netcharge_energy

Bindings for core::scoring::netcharge_energy namespace

class pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint

Bases: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint

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.netcharge_energy.NetChargeConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

Clone operator

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

dist(*args, **kwargs)

Overloaded function.

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

  2. 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.netcharge_energy.NetChargeConstraint, filename: str) None

Initialize the NetChargeEnergySetup object from a file.

C++: core::scoring::netcharge_energy::NetChargeConstraint::initialize_from_file(const std::string &) –> void

initialize_from_file_contents(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint, filecontents: str) None

Initialize the NetChargeEnergySetup 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::netcharge_energy::NetChargeConstraint::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

netcharge_energy_setup(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint) pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup

Const access to the NetChargeEnergySetup object.

C++: core::scoring::netcharge_energy::NetChargeConstraint::netcharge_energy_setup() const –> class std::shared_ptr<const class core::scoring::netcharge_energy::NetChargeEnergySetup>

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.netcharge_energy.NetChargeConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

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

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

  2. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

  3. 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.netcharge_energy.NetChargeConstraint) 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::netcharge_energy::NetChargeConstraint::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_selector(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint, 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::netcharge_energy::NetChargeConstraint::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.netcharge_energy.NetChargeConstraint, TO: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

Print info on the constraint

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

show_violations(*args, **kwargs)

Overloaded function.

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

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

Prints the violations of this constraint to the given

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

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

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

take coordinates, distances, angles, etc from given pose

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

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

Not to be overriden by derived classes.

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

type(self: pyrosetta.rosetta.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.netcharge_energy.NetChargeEnergySetup

Bases: pybind11_builtins.pybind11_object

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

assign(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup, : pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup) pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::operator=(const class core::scoring::netcharge_energy::NetChargeEnergySetup &) –> class core::scoring::netcharge_energy::NetChargeEnergySetup &

clone(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup) pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup
Clone: create a copy of this object, and return an owning pointer

to the copy.

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::clone() const –> class std::shared_ptr<class core::scoring::netcharge_energy::NetChargeEnergySetup>

desired_charge(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup) int

Get the desired charge.

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::desired_charge() const –> unsigned long

get_tailfunction_from_name(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup, name: str) pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction

Get tail function enum from name.

This is slow; it calls get_tailfunction_name repeatedly. Intended only for use during setup. Returns tf_unknown if tail function couldn’t be parsed.

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

get_tailfunction_name(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup, tf: pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction) str

Get tail function name from enum.

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::get_tailfunction_name(const enum core::scoring::netcharge_energy::TailFunction) const –> std::string

initialize_from_file(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup, filename: str) None

Initialize from a .charge file.

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::initialize_from_file(const std::string &) –> void

initialize_from_file_contents(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup, filecontents: str) None

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

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

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::initialize_from_file_contents(const std::string &) –> void

penalty(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup, observed: int) float

Look up the penalty given the net charge observed.

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::penalty(const long) const –> double

report(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup) str

Get a summary of the data stored in this object

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::report() const –> std::string

reset(self: pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup) None

Reset all data in this data storage object.

C++: core::scoring::netcharge_energy::NetChargeEnergySetup::reset() –> void

class pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction

Bases: pybind11_builtins.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 NetChargeEnergySetup::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>