mhc_epitope_energy

Bindings for core::scoring::mhc_epitope_energy namespace

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

Bases: pybind11_builtins.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: 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.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.

  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_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.

  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.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.

  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.mhc_epitope_energy.MHCEpitopeEnergySetup

Bases: pybind11_builtins.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_builtins.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: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.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: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.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: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.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: pyrosetta.rosetta.core.scoring.mhc_epitope_energy.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