nmr

Bindings for core::scoring::nmr namespace

class pyrosetta.rosetta.core.scoring.nmr.EULER_CONVENTION

Bases: pybind11_builtins.pybind11_object

possible sequences of euler rotation axes

Members:

ZXZ_CONVENTION

ZYZ_CONVENTION

ZYX_CONVENTION

ZXZ_CONVENTION = <EULER_CONVENTION.ZXZ_CONVENTION: 1>
ZYX_CONVENTION = <EULER_CONVENTION.ZYX_CONVENTION: 3>
ZYZ_CONVENTION = <EULER_CONVENTION.ZYZ_CONVENTION: 2>
property name
class pyrosetta.rosetta.core.scoring.nmr.NMRDataFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_core_scoring_nmr_NMRDataFactory_t

create_attach_nmr_data_to_pose(self: pyrosetta.rosetta.core.scoring.nmr.NMRDataFactory, nmr_data_type: str, filename: str, pose: pyrosetta.rosetta.core.pose.Pose) None
Factory function that takes an NMR data type and input filename

as arguments, creates NMR data and attaches them directly to the pose.

C++: core::scoring::nmr::NMRDataFactory::create_attach_nmr_data_to_pose(const std::string &, const std::string &, class core::pose::Pose &) –> void

static get_instance() core::scoring::nmr::NMRDataFactory

C++: utility::SingletonBase<core::scoring::nmr::NMRDataFactory>::get_instance() –> class core::scoring::nmr::NMRDataFactory *

get_nmr_data(self: pyrosetta.rosetta.core.scoring.nmr.NMRDataFactory, nmr_data_type: str, filename: str, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.basic.datacache.CacheableData
Factory function that takes an NMR data type and input filename

as arguments and returns a pointer to the NMR data.

C++: core::scoring::nmr::NMRDataFactory::get_nmr_data(const std::string &, const std::string &, const class core::pose::Pose &) –> class std::shared_ptr<class basic::datacache::CacheableData>

class pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom

Bases: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint

Derived class of VoxelGridPoint to store the 3D coordinates of one atom of a NMRDummySpinlabelConformer. NMRDummySpinlabelAtom is also a member of NMRDummySpinlabelConformer and holds a const pointer to its outer class.

assign(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom, : pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom) pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom

C++: core::scoring::nmr::NMRDummySpinlabelAtom::operator=(const class core::scoring::nmr::NMRDummySpinlabelAtom &) –> class core::scoring::nmr::NMRDummySpinlabelAtom &

atom_name(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) str

C++: core::scoring::nmr::VoxelGridPoint::atom_name() const –> std::string

conformer(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom) pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer

C++: core::scoring::nmr::NMRDummySpinlabelAtom::conformer() const –> const class core::scoring::nmr::NMRDummySpinlabelConformer *

get_coordinates(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::nmr::VoxelGridPoint::get_coordinates() const –> const class numeric::xyzVector<double> &

id(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) int
Integer key to identify membership of this point to a group (e.g. a conformer or residue).

Points belonging to the same group will have the same key. A key is a fast way in retrieving information about the group. Locking up the derived classes’ member pointer and eventual casts would take too long.

C++: core::scoring::nmr::VoxelGridPoint::id() const –> unsigned long

is_relevant_neighbor(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom) bool

Is relevant for neighbor search

C++: core::scoring::nmr::NMRDummySpinlabelAtom::is_relevant_neighbor() const –> bool

type(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom) str

Type name of this voxel grid point

C++: core::scoring::nmr::NMRDummySpinlabelAtom::type() const –> std::string

class pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer

Bases: pybind11_builtins.pybind11_object

Class that stores information about one dummy spinlabel conformer (e.g. atom names and xyz coordinates, and whether it clashes with neighboring amino acid residues or not). A vector of NMRDummySpinlabelConformer objects is member of class NMRDummySpinlabelEnsemble.

assign(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer, rhs: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer

assignment operator

C++: core::scoring::nmr::NMRDummySpinlabelConformer::operator=(const class core::scoring::nmr::NMRDummySpinlabelConformer &) –> class core::scoring::nmr::NMRDummySpinlabelConformer &

clash_off(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) None

C++: core::scoring::nmr::NMRDummySpinlabelConformer::clash_off() –> void

clash_on(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) None

C++: core::scoring::nmr::NMRDummySpinlabelConformer::clash_on() –> void

clash_score(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) float

C++: core::scoring::nmr::NMRDummySpinlabelConformer::clash_score() –> double &

frequency(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) float

C++: core::scoring::nmr::NMRDummySpinlabelConformer::frequency() –> double &

get_clash_score(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) float

C++: core::scoring::nmr::NMRDummySpinlabelConformer::get_clash_score() const –> double

get_frequency(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) float

C++: core::scoring::nmr::NMRDummySpinlabelConformer::get_frequency() const –> double

get_id(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) int

Getters and Setters

C++: core::scoring::nmr::NMRDummySpinlabelConformer::get_id() const –> unsigned long

get_nobs(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) int

C++: core::scoring::nmr::NMRDummySpinlabelConformer::get_nobs() const –> unsigned long

get_residue(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) pyrosetta.rosetta.core.conformation.Residue

C++: core::scoring::nmr::NMRDummySpinlabelConformer::get_residue() –> class std::shared_ptr<class core::conformation::Residue>

has_clash(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer) bool

C++: core::scoring::nmr::NMRDummySpinlabelConformer::has_clash() const –> bool

set_clash_score(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer, score: float) None

C++: core::scoring::nmr::NMRDummySpinlabelConformer::set_clash_score(double) –> void

class pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble

Bases: pybind11_builtins.pybind11_object

Class that represents a “dummy” spinlabel ensemble. It holds information about each individual conformer member (atom coordinates, number of observations) and data to score those based on atom clashes with the neighborhood of the ensemble. To speed up the clash score calculation, this class holds also an object of type NMRDummySpinlabelVoxelGrid which gets filled with constant pointers to NMRDummySpinlabelAtoms.

assign(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble, rhs: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble) pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble

assignment operator

C++: core::scoring::nmr::NMRDummySpinlabelEnsemble::operator=(const class core::scoring::nmr::NMRDummySpinlabelEnsemble &) –> class core::scoring::nmr::NMRDummySpinlabelEnsemble &

clash_check(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble, pose: pyrosetta.rosetta.core.pose.Pose, target_resid: int, radius: float) None
Perform a clash score calculation for every spinlabel conformer in the ensemble by

calculating pairwise distances to neighborhood residues which are within a given radius. Specifically, the distance between every side-chain heavy atom in the spinlabel conformer and the neighbor atom of a pose residue is calculated. If the distance is smaller than the pose residue’s neighbor radius, is is assumed that the spinlabel conformer will fall within the side-chain radius of the neighborhood residue and thus it will be labeled as clashing otherwise it will not.

C++: core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(const class core::pose::Pose &, const unsigned long, const double) –> void

coordinate_transform_onto_target_site(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) pyrosetta.rosetta.numeric.HomogeneousTransform_double_t
returns the transformation matrix which transforms a xyz coordinate from

the frame of the spinlabel ensemble into the frame of the target site residue.

C++: core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_onto_target_site(const class core::pose::Pose &, const unsigned long) const –> class numeric::HomogeneousTransform<double>

get_conformer_table(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_nmr_NMRDummySpinlabelConformer_t

Getters

C++: core::scoring::nmr::NMRDummySpinlabelEnsemble::get_conformer_table() –> class utility::vector1<class std::shared_ptr<class core::scoring::nmr::NMRDummySpinlabelConformer>, class std::allocator<class std::shared_ptr<class core::scoring::nmr::NMRDummySpinlabelConformer> > > &

get_ensemble_size(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble) int

C++: core::scoring::nmr::NMRDummySpinlabelEnsemble::get_ensemble_size() const –> unsigned long

get_rmsd_mat(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble) pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: core::scoring::nmr::NMRDummySpinlabelEnsemble::get_rmsd_mat() –> const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &

get_voxel_grid(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble) core::scoring::nmr::NMRDummySpinlabelVoxelGrid

C++: core::scoring::nmr::NMRDummySpinlabelEnsemble::get_voxel_grid() –> class std::shared_ptr<class core::scoring::nmr::NMRDummySpinlabelVoxelGrid>

class pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid

Bases: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t

Derived class of VoxelGrid to create a grid of VoxelGridPoint objects.

Clear(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t) None

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::Clear() –> void

ExtractPosition(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid, point: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) pyrosetta.rosetta.numeric.xyzVector_double_t

Extract the 3D coordinate of a given object of type VoxelGridPoint.

C++: core::scoring::nmr::NMRDummySpinlabelVoxelGrid::ExtractPosition(const class core::scoring::nmr::VoxelGridPoint &) const –> const class numeric::xyzVector<double> *

GetBoundingBox(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t) pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::GetBoundingBox() const –> const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &

GetDimension(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t) int

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::GetDimension() const –> unsigned long

GetGridItems(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t) pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint_*_const_numeric_xyzVector_double_*_std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint_*_const_numeric_xyzVector_double_*_t

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::GetGridItems() const –> const class utility::vector1<class utility::vector1<struct std::pair<const class core::scoring::nmr::VoxelGridPoint *, const class numeric::xyzVector<double> *>, class std::allocator<struct std::pair<const class core::scoring::nmr::VoxelGridPoint *, const class numeric::xyzVector<double> *> > >, class std::allocator<class utility::vector1<struct std::pair<const class core::scoring::nmr::VoxelGridPoint *, const class numeric::xyzVector<double> *>, class std::allocator<struct std::pair<const class core::scoring::nmr::VoxelGridPoint *, const class numeric::xyzVector<double> *> > > > > &

GetNumberItems(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t) int

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::GetNumberItems() const –> unsigned long

GetResolution(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t) float

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::GetResolution() const –> double

HasNeighbors(*args, **kwargs)

Overloaded function.

  1. HasNeighbors(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t, input: core::scoring::nmr::VoxelGridPoint, neighborhood: float) -> bool

  2. HasNeighbors(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t, input: core::scoring::nmr::VoxelGridPoint, neighborhood: float, check_relevance: bool) -> bool

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::HasNeighbors(const class core::scoring::nmr::VoxelGridPoint &, const double &, bool) const –> bool

InsertObject(*args, **kwargs)

Overloaded function.

  1. InsertObject(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t, new_item: core::scoring::nmr::VoxelGridPoint) -> None

  2. InsertObject(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t, new_item: core::scoring::nmr::VoxelGridPoint, check_relevance: bool) -> None

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::InsertObject(const class core::scoring::nmr::VoxelGridPoint &, bool) –> void

IsRelevantItem(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid, point: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) bool

Check if this item is relevant for neighbor search

C++: core::scoring::nmr::NMRDummySpinlabelVoxelGrid::IsRelevantItem(const class core::scoring::nmr::VoxelGridPoint &) const –> bool

IsSameItem(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid, point1: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint, point2: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) bool

Check if two grid points are the same.

C++: core::scoring::nmr::NMRDummySpinlabelVoxelGrid::IsSameItem(const class core::scoring::nmr::VoxelGridPoint &, const class core::scoring::nmr::VoxelGridPoint &) const –> bool

RemoveObject(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t, item_to_remove: core::scoring::nmr::VoxelGridPoint) None

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::RemoveObject(const class core::scoring::nmr::VoxelGridPoint &) –> void

Translate(self: pyrosetta.rosetta.numeric.VoxelGrid_core_scoring_nmr_VoxelGridPoint_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: numeric::VoxelGrid<core::scoring::nmr::VoxelGridPoint>::Translate(const class numeric::xyzVector<double> &) –> void

assign(self: pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid, : pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid) pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid

C++: core::scoring::nmr::NMRDummySpinlabelVoxelGrid::operator=(const class core::scoring::nmr::NMRDummySpinlabelVoxelGrid &) –> class core::scoring::nmr::NMRDummySpinlabelVoxelGrid &

class pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, rhs: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch

assignment operator

C++: core::scoring::nmr::NMRGridSearch::operator=(const class core::scoring::nmr::NMRGridSearch &) –> class core::scoring::nmr::NMRGridSearch &

get_best_grid_point(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::nmr::NMRGridSearch::get_best_grid_point() const –> class numeric::xyzVector<double>

get_distance_center_to_atom1(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) float

C++: core::scoring::nmr::NMRGridSearch::get_distance_center_to_atom1() const –> double

get_grid_atom1(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) pyrosetta.rosetta.core.id.AtomID

C++: core::scoring::nmr::NMRGridSearch::get_grid_atom1() const –> const class core::id::AtomID &

get_grid_atom2(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) pyrosetta.rosetta.core.id.AtomID

C++: core::scoring::nmr::NMRGridSearch::get_grid_atom2() const –> const class core::id::AtomID &

get_grid_max_radius(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) float

C++: core::scoring::nmr::NMRGridSearch::get_grid_max_radius() const –> double

get_grid_min_radius(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) float

C++: core::scoring::nmr::NMRGridSearch::get_grid_min_radius() const –> double

get_grid_search_center(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::nmr::NMRGridSearch::get_grid_search_center() const –> class numeric::xyzVector<double>

get_stepsize(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch) float

C++: core::scoring::nmr::NMRGridSearch::get_stepsize() const –> double

set_best_grid_point(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, point: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::scoring::nmr::NMRGridSearch::set_best_grid_point(const class numeric::xyzVector<double> &) –> void

set_distance_center_to_atom1(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, distance: float) None

C++: core::scoring::nmr::NMRGridSearch::set_distance_center_to_atom1(double) –> void

set_grid_atom1(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, atom: pyrosetta.rosetta.core.id.AtomID) None

C++: core::scoring::nmr::NMRGridSearch::set_grid_atom1(const class core::id::AtomID &) –> void

set_grid_atom2(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, atom: pyrosetta.rosetta.core.id.AtomID) None

C++: core::scoring::nmr::NMRGridSearch::set_grid_atom2(const class core::id::AtomID &) –> void

set_grid_max_radius(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, radius: float) None

C++: core::scoring::nmr::NMRGridSearch::set_grid_max_radius(double) –> void

set_grid_min_radius(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, radius: float) None

C++: core::scoring::nmr::NMRGridSearch::set_grid_min_radius(double) –> void

set_grid_search_center(*args, **kwargs)

Overloaded function.

  1. set_grid_search_center(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Calculate and set grid search center from coordinates

of atoms 1 and 2 found in the input pose and from the geometric definition of the grid search

C++: core::scoring::nmr::NMRGridSearch::set_grid_search_center(const class core::pose::Pose &) –> void

  1. set_grid_search_center(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, point: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Set grid search center directly to specified input point

C++: core::scoring::nmr::NMRGridSearch::set_grid_search_center(const class numeric::xyzVector<double> &) –> void

set_stepsize(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, step: float) None

C++: core::scoring::nmr::NMRGridSearch::set_stepsize(double) –> void

valid_next_grid_point(self: pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch, metal_coords: pyrosetta.rosetta.numeric.xyzVector_double_t) bool
checks if grid point is within the predefined sphere and updates metal coordinates

returns false when last grid point is reached

C++: core::scoring::nmr::NMRGridSearch::valid_next_grid_point(class numeric::xyzVector<double> &) –> bool

class pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel

Bases: pybind11_builtins.pybind11_object

BUMP_ENERGY = <CONFORMER_FILTER.BUMP_ENERGY: 2>
class CONFORMER_FILTER

Bases: pybind11_builtins.pybind11_object

type of spinlabel conformer filtering
DISTANCE = measure the distance of spinlabel side chain heavy atoms to the

NBR_ATOM in every neighborhood residue in the spinlabel environment and count how many atoms are within the NBR_RADIUS

BUMP_ENERGY = filter based on packer energy of a spinlabel conformer with all

neighboring residues and keep conformers with energy lower than bump energy threshold

Members:

DISTANCE

BUMP_ENERGY

BUMP_ENERGY = <CONFORMER_FILTER.BUMP_ENERGY: 2>
DISTANCE = <CONFORMER_FILTER.DISTANCE: 1>
property name
DISTANCE = <CONFORMER_FILTER.DISTANCE: 1>
assign(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel, rhs: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel

assignment operator

C++: core::scoring::nmr::NMRSpinlabel::operator=(const class core::scoring::nmr::NMRSpinlabel &) –> class core::scoring::nmr::NMRSpinlabel &

filter_spinlabel_ensemble_by_distance_check(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel, pose: pyrosetta.rosetta.core.pose.Pose, target_resid: int) pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t
filter dummy spinlabel ensemble given the neighborhood

of a particular target residue in the pose. Return a vector of each spinlabel conformer’s weight and radical atom coordinates. Performs also clustering of coordinates internally such that the vector size does not exceed the maximal number of spinlabel conformers.

C++: core::scoring::nmr::NMRSpinlabel::filter_spinlabel_ensemble_by_distance_check(const class core::pose::Pose &, const unsigned long &) –> class utility::vector1<struct std::pair<double, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<double, class numeric::xyzVector<double> > > >

filter_spinlabel_ensemble_by_mask(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel, pose: pyrosetta.rosetta.core.pose.Pose, target_resid: int, mask: pyrosetta.rosetta.utility.vector1_bool, scores: pyrosetta.rosetta.utility.vector1_double) pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t

filter dummy ensemble and keep those spinlabels provided in boolean mask

C++: core::scoring::nmr::NMRSpinlabel::filter_spinlabel_ensemble_by_mask(const class core::pose::Pose &, const unsigned long &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<double, class std::allocator<double> > &) –> class utility::vector1<struct std::pair<double, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<double, class numeric::xyzVector<double> > > >

get_boltzman_factor(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) float

C++: core::scoring::nmr::NMRSpinlabel::get_boltzman_factor() const –> double

get_code(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) str

C++: core::scoring::nmr::NMRSpinlabel::get_code() const –> std::string

get_current_ensemble_size(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) int

C++: core::scoring::nmr::NMRSpinlabel::get_current_ensemble_size() const –> unsigned long

get_distance_potential_histogram_file(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) str

C++: core::scoring::nmr::NMRSpinlabel::get_distance_potential_histogram_file() const –> std::string

get_dummy_ensemble(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble

C++: core::scoring::nmr::NMRSpinlabel::get_dummy_ensemble() –> class std::shared_ptr<class core::scoring::nmr::NMRDummySpinlabelEnsemble>

get_highres_conformer_filter_type(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel.CONFORMER_FILTER

C++: core::scoring::nmr::NMRSpinlabel::get_highres_conformer_filter_type() const –> enum core::scoring::nmr::NMRSpinlabel::CONFORMER_FILTER

get_max_ensemble_size(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) int

C++: core::scoring::nmr::NMRSpinlabel::get_max_ensemble_size() const –> unsigned long

get_name(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) str

Getters

C++: core::scoring::nmr::NMRSpinlabel::get_name() const –> std::string

get_radical_atom(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) str

C++: core::scoring::nmr::NMRSpinlabel::get_radical_atom() const –> std::string

get_radical_atom_coordinates(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t

C++: core::scoring::nmr::NMRSpinlabel::get_radical_atom_coordinates() const –> const class utility::vector1<struct std::pair<double, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<double, class numeric::xyzVector<double> > > > &

get_residue_type(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel) pyrosetta.rosetta.core.chemical.ResidueType

C++: core::scoring::nmr::NMRSpinlabel::get_residue_type() const –> class std::shared_ptr<const class core::chemical::ResidueType>

set_boltzmann_factor(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel, kt: float) None

C++: core::scoring::nmr::NMRSpinlabel::set_boltzmann_factor(const double) –> void

set_highres_conformer_filter_type(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel, filter_type: str) None

C++: core::scoring::nmr::NMRSpinlabel::set_highres_conformer_filter_type(const std::string &) –> void

set_path_to_distance_potential_histogram_file(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel, filename: str) None

C++: core::scoring::nmr::NMRSpinlabel::set_path_to_distance_potential_histogram_file(const std::string &) –> void

show(self: pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel, TR: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::nmr::NMRSpinlabel::show(std::ostream &) –> void

class pyrosetta.rosetta.core.scoring.nmr.NMRTensor

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, rhs: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) pyrosetta.rosetta.core.scoring.nmr.NMRTensor

assignment operator

C++: core::scoring::nmr::NMRTensor::operator=(const class core::scoring::nmr::NMRTensor &) –> class core::scoring::nmr::NMRTensor &

deserialize(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) None

deserialize a json_spirit object to an NMRTensor

C++: core::scoring::nmr::NMRTensor::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diagonalize_tensor(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) None

bring NMR tensor in principal axis frame by diagonalization

C++: core::scoring::nmr::NMRTensor::diagonalize_tensor() –> void

get_Eig_xx(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_Eig_xx() const –> double

get_Eig_yy(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_Eig_yy() const –> double

get_Eig_zz(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_Eig_zz() const –> double

get_T_xx(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_T_xx() const –> double

get_T_xy(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_T_xy() const –> double

get_T_xz(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_T_xz() const –> double

get_T_yy(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_T_yy() const –> double

get_T_yz(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_T_yz() const –> double

get_alpha(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_alpha() const –> double

get_ax(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_ax() const –> double

get_beta(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_beta() const –> double

get_euler_convention(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) pyrosetta.rosetta.core.scoring.nmr.EULER_CONVENTION

C++: core::scoring::nmr::NMRTensor::get_euler_convention() const –> enum core::scoring::nmr::EULER_CONVENTION

get_gamma(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_gamma() const –> double

get_rh(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) float

C++: core::scoring::nmr::NMRTensor::get_rh() const –> double

reorder_tensor(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) None
Bring the NMR tensor principal values in correct order

and reconfigure tensor into unique tensor representation

C++: core::scoring::nmr::NMRTensor::reorder_tensor() –> void

serialize(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize an NMRTensor to a json_spirit object

C++: core::scoring::nmr::NMRTensor::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_Eig_xx(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, Eig_xx: float) None

C++: core::scoring::nmr::NMRTensor::set_Eig_xx(double) –> void

set_Eig_yy(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, Eig_yy: float) None

C++: core::scoring::nmr::NMRTensor::set_Eig_yy(double) –> void

set_Eig_zz(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, Eig_zz: float) None

C++: core::scoring::nmr::NMRTensor::set_Eig_zz(double) –> void

set_T_xx(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, T_xx: float) None

C++: core::scoring::nmr::NMRTensor::set_T_xx(double) –> void

set_T_xy(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, T_xy: float) None

C++: core::scoring::nmr::NMRTensor::set_T_xy(double) –> void

set_T_xz(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, T_xz: float) None

C++: core::scoring::nmr::NMRTensor::set_T_xz(double) –> void

set_T_yy(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, T_yy: float) None

C++: core::scoring::nmr::NMRTensor::set_T_yy(double) –> void

set_T_yz(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, T_yz: float) None

C++: core::scoring::nmr::NMRTensor::set_T_yz(double) –> void

set_alpha(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, alpha: float) None

C++: core::scoring::nmr::NMRTensor::set_alpha(double) –> void

set_ax(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, ax: float) None

C++: core::scoring::nmr::NMRTensor::set_ax(double) –> void

set_beta(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, beta: float) None

C++: core::scoring::nmr::NMRTensor::set_beta(double) –> void

set_gamma(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, gamma: float) None

C++: core::scoring::nmr::NMRTensor::set_gamma(double) –> void

set_rh(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, rh: float) None

C++: core::scoring::nmr::NMRTensor::set_rh(double) –> void

set_tensor_in_arbitrary_frame(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, tensor_params: pyrosetta.rosetta.utility.vector1_double) None
every NMR tensor should offer a function to set and update its upper diagonal elements

in this way the NMR tensor is represented in the arbitrary (molecular) frame

C++: core::scoring::nmr::NMRTensor::set_tensor_in_arbitrary_frame(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_tensor_in_pas(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, tensor_params: pyrosetta.rosetta.utility.vector1_double) None
every NMR tensor should offer a function to set and update its axial and rhombic component and three Euler angles

in this way the NMR tensor is represented in its principal axis system (PAS)

C++: core::scoring::nmr::NMRTensor::set_tensor_in_pas(const class utility::vector1<double, class std::allocator<double> > &) –> void

show_tensor_stats(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor, : pyrosetta.rosetta.std.ostream, : bool) None

show summary of tensor statistics

C++: core::scoring::nmr::NMRTensor::show_tensor_stats(std::ostream &, bool) const –> void

tensor_name(self: pyrosetta.rosetta.core.scoring.nmr.NMRTensor) str

every tensor should offer a function that returns its name

C++: core::scoring::nmr::NMRTensor::tensor_name() const –> std::string

class pyrosetta.rosetta.core.scoring.nmr.NMR_VALUE_AVERAGING_TYPE

Bases: pybind11_builtins.pybind11_object

the type how equivalent, ambiguous spins are averaged

Members:

SUM

MEAN

MEAN = <NMR_VALUE_AVERAGING_TYPE.MEAN: 2>
SUM = <NMR_VALUE_AVERAGING_TYPE.SUM: 1>
property name
class pyrosetta.rosetta.core.scoring.nmr.PRE_RATE_TYPE

Bases: pybind11_builtins.pybind11_object

type of the paramagnetic relaxation rate

Members:

R2_PARA

R1_PARA

R1_PARA = <PRE_RATE_TYPE.R1_PARA: 2>
R2_PARA = <PRE_RATE_TYPE.R2_PARA: 1>
property name
class pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE

Bases: pybind11_builtins.pybind11_object

type of PRE nuclear spin

Members:

PRE_SPIN_TYPE_H

PRE_SPIN_TYPE_N

PRE_SPIN_TYPE_C

PRE_SPIN_TYPE_C = <PRE_SPIN_TYPE.PRE_SPIN_TYPE_C: 3>
PRE_SPIN_TYPE_H = <PRE_SPIN_TYPE.PRE_SPIN_TYPE_H: 1>
PRE_SPIN_TYPE_N = <PRE_SPIN_TYPE.PRE_SPIN_TYPE_N: 2>
property name
class pyrosetta.rosetta.core.scoring.nmr.RDC_NORM_TYPE

Bases: pybind11_builtins.pybind11_object

type of RDC normalization

NORM_TYPE_NH = relative to N-H RDCs NORM_TYPE_CH = relative to CA-HA RDCs NORM_TYPE_NONE = it is assumed that input RDCs have been normalized to N-H RDCs in beforehand

(which is the NMR convention). Thus no additional scaling will be applied here

Members:

NORM_TYPE_NH

NORM_TYPE_CH

NORM_TYPE_NONE

NORM_TYPE_CH = <RDC_NORM_TYPE.NORM_TYPE_CH: 2>
NORM_TYPE_NH = <RDC_NORM_TYPE.NORM_TYPE_NH: 1>
NORM_TYPE_NONE = <RDC_NORM_TYPE.NORM_TYPE_NONE: 3>
property name
class pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE

Bases: pybind11_builtins.pybind11_object

the type of the residual dipolar coupling measured between two nuclei

Members:

RDC_TYPE_NH

RDC_TYPE_NCO

RDC_TYPE_CAHA

RDC_TYPE_CACO

RDC_TYPE_CACB

RDC_TYPE_NCA

RDC_TYPE_CAHN

RDC_TYPE_COHN

RDC_TYPE_CACB = <RDC_TYPE.RDC_TYPE_CACB: 5>
RDC_TYPE_CACO = <RDC_TYPE.RDC_TYPE_CACO: 4>
RDC_TYPE_CAHA = <RDC_TYPE.RDC_TYPE_CAHA: 3>
RDC_TYPE_CAHN = <RDC_TYPE.RDC_TYPE_CAHN: 7>
RDC_TYPE_COHN = <RDC_TYPE.RDC_TYPE_COHN: 8>
RDC_TYPE_NCA = <RDC_TYPE.RDC_TYPE_NCA: 6>
RDC_TYPE_NCO = <RDC_TYPE.RDC_TYPE_NCO: 2>
RDC_TYPE_NH = <RDC_TYPE.RDC_TYPE_NH: 1>
property name
class pyrosetta.rosetta.core.scoring.nmr.SINGLE_NMR_VALUE_WEIGHTING

Bases: pybind11_builtins.pybind11_object

type of weighting of single PCS/RDC/PRE values

CONST = constant weighting, 1.0 for every value

SIGMA = weighting based on error, 1.0/(error * error) OBSIG = weighting based on observed NMR value and error

val_obs/val_max/ (error * error)

Members:

CONST

SIGMA

OBSIG

CONST = <SINGLE_NMR_VALUE_WEIGHTING.CONST: 1>
OBSIG = <SINGLE_NMR_VALUE_WEIGHTING.OBSIG: 3>
SIGMA = <SINGLE_NMR_VALUE_WEIGHTING.SIGMA: 2>
property name
class pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint

Bases: pybind11_builtins.pybind11_object

Base class of a point object from which the voxel grid is created.

assign(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint, : pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint

C++: core::scoring::nmr::VoxelGridPoint::operator=(const class core::scoring::nmr::VoxelGridPoint &) –> class core::scoring::nmr::VoxelGridPoint &

atom_name(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) str

C++: core::scoring::nmr::VoxelGridPoint::atom_name() const –> std::string

get_coordinates(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::nmr::VoxelGridPoint::get_coordinates() const –> const class numeric::xyzVector<double> &

id(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) int
Integer key to identify membership of this point to a group (e.g. a conformer or residue).

Points belonging to the same group will have the same key. A key is a fast way in retrieving information about the group. Locking up the derived classes’ member pointer and eventual casts would take too long.

C++: core::scoring::nmr::VoxelGridPoint::id() const –> unsigned long

is_relevant_neighbor(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) bool

Is relevant for neighbor search

C++: core::scoring::nmr::VoxelGridPoint::is_relevant_neighbor() const –> bool

type(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) str

Type name of this voxel grid point

C++: core::scoring::nmr::VoxelGridPoint::type() const –> std::string

class pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA

Bases: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint

Derived class of VoxelGridPoint to store the 3D coordinates of one atom of an amino acid residue. In addition, it holds a const pointer to the residue object to which it refers to.

assign(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA, : pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA) pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA

C++: core::scoring::nmr::VoxelGridPoint_AA::operator=(const class core::scoring::nmr::VoxelGridPoint_AA &) –> class core::scoring::nmr::VoxelGridPoint_AA &

atom_name(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) str

C++: core::scoring::nmr::VoxelGridPoint::atom_name() const –> std::string

get_coordinates(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::nmr::VoxelGridPoint::get_coordinates() const –> const class numeric::xyzVector<double> &

id(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) int
Integer key to identify membership of this point to a group (e.g. a conformer or residue).

Points belonging to the same group will have the same key. A key is a fast way in retrieving information about the group. Locking up the derived classes’ member pointer and eventual casts would take too long.

C++: core::scoring::nmr::VoxelGridPoint::id() const –> unsigned long

is_relevant_neighbor(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint) bool

Is relevant for neighbor search

C++: core::scoring::nmr::VoxelGridPoint::is_relevant_neighbor() const –> bool

residue(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA) pyrosetta.rosetta.core.conformation.Residue

C++: core::scoring::nmr::VoxelGridPoint_AA::residue() const –> const class core::conformation::Residue *

type(self: pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA) str

Type name of this voxel grid point

C++: core::scoring::nmr::VoxelGridPoint_AA::type() const –> std::string

pyrosetta.rosetta.core.scoring.nmr.apply_tensor_transformation(pose: pyrosetta.rosetta.core.pose.Pose, Min: pyrosetta.rosetta.numeric.xyzMatrix_double_t, resid_from: int, resid_to: int) pyrosetta.rosetta.numeric.xyzMatrix_double_t
Utility function that transforms an NMR tensor from the frame of residue_from

into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original matrix if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to.

C++: core::scoring::nmr::apply_tensor_transformation(class core::pose::Pose &, const class numeric::xyzMatrix<double> &, unsigned long, unsigned long) –> class numeric::xyzMatrix<double>

pyrosetta.rosetta.core.scoring.nmr.apply_vector_rotation(pose: pyrosetta.rosetta.core.pose.Pose, Vin: pyrosetta.rosetta.numeric.xyzVector_double_t, resid_from: int, resid_to: int) pyrosetta.rosetta.numeric.xyzVector_double_t
Utility function that rotates a vector from the frame of residue_from

into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original vector if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to.

C++: core::scoring::nmr::apply_vector_rotation(class core::pose::Pose &, const class numeric::xyzVector<double> &, unsigned long, unsigned long) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.nmr.apply_vector_transformation(pose: pyrosetta.rosetta.core.pose.Pose, Vin: pyrosetta.rosetta.numeric.xyzVector_double_t, resid_from: int, resid_to: int) pyrosetta.rosetta.numeric.xyzVector_double_t
Utility function that transforms a vector of metal (or spinlabel) coordinates from

the frame of residue_from into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original vector if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to.

C++: core::scoring::nmr::apply_vector_transformation(class core::pose::Pose &, const class numeric::xyzVector<double> &, unsigned long, unsigned long) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.nmr.convert_pre_spin_type_to_string(type: pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE) str

C++: core::scoring::nmr::convert_pre_spin_type_to_string(const enum core::scoring::nmr::PRE_SPIN_TYPE &) –> std::string

pyrosetta.rosetta.core.scoring.nmr.convert_rdc_type_to_string(type: pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE) str

C++: core::scoring::nmr::convert_rdc_type_to_string(const enum core::scoring::nmr::RDC_TYPE &) –> std::string

pyrosetta.rosetta.core.scoring.nmr.convert_string_to_averaging_type(averaging_type: str) pyrosetta.rosetta.core.scoring.nmr.NMR_VALUE_AVERAGING_TYPE

C++: core::scoring::nmr::convert_string_to_averaging_type(const std::string &) –> enum core::scoring::nmr::NMR_VALUE_AVERAGING_TYPE

pyrosetta.rosetta.core.scoring.nmr.convert_string_to_normalization_type(normalization_type: str) pyrosetta.rosetta.core.scoring.nmr.RDC_NORM_TYPE

C++: core::scoring::nmr::convert_string_to_normalization_type(const std::string &) –> enum core::scoring::nmr::RDC_NORM_TYPE

pyrosetta.rosetta.core.scoring.nmr.convert_string_to_rate_type(rate_type: str) pyrosetta.rosetta.core.scoring.nmr.PRE_RATE_TYPE

C++: core::scoring::nmr::convert_string_to_rate_type(const std::string &) –> enum core::scoring::nmr::PRE_RATE_TYPE

pyrosetta.rosetta.core.scoring.nmr.convert_string_to_weighting_scheme(weighting_scheme: str) pyrosetta.rosetta.core.scoring.nmr.SINGLE_NMR_VALUE_WEIGHTING

C++: core::scoring::nmr::convert_string_to_weighting_scheme(const std::string &) –> enum core::scoring::nmr::SINGLE_NMR_VALUE_WEIGHTING

pyrosetta.rosetta.core.scoring.nmr.define_local_frame(CA: pyrosetta.rosetta.numeric.xyzVector_double_t, CB: pyrosetta.rosetta.numeric.xyzVector_double_t, C: pyrosetta.rosetta.numeric.xyzVector_double_t) pyrosetta.rosetta.numeric.HomogeneousTransform_double_t
Create a local coordinate frame from backbone coordinates.

The local frame is defined by a homogeneous transform object which can be created from three axes and one point. The center is located at CA. The z’-axis is along CA - CB. The x’-axis is within the CA-CB - CA-C plane and the y’-axis is perpendicular to the CB - CA - C plane.

C++: core::scoring::nmr::define_local_frame(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> class numeric::HomogeneousTransform<double>

pyrosetta.rosetta.core.scoring.nmr.euler_angles_from_rotation_matrix(rotM: pyrosetta.rosetta.numeric.xyzMatrix_double_t, convention: pyrosetta.rosetta.core.scoring.nmr.EULER_CONVENTION) pyrosetta.rosetta.numeric.xyzVector_double_t
determines the three Euler angles given a rotation matrix

and the respective Euler convention as determined at runtime

C++: core::scoring::nmr::euler_angles_from_rotation_matrix(const class numeric::xyzMatrix<double> &, enum core::scoring::nmr::EULER_CONVENTION) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.nmr.lookup_pseudoprotons(rsd: int, atomname: str, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_core_id_AtomID

function that handles conversion from pseudoatom identifier for degenerate protons to fullatom name

C++: core::scoring::nmr::lookup_pseudoprotons(const unsigned long, const std::string &, const class core::pose::Pose &) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.core.scoring.nmr.order_tensor_parameters(params: pyrosetta.rosetta.utility.vector1_double, convention: pyrosetta.rosetta.core.scoring.nmr.EULER_CONVENTION) None
orders the three eigenvalues of NMRTensor and brings NMRTensor

in unique tensor representation

C++: core::scoring::nmr::order_tensor_parameters(class utility::vector1<double, class std::allocator<double> > &, enum core::scoring::nmr::EULER_CONVENTION) –> void

pyrosetta.rosetta.core.scoring.nmr.pcs_func(*args, **kwargs)

Overloaded function.

  1. pcs_func(par: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rotM: pyrosetta.rosetta.numeric.xyzMatrix_double_t, spin_coord: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

  2. pcs_func(par: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rotM: pyrosetta.rosetta.numeric.xyzMatrix_double_t, spin_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, scal: float) -> float

Auxiliary PCS function

Tensor values [xM, yM, zM, Xax, Xrh] rotM: Rotation matrix to transform spin coordinates in tensor frame spin_coord: Spin xyz coordinates scal: optional scaling factor

C++: core::scoring::nmr::pcs_func(const class utility::fixedsizearray1<double, 5> &, const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, const double &) –> double

pyrosetta.rosetta.core.scoring.nmr.pre_spin_type_from_atom_name(atom: pyrosetta.rosetta.core.io.nmr.AtomSelection) pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE

C++: core::scoring::nmr::pre_spin_type_from_atom_name(const class core::io::nmr::AtomSelection &) –> enum core::scoring::nmr::PRE_SPIN_TYPE

pyrosetta.rosetta.core.scoring.nmr.rdc_type_from_atom_names(spinsAB: Tuple[pyrosetta.rosetta.core.io.nmr.AtomSelection, pyrosetta.rosetta.core.io.nmr.AtomSelection]) pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE

determine the RDC type from the spins’ atom names

C++: core::scoring::nmr::rdc_type_from_atom_names(const struct std::pair<class core::io::nmr::AtomSelection, class core::io::nmr::AtomSelection> &) –> enum core::scoring::nmr::RDC_TYPE

pyrosetta.rosetta.core.scoring.nmr.rotation_matrix_from_euler_angles(angles: pyrosetta.rosetta.numeric.xyzVector_double_t, convention: pyrosetta.rosetta.core.scoring.nmr.EULER_CONVENTION) pyrosetta.rosetta.numeric.xyzMatrix_double_t
creates a rotation matrix given three Euler angles

and a convention as determined at runtime

C++: core::scoring::nmr::rotation_matrix_from_euler_angles(const class numeric::xyzVector<double> &, enum core::scoring::nmr::EULER_CONVENTION) –> class numeric::xyzMatrix<double>