noesy_assign¶

Bindings for protocols::noesy_assign namespace

class pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶

Bases: pybind11_object

Members:

BACKBONE

BETA_NON_METHYL

METHYL

SIDECHAIN

MAX_TYPE

BACKBONE = <CALIBRATION_ATOM_TYPE.BACKBONE: 1>¶

BETA_NON_METHYL = <CALIBRATION_ATOM_TYPE.BETA_NON_METHYL: 2>¶

MAX_TYPE = <CALIBRATION_ATOM_TYPE.MAX_TYPE: 5>¶

METHYL = <CALIBRATION_ATOM_TYPE.METHYL: 3>¶

SIDECHAIN = <CALIBRATION_ATOM_TYPE.SIDECHAIN: 4>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance¶

Bases: SingletonBase_protocols_noesy_assign_CovalentCompliance_t

WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST JOB-SPECIFIC DATA AND MAKES EVERYTHING THAT RELIES ON IT THREAD-UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED.

distance(self: pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance, atom1: pyrosetta.rosetta.core.id.NamedAtomID, atom2: pyrosetta.rosetta.core.id.NamedAtomID) → float¶: C++: protocols::noesy_assign::CovalentCompliance::distance(const class core::id::NamedAtomID &, const class core::id::NamedAtomID &) const –> double

static get_instance() → protocols::noesy_assign::CovalentCompliance¶: C++: utility::SingletonBase<protocols::noesy_assign::CovalentCompliance>::get_instance() –> class protocols::noesy_assign::CovalentCompliance *

is_compliant(*args, **kwargs)¶

Overloaded function.

is_compliant(self: pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance, atom1: pyrosetta.rosetta.core.id.NamedAtomID, atom2: pyrosetta.rosetta.core.id.NamedAtomID) -> bool
is_compliant(self: pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance, atom1: pyrosetta.rosetta.core.id.NamedAtomID, atom2: pyrosetta.rosetta.core.id.NamedAtomID, cutoff: float) -> bool

C++: protocols::noesy_assign::CovalentCompliance::is_compliant(const class core::id::NamedAtomID &, const class core::id::NamedAtomID &, double) const –> bool

load_dist_table(self: pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance, file: str) → None¶

This is clearly thread-unsafe.

C++: protocols::noesy_assign::CovalentCompliance::load_dist_table(const std::string &) –> void

class pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶

Bases: pybind11_object

BAD_LOW_PROB = <QualityClass.BAD_LOW_PROB: 5>¶

EL_DISTVIOL = <EliminationReason.EL_DISTVIOL: 1>¶

EL_MAXASSIGN = <EliminationReason.EL_MAXASSIGN: 4>¶

EL_MINPEAKVOL = <EliminationReason.EL_MINPEAKVOL: 3>¶

EL_NETWORK = <EliminationReason.EL_NETWORK: 2>¶

class EliminationReason¶

Bases: pybind11_object

Members:

NOT_ELIMINATED

EL_DISTVIOL

EL_NETWORK

EL_MINPEAKVOL

EL_MAXASSIGN

EL_DISTVIOL = <EliminationReason.EL_DISTVIOL: 1>¶

EL_MAXASSIGN = <EliminationReason.EL_MAXASSIGN: 4>¶

EL_MINPEAKVOL = <EliminationReason.EL_MINPEAKVOL: 3>¶

EL_NETWORK = <EliminationReason.EL_NETWORK: 2>¶

NOT_ELIMINATED = <EliminationReason.NOT_ELIMINATED: 0>¶

property name¶

property value¶

HI_AMBIG = <QualityClass.HI_AMBIG: 2>¶

HI_NEAR_UNAMBIG = <QualityClass.HI_NEAR_UNAMBIG: 1>¶

HI_UNAMBIG = <QualityClass.HI_UNAMBIG: 0>¶

MAX_CLASS = <QualityClass.MAX_CLASS: 6>¶

MED_AMBIG = <QualityClass.MED_AMBIG: 3>¶

NOT_ELIMINATED = <EliminationReason.NOT_ELIMINATED: 0>¶

class QualityClass¶

Bases: pybind11_object

Members:

HI_UNAMBIG

HI_NEAR_UNAMBIG

HI_AMBIG

MED_AMBIG

UNAMBIG_MED_PROB

BAD_LOW_PROB

MAX_CLASS

BAD_LOW_PROB = <QualityClass.BAD_LOW_PROB: 5>¶

HI_AMBIG = <QualityClass.HI_AMBIG: 2>¶

HI_NEAR_UNAMBIG = <QualityClass.HI_NEAR_UNAMBIG: 1>¶

HI_UNAMBIG = <QualityClass.HI_UNAMBIG: 0>¶

MAX_CLASS = <QualityClass.MAX_CLASS: 6>¶

MED_AMBIG = <QualityClass.MED_AMBIG: 3>¶

UNAMBIG_MED_PROB = <QualityClass.UNAMBIG_MED_PROB: 4>¶

property name¶

property value¶

class Spin¶

Bases: pybind11_object

a single dimension of a multidimensional peak, stores putative assignments as indices into Resonance table

add_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, assignment: int) → None¶

add index-pointer into Resonance table to assign peak to putative spin

C++: protocols::noesy_assign::CrossPeak::Spin::add_assignment(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin¶: C++: protocols::noesy_assign::CrossPeak::Spin::operator=(const class protocols::noesy_assign::CrossPeak::Spin &) –> class protocols::noesy_assign::CrossPeak::Spin &

assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, nr: int) → int¶

return index-pointer into Resonance table

C++: protocols::noesy_assign::CrossPeak::Spin::assignment(unsigned long) const –> unsigned long

assignment_index(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, assignment: int) → int¶: C++: protocols::noesy_assign::CrossPeak::Spin::assignment_index(unsigned long) const –> unsigned long

freq(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → float¶

resonance frequency of peak

C++: protocols::noesy_assign::CrossPeak::Spin::freq() const –> double

n_assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → int¶: C++: protocols::noesy_assign::CrossPeak::Spin::n_assigned() const –> unsigned long

set_freq(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, freq: float) → None¶: C++: protocols::noesy_assign::CrossPeak::Spin::set_freq(double) –> void

UNAMBIG_MED_PROB = <QualityClass.UNAMBIG_MED_PROB: 4>¶

ambiguous(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::ambiguous() const –> bool

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::CrossPeak::operator=(const class protocols::noesy_assign::CrossPeak &) –> class protocols::noesy_assign::CrossPeak &

assign_spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, spin_id: int) → None¶: C++: protocols::noesy_assign::CrossPeak::assign_spin(unsigned long) –> void

assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::assigned() const –> bool

assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t¶: C++: protocols::noesy_assign::CrossPeak::assignments() const –> const class utility::vector1<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment>, class std::allocator<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment> > > &

create_fa_and_cen_constraint(*args, **kwargs)¶

Overloaded function.

create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int) -> None
create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int, padding: float) -> None
create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int, padding: float, fa_only: bool) -> None

C++: protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(class std::shared_ptr<class core::scoring::constraints::Constraint> &, class std::shared_ptr<class core::scoring::constraints::Constraint> &, const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, double, bool) const –> void

cumulative_peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the cumulative cyana-type weights for all assignments Vk

C++: protocols::noesy_assign::CrossPeak::cumulative_peak_volume() const –> double

dimension(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::dimension() const –> unsigned long

distance_bound(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::distance_bound() const –> double

eliminated(*args, **kwargs)¶

Overloaded function.

eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) -> bool
eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, recompute: bool) -> bool
eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, recompute: bool, do_not_compute: bool) -> bool

returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227: do_not_compute … for outputter that does not want to change state…

C++: protocols::noesy_assign::CrossPeak::eliminated(bool, bool) const –> bool

elimination_reason(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::elimination_reason() const –> std::string

empty_clone(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::CrossPeak::empty_clone() –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

exp_hash(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::exp_hash() const –> unsigned long

filename(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::filename() const –> const std::string &

find_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::CrossPeak::find_assignments() –> void

fold_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, freq: float, i: int) → float¶: C++: protocols::noesy_assign::CrossPeak::fold_resonance(double, unsigned long) –> double

folder(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → pyrosetta.rosetta.protocols.noesy_assign.FoldResonance¶: C++: protocols::noesy_assign::CrossPeak::folder(unsigned long) –> const class protocols::noesy_assign::FoldResonance &

has_label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : int) → bool¶: C++: protocols::noesy_assign::CrossPeak::has_label(unsigned long) const –> bool

has_proton(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : int) → bool¶: C++: protocols::noesy_assign::CrossPeak::has_proton(unsigned long) const –> bool

info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo¶: C++: protocols::noesy_assign::CrossPeak::info(unsigned long) const –> const class protocols::noesy_assign::CrossPeakInfo &

is4D(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::is4D() const –> bool

is_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::is_elimination_candidate() –> bool

label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : int) → protocols::noesy_assign::CrossPeak::Spin¶: C++: protocols::noesy_assign::CrossPeak::label(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

max_volume_contribution(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the largest volume contribution (normalized) any of the assignments has

C++: protocols::noesy_assign::CrossPeak::max_volume_contribution() const –> double

min_seq_separation_residue_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, volume_threshold: float) → int¶: C++: protocols::noesy_assign::CrossPeak::min_seq_separation_residue_assignment(double) const –> unsigned long

n_Vmin_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶

number of assignments with peak volume higher than params.min_volume_

C++: protocols::noesy_assign::CrossPeak::n_Vmin_assignments() –> unsigned long

n_assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::n_assigned() const –> unsigned long

nudge_distance_bound(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, offset: float) → None¶: C++: protocols::noesy_assign::CrossPeak::nudge_distance_bound(double) –> void

peak_id(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::peak_id() const –> unsigned long

print_peak_info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::CrossPeak::print_peak_info(std::ostream &) const –> void

probability(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::probability() const –> double

proton(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → protocols::noesy_assign::CrossPeak::Spin¶: C++: protocols::noesy_assign::CrossPeak::proton(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

quality_class(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass¶: C++: protocols::noesy_assign::CrossPeak::quality_class() const –> enum protocols::noesy_assign::CrossPeak::QualityClass

quality_class_str(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::quality_class_str() const –> std::string

resonances(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → protocols::noesy_assign::ResonanceList¶: C++: protocols::noesy_assign::CrossPeak::resonances() const –> const class protocols::noesy_assign::ResonanceList &

same_peak(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, other: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::same_peak(const class protocols::noesy_assign::CrossPeak &) const –> bool

set_cumulative_peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: float) → None¶: C++: protocols::noesy_assign::CrossPeak::set_cumulative_peak_volume(double) –> void

set_eliminated_due_to_dist_violations(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: bool) → None¶: C++: protocols::noesy_assign::CrossPeak::set_eliminated_due_to_dist_violations(bool) –> void

set_elimination_candidate(*args, **kwargs)¶

Overloaded function.

set_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) -> None
set_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: bool) -> None

C++: protocols::noesy_assign::CrossPeak::set_elimination_candidate(bool) –> void

set_elimination_comment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, str: str) → None¶: C++: protocols::noesy_assign::CrossPeak::set_elimination_comment(const std::string &) –> void

set_info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int, info: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → None¶: C++: protocols::noesy_assign::CrossPeak::set_info(unsigned long, class std::shared_ptr<const class protocols::noesy_assign::CrossPeakInfo>) –> void

set_peak_id(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, val: int) → None¶: C++: protocols::noesy_assign::CrossPeak::set_peak_id(unsigned long) –> void

set_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, res_in: protocols::noesy_assign::ResonanceList) → None¶: C++: protocols::noesy_assign::CrossPeak::set_resonances(class std::shared_ptr<class protocols::noesy_assign::ResonanceList>) –> void

set_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, val: float) → None¶: C++: protocols::noesy_assign::CrossPeak::set_volume(double) –> void

smallest_native_violation(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::smallest_native_violation() const –> double

spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → protocols::noesy_assign::CrossPeak::Spin¶: C++: protocols::noesy_assign::CrossPeak::spin(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, d: int) → float¶: C++: protocols::noesy_assign::CrossPeak::tolerance(unsigned long) –> double

volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the measured integral of the peak

C++: protocols::noesy_assign::CrossPeak::volume() const –> double

class pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D¶

Bases: CrossPeak

BAD_LOW_PROB = <QualityClass.BAD_LOW_PROB: 5>¶

EL_DISTVIOL = <EliminationReason.EL_DISTVIOL: 1>¶

EL_MAXASSIGN = <EliminationReason.EL_MAXASSIGN: 4>¶

EL_MINPEAKVOL = <EliminationReason.EL_MINPEAKVOL: 3>¶

EL_NETWORK = <EliminationReason.EL_NETWORK: 2>¶

class EliminationReason¶

Bases: pybind11_object

Members:

NOT_ELIMINATED

EL_DISTVIOL

EL_NETWORK

EL_MINPEAKVOL

EL_MAXASSIGN

EL_DISTVIOL = <EliminationReason.EL_DISTVIOL: 1>¶

EL_MAXASSIGN = <EliminationReason.EL_MAXASSIGN: 4>¶

EL_MINPEAKVOL = <EliminationReason.EL_MINPEAKVOL: 3>¶

EL_NETWORK = <EliminationReason.EL_NETWORK: 2>¶

NOT_ELIMINATED = <EliminationReason.NOT_ELIMINATED: 0>¶

property name¶

property value¶

HI_AMBIG = <QualityClass.HI_AMBIG: 2>¶

HI_NEAR_UNAMBIG = <QualityClass.HI_NEAR_UNAMBIG: 1>¶

HI_UNAMBIG = <QualityClass.HI_UNAMBIG: 0>¶

MAX_CLASS = <QualityClass.MAX_CLASS: 6>¶

MED_AMBIG = <QualityClass.MED_AMBIG: 3>¶

NOT_ELIMINATED = <EliminationReason.NOT_ELIMINATED: 0>¶

class QualityClass¶

Bases: pybind11_object

Members:

HI_UNAMBIG

HI_NEAR_UNAMBIG

HI_AMBIG

MED_AMBIG

UNAMBIG_MED_PROB

BAD_LOW_PROB

MAX_CLASS

BAD_LOW_PROB = <QualityClass.BAD_LOW_PROB: 5>¶

HI_AMBIG = <QualityClass.HI_AMBIG: 2>¶

HI_NEAR_UNAMBIG = <QualityClass.HI_NEAR_UNAMBIG: 1>¶

HI_UNAMBIG = <QualityClass.HI_UNAMBIG: 0>¶

MAX_CLASS = <QualityClass.MAX_CLASS: 6>¶

MED_AMBIG = <QualityClass.MED_AMBIG: 3>¶

UNAMBIG_MED_PROB = <QualityClass.UNAMBIG_MED_PROB: 4>¶

property name¶

property value¶

class Spin¶

Bases: pybind11_object

a single dimension of a multidimensional peak, stores putative assignments as indices into Resonance table

add_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, assignment: int) → None¶

add index-pointer into Resonance table to assign peak to putative spin

C++: protocols::noesy_assign::CrossPeak::Spin::add_assignment(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin¶: C++: protocols::noesy_assign::CrossPeak::Spin::operator=(const class protocols::noesy_assign::CrossPeak::Spin &) –> class protocols::noesy_assign::CrossPeak::Spin &

assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, nr: int) → int¶

return index-pointer into Resonance table

C++: protocols::noesy_assign::CrossPeak::Spin::assignment(unsigned long) const –> unsigned long

assignment_index(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, assignment: int) → int¶: C++: protocols::noesy_assign::CrossPeak::Spin::assignment_index(unsigned long) const –> unsigned long

freq(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → float¶

resonance frequency of peak

C++: protocols::noesy_assign::CrossPeak::Spin::freq() const –> double

n_assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → int¶: C++: protocols::noesy_assign::CrossPeak::Spin::n_assigned() const –> unsigned long

set_freq(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, freq: float) → None¶: C++: protocols::noesy_assign::CrossPeak::Spin::set_freq(double) –> void

UNAMBIG_MED_PROB = <QualityClass.UNAMBIG_MED_PROB: 4>¶

ambiguous(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::ambiguous() const –> bool

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D¶: C++: protocols::noesy_assign::CrossPeak3D::operator=(const class protocols::noesy_assign::CrossPeak3D &) –> class protocols::noesy_assign::CrossPeak3D &

assign_labelled_spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D, proton: int) → None¶: C++: protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(unsigned long) –> void

assign_spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D, spin_id: int) → None¶: C++: protocols::noesy_assign::CrossPeak3D::assign_spin(unsigned long) –> void

assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::assigned() const –> bool

assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t¶: C++: protocols::noesy_assign::CrossPeak::assignments() const –> const class utility::vector1<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment>, class std::allocator<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment> > > &

create_fa_and_cen_constraint(*args, **kwargs)¶

Overloaded function.

create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int) -> None
create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int, padding: float) -> None
create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int, padding: float, fa_only: bool) -> None

C++: protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(class std::shared_ptr<class core::scoring::constraints::Constraint> &, class std::shared_ptr<class core::scoring::constraints::Constraint> &, const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, double, bool) const –> void

cumulative_peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the cumulative cyana-type weights for all assignments Vk

C++: protocols::noesy_assign::CrossPeak::cumulative_peak_volume() const –> double

dimension(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::dimension() const –> unsigned long

distance_bound(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::distance_bound() const –> double

eliminated(*args, **kwargs)¶

Overloaded function.

eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) -> bool
eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, recompute: bool) -> bool
eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, recompute: bool, do_not_compute: bool) -> bool

returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227: do_not_compute … for outputter that does not want to change state…

C++: protocols::noesy_assign::CrossPeak::eliminated(bool, bool) const –> bool

elimination_reason(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::elimination_reason() const –> std::string

empty_clone(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::CrossPeak3D::empty_clone() –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

exp_hash(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::exp_hash() const –> unsigned long

filename(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::filename() const –> const std::string &

find_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::CrossPeak::find_assignments() –> void

fold_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, freq: float, i: int) → float¶: C++: protocols::noesy_assign::CrossPeak::fold_resonance(double, unsigned long) –> double

folder(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → pyrosetta.rosetta.protocols.noesy_assign.FoldResonance¶: C++: protocols::noesy_assign::CrossPeak::folder(unsigned long) –> const class protocols::noesy_assign::FoldResonance &

has_label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D, i: int) → bool¶: C++: protocols::noesy_assign::CrossPeak3D::has_label(unsigned long) const –> bool

has_proton(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : int) → bool¶: C++: protocols::noesy_assign::CrossPeak::has_proton(unsigned long) const –> bool

info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo¶: C++: protocols::noesy_assign::CrossPeak::info(unsigned long) const –> const class protocols::noesy_assign::CrossPeakInfo &

is4D(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::is4D() const –> bool

is_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::is_elimination_candidate() –> bool

label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D, : int) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin¶: C++: protocols::noesy_assign::CrossPeak3D::label(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

max_volume_contribution(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the largest volume contribution (normalized) any of the assignments has

C++: protocols::noesy_assign::CrossPeak::max_volume_contribution() const –> double

min_seq_separation_residue_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, volume_threshold: float) → int¶: C++: protocols::noesy_assign::CrossPeak::min_seq_separation_residue_assignment(double) const –> unsigned long

n_Vmin_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶

number of assignments with peak volume higher than params.min_volume_

C++: protocols::noesy_assign::CrossPeak::n_Vmin_assignments() –> unsigned long

n_assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::n_assigned() const –> unsigned long

nudge_distance_bound(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, offset: float) → None¶: C++: protocols::noesy_assign::CrossPeak::nudge_distance_bound(double) –> void

peak_id(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::peak_id() const –> unsigned long

print_peak_info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::CrossPeak::print_peak_info(std::ostream &) const –> void

probability(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::probability() const –> double

proton(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → protocols::noesy_assign::CrossPeak::Spin¶: C++: protocols::noesy_assign::CrossPeak::proton(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

quality_class(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass¶: C++: protocols::noesy_assign::CrossPeak::quality_class() const –> enum protocols::noesy_assign::CrossPeak::QualityClass

quality_class_str(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::quality_class_str() const –> std::string

resonances(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → protocols::noesy_assign::ResonanceList¶: C++: protocols::noesy_assign::CrossPeak::resonances() const –> const class protocols::noesy_assign::ResonanceList &

same_peak(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, other: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::same_peak(const class protocols::noesy_assign::CrossPeak &) const –> bool

set_cumulative_peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: float) → None¶: C++: protocols::noesy_assign::CrossPeak::set_cumulative_peak_volume(double) –> void

set_eliminated_due_to_dist_violations(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: bool) → None¶: C++: protocols::noesy_assign::CrossPeak::set_eliminated_due_to_dist_violations(bool) –> void

set_elimination_candidate(*args, **kwargs)¶

Overloaded function.

set_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) -> None
set_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: bool) -> None

C++: protocols::noesy_assign::CrossPeak::set_elimination_candidate(bool) –> void

set_elimination_comment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, str: str) → None¶: C++: protocols::noesy_assign::CrossPeak::set_elimination_comment(const std::string &) –> void

set_info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int, info: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → None¶: C++: protocols::noesy_assign::CrossPeak::set_info(unsigned long, class std::shared_ptr<const class protocols::noesy_assign::CrossPeakInfo>) –> void

set_peak_id(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, val: int) → None¶: C++: protocols::noesy_assign::CrossPeak::set_peak_id(unsigned long) –> void

set_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, res_in: protocols::noesy_assign::ResonanceList) → None¶: C++: protocols::noesy_assign::CrossPeak::set_resonances(class std::shared_ptr<class protocols::noesy_assign::ResonanceList>) –> void

set_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, val: float) → None¶: C++: protocols::noesy_assign::CrossPeak::set_volume(double) –> void

smallest_native_violation(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::smallest_native_violation() const –> double

spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → protocols::noesy_assign::CrossPeak::Spin¶: C++: protocols::noesy_assign::CrossPeak::spin(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, d: int) → float¶: C++: protocols::noesy_assign::CrossPeak::tolerance(unsigned long) –> double

volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the measured integral of the peak

C++: protocols::noesy_assign::CrossPeak::volume() const –> double

class pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D¶

Bases: CrossPeak3D

BAD_LOW_PROB = <QualityClass.BAD_LOW_PROB: 5>¶

EL_DISTVIOL = <EliminationReason.EL_DISTVIOL: 1>¶

EL_MAXASSIGN = <EliminationReason.EL_MAXASSIGN: 4>¶

EL_MINPEAKVOL = <EliminationReason.EL_MINPEAKVOL: 3>¶

EL_NETWORK = <EliminationReason.EL_NETWORK: 2>¶

class EliminationReason¶

Bases: pybind11_object

Members:

NOT_ELIMINATED

EL_DISTVIOL

EL_NETWORK

EL_MINPEAKVOL

EL_MAXASSIGN

EL_DISTVIOL = <EliminationReason.EL_DISTVIOL: 1>¶

EL_MAXASSIGN = <EliminationReason.EL_MAXASSIGN: 4>¶

EL_MINPEAKVOL = <EliminationReason.EL_MINPEAKVOL: 3>¶

EL_NETWORK = <EliminationReason.EL_NETWORK: 2>¶

NOT_ELIMINATED = <EliminationReason.NOT_ELIMINATED: 0>¶

property name¶

property value¶

HI_AMBIG = <QualityClass.HI_AMBIG: 2>¶

HI_NEAR_UNAMBIG = <QualityClass.HI_NEAR_UNAMBIG: 1>¶

HI_UNAMBIG = <QualityClass.HI_UNAMBIG: 0>¶

MAX_CLASS = <QualityClass.MAX_CLASS: 6>¶

MED_AMBIG = <QualityClass.MED_AMBIG: 3>¶

NOT_ELIMINATED = <EliminationReason.NOT_ELIMINATED: 0>¶

class QualityClass¶

Bases: pybind11_object

Members:

HI_UNAMBIG

HI_NEAR_UNAMBIG

HI_AMBIG

MED_AMBIG

UNAMBIG_MED_PROB

BAD_LOW_PROB

MAX_CLASS

BAD_LOW_PROB = <QualityClass.BAD_LOW_PROB: 5>¶

HI_AMBIG = <QualityClass.HI_AMBIG: 2>¶

HI_NEAR_UNAMBIG = <QualityClass.HI_NEAR_UNAMBIG: 1>¶

HI_UNAMBIG = <QualityClass.HI_UNAMBIG: 0>¶

MAX_CLASS = <QualityClass.MAX_CLASS: 6>¶

MED_AMBIG = <QualityClass.MED_AMBIG: 3>¶

UNAMBIG_MED_PROB = <QualityClass.UNAMBIG_MED_PROB: 4>¶

property name¶

property value¶

class Spin¶

Bases: pybind11_object

a single dimension of a multidimensional peak, stores putative assignments as indices into Resonance table

add_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, assignment: int) → None¶

add index-pointer into Resonance table to assign peak to putative spin

C++: protocols::noesy_assign::CrossPeak::Spin::add_assignment(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin¶: C++: protocols::noesy_assign::CrossPeak::Spin::operator=(const class protocols::noesy_assign::CrossPeak::Spin &) –> class protocols::noesy_assign::CrossPeak::Spin &

assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, nr: int) → int¶

return index-pointer into Resonance table

C++: protocols::noesy_assign::CrossPeak::Spin::assignment(unsigned long) const –> unsigned long

assignment_index(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, assignment: int) → int¶: C++: protocols::noesy_assign::CrossPeak::Spin::assignment_index(unsigned long) const –> unsigned long

freq(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → float¶

resonance frequency of peak

C++: protocols::noesy_assign::CrossPeak::Spin::freq() const –> double

n_assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin) → int¶: C++: protocols::noesy_assign::CrossPeak::Spin::n_assigned() const –> unsigned long

set_freq(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin, freq: float) → None¶: C++: protocols::noesy_assign::CrossPeak::Spin::set_freq(double) –> void

UNAMBIG_MED_PROB = <QualityClass.UNAMBIG_MED_PROB: 4>¶

ambiguous(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::ambiguous() const –> bool

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D¶: C++: protocols::noesy_assign::CrossPeak4D::operator=(const class protocols::noesy_assign::CrossPeak4D &) –> class protocols::noesy_assign::CrossPeak4D &

assign_labelled_spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D, proton: int) → None¶: C++: protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(unsigned long) –> void

assign_spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D, proton: int) → None¶: C++: protocols::noesy_assign::CrossPeak4D::assign_spin(unsigned long) –> void

assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::assigned() const –> bool

assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t¶: C++: protocols::noesy_assign::CrossPeak::assignments() const –> const class utility::vector1<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment>, class std::allocator<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment> > > &

create_fa_and_cen_constraint(*args, **kwargs)¶

Overloaded function.

create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int) -> None
create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int, padding: float) -> None
create_fa_and_cen_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, fa_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, cen_cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, normalization: int, padding: float, fa_only: bool) -> None

C++: protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(class std::shared_ptr<class core::scoring::constraints::Constraint> &, class std::shared_ptr<class core::scoring::constraints::Constraint> &, const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, double, bool) const –> void

cumulative_peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the cumulative cyana-type weights for all assignments Vk

C++: protocols::noesy_assign::CrossPeak::cumulative_peak_volume() const –> double

dimension(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::dimension() const –> unsigned long

distance_bound(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::distance_bound() const –> double

eliminated(*args, **kwargs)¶

Overloaded function.

eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) -> bool
eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, recompute: bool) -> bool
eliminated(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, recompute: bool, do_not_compute: bool) -> bool

returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227: do_not_compute … for outputter that does not want to change state…

C++: protocols::noesy_assign::CrossPeak::eliminated(bool, bool) const –> bool

elimination_reason(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::elimination_reason() const –> std::string

empty_clone(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::CrossPeak4D::empty_clone() –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

exp_hash(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::exp_hash() const –> unsigned long

filename(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::filename() const –> const std::string &

find_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::CrossPeak::find_assignments() –> void

fold_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, freq: float, i: int) → float¶: C++: protocols::noesy_assign::CrossPeak::fold_resonance(double, unsigned long) –> double

folder(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → pyrosetta.rosetta.protocols.noesy_assign.FoldResonance¶: C++: protocols::noesy_assign::CrossPeak::folder(unsigned long) –> const class protocols::noesy_assign::FoldResonance &

has_label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D, : int) → bool¶: C++: protocols::noesy_assign::CrossPeak4D::has_label(unsigned long) const –> bool

has_proton(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : int) → bool¶: C++: protocols::noesy_assign::CrossPeak::has_proton(unsigned long) const –> bool

info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo¶: C++: protocols::noesy_assign::CrossPeak::info(unsigned long) const –> const class protocols::noesy_assign::CrossPeakInfo &

is4D(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::is4D() const –> bool

is_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::is_elimination_candidate() –> bool

label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D, i: int) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin¶: C++: protocols::noesy_assign::CrossPeak4D::label(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

max_volume_contribution(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the largest volume contribution (normalized) any of the assignments has

C++: protocols::noesy_assign::CrossPeak::max_volume_contribution() const –> double

min_seq_separation_residue_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, volume_threshold: float) → int¶: C++: protocols::noesy_assign::CrossPeak::min_seq_separation_residue_assignment(double) const –> unsigned long

n_Vmin_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶

number of assignments with peak volume higher than params.min_volume_

C++: protocols::noesy_assign::CrossPeak::n_Vmin_assignments() –> unsigned long

n_assigned(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::n_assigned() const –> unsigned long

nudge_distance_bound(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, offset: float) → None¶: C++: protocols::noesy_assign::CrossPeak::nudge_distance_bound(double) –> void

peak_id(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → int¶: C++: protocols::noesy_assign::CrossPeak::peak_id() const –> unsigned long

print_peak_info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::CrossPeak::print_peak_info(std::ostream &) const –> void

probability(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::probability() const –> double

proton(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → protocols::noesy_assign::CrossPeak::Spin¶: C++: protocols::noesy_assign::CrossPeak::proton(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

quality_class(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass¶: C++: protocols::noesy_assign::CrossPeak::quality_class() const –> enum protocols::noesy_assign::CrossPeak::QualityClass

quality_class_str(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → str¶: C++: protocols::noesy_assign::CrossPeak::quality_class_str() const –> std::string

resonances(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → protocols::noesy_assign::ResonanceList¶: C++: protocols::noesy_assign::CrossPeak::resonances() const –> const class protocols::noesy_assign::ResonanceList &

same_peak(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, other: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::CrossPeak::same_peak(const class protocols::noesy_assign::CrossPeak &) const –> bool

set_cumulative_peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: float) → None¶: C++: protocols::noesy_assign::CrossPeak::set_cumulative_peak_volume(double) –> void

set_eliminated_due_to_dist_violations(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: bool) → None¶: C++: protocols::noesy_assign::CrossPeak::set_eliminated_due_to_dist_violations(bool) –> void

set_elimination_candidate(*args, **kwargs)¶

Overloaded function.

set_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) -> None
set_elimination_candidate(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, setting: bool) -> None

C++: protocols::noesy_assign::CrossPeak::set_elimination_candidate(bool) –> void

set_elimination_comment(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, str: str) → None¶: C++: protocols::noesy_assign::CrossPeak::set_elimination_comment(const std::string &) –> void

set_info(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int, info: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → None¶: C++: protocols::noesy_assign::CrossPeak::set_info(unsigned long, class std::shared_ptr<const class protocols::noesy_assign::CrossPeakInfo>) –> void

set_peak_id(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, val: int) → None¶: C++: protocols::noesy_assign::CrossPeak::set_peak_id(unsigned long) –> void

set_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, res_in: protocols::noesy_assign::ResonanceList) → None¶: C++: protocols::noesy_assign::CrossPeak::set_resonances(class std::shared_ptr<class protocols::noesy_assign::ResonanceList>) –> void

set_volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, val: float) → None¶: C++: protocols::noesy_assign::CrossPeak::set_volume(double) –> void

smallest_native_violation(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶: C++: protocols::noesy_assign::CrossPeak::smallest_native_violation() const –> double

spin(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, i: int) → protocols::noesy_assign::CrossPeak::Spin¶: C++: protocols::noesy_assign::CrossPeak::spin(unsigned long) –> class protocols::noesy_assign::CrossPeak::Spin &

tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, d: int) → float¶: C++: protocols::noesy_assign::CrossPeak::tolerance(unsigned long) –> double

volume(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → float¶

the measured integral of the peak

C++: protocols::noesy_assign::CrossPeak::volume() const –> double

class pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo¶

Bases: pybind11_object

shared information about CrossPeak (one for each proton dimension)

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo¶: C++: protocols::noesy_assign::CrossPeakInfo::operator=(const class protocols::noesy_assign::CrossPeakInfo &) –> class protocols::noesy_assign::CrossPeakInfo &

exp_hash(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → int¶: C++: protocols::noesy_assign::CrossPeakInfo::exp_hash() const –> unsigned long

filename(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → str¶: C++: protocols::noesy_assign::CrossPeakInfo::filename() const –> const std::string &

fold_label_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → pyrosetta.rosetta.protocols.noesy_assign.FoldResonance¶: C++: protocols::noesy_assign::CrossPeakInfo::fold_label_resonance() const –> const class protocols::noesy_assign::FoldResonance &

fold_proton_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → pyrosetta.rosetta.protocols.noesy_assign.FoldResonance¶: C++: protocols::noesy_assign::CrossPeakInfo::fold_proton_resonance() const –> const class protocols::noesy_assign::FoldResonance &

has_label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → bool¶: C++: protocols::noesy_assign::CrossPeakInfo::has_label() const –> bool

label_atom_name(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, proton_name: str, aa: pyrosetta.rosetta.core.chemical.AA) → str¶: C++: protocols::noesy_assign::CrossPeakInfo::label_atom_name(const std::string &, enum core::chemical::AA) const –> std::string

label_atom_type(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → str¶: C++: protocols::noesy_assign::CrossPeakInfo::label_atom_type() const –> const std::string &

label_tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → float¶: C++: protocols::noesy_assign::CrossPeakInfo::label_tolerance() const –> const double &

main_atom(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → str¶: C++: protocols::noesy_assign::CrossPeakInfo::main_atom() const –> const std::string &

max_noe_distance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → float¶: C++: protocols::noesy_assign::CrossPeakInfo::max_noe_distance() const –> double

proton_tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo) → float¶: C++: protocols::noesy_assign::CrossPeakInfo::proton_tolerance() const –> const double &

set_filename(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, filename: str) → None¶: C++: protocols::noesy_assign::CrossPeakInfo::set_filename(std::string) –> void

set_folding_window(*args, **kwargs)¶

Overloaded function.

set_folding_window(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, start: float, end: float) -> None
set_folding_window(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, start: float, end: float, label: bool) -> None

C++: protocols::noesy_assign::CrossPeakInfo::set_folding_window(double, double, bool) –> void

set_label(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, label: str, tolerance: float) → None¶: C++: protocols::noesy_assign::CrossPeakInfo::set_label(std::string, double) –> void

set_proton(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, name: str, tolerance: float) → None¶: C++: protocols::noesy_assign::CrossPeakInfo::set_proton(std::string, double) –> void

show(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::CrossPeakInfo::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList¶: C++: protocols::noesy_assign::CrossPeakList::operator=(const class protocols::noesy_assign::CrossPeakList &) –> class protocols::noesy_assign::CrossPeakList &

assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → protocols::noesy_assign::PeakAssignmentResidueMap¶: C++: protocols::noesy_assign::CrossPeakList::assignments() –> class protocols::noesy_assign::PeakAssignmentResidueMap &

count_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → int¶: C++: protocols::noesy_assign::CrossPeakList::count_assignments() const –> unsigned long

delete_diagonal_peaks(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::delete_diagonal_peaks() –> void

eliminate_spurious_peaks(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::eliminate_spurious_peaks() –> void

find_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::find_assignments() –> void

generate_fa_and_cen_constraints(*args, **kwargs)¶

Overloaded function.

generate_fa_and_cen_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, fa_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cen_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, min_seq_separation: int, min_quali: int, max_quali: int) -> None
generate_fa_and_cen_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, fa_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cen_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, min_seq_separation: int, min_quali: int, max_quali: int, padding: float) -> None
generate_fa_and_cen_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, fa_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cen_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, min_seq_separation: int, min_quali: int, max_quali: int, padding: float, ignore_elimination_candidates: bool) -> None
generate_fa_and_cen_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, fa_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cen_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, centroid_pose: pyrosetta.rosetta.core.pose.Pose, min_seq_separation: int, min_quali: int, max_quali: int, padding: float, ignore_elimination_candidates: bool, elimination_candidates: bool) -> None

C++: protocols::noesy_assign::CrossPeakList::generate_fa_and_cen_constraints(class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, double, bool, bool) const –> void

network_analysis(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::network_analysis() –> void

peaks(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t¶: C++: protocols::noesy_assign::CrossPeakList::peaks() const –> const class std::list<class std::shared_ptr<class protocols::noesy_assign::CrossPeak>, class std::allocator<class std::shared_ptr<class protocols::noesy_assign::CrossPeak> > > &

read_from_stream(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, : pyrosetta.rosetta.std.istream, input_adaptor: protocols::noesy_assign::PeakFileFormat, resonances: protocols::noesy_assign::ResonanceList) → None¶: C++: protocols::noesy_assign::CrossPeakList::read_from_stream(std::istream &, class protocols::noesy_assign::PeakFileFormat &, class std::shared_ptr<class protocols::noesy_assign::ResonanceList>) –> void

set_trivial_decoy_compatibility_score(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::set_trivial_decoy_compatibility_score() –> void

size(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → int¶: C++: protocols::noesy_assign::CrossPeakList::size() const –> unsigned long

update_chemshiftscore(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::update_chemshiftscore() –> void

update_peak_volumina(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::update_peak_volumina() –> void

update_symmetry_score(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::update_symmetry_score() –> void

update_upperdistance_score(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) → None¶: C++: protocols::noesy_assign::CrossPeakList::update_upperdistance_score() –> void

write_peak_files(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, prefix: str, output_adaptor: protocols::noesy_assign::PeakFileFormat) → None¶: C++: protocols::noesy_assign::CrossPeakList::write_peak_files(const std::string &, class protocols::noesy_assign::PeakFileFormat &) const –> void

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, : pyrosetta.rosetta.std.ostream, output_adaptor: protocols::noesy_assign::PeakFileFormat) → None¶: C++: protocols::noesy_assign::CrossPeakList::write_to_stream(std::ostream &, class protocols::noesy_assign::PeakFileFormat &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover¶

Bases: Mover

maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility)

apply(self: pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

sum up decoy_compatibility score in PeakAssignments

C++: protocols::noesy_assign::DistanceScoreMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_scoring(self: pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover) → None¶

normalize decoy_compatibility of PeakAssignments by count_decoys_

C++: protocols::noesy_assign::DistanceScoreMover::finalize_scoring() const –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover) → str¶: C++: protocols::noesy_assign::DistanceScoreMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

prepare_scoring(*args, **kwargs)¶

Overloaded function.

prepare_scoring(self: pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover) -> None
prepare_scoring(self: pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover, use_for_calibration: bool) -> None

set decoy_compatibility in PeakAssignments to zero

C++: protocols::noesy_assign::DistanceScoreMover::prepare_scoring(bool) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_dcut(self: pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover, setting: float) → None¶: C++: protocols::noesy_assign::DistanceScoreMover::set_dcut(double) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound¶

Bases: EXCN_NoesyAssign

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound, : pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound) → pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound¶: C++: protocols::noesy_assign::EXCN_AssignmentNotFound::operator=(const class protocols::noesy_assign::EXCN_AssignmentNotFound &) –> class protocols::noesy_assign::EXCN_AssignmentNotFound &

property assignment_¶

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str¶

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat¶

Bases: EXCN_NoesyAssign

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat, : pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat) → pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat¶: C++: protocols::noesy_assign::EXCN_FileFormat::operator=(const class protocols::noesy_assign::EXCN_FileFormat &) –> class protocols::noesy_assign::EXCN_FileFormat &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str¶

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign¶

Bases: Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign, : pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign) → pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign¶: C++: protocols::noesy_assign::EXCN_NoesyAssign::operator=(const class protocols::noesy_assign::EXCN_NoesyAssign &) –> class protocols::noesy_assign::EXCN_NoesyAssign &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str¶

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname¶

Bases: EXCN_NoesyAssign

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname, : pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname) → pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname¶: C++: protocols::noesy_assign::EXCN_UnknownAtomname::operator=(const class protocols::noesy_assign::EXCN_UnknownAtomname &) –> class protocols::noesy_assign::EXCN_UnknownAtomname &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str¶

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance¶

Bases: EXCN_NoesyAssign

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance, : pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance) → pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance¶: C++: protocols::noesy_assign::EXCN_UnknownResonance::operator=(const class protocols::noesy_assign::EXCN_UnknownResonance &) –> class protocols::noesy_assign::EXCN_UnknownResonance &

atom(self: pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance) → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: protocols::noesy_assign::EXCN_UnknownResonance::atom() –> const class core::id::NamedAtomID &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str¶

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance¶

Bases: Resonance

FloatingResonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid) (provided accessor methods of “FloatingResonance”: label, atom, resid, name, freq, error, tolerance, calibration_atom_type )

_pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::Resonance::_pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

aa(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.chemical.AA¶: C++: protocols::noesy_assign::Resonance::aa() const –> enum core::chemical::AA

add_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, ptr: pyrosetta.rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) → None¶: C++: protocols::noesy_assign::Resonance::add_connected_resonance(class std::weak_ptr<class protocols::noesy_assign::Resonance>) –> void

ambiguity(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance) → int¶: C++: protocols::noesy_assign::FloatingResonance::ambiguity() const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance, : pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance) → pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance¶: C++: protocols::noesy_assign::FloatingResonance::operator=(const class protocols::noesy_assign::FloatingResonance &) –> class protocols::noesy_assign::FloatingResonance &

atom(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.id.NamedAtomID¶

Atom

C++: protocols::noesy_assign::Resonance::atom() const –> const class core::id::NamedAtomID &

calibration_atom_type(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶

classification for calibration… e.g., Backbone, sidechain, etc..

C++: protocols::noesy_assign::Resonance::calibration_atom_type() const –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

clear_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → None¶: C++: protocols::noesy_assign::Resonance::clear_connected_resonances() –> void

clone(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::FloatingResonance::clone() –> class std::shared_ptr<class protocols::noesy_assign::Resonance>

connected_resonance_ids(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::noesy_assign::Resonance::connected_resonance_ids() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t¶: C++: protocols::noesy_assign::Resonance::connected_resonances() const –> const class utility::vector1<class std::weak_ptr<class protocols::noesy_assign::Resonance>, class std::allocator<class std::weak_ptr<class protocols::noesy_assign::Resonance> > > &

error(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::error() const –> double

first_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::Resonance::first_connected_resonance() const –> const class protocols::noesy_assign::Resonance &

float_label(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance, ifloat: int) → int¶: C++: protocols::noesy_assign::FloatingResonance::float_label(unsigned long) const –> unsigned long

freq(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

resonance frequency (chemical shift)

C++: protocols::noesy_assign::Resonance::freq() const –> double

has_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::has_connected_resonances() const –> bool

intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,: whereas I delta methyls are labelled 100%

C++: protocols::noesy_assign::Resonance::intensity() const –> double

is_proton(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::is_proton() const –> bool

label(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶

ResonanceID

C++: protocols::noesy_assign::Resonance::label() const –> unsigned long

match(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → bool¶

Resonance matches the given cross-peaks frequency

C++: protocols::noesy_assign::Resonance::match(double, double, const class protocols::noesy_assign::FoldResonance &) const –> bool

match2D(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance, proton_freq: float, proton_error: float, proton_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, label_freq: float, label_error: float, label_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, matches: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → bool¶

match the proton and corresponding label atom at same time

C++: protocols::noesy_assign::FloatingResonance::match2D(double, double, const class protocols::noesy_assign::FoldResonance &, double, double, const class protocols::noesy_assign::FoldResonance &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> bool

name(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → str¶: C++: protocols::noesy_assign::Resonance::name() const –> const std::string &

pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance, peakfreq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::FloatingResonance::pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

resid(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶: C++: protocols::noesy_assign::Resonance::resid() const –> unsigned long

set_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, setting: float) → None¶: C++: protocols::noesy_assign::Resonance::set_intensity(double) –> void

tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::tolerance() const –> double

write_to_stream(*args, **kwargs)¶

Overloaded function.

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance, os: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::noesy_assign::FloatingResonance::write_to_stream(std::ostream &) const –> void

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance, : pyrosetta.rosetta.std.ostream, aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::noesy_assign::FloatingResonance::write_to_stream(std::ostream &, enum core::chemical::AA) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.FoldResonance¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, : pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → pyrosetta.rosetta.protocols.noesy_assign.FoldResonance¶: C++: protocols::noesy_assign::FoldResonance::operator=(const class protocols::noesy_assign::FoldResonance &) –> class protocols::noesy_assign::FoldResonance &

end(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::FoldResonance::end() const –> double

is_folded(*args, **kwargs)¶

Overloaded function.

is_folded(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, freq: float) -> bool

C++: protocols::noesy_assign::FoldResonance::is_folded(double) const –> bool

is_folded(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) -> bool

C++: protocols::noesy_assign::FoldResonance::is_folded() const –> bool

is_folded_down(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, freq: float) → bool¶: C++: protocols::noesy_assign::FoldResonance::is_folded_down(double) const –> bool

is_folded_up(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, freq: float) → bool¶: C++: protocols::noesy_assign::FoldResonance::is_folded_up(double) const –> bool

set_window(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, start: float, end: float) → None¶: C++: protocols::noesy_assign::FoldResonance::set_window(double, double) –> void

show(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, os: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::FoldResonance::show(std::ostream &) const –> void

start(self: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::FoldResonance::start() const –> double

class pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist¶

Bases: pybind11_object

class DistanceRecord¶

Bases: pybind11_object

average_dist(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord) → float¶: C++: protocols::noesy_assign::FragsToAtomDist::DistanceRecord::average_dist() const –> double

average_dist6(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord) → float¶: C++: protocols::noesy_assign::FragsToAtomDist::DistanceRecord::average_dist6() const –> double

dist_track(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::noesy_assign::FragsToAtomDist::DistanceRecord::dist_track() const –> class utility::vector1<double, class std::allocator<double> >

is_valid(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord) → bool¶: C++: protocols::noesy_assign::FragsToAtomDist::DistanceRecord::is_valid() const –> bool

min_dist(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord) → float¶: C++: protocols::noesy_assign::FragsToAtomDist::DistanceRecord::min_dist() const –> double

record(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord, : float) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::DistanceRecord::record(double) –> void

record_inv6(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord, : float) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::DistanceRecord::record_inv6(double) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, : pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist) → pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist¶: C++: protocols::noesy_assign::FragsToAtomDist::operator=(const class protocols::noesy_assign::FragsToAtomDist &) –> class protocols::noesy_assign::FragsToAtomDist &

check_sequence(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, other_sequence: str) → bool¶: C++: protocols::noesy_assign::FragsToAtomDist::check_sequence(const std::string &) const –> bool

distance(*args, **kwargs)¶

Overloaded function.

distance(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, atom1: pyrosetta.rosetta.core.id.NamedAtomID, atom2: pyrosetta.rosetta.core.id.NamedAtomID) -> float
distance(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, atom1: pyrosetta.rosetta.core.id.NamedAtomID, atom2: pyrosetta.rosetta.core.id.NamedAtomID, r6_averaged: bool) -> float

C++: protocols::noesy_assign::FragsToAtomDist::distance(class core::id::NamedAtomID, class core::id::NamedAtomID, bool) const –> double

distance_record(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, atom1: pyrosetta.rosetta.core.id.NamedAtomID, atom2: pyrosetta.rosetta.core.id.NamedAtomID) → protocols::noesy_assign::FragsToAtomDist::DistanceRecord¶: C++: protocols::noesy_assign::FragsToAtomDist::distance_record(class core::id::NamedAtomID, class core::id::NamedAtomID) const –> const class protocols::noesy_assign::FragsToAtomDist::DistanceRecord &

generate_from_frag_file(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, filename: str, sequence: str, cycles: int, dump_freq: int) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::generate_from_frag_file(const std::string &, const std::string &, unsigned long, unsigned long) –> void

generate_from_fragments(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, fragments: pyrosetta.rosetta.core.fragment.FragSet, sequence: str, cycles: int, dump_freq: int) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::generate_from_fragments(class std::shared_ptr<class core::fragment::FragSet>, const std::string &, unsigned long, unsigned long) –> void

read_from_file(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, filename: str) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::read_from_file(const std::string &) –> void

read_from_stream(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, : pyrosetta.rosetta.std.istream) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::read_from_stream(std::istream &) –> void

sequence(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist) → str¶: C++: protocols::noesy_assign::FragsToAtomDist::sequence() const –> const std::string &

write_hist_to_file(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, filename: str) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::write_hist_to_file(const std::string &) const –> void

write_hist_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::write_hist_to_stream(std::ostream &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, filename: str) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::write_to_file(const std::string &) const –> void

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::FragsToAtomDist::write_to_stream(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.LabelResonance¶

Bases: Resonance

LabelResonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid) (provided accessor methods of “LabelResonance”: label, atom, resid, name, freq, error, tolerance, calibration_atom_type )

_pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::Resonance::_pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

aa(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.chemical.AA¶: C++: protocols::noesy_assign::Resonance::aa() const –> enum core::chemical::AA

add_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, ptr: pyrosetta.rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) → None¶: C++: protocols::noesy_assign::Resonance::add_connected_resonance(class std::weak_ptr<class protocols::noesy_assign::Resonance>) –> void

ambiguity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶: C++: protocols::noesy_assign::Resonance::ambiguity() const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.noesy_assign.LabelResonance, : pyrosetta.rosetta.protocols.noesy_assign.LabelResonance) → pyrosetta.rosetta.protocols.noesy_assign.LabelResonance¶: C++: protocols::noesy_assign::LabelResonance::operator=(const class protocols::noesy_assign::LabelResonance &) –> class protocols::noesy_assign::LabelResonance &

atom(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.id.NamedAtomID¶

Atom

C++: protocols::noesy_assign::Resonance::atom() const –> const class core::id::NamedAtomID &

calibration_atom_type(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶

classification for calibration… e.g., Backbone, sidechain, etc..

C++: protocols::noesy_assign::Resonance::calibration_atom_type() const –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

clear_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → None¶: C++: protocols::noesy_assign::Resonance::clear_connected_resonances() –> void

clone(self: pyrosetta.rosetta.protocols.noesy_assign.LabelResonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::LabelResonance::clone() –> class std::shared_ptr<class protocols::noesy_assign::Resonance>

connected_resonance_ids(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::noesy_assign::Resonance::connected_resonance_ids() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t¶: C++: protocols::noesy_assign::Resonance::connected_resonances() const –> const class utility::vector1<class std::weak_ptr<class protocols::noesy_assign::Resonance>, class std::allocator<class std::weak_ptr<class protocols::noesy_assign::Resonance> > > &

error(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::error() const –> double

first_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::Resonance::first_connected_resonance() const –> const class protocols::noesy_assign::Resonance &

float_label(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : int) → int¶: C++: protocols::noesy_assign::Resonance::float_label(unsigned long) const –> unsigned long

freq(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

resonance frequency (chemical shift)

C++: protocols::noesy_assign::Resonance::freq() const –> double

has_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::has_connected_resonances() const –> bool

intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,: whereas I delta methyls are labelled 100%

C++: protocols::noesy_assign::Resonance::intensity() const –> double

is_proton(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::is_proton() const –> bool

label(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶

ResonanceID

C++: protocols::noesy_assign::Resonance::label() const –> unsigned long

match(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → bool¶

Resonance matches the given cross-peaks frequency

C++: protocols::noesy_assign::Resonance::match(double, double, const class protocols::noesy_assign::FoldResonance &) const –> bool

match2D(self: pyrosetta.rosetta.protocols.noesy_assign.LabelResonance, proton_freq: float, proton_error: float, proton_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, label_freq: float, label_error: float, label_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, matches: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → bool¶

match the proton and corresponding label atom at same time

C++: protocols::noesy_assign::LabelResonance::match2D(double, double, const class protocols::noesy_assign::FoldResonance &, double, double, const class protocols::noesy_assign::FoldResonance &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> bool

name(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → str¶: C++: protocols::noesy_assign::Resonance::name() const –> const std::string &

pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::Resonance::pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

resid(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶: C++: protocols::noesy_assign::Resonance::resid() const –> unsigned long

set_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, setting: float) → None¶: C++: protocols::noesy_assign::Resonance::set_intensity(double) –> void

tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::tolerance() const –> double

write_to_stream(*args, **kwargs)¶

Overloaded function.

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : pyrosetta.rosetta.std.ostream) -> None

output

C++: protocols::noesy_assign::Resonance::write_to_stream(std::ostream &) const –> void

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : pyrosetta.rosetta.std.ostream, aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::noesy_assign::Resonance::write_to_stream(std::ostream &, enum core::chemical::AA) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.MethylNameLibrary¶

Bases: SingletonBase_protocols_noesy_assign_MethylNameLibrary_t

static get_instance() → protocols::noesy_assign::MethylNameLibrary¶: C++: utility::SingletonBase<protocols::noesy_assign::MethylNameLibrary>::get_instance() –> class protocols::noesy_assign::MethylNameLibrary *

class pyrosetta.rosetta.protocols.noesy_assign.MethylNames¶

Bases: pybind11_object

aa(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames) → pyrosetta.rosetta.core.chemical.AA¶: C++: protocols::noesy_assign::MethylNames::aa() const –> enum core::chemical::AA

aa_name(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames) → str¶: C++: protocols::noesy_assign::MethylNames::aa_name() const –> std::string

add_methyl(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames, rosetta: str, methyl: str) → None¶: C++: protocols::noesy_assign::MethylNames::add_methyl(const std::string &, const std::string &) –> void

add_proton(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames, nmr: str, rosetta: str) → None¶: C++: protocols::noesy_assign::MethylNames::add_proton(const std::string &, const std::string &) –> void

nmr2rosetta(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames, proton: str) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::noesy_assign::MethylNames::nmr2rosetta(const std::string &) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

proton_index(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames, : str) → int¶: C++: protocols::noesy_assign::MethylNames::proton_index(const std::string &) const –> unsigned long

rosetta2methyl(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames, proton: str) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::noesy_assign::MethylNames::rosetta2methyl(const std::string &) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

rosetta2nmr(self: pyrosetta.rosetta.protocols.noesy_assign.MethylNames, proton: str) → str¶: C++: protocols::noesy_assign::MethylNames::rosetta2nmr(const std::string &) const –> const std::string &

class pyrosetta.rosetta.protocols.noesy_assign.NoesyModule¶

Bases: pybind11_object

WARNING WARNING WARNING THREAD UNSAFE FOR USING THE COVALENTCOMPLIANCE CLASS IN A NON-CONST WAY

add_dist_viol_to_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, native_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::noesy_assign::NoesyModule::add_dist_viol_to_assignments(class core::pose::Pose) –> void

assign(*args, **kwargs)¶

Overloaded function.

assign(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule) -> None

same as above, but decoy file will be determined from commandline and read directly

C++: protocols::noesy_assign::NoesyModule::assign() –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, : pyrosetta.rosetta.protocols.noesy_assign.NoesyModule) -> pyrosetta.rosetta.protocols.noesy_assign.NoesyModule

C++: protocols::noesy_assign::NoesyModule::operator=(const class protocols::noesy_assign::NoesyModule &) –> class protocols::noesy_assign::NoesyModule &

static cmdline_options_activated() → bool¶

returns true if -noesy::in::resonances and -noesy::in::peaks are in cmd-line

C++: protocols::noesy_assign::NoesyModule::cmdline_options_activated() –> bool

crosspeaks(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList¶

return (cross)peak-list (peak-file)

C++: protocols::noesy_assign::NoesyModule::crosspeaks() const –> const class protocols::noesy_assign::CrossPeakList &

generate_constraint_files(*args, **kwargs)¶

Overloaded function.

generate_constraint_files(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, pose: pyrosetta.rosetta.core.pose.Pose, cst_fa_file: str, cst_centroid_file: str, min_seq_separation: int) -> None
generate_constraint_files(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, pose: pyrosetta.rosetta.core.pose.Pose, cst_fa_file: str, cst_centroid_file: str, min_seq_separation: int, min_quali: int) -> None
generate_constraint_files(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, pose: pyrosetta.rosetta.core.pose.Pose, cst_fa_file: str, cst_centroid_file: str, min_seq_separation: int, min_quali: int, max_quali: int) -> None
generate_constraint_files(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, pose: pyrosetta.rosetta.core.pose.Pose, cst_fa_file: str, cst_centroid_file: str, min_seq_separation: int, min_quali: int, max_quali: int, ignore_elimination_candidates: bool) -> None
generate_constraint_files(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, pose: pyrosetta.rosetta.core.pose.Pose, cst_fa_file: str, cst_centroid_file: str, min_seq_separation: int, min_quali: int, max_quali: int, ignore_elimination_candidates: bool, elimination_candidates: bool) -> None

after assignment –> create appropriate constraints

C++: protocols::noesy_assign::NoesyModule::generate_constraint_files(const class core::pose::Pose &, const std::string &, const std::string &, unsigned long, unsigned long, unsigned long, bool, bool) const –> void

static register_options() → None¶

register options

C++: protocols::noesy_assign::NoesyModule::register_options() –> void

reset(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule) → None¶

reset assignments… – call before re-assigning peaks

C++: protocols::noesy_assign::NoesyModule::reset() –> void

sequence(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule) → str¶: C++: protocols::noesy_assign::NoesyModule::sequence() –> const std::string &

write_assignments(*args, **kwargs)¶

Overloaded function.

write_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule) -> None
write_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.NoesyModule, file: str) -> None

write assignments into peak-file…

C++: protocols::noesy_assign::NoesyModule::write_assignments(std::string) –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment¶

Bases: pybind11_object

fast access to assignments that are stored in CrossPeak – similar to FragID WARNING WARNING WARNING THREAD UNSAFE. THIS CLASS USES THE FUNCTION covalent_compliance WHICH RELIES ON THREAD-UNSAFE SINGLETON CovalentCompliance

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment¶: C++: protocols::noesy_assign::PeakAssignment::operator=(const class protocols::noesy_assign::PeakAssignment &) –> class protocols::noesy_assign::PeakAssignment &

atom(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, iatom: int) → pyrosetta.rosetta.core.id.NamedAtomID¶

returns atom 1 or 2 of the assigned cross-peak. — might throw Exception if atom not found in ResonanceList

C++: protocols::noesy_assign::PeakAssignment::atom(unsigned long) const –> const class core::id::NamedAtomID &

calibration_atom_type(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, iatom: int) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶: C++: protocols::noesy_assign::PeakAssignment::calibration_atom_type(unsigned long) const –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

chemshift_compliance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶: C++: protocols::noesy_assign::PeakAssignment::chemshift_compliance() const –> double

create_constraint(*args, **kwargs)¶

Overloaded function.

create_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.Constraint
create_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.func.Func) -> pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::noesy_assign::PeakAssignment::create_constraint(const class core::pose::Pose &, class std::shared_ptr<class core::scoring::func::Func>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

create_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, pose: pyrosetta.rosetta.core.pose.Pose, ifloat: int) -> pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint
create_constraint(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, pose: pyrosetta.rosetta.core.pose.Pose, ifloat: int, : pyrosetta.rosetta.core.scoring.func.Func) -> pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint

C++: protocols::noesy_assign::PeakAssignment::create_constraint(const class core::pose::Pose &, unsigned long, class std::shared_ptr<class core::scoring::func::Func>) const –> class std::shared_ptr<class core::scoring::constraints::AmbiguousNMRDistanceConstraint>

crosspeak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::PeakAssignment::crosspeak() –> class protocols::noesy_assign::CrossPeak &

decoy_compatibility(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶: C++: protocols::noesy_assign::PeakAssignment::decoy_compatibility() const –> double

dump_weights(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, os: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakAssignment::dump_weights(std::ostream &) const –> void

float_ambiguity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → int¶: C++: protocols::noesy_assign::PeakAssignment::float_ambiguity() const –> unsigned long

has_label(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, select: int) → bool¶: C++: protocols::noesy_assign::PeakAssignment::has_label(unsigned long) const –> bool

has_proton(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, select: int) → bool¶: C++: protocols::noesy_assign::PeakAssignment::has_proton(unsigned long) const –> bool

is_symmetric_partner_of(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, other: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → bool¶: C++: protocols::noesy_assign::PeakAssignment::is_symmetric_partner_of(const class protocols::noesy_assign::PeakAssignment &) const –> bool

label_atom(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, iatom: int) → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: protocols::noesy_assign::PeakAssignment::label_atom(unsigned long) const –> const class core::id::NamedAtomID &

label_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, iatom: int) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::PeakAssignment::label_resonance(unsigned long) const –> const class protocols::noesy_assign::Resonance &

label_resonance_id(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, select: int) → int¶

return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom

C++: protocols::noesy_assign::PeakAssignment::label_resonance_id(unsigned long) const –> unsigned long

native_distance_viol(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶: C++: protocols::noesy_assign::PeakAssignment::native_distance_viol() –> double

network_anchoring(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶: C++: protocols::noesy_assign::PeakAssignment::network_anchoring() const –> double

network_anchoring_per_residue(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶: C++: protocols::noesy_assign::PeakAssignment::network_anchoring_per_residue() const –> double

normalized_peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶

only correct if peak_volumes have been update in CrossPeaks.

C++: protocols::noesy_assign::PeakAssignment::normalized_peak_volume() const –> double

peak_volume(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶

this is not normalized

C++: protocols::noesy_assign::PeakAssignment::peak_volume() const –> double

resid(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, iatom: int) → int¶

returns residue number of a1 or a2 of the assigned cross-peak, — might throw Exception if atom not found

C++: protocols::noesy_assign::PeakAssignment::resid(unsigned long) const –> unsigned long

resonance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, iatom: int) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::PeakAssignment::resonance(unsigned long) const –> const class protocols::noesy_assign::Resonance &

resonance_id(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, select: int) → int¶

return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom

C++: protocols::noesy_assign::PeakAssignment::resonance_id(unsigned long) const –> unsigned long

resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → pyrosetta.rosetta.protocols.noesy_assign.ResonanceList¶: C++: protocols::noesy_assign::PeakAssignment::resonances() const –> const class protocols::noesy_assign::ResonanceList &

set_decoy_compatibility(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, setting: float) → None¶: C++: protocols::noesy_assign::PeakAssignment::set_decoy_compatibility(double) –> void

set_native_distance_viol(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, setting: float) → None¶: C++: protocols::noesy_assign::PeakAssignment::set_native_distance_viol(double) –> void

set_network_anchoring(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, setting: float) → None¶: C++: protocols::noesy_assign::PeakAssignment::set_network_anchoring(double) –> void

set_network_anchoring_per_residue(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, reswise_setting: float) → None¶: C++: protocols::noesy_assign::PeakAssignment::set_network_anchoring_per_residue(double) –> void

set_symmetry(*args, **kwargs)¶

Overloaded function.

set_symmetry(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) -> None
set_symmetry(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, setting: float) -> None

C++: protocols::noesy_assign::PeakAssignment::set_symmetry(double) –> void

show(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, os: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakAssignment::show(std::ostream &) const –> void

spin_id(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment, select: int) → int¶: C++: protocols::noesy_assign::PeakAssignment::spin_id(unsigned long) const –> unsigned long

symmetry_compliance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → float¶: C++: protocols::noesy_assign::PeakAssignment::symmetry_compliance() const –> double

update_chemshiftscore_from_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakAssignment::update_chemshiftscore_from_peak() –> void

update_upperdistance_score(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakAssignment::update_upperdistance_score() –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters) → pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters¶: C++: protocols::noesy_assign::PeakAssignmentParameters::operator=(const class protocols::noesy_assign::PeakAssignmentParameters &) –> class protocols::noesy_assign::PeakAssignmentParameters &

property atom_dependent_calibration_¶

property calibration_convergence_¶

property calibration_cycles_¶

property calibration_eliminate_¶

property calibration_ignore_eliminated_peaks_¶

property calibration_max_noe_dist_¶

property calibration_max_nudging_¶

property calibration_start_nudging_¶

property calibration_stop_nudging_¶

property calibration_target_¶

property calibration_use_median_¶

property centroid_mapping_distance_padding_¶

property chemshift_overlap_weight_¶

property covalent_compliance_weight_¶

property cst_strength_¶

property dcalibrate_¶

property dcut_¶

static get_instance() → pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters¶: C++: protocols::noesy_assign::PeakAssignmentParameters::get_instance() –> const class protocols::noesy_assign::PeakAssignmentParameters *

static get_nonconst_instance() → pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters¶: C++: protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance() –> class protocols::noesy_assign::PeakAssignmentParameters *

property ignore_resonancefile_intensities_¶

property ignore_resonancefile_tolerances_¶

property local_distviol_cutoff_¶

property local_distviol_cutoff_buffer_¶

property local_distviol_global_buffer_¶

property local_distviol_global_factor_¶

property local_distviol_range_¶

property map_to_cen_atom_¶

property min_contribution_symmetric_peaks_¶

property min_volume_¶

property network_allow_same_residue_connect_¶

property network_atom_min_¶

property network_include_reverse_dir_¶

property network_mode_¶

property network_reswise_high_¶

property network_reswise_min_¶

property network_use_all_covalent_atoms_¶

property nmax_¶

property no_network_¶

property nr_conformers_violatable_¶

property prob_level_¶

property prob_sigmoid_m_¶

property prob_sigmoid_tau_¶

property prob_sigmoid_w_¶

static register_options() → None¶: C++: protocols::noesy_assign::PeakAssignmentParameters::register_options() –> void

static reset() → None¶: C++: protocols::noesy_assign::PeakAssignmentParameters::reset() –> void

static set_cycle(: int) → None¶: C++: protocols::noesy_assign::PeakAssignmentParameters::set_cycle(unsigned long) –> void

show(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakAssignmentParameters::show(std::ostream &) const –> void

show_on_tracer(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters) → None¶: C++: protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer() const –> void

property smax_¶

property symmetry_compliance_weight_¶

property use_local_distviol_¶

property vmax_¶

property vmin_¶

class pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap¶

Bases: pybind11_object

fast access to assignments by residue number

add(*args, **kwargs)¶

Overloaded function.

add(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList) -> None

add all PeakAssignments in all Crosspeaks of list

C++: protocols::noesy_assign::PeakAssignmentResidueMap::add(const class protocols::noesy_assign::CrossPeakList &) –> void

add(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) -> None

add individual PeakAssignment

C++: protocols::noesy_assign::PeakAssignmentResidueMap::add(const class std::shared_ptr<class protocols::noesy_assign::PeakAssignment> &) –> void

add_all_atoms(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : pyrosetta.rosetta.protocols.noesy_assign.ResonanceList) → None¶

add all resonances for backward compatibility in covalent-part of network-analysis

C++: protocols::noesy_assign::PeakAssignmentResidueMap::add_all_atoms(const class protocols::noesy_assign::ResonanceList &) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap) → pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap¶: C++: protocols::noesy_assign::PeakAssignmentResidueMap::operator=(const class protocols::noesy_assign::PeakAssignmentResidueMap &) –> class protocols::noesy_assign::PeakAssignmentResidueMap &

assignments(*args, **kwargs)¶

Overloaded function.

assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, resi: int, resj: int) -> pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t

C++: protocols::noesy_assign::PeakAssignmentResidueMap::assignments(unsigned long, unsigned long) –> class std::list<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment>, class std::allocator<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment> > > &

assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, resi: int, resj: int, collector: pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t) -> None

add assignments found between resi and resj to collector

C++: protocols::noesy_assign::PeakAssignmentResidueMap::assignments(unsigned long, unsigned long, class std::list<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment>, class std::allocator<class std::shared_ptr<class protocols::noesy_assign::PeakAssignment> > > &) const –> void

check_for_symmetric_peaks(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList, accumulate_symmetry: bool) → None¶

invalidate non symmetric peaks

C++: protocols::noesy_assign::PeakAssignmentResidueMap::check_for_symmetric_peaks(class protocols::noesy_assign::CrossPeakList &, bool) –> void

has(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, resi: int, resj: int) → bool¶

has some (valid or invalid) assignments between residue pair

C++: protocols::noesy_assign::PeakAssignmentResidueMap::has(unsigned long, unsigned long) –> bool

network_analysis(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, n_total_assignments: int) → None¶: C++: protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis(unsigned long) –> void

network_analysis2(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap) → None¶: C++: protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2() –> void

remove(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶

remove individual PeakAssignment

C++: protocols::noesy_assign::PeakAssignmentResidueMap::remove(const class protocols::noesy_assign::PeakAssignment &) –> void

total_residue(self: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap) → int¶: C++: protocols::noesy_assign::PeakAssignmentResidueMap::total_residue() const –> unsigned long

class pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator¶

Bases: pybind11_object

add_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, peak: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakCalibrator::add_peak(class std::shared_ptr<class protocols::noesy_assign::CrossPeak>) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, : pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator¶: C++: protocols::noesy_assign::PeakCalibrator::operator=(const class protocols::noesy_assign::PeakCalibrator &) –> class protocols::noesy_assign::PeakCalibrator &

static atom_type(atom: pyrosetta.rosetta.core.id.NamedAtomID, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶: C++: protocols::noesy_assign::PeakCalibrator::atom_type(const class core::id::NamedAtomID &, enum core::chemical::AA) –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

calibration_constant(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) → float¶: C++: protocols::noesy_assign::PeakCalibrator::calibration_constant(enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE) const –> double

do_calibration(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::do_calibration() –> void

eliminate_violated_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::eliminate_violated_constraints() –> void

fresh_instance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator¶: C++: protocols::noesy_assign::PeakCalibrator::fresh_instance() –> class std::shared_ptr<class protocols::noesy_assign::PeakCalibrator>

init_calibrator(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::init_calibrator() –> void

interpolate_on_statistics(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → bool¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics() –> bool

interpolate_too_big(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: int) → None¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_too_big(unsigned long) –> void

interpolate_too_small(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: int) → None¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_too_small(unsigned long) –> void

reset_calibration_constants(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::reset_calibration_constants() –> void

reset_statistics(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::reset_statistics() –> void

set_new_upper_bounds(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::set_new_upper_bounds() –> void

set_target_and_tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, target: float, tolerance: float) → None¶: C++: protocols::noesy_assign::PeakCalibrator::set_target_and_tolerance(double, double) –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap, : pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap) → pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap¶: C++: protocols::noesy_assign::PeakCalibratorMap::operator=(const class protocols::noesy_assign::PeakCalibratorMap &) –> class protocols::noesy_assign::PeakCalibratorMap &

do_calibration(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap) → None¶: C++: protocols::noesy_assign::PeakCalibratorMap::do_calibration() –> void

eliminate_violated_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap) → None¶: C++: protocols::noesy_assign::PeakCalibratorMap::eliminate_violated_constraints() –> void

set_new_upper_bounds(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap) → None¶: C++: protocols::noesy_assign::PeakCalibratorMap::set_new_upper_bounds() –> void

set_target_and_tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap, target: float, tolerance: float) → None¶: C++: protocols::noesy_assign::PeakCalibratorMap::set_target_and_tolerance(double, double) –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat¶

Bases: PeakFileFormat_Base

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat¶: C++: protocols::noesy_assign::PeakFileFormat::operator=(const class protocols::noesy_assign::PeakFileFormat &) –> class protocols::noesy_assign::PeakFileFormat &

compatible_with_current_format(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::compatible_with_current_format(const class protocols::noesy_assign::CrossPeak &) const –> bool

filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → str¶: C++: protocols::noesy_assign::PeakFileFormat_Base::filename() const –> const std::string &

ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments() const –> bool

ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity() const –> bool

min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write() const –> double

minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity() const –> double

ncol(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → int¶: C++: protocols::noesy_assign::PeakFileFormat::ncol() const –> unsigned long

output_diagnosis(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::output_diagnosis(std::ostream &) const –> void

read_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, is: pyrosetta.rosetta.std.istream, rest_line: pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_assignments(std::istream &, std::istream &, class protocols::noesy_assign::CrossPeak &, std::string &) const –> void

read_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_header(std::istream &, std::string &) –> void

read_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::PeakFileFormat::read_peak(std::istream &, std::string &) const –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

read_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_resonances(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

read_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_strength(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

static register_options() → None¶: C++: protocols::noesy_assign::PeakFileFormat::register_options() –> void

set_filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, str: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_filename(std::string) –> void

set_format_from_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::set_format_from_peak(const class protocols::noesy_assign::CrossPeak &) –> void

set_ignore_assignments(*args, **kwargs)¶

Overloaded function.

set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_assignments(bool) –> void

set_ignore_negative_intensity(*args, **kwargs)¶

Overloaded function.

set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_negative_intensity(bool) –> void

set_min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_min_VC_to_write(double) –> void

set_minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_minimum_peak_intensity(double) –> void

set_write_atom_names(*args, **kwargs)¶

Overloaded function.

set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) -> None
set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat::set_write_atom_names(bool) –> void

set_write_only_highest_VC(*args, **kwargs)¶

Overloaded function.

set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_write_only_highest_VC(bool) –> void

write_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignment(std::ostream &, const class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignment_indent(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignment_indent(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_assignment_stats(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, os: pyrosetta.rosetta.std.ostream, pa: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignment_stats(std::ostream &, class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, first_line_end: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignments(std::ostream &, const class protocols::noesy_assign::CrossPeak &, const std::string &) const –> void

write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::write_atom_names() const –> bool

write_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_header(std::ostream &) –> void

write_nil_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_nil_assignment(std::ostream &) const –> void

write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC() const –> bool

write_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, ct: int, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_peak(std::ostream &, unsigned long, const class protocols::noesy_assign::CrossPeak &) const –> void

write_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_resonances(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_strength(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base¶: C++: protocols::noesy_assign::PeakFileFormat_Base::operator=(const class protocols::noesy_assign::PeakFileFormat_Base &) –> class protocols::noesy_assign::PeakFileFormat_Base &

compatible_with_current_format(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::compatible_with_current_format(const class protocols::noesy_assign::CrossPeak &) const –> bool

filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → str¶: C++: protocols::noesy_assign::PeakFileFormat_Base::filename() const –> const std::string &

ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments() const –> bool

ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity() const –> bool

min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write() const –> double

minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity() const –> double

output_diagnosis(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::output_diagnosis(std::ostream &) const –> void

read_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, is: pyrosetta.rosetta.std.istream, rest_line: pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, new_peak_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::read_assignments(std::istream &, std::istream &, class protocols::noesy_assign::CrossPeak &, std::string &) const –> void

read_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.istream, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::read_header(std::istream &, std::string &) –> void

read_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.istream, next_line: str) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::PeakFileFormat_Base::read_peak(std::istream &, std::string &) const –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

read_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::read_resonances(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

read_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::read_strength(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

set_filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, str: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_filename(std::string) –> void

set_format_from_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_format_from_peak(const class protocols::noesy_assign::CrossPeak &) –> void

set_ignore_assignments(*args, **kwargs)¶

Overloaded function.

set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_assignments(bool) –> void

set_ignore_negative_intensity(*args, **kwargs)¶

Overloaded function.

set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_negative_intensity(bool) –> void

set_min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_min_VC_to_write(double) –> void

set_minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_minimum_peak_intensity(double) –> void

set_write_only_highest_VC(*args, **kwargs)¶

Overloaded function.

set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_write_only_highest_VC(bool) –> void

write_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, first_line_end: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_assignments(std::ostream &, const class protocols::noesy_assign::CrossPeak &, const std::string &) const –> void

write_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_header(std::ostream &) –> void

write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC() const –> bool

write_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.ostream, ct: int, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_peak(std::ostream &, unsigned long, const class protocols::noesy_assign::CrossPeak &) const –> void

write_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_resonances(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_strength(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky¶

Bases: PeakFileFormat

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky) → pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::operator=(const class protocols::noesy_assign::PeakFileFormat_Sparky &) –> class protocols::noesy_assign::PeakFileFormat_Sparky &

compatible_with_current_format(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::compatible_with_current_format(const class protocols::noesy_assign::CrossPeak &) const –> bool

filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → str¶: C++: protocols::noesy_assign::PeakFileFormat_Base::filename() const –> const std::string &

ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments() const –> bool

ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity() const –> bool

min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write() const –> double

minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity() const –> double

ncol(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → int¶: C++: protocols::noesy_assign::PeakFileFormat::ncol() const –> unsigned long

output_diagnosis(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::output_diagnosis(std::ostream &) const –> void

read_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, is: pyrosetta.rosetta.std.istream, rest_line: pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_assignments(std::istream &, std::istream &, class protocols::noesy_assign::CrossPeak &, std::string &) const –> void

read_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_header(std::istream &, std::string &) –> void

read_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::PeakFileFormat::read_peak(std::istream &, std::string &) const –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

read_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_resonances(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

read_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_strength(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

static register_options() → None¶: C++: protocols::noesy_assign::PeakFileFormat::register_options() –> void

set_filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, str: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_filename(std::string) –> void

set_format_from_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::set_format_from_peak(const class protocols::noesy_assign::CrossPeak &) –> void

set_ignore_assignments(*args, **kwargs)¶

Overloaded function.

set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_assignments(bool) –> void

set_ignore_negative_intensity(*args, **kwargs)¶

Overloaded function.

set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_negative_intensity(bool) –> void

set_min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_min_VC_to_write(double) –> void

set_minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_minimum_peak_intensity(double) –> void

set_write_atom_names(*args, **kwargs)¶

Overloaded function.

set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) -> None
set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat::set_write_atom_names(bool) –> void

set_write_only_highest_VC(*args, **kwargs)¶

Overloaded function.

set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_write_only_highest_VC(bool) –> void

write_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(std::ostream &, const class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignment_indent(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment_indent(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_assignment_stats(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment_stats(std::ostream &, class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, first_line_end: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignments(std::ostream &, const class protocols::noesy_assign::CrossPeak &, const std::string &) const –> void

write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::write_atom_names() const –> bool

write_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::write_header(std::ostream &) –> void

write_nil_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::write_nil_assignment(std::ostream &) const –> void

write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC() const –> bool

write_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : pyrosetta.rosetta.std.ostream, ct: int, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Sparky::write_peak(std::ostream &, unsigned long, const class protocols::noesy_assign::CrossPeak &) const –> void

write_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_resonances(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_strength(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy¶

Bases: PeakFileFormat

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy, : pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy) → pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy¶: C++: protocols::noesy_assign::PeakFileFormat_xeasy::operator=(const class protocols::noesy_assign::PeakFileFormat_xeasy &) –> class protocols::noesy_assign::PeakFileFormat_xeasy &

compatible_with_current_format(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::compatible_with_current_format(const class protocols::noesy_assign::CrossPeak &) const –> bool

filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → str¶: C++: protocols::noesy_assign::PeakFileFormat_Base::filename() const –> const std::string &

ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments() const –> bool

ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity() const –> bool

min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write() const –> double

minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity() const –> double

ncol(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → int¶: C++: protocols::noesy_assign::PeakFileFormat::ncol() const –> unsigned long

output_diagnosis(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::output_diagnosis(std::ostream &) const –> void

read_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, is: pyrosetta.rosetta.std.istream, rest_line: pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_assignments(std::istream &, std::istream &, class protocols::noesy_assign::CrossPeak &, std::string &) const –> void

read_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_header(std::istream &, std::string &) –> void

read_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::PeakFileFormat::read_peak(std::istream &, std::string &) const –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

read_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_resonances(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

read_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_strength(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

static register_options() → None¶: C++: protocols::noesy_assign::PeakFileFormat::register_options() –> void

set_filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, str: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_filename(std::string) –> void

set_format_from_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::set_format_from_peak(const class protocols::noesy_assign::CrossPeak &) –> void

set_ignore_assignments(*args, **kwargs)¶

Overloaded function.

set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_assignments(bool) –> void

set_ignore_negative_intensity(*args, **kwargs)¶

Overloaded function.

set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_negative_intensity(bool) –> void

set_min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_min_VC_to_write(double) –> void

set_minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_minimum_peak_intensity(double) –> void

set_write_atom_names(*args, **kwargs)¶

Overloaded function.

set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) -> None
set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat::set_write_atom_names(bool) –> void

set_write_only_highest_VC(*args, **kwargs)¶

Overloaded function.

set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_write_only_highest_VC(bool) –> void

write_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignment(std::ostream &, const class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignment_indent(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignment_indent(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_assignment_stats(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, os: pyrosetta.rosetta.std.ostream, pa: pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignment_stats(std::ostream &, class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, first_line_end: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignments(std::ostream &, const class protocols::noesy_assign::CrossPeak &, const std::string &) const –> void

write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::write_atom_names() const –> bool

write_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_header(std::ostream &) –> void

write_nil_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_nil_assignment(std::ostream &) const –> void

write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC() const –> bool

write_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, ct: int, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_peak(std::ostream &, unsigned long, const class protocols::noesy_assign::CrossPeak &) const –> void

write_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_resonances(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_strength(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk¶

Bases: PeakFileFormat

assign(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk) → pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::operator=(const class protocols::noesy_assign::PeakFileFormat_xpk &) –> class protocols::noesy_assign::PeakFileFormat_xpk &

compatible_with_current_format(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::compatible_with_current_format(const class protocols::noesy_assign::CrossPeak &) const –> bool

filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → str¶: C++: protocols::noesy_assign::PeakFileFormat_Base::filename() const –> const std::string &

ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments() const –> bool

ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity() const –> bool

min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write() const –> double

minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → float¶: C++: protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity() const –> double

ncol(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → int¶: C++: protocols::noesy_assign::PeakFileFormat::ncol() const –> unsigned long

output_diagnosis(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat::output_diagnosis(std::ostream &) const –> void

read_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, is: pyrosetta.rosetta.std.istream, rest_line: pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_assignments(std::istream &, std::istream &, class protocols::noesy_assign::CrossPeak &, std::string &) const –> void

read_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_header(std::istream &, std::string &) –> void

read_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, next_line: str) → pyrosetta.rosetta.protocols.noesy_assign.CrossPeak¶: C++: protocols::noesy_assign::PeakFileFormat::read_peak(std::istream &, std::string &) const –> class std::shared_ptr<class protocols::noesy_assign::CrossPeak>

read_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_resonances(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

read_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::read_strength(std::istream &, class protocols::noesy_assign::CrossPeak &) const –> void

static register_options() → None¶: C++: protocols::noesy_assign::PeakFileFormat::register_options() –> void

set_filename(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, str: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_filename(std::string) –> void

set_format_from_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::set_format_from_peak(const class protocols::noesy_assign::CrossPeak &) –> void

set_ignore_assignments(*args, **kwargs)¶

Overloaded function.

set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_assignments(bool) –> void

set_ignore_negative_intensity(*args, **kwargs)¶

Overloaded function.

set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_ignore_negative_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_ignore_negative_intensity(bool) –> void

set_min_VC_to_write(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_min_VC_to_write(double) –> void

set_minimum_peak_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: float) → None¶: C++: protocols::noesy_assign::PeakFileFormat_Base::set_minimum_peak_intensity(double) –> void

set_write_atom_names(*args, **kwargs)¶

Overloaded function.

set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) -> None
set_write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat::set_write_atom_names(bool) –> void

set_write_only_highest_VC(*args, **kwargs)¶

Overloaded function.

set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> None
set_write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting: bool) -> None

C++: protocols::noesy_assign::PeakFileFormat_Base::set_write_only_highest_VC(bool) –> void

write_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(std::ostream &, const class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignment_indent(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::write_assignment_indent(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_assignment_stats(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment) → None¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::write_assignment_stats(std::ostream &, class protocols::noesy_assign::PeakAssignment &) const –> void

write_assignments(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak, first_line_end: str) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_assignments(std::ostream &, const class protocols::noesy_assign::CrossPeak &, const std::string &) const –> void

write_atom_names(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat) → bool¶: C++: protocols::noesy_assign::PeakFileFormat::write_atom_names() const –> bool

write_header(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::write_header(std::ostream &) –> void

write_nil_assignment(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::write_nil_assignment(std::ostream &) const –> void

write_only_highest_VC(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base) → bool¶: C++: protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC() const –> bool

write_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : pyrosetta.rosetta.std.ostream, ct: int, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat_xpk::write_peak(std::ostream &, unsigned long, const class protocols::noesy_assign::CrossPeak &) const –> void

write_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_resonances(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

write_strength(self: pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakFileFormat::write_strength(std::ostream &, const class protocols::noesy_assign::CrossPeak &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance¶

Bases: Resonance

ProtonResonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid) (provided accessor methods of “ProtonResonance”: label, atom, resid, name, freq, error, tolerance, calibration_atom_type )

_pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::Resonance::_pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

aa(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.chemical.AA¶: C++: protocols::noesy_assign::Resonance::aa() const –> enum core::chemical::AA

add_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, ptr: pyrosetta.rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) → None¶: C++: protocols::noesy_assign::Resonance::add_connected_resonance(class std::weak_ptr<class protocols::noesy_assign::Resonance>) –> void

ambiguity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶: C++: protocols::noesy_assign::Resonance::ambiguity() const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance, : pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance) → pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance¶: C++: protocols::noesy_assign::ProtonResonance::operator=(const class protocols::noesy_assign::ProtonResonance &) –> class protocols::noesy_assign::ProtonResonance &

atom(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.id.NamedAtomID¶

Atom

C++: protocols::noesy_assign::Resonance::atom() const –> const class core::id::NamedAtomID &

calibration_atom_type(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶

classification for calibration… e.g., Backbone, sidechain, etc..

C++: protocols::noesy_assign::Resonance::calibration_atom_type() const –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

clear_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → None¶: C++: protocols::noesy_assign::Resonance::clear_connected_resonances() –> void

clone(self: pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::ProtonResonance::clone() –> class std::shared_ptr<class protocols::noesy_assign::Resonance>

connected_resonance_ids(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::noesy_assign::Resonance::connected_resonance_ids() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t¶: C++: protocols::noesy_assign::Resonance::connected_resonances() const –> const class utility::vector1<class std::weak_ptr<class protocols::noesy_assign::Resonance>, class std::allocator<class std::weak_ptr<class protocols::noesy_assign::Resonance> > > &

error(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::error() const –> double

first_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::Resonance::first_connected_resonance() const –> const class protocols::noesy_assign::Resonance &

float_label(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : int) → int¶: C++: protocols::noesy_assign::Resonance::float_label(unsigned long) const –> unsigned long

freq(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

resonance frequency (chemical shift)

C++: protocols::noesy_assign::Resonance::freq() const –> double

has_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::has_connected_resonances() const –> bool

intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,: whereas I delta methyls are labelled 100%

C++: protocols::noesy_assign::Resonance::intensity() const –> double

is_proton(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::is_proton() const –> bool

label(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶

ResonanceID

C++: protocols::noesy_assign::Resonance::label() const –> unsigned long

match(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → bool¶

Resonance matches the given cross-peaks frequency

C++: protocols::noesy_assign::Resonance::match(double, double, const class protocols::noesy_assign::FoldResonance &) const –> bool

match2D(self: pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance, proton_freq: float, proton_error: float, proton_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, label_freq: float, label_error: float, label_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, matches: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → bool¶

match the proton and corresponding label atom at same time

C++: protocols::noesy_assign::ProtonResonance::match2D(double, double, const class protocols::noesy_assign::FoldResonance &, double, double, const class protocols::noesy_assign::FoldResonance &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> bool

name(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → str¶: C++: protocols::noesy_assign::Resonance::name() const –> const std::string &

pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::Resonance::pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

resid(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶: C++: protocols::noesy_assign::Resonance::resid() const –> unsigned long

set_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, setting: float) → None¶: C++: protocols::noesy_assign::Resonance::set_intensity(double) –> void

tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::tolerance() const –> double

write_to_stream(*args, **kwargs)¶

Overloaded function.

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : pyrosetta.rosetta.std.ostream) -> None

output

C++: protocols::noesy_assign::Resonance::write_to_stream(std::ostream &) const –> void

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : pyrosetta.rosetta.std.ostream, aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::noesy_assign::Resonance::write_to_stream(std::ostream &, enum core::chemical::AA) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.Resonance¶

Bases: pybind11_object

Resonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid) (provided accessor methods of “Resonance”: label, atom, resid, name, freq, error, tolerance, calibration_atom_type )

_pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::Resonance::_pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

aa(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.chemical.AA¶: C++: protocols::noesy_assign::Resonance::aa() const –> enum core::chemical::AA

add_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, ptr: pyrosetta.rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) → None¶: C++: protocols::noesy_assign::Resonance::add_connected_resonance(class std::weak_ptr<class protocols::noesy_assign::Resonance>) –> void

ambiguity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶: C++: protocols::noesy_assign::Resonance::ambiguity() const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::Resonance::operator=(const class protocols::noesy_assign::Resonance &) –> class protocols::noesy_assign::Resonance &

atom(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.core.id.NamedAtomID¶

Atom

C++: protocols::noesy_assign::Resonance::atom() const –> const class core::id::NamedAtomID &

calibration_atom_type(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶

classification for calibration… e.g., Backbone, sidechain, etc..

C++: protocols::noesy_assign::Resonance::calibration_atom_type() const –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

clear_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → None¶: C++: protocols::noesy_assign::Resonance::clear_connected_resonances() –> void

clone(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::Resonance::clone() –> class std::shared_ptr<class protocols::noesy_assign::Resonance>

connected_resonance_ids(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::noesy_assign::Resonance::connected_resonance_ids() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t¶: C++: protocols::noesy_assign::Resonance::connected_resonances() const –> const class utility::vector1<class std::weak_ptr<class protocols::noesy_assign::Resonance>, class std::allocator<class std::weak_ptr<class protocols::noesy_assign::Resonance> > > &

error(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::error() const –> double

first_connected_resonance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → pyrosetta.rosetta.protocols.noesy_assign.Resonance¶: C++: protocols::noesy_assign::Resonance::first_connected_resonance() const –> const class protocols::noesy_assign::Resonance &

float_label(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : int) → int¶: C++: protocols::noesy_assign::Resonance::float_label(unsigned long) const –> unsigned long

freq(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

resonance frequency (chemical shift)

C++: protocols::noesy_assign::Resonance::freq() const –> double

has_connected_resonances(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::has_connected_resonances() const –> bool

intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶

in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,: whereas I delta methyls are labelled 100%

C++: protocols::noesy_assign::Resonance::intensity() const –> double

is_proton(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → bool¶: C++: protocols::noesy_assign::Resonance::is_proton() const –> bool

label(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶

ResonanceID

C++: protocols::noesy_assign::Resonance::label() const –> unsigned long

match(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → bool¶

Resonance matches the given cross-peaks frequency

C++: protocols::noesy_assign::Resonance::match(double, double, const class protocols::noesy_assign::FoldResonance &) const –> bool

match2D(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, proton_freq: float, proton_error: float, proton_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, label_freq: float, label_error: float, label_folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance, matches: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → bool¶

match the proton and corresponding label atom at same time

C++: protocols::noesy_assign::Resonance::match2D(double, double, const class protocols::noesy_assign::FoldResonance &, double, double, const class protocols::noesy_assign::FoldResonance &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> bool

name(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → str¶: C++: protocols::noesy_assign::Resonance::name() const –> const std::string &

pmatch(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, freq: float, error: float, folder: pyrosetta.rosetta.protocols.noesy_assign.FoldResonance) → float¶: C++: protocols::noesy_assign::Resonance::pmatch(double, double, const class protocols::noesy_assign::FoldResonance &) const –> double

resid(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → int¶: C++: protocols::noesy_assign::Resonance::resid() const –> unsigned long

set_intensity(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, setting: float) → None¶: C++: protocols::noesy_assign::Resonance::set_intensity(double) –> void

tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance) → float¶: C++: protocols::noesy_assign::Resonance::tolerance() const –> double

write_to_stream(*args, **kwargs)¶

Overloaded function.

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : pyrosetta.rosetta.std.ostream) -> None

output

C++: protocols::noesy_assign::Resonance::write_to_stream(std::ostream &) const –> void

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.Resonance, : pyrosetta.rosetta.std.ostream, aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::noesy_assign::Resonance::write_to_stream(std::ostream &, enum core::chemical::AA) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.ResonanceList¶

Bases: pybind11_object

: the ResonanceList provides a map of chemical shifts. each atom-chemical shift tupel has a “resonanceID” as a key. (integer)

used classes:

Resonance is an atom with chemical shift information ResonanceIDs (typedef) is a map from ID to Resonance ResidueMap (typedef) is a map from residue number to a vector of Resonances.

aa_from_resid(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList, resi: int) → pyrosetta.rosetta.core.chemical.AA¶

retrieve aminoacid of residue “resi”

C++: protocols::noesy_assign::ResonanceList::aa_from_resid(unsigned long) const –> enum core::chemical::AA

has_residue(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList, resi: int) → bool¶

have at least one resonance for residue “resi”

C++: protocols::noesy_assign::ResonanceList::has_residue(unsigned long) const –> bool

last_key(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList) → int¶

last ResonanceID ( given by input file )

C++: protocols::noesy_assign::ResonanceList::last_key() const –> unsigned long

read_from_stream(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList, : pyrosetta.rosetta.std.istream) → None¶

read chemical shift assignments

C++: protocols::noesy_assign::ResonanceList::read_from_stream(std::istream &) –> void

resonances_at_residue(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList, resid: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_Resonance_t¶

all resonances of a certain residue

— requires that update_residue_map() has been called (which is done by read_from_stream() )

C++: protocols::noesy_assign::ResonanceList::resonances_at_residue(unsigned long) const –> const class utility::vector1<class std::shared_ptr<class protocols::noesy_assign::Resonance>, class std::allocator<class std::shared_ptr<class protocols::noesy_assign::Resonance> > > &

sequence(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList) → str¶

retrieve the protein sequence

C++: protocols::noesy_assign::ResonanceList::sequence() const –> const std::string &

size(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList) → int¶

number of Resonances

C++: protocols::noesy_assign::ResonanceList::size() const –> unsigned long

start_key(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList) → int¶

first ResonanceID (given by input file)

C++: protocols::noesy_assign::ResonanceList::start_key() const –> unsigned long

write_talos_format(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList, : pyrosetta.rosetta.std.ostream, backbone_only: bool) → None¶

write in talos format

C++: protocols::noesy_assign::ResonanceList::write_talos_format(std::ostream &, bool) const –> void

write_to_stream(self: pyrosetta.rosetta.protocols.noesy_assign.ResonanceList, : pyrosetta.rosetta.std.ostream) → None¶

write chemical shift assignments

C++: protocols::noesy_assign::ResonanceList::write_to_stream(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator¶

Bases: PeakCalibrator

add_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, peak: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakCalibrator::add_peak(class std::shared_ptr<class protocols::noesy_assign::CrossPeak>) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator, : pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) → pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator¶: C++: protocols::noesy_assign::StructureDependentPeakCalibrator::operator=(const class protocols::noesy_assign::StructureDependentPeakCalibrator &) –> class protocols::noesy_assign::StructureDependentPeakCalibrator &

static atom_type(atom: pyrosetta.rosetta.core.id.NamedAtomID, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶: C++: protocols::noesy_assign::PeakCalibrator::atom_type(const class core::id::NamedAtomID &, enum core::chemical::AA) –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

calibration_constant(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) → float¶: C++: protocols::noesy_assign::PeakCalibrator::calibration_constant(enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE) const –> double

do_calibration(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::do_calibration() –> void

eliminate_violated_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) → None¶: C++: protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints() –> void

fresh_instance(self: pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) → pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator¶: C++: protocols::noesy_assign::StructureDependentPeakCalibrator::fresh_instance() –> class std::shared_ptr<class protocols::noesy_assign::PeakCalibrator>

generate_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) → None¶: C++: protocols::noesy_assign::StructureDependentPeakCalibrator::generate_constraints() –> void

init_calibrator(self: pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) → None¶: C++: protocols::noesy_assign::StructureDependentPeakCalibrator::init_calibrator() –> void

interpolate_on_statistics(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → bool¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics() –> bool

interpolate_too_big(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: int) → None¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_too_big(unsigned long) –> void

interpolate_too_small(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: int) → None¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_too_small(unsigned long) –> void

reset_calibration_constants(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::reset_calibration_constants() –> void

reset_statistics(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::reset_statistics() –> void

set_new_upper_bounds(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::set_new_upper_bounds() –> void

set_target_and_tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, target: float, tolerance: float) → None¶: C++: protocols::noesy_assign::PeakCalibrator::set_target_and_tolerance(double, double) –> void

class pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator¶

Bases: PeakCalibrator

add_peak(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, peak: pyrosetta.rosetta.protocols.noesy_assign.CrossPeak) → None¶: C++: protocols::noesy_assign::PeakCalibrator::add_peak(class std::shared_ptr<class protocols::noesy_assign::CrossPeak>) –> void

assign(self: pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator, : pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator) → pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator¶: C++: protocols::noesy_assign::StructureIndependentPeakCalibrator::operator=(const class protocols::noesy_assign::StructureIndependentPeakCalibrator &) –> class protocols::noesy_assign::StructureIndependentPeakCalibrator &

static atom_type(atom: pyrosetta.rosetta.core.id.NamedAtomID, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE¶: C++: protocols::noesy_assign::PeakCalibrator::atom_type(const class core::id::NamedAtomID &, enum core::chemical::AA) –> enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

calibration_constant(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) → float¶: C++: protocols::noesy_assign::PeakCalibrator::calibration_constant(enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE) const –> double

do_calibration(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::do_calibration() –> void

eliminate_violated_constraints(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::eliminate_violated_constraints() –> void

fresh_instance(self: pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator) → pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator¶: C++: protocols::noesy_assign::StructureIndependentPeakCalibrator::fresh_instance() –> class std::shared_ptr<class protocols::noesy_assign::PeakCalibrator>

init_calibrator(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::init_calibrator() –> void

interpolate_on_statistics(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → bool¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics() –> bool

interpolate_too_big(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: int) → None¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_too_big(unsigned long) –> void

interpolate_too_small(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, type: int) → None¶: C++: protocols::noesy_assign::PeakCalibrator::interpolate_too_small(unsigned long) –> void

reset_calibration_constants(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::reset_calibration_constants() –> void

reset_statistics(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::reset_statistics() –> void

set_new_upper_bounds(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator) → None¶: C++: protocols::noesy_assign::PeakCalibrator::set_new_upper_bounds() –> void

set_target_and_tolerance(self: pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator, target: float, tolerance: float) → None¶: C++: protocols::noesy_assign::PeakCalibrator::set_target_and_tolerance(double, double) –> void

pyrosetta.rosetta.protocols.noesy_assign.covalent_compliance(atom1: pyrosetta.rosetta.core.id.NamedAtomID, atom2: pyrosetta.rosetta.core.id.NamedAtomID) → bool¶

WARNING WARNING WARNING THREAD UNSAFE covalent_compliance RELIES ON THREAD-UNSAFE SINGLETON CovalentCompliance

C++: protocols::noesy_assign::covalent_compliance(const class core::id::NamedAtomID &, const class core::id::NamedAtomID &) –> bool