mhc_epitope_energy¶

Bindings for core::scoring::mhc_epitope_energy namespace

class pyrosetta.rosetta.core.scoring.mhc_epitope_energy.AlleleMatrix¶

Bases: pybind11_object

The scoring matrix for one specific allele

A position weight matrix (PWM) specifies the value for each amino acid type. A set of threshold specify the minimum score required to be in the top percentile of predicted binders.

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

is_hit(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.AlleleMatrix, pep: str, thresh: float) → bool¶

Predicts whether the peptide will bind the MHC allele, with respect to the threshold for binding strength / likelihood

C++: core::scoring::mhc_epitope_energy::AlleleMatrix::is_hit(const std::string &, double) –> bool

class pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint¶

Bases: 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.mhc_epitope_energy.MHCEpitopeConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶

Clone operator

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::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_cst_weight(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint) → float¶

Get the cst_weight_

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::get_cst_weight() 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_selector_name(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint) → str¶

Returns the name of the selector used to mask the constraint.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::get_selector_name() –> std::string

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

Initialize the MHCEpitopeEnergySetup object from a file.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::initialize_from_file(const std::string &) –> void

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

Initialize the MHCEpitopeEnergySetup 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::mhc_epitope_energy::MHCEpitopeConstraint::initialize_from_file_contents(const std::string &) –> void

mhc_epitope_energy_setup(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint) → pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup¶

Const access to the MHCEpitopeEnergySetup object.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::mhc_epitope_energy_setup() const –> class std::shared_ptr<const class core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup>

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.mhc_epitope_energy.MHCEpitopeConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::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.mhc_epitope_energy.MHCEpitopeConstraint) → 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::mhc_epitope_energy::MHCEpitopeConstraint::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_cst_weight(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint, cst_weight: float) → None¶

Set the cst_weight_

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::set_cst_weight(double) –> void

set_selector(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint, 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::mhc_epitope_energy::MHCEpitopeConstraint::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_selector_name(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint, selector_name: str) → None¶

Stores the name of the selector used to mask the constraint.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::set_selector_name(const std::string &) –> 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.mhc_epitope_energy.MHCEpitopeConstraint, TO: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Print info on the constraint

C++: core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::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.mhc_epitope_energy.MHCEpitopeEnergySetup¶

Bases: pybind11_object

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

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

clone(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup¶

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

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::clone() const –> class std::shared_ptr<class core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup>

get_apply_offset(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → bool¶

Return whether to apply an offset to the score.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_apply_offset() const –> bool

get_overhang_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → int¶

If the peptide has a core peptide plus overhangs, how many residues are in the overhangs (on both the N- and C-terminus)?

For example, if we have a total peptide length of 15, with a core of 9 residues and overhangs of 3 residues on both sides, peptide_length_ should be 15 and overhang_length should be 3.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_overhang_length() const –> unsigned long

get_peptide_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → int¶

How long are the peptides to be predicted?

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_peptide_length() const –> unsigned long

get_predictor(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor¶

Getter for predictor_ (MHCEpitopePredictorOP)

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_predictor() const –> class std::shared_ptr<class core::scoring::mhc_epitope_energy::MHCEpitopePredictor>

get_relative(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → bool¶

Return whether using relative or absolute scoring.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_relative() const –> bool

get_relative_additive(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → bool¶

Return whether the relative score is in additive (true) or multiplicative (false) mode

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_relative_additive() const –> bool

get_score_offset(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → float¶

Return the score_offset_ value

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_score_offset() const –> double

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

Initialize from a .mhc file.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file(const std::string &) –> void

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

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

Allows external code to initialize object without having it read directly from disk. Note however that the specs in the file may require subsequent disk reads depending on the type of predictor indicated.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file_contents(const std::string &) –> void

is_default(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → bool¶

Is is just the default, always-zero, predictor?

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::is_default() const –> bool

raw_score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup, peptide: str) → float¶

The MHC epitope score for the peptide, as returned by the predictor

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::raw_score(std::string) const –> double

report(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → str¶

Get a summary of the data stored in this object

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::report() const –> std::string

reset(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup) → None¶

Reset all data in this data storage object.

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::reset() –> void

score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup, peptide: str, native: float) → float¶

The xformed MHC epitope score, in a single step

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::score(std::string, double) const –> double

xform(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup, : float, : float) → float¶

Transform the MHC epitope score, as specified for this helper

C++: core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::xform(double, double) const –> double

class pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor¶

Bases: pybind11_object

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

get_overhang_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_overhang_length() const –> unsigned long

get_peptide_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶

The length required by this predictor for peptides

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length() const –> unsigned long

provide_citation_info(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

The default Predictor does not add citation info. Derived classes can add specific citation information, which will be automatically during setup by MHCEpitopeEnergySetup.

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

report(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → str¶

Get a summary of the data stored in this object

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::report() const –> std::string

score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor, : str) → float¶

The MHC epitope score, predicting “immunogenicity” of the peptide (lower is lower risk, with 0 being none)

The peptide must be of the length specified for this predictor (get_peptide_length()))

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::score(const std::string &) –> double

class pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal¶

Bases: MHCEpitopePredictor

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

connect(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal, db_filename: str) → None¶

Establishes the connection to the sqlite database and gets the meta information about the predictor

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::connect(const std::string &) –> void

get_database(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal) → pyrosetta.rosetta.utility.sql_database.session¶

Return the sqlite database connection pointer

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::get_database() –> class std::shared_ptr<class utility::sql_database::session>

get_overhang_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_overhang_length() const –> unsigned long

get_peptide_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶

The length required by this predictor for peptides

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length() const –> unsigned long

get_unseen_score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal) → int¶

Accessor for the unseen_score_

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::get_unseen_score() –> unsigned long

provide_citation_info(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

The default Predictor does not add citation info. Derived classes can add specific citation information, which will be automatically during setup by MHCEpitopeEnergySetup.

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

report(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal) → str¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::report() const –> std::string

score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal, pep: str) → float¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::score(const std::string &) –> double

set_unseen_score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal, u: int) → None¶

Sets the score for a peptide not in the database

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::set_unseen_score(unsigned long) –> void

class pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix¶

Bases: MHCEpitopePredictor

An predictor based on a set of allele-specific profiles of which peptides are likely to be binders

Each allele’s binding is predicted separately, thresholded with respect to the top % of binders, and the score is then the number of predicted binding events

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

get_overhang_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_overhang_length() const –> unsigned long

get_peptide_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶

The length required by this predictor for peptides

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length() const –> unsigned long

get_thresh(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix) → float¶

Gets the threshold for what is considered to be an epitope – top thresh% of peptides in this implementation

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::get_thresh() –> double

load_matrix(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix, filename: str) → None¶

Loads the matrices from the file

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(const std::string &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations for ProPred.

If ProPred is being used, add the appropriate citation information

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

report(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix) → str¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::report() const –> std::string

score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix, pep: str) → float¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::score(const std::string &) –> double

set_thresh(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix, thresh: float) → None¶

Sets the threshold for what is considered to be an epitope – top thresh% of peptides in this implementation

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::set_thresh(double) –> void

class pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded¶

Bases: MHCEpitopePredictor

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

static check_file_size(filename: str, warn_threshold: int) → None¶

Check for the size of a file and print a warning if appropriate.

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::check_file_size(const std::string &, const unsigned long) –> void

get_overhang_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_overhang_length() const –> unsigned long

get_peptide_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶

The length required by this predictor for peptides

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length() const –> unsigned long

get_scores_map(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded) → pyrosetta.rosetta.std.map_std_string_double¶

Accessor for the peptide->score map object

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::get_scores_map() const –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

get_unseen_score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded) → int¶

Accessor for the unseen_score_

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::get_unseen_score() const –> unsigned long

load_csv(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded, filename: str) → None¶

Initializes from a csv file with header, such that the first column is the peptide and the second column the score; other columns ignored

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::load_csv(const std::string &) –> void

load_database(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded, filename: str) → None¶

Initializes from an sqlite database

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::load_database(const std::string &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations for IEDB.

If IEDB is being used, add the appropriate citation information

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

report(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded) → str¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::report() const –> std::string

score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded, pep: str) → float¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::score(const std::string &) –> double

set_unseen_score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded, us: int) → None¶

Sets the score for a peptide not in the map

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::set_unseen_score(unsigned long) –> void

class pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM¶

Bases: MHCEpitopePredictor

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

get_overhang_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_overhang_length() const –> unsigned long

get_peptide_length(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor) → int¶

The length required by this predictor for peptides

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length() const –> unsigned long

get_svm(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM) → core::scoring::methods::NMerSVMEnergy¶

Accessor for the svm_ (NMerSVMEnergy object) being used by the Predictor for scoring.

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::get_svm() const –> class std::shared_ptr<class core::scoring::methods::NMerSVMEnergy>

provide_citation_info(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations for NMer.

Add the appropriate citation information to the CitationManager

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

report(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM) → str¶: C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::report() const –> std::string

score(self: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM, pep: str) → float¶

Scores a peptide

C++: core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::score(const std::string &) –> double