

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_absolute(const unsigned long) const –> long

expected_by_properties_fraction(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index: int) → float¶

Get the expected fractional number of residues for a given set of properties, by property set index.

Warning! For speed, there’s no check that the index is in range!

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_fraction(const unsigned long) const –> double

fract_property_penalty(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, delta_fract: float, property_set_index: int) → float¶

Look up the penalty for a property set of internal index property_set_index, given a fractional content given by fract.

This version is for fractional property penalties.

The measured fractional content of amino acids matching this property set in the pose or pose subset minus the expected.

The index of this property set.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::fract_property_penalty(const double, const unsigned long) const –> double

get_tailfunction_from_name(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, name: str) → pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction¶

Get tail function enum from name.

This is slow; it calls get_tailfunction_name repeatedly. Intended only for use during setup.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::get_tailfunction_from_name(const std::string &) const –> enum core::scoring::aa_composition_energy::TailFunction

get_tailfunction_name(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, tf: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) → str¶

Get tail function name from enum.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::get_tailfunction_name(const enum core::scoring::aa_composition_energy::TailFunction) const –> std::string

initialize_from_file(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, filename: str) → None¶

Initialize from a .comp file.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file(const std::string &) –> void

initialize_from_file_contents(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, filecontents: str) → None¶

Initialize from a string in the format of a .comp file.

Allows external code to initialize object without having it read directly from disk.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file_contents(const std::string &) –> void

n_property_sets(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → int¶

Get the number of sets of properties that we’ll be counting.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::n_property_sets() const –> unsigned long

property_penalty(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, delta_expected: int, property_set_index: int) → float¶

Look up the penalty for a property set of internal index property_set_index, given a deviation from: the desired count given by delta_expected.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::property_penalty(const long, const unsigned long) const –> double

property_set_indices_matching_residue(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, indices_out: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Get the indices of all of the property sets corresponding to the current residue.

Returns empty vector if none of the property sets that we’re counting corresponds to the current residue.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::property_set_indices_matching_residue(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

report(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → str¶

Get a summary of the data stored in this object

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::report() const –> std::string

reset(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → None¶

Reset all data in this data storage object.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::reset() –> void

use_fract_expected_values_any(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → bool¶

Determine whether ANY of the property sets of this helper object use fractional expected values.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_expected_values_any() const –> bool

use_fract_ranges(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index: int) → bool¶

Look up whether we’re using absolute (return false) or fractional (return true) penalty ranges.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_ranges(const unsigned long) const –> bool

use_fract_ranges_any(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → bool¶

Determine whether ANY of the property sets of this helper object use fractional ranges.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_ranges_any() const –> bool

class pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet¶

Bases: pybind11_object

AACompositionPropertiesSet, a helper class that stores: - names of residue types that WILL be counted (TYPE) - names of residue types that WILL NOT be counted (NOT_TYPE) - properties that MUST be present in order for a residue to be counted (PROPERTIES). - properties, any of which is sufficient for a residue to be counted (OR_PROPERTIES). - properties that MUST NOT be present in order for a residue to be counted (NOT_PROPERTIES).

The logic is as follows: a residue is counted if and only if [any TYPE matches] OR [ (no NOT_TYPE matches) AND ( {all PROPERTIES match} OR {any OR_PROPERTIES match} OR {no TYPEs defined AND no PROPERTIES defined AND no OR_PROPERTIES defined } ) AND ( no NOT_PROPERTIES match) ]

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

clone(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet¶

Clone: create a copy of this object, and return an owning pointer: to the copy.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::clone() const –> class std::shared_ptr<class core::scoring::aa_composition_energy::AACompositionPropertiesSet>

one_line_report(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) → str¶

Generate a one-line summary of the properties stored in this AACompositionPropertySet

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::one_line_report() const –> std::string

parse_excluded_properites(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Take a list of excluded property strings and parse it.

Populates the excluded_properties_ vector based on the properties named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_excluded_properites(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

parse_excluded_types(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, typelist: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Take a list of excluded type strings and add it to the list of excluded types, checking that

none of the types has already been added.

Populates the excluded_types_ vector based on the types named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_excluded_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

parse_included_properites(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Take a list of included property strings and parse it.

Populates the included_properties_ vector based on the properties named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_included_properites(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

parse_included_types(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, typelist: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Take a list of included type strings and add it to the list of included types, checking that

none of the types has already been added.

Populates the included_types_ vector based on the types named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_included_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

parse_or_properties(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Take a list of included property strings and parse it.

Populates the included_properties_ vector based on the properties named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_or_properties(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

properties_match_this(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Check whether the properties of a residue type match those of this set.

This checks: 1. Whether the residue name matches an exlcuded name -> return false. 2. Whether the residue name matches an included name -> return true. 3. Whether the residue properties match an excluded property -> return false. 4. Whether all three of the included_types and or_properties and included_property lists are empty -> return true. 5. Whether any or_property is matched -> return true. 6. Whether there exist any proprties to match -> if not, return false. 7. Whether any properties are not matched -> return false. Returns true

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::properties_match_this(const class core::chemical::ResidueType &) const –> bool

class pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint¶

Bases: Constraint

atom(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : int) → pyrosetta.rosetta.core.id.AtomID¶

Implemented because the base class requires it; not used by a sequence constraint.

Always returns AtomID(0,0).

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

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) → int¶: C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(*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.aa_composition_energy.SequenceConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
dist(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func) -> float

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::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.aa_composition_energy.SequenceConstraint, : pyrosetta.rosetta.core.id.AtomID, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) → None¶

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::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.aa_composition_energy.SequenceConstraint) → int¶

Implemented because the base class requires it; not used by a sequence constraint.

Always returns zero.

C++: core::scoring::aa_composition_energy::SequenceConstraint::natoms() const –> unsigned long

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

This method is totally redundant with read_def YAY: DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

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

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) → None¶

initialize this Constraint from the given std::istream. It’s amazing: that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

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

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

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

apply a resid remapping to this constraint, returns the remapped: constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

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

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

Copies the data from this Constraint into a new object and returns: an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

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

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

same_type_as_me(self: pyrosetta.rosetta.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.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::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.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(std::ostream &) 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(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

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

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

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

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

take coordinates, distances, angles, etc from given pose

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

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

Convenience function, returns the results of show() as a string.: Not to be overriden by derived classes.

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

type(self: pyrosetta.rosetta.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.aa_composition_energy.TailFunction¶

Bases: pybind11_object

The different types of behaviour for the penalty values past the defined range.

When values are added to this enum, they should also be added to the AACompositionEnergySetup::get_tailfunction_name() function.

Members:

tf_linear

tf_quadratic

tf_constant

tf_unknown

tf_end_of_list

property name¶

tf_constant = <TailFunction.tf_constant: 3>¶

tf_end_of_list = <TailFunction.tf_unknown: 4>¶

tf_linear = <TailFunction.tf_linear: 1>¶

tf_quadratic = <TailFunction.tf_quadratic: 2>¶

tf_unknown = <TailFunction.tf_unknown: 4>¶

property value¶