rings

Bindings for core::chemical::rings namespace

class pyrosetta.rosetta.core.chemical.rings.AxEqDesignation

Bases: pybind11_builtins.pybind11_object

: The axial/equatorial designation for bonds/substituents on ring systems.

Axial: “…[B]onds to ring atoms (and molecular entities attached to such bonds) are… axial… [if] the bonds make a relatively large… angle… with the plane containing or passing closest to a majority of the ring atoms. …[A]xial bonds are approximately parallel to the C3 axis…. Equatorial: “…[B]onds to ring atoms (and molecular entities attached to such bonds) are… equatorial… [if] the bonds make a relatively small… angle… with the plane containing or passing closest to a majority of the ring atoms. …[E]quatorial bonds [are] approximately parallel to two of the ring bonds.

NEITHER has the value of 0 and so can be used in conditionals as false.

Members:

NEITHER

AXIAL

EQUATORIAL

AXIAL = <AxEqDesignation.AXIAL: 1>
EQUATORIAL = <AxEqDesignation.EQUATORIAL: 2>
NEITHER = <AxEqDesignation.NEITHER: 0>
property name
class pyrosetta.rosetta.core.chemical.rings.CPParameter

Bases: pybind11_builtins.pybind11_object

Enumerators for the three Cremer-Pople “ring-puckering” parameters used to describe 4-, 5-, and 6-membered

ring conformers

Members:

q

PHI

THETA

PHI = <CPParameter.PHI: 2>
THETA = <CPParameter.THETA: 3>
property name
q = <CPParameter.q: 1>
class pyrosetta.rosetta.core.chemical.rings.RingConformer

Bases: pybind11_builtins.pybind11_object

A structure for storing information for specific, idealized ring conformers.

property CP_parameters
assign(self: pyrosetta.rosetta.core.chemical.rings.RingConformer, : pyrosetta.rosetta.core.chemical.rings.RingConformer) pyrosetta.rosetta.core.chemical.rings.RingConformer

C++: core::chemical::rings::RingConformer::operator=(const struct core::chemical::rings::RingConformer &) –> struct core::chemical::rings::RingConformer &

property degeneracy
property general_name
property nu_angles
property specific_name
property tau_angles
class pyrosetta.rosetta.core.chemical.rings.RingConformerManager

Bases: pyrosetta.rosetta.utility.SingletonBase_core_chemical_rings_RingConformerManager_t

This class is a singleton and manages RingConformer data that should only be read from the database one time and shared among all RingConformerSets.

static conformers_for_ring_size_and_type(ring_size: int, type: pyrosetta.rosetta.core.chemical.rings.RingSaturationType) pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer

Return a set of ring conformers for the requested ring size.

C++: core::chemical::rings::RingConformerManager::conformers_for_ring_size_and_type(const unsigned long, const enum core::chemical::rings::RingSaturationType) –> const class utility::vector1<struct core::chemical::rings::RingConformer, class std::allocator<struct core::chemical::rings::RingConformer> > &

static get_instance() core::chemical::rings::RingConformerManager

C++: utility::SingletonBase<core::chemical::rings::RingConformerManager>::get_instance() –> class core::chemical::rings::RingConformerManager *

class pyrosetta.rosetta.core.chemical.rings.RingConformerSet

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet, object_to_copy: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) pyrosetta.rosetta.core.chemical.rings.RingConformerSet

C++: core::chemical::rings::RingConformerSet::operator=(const class core::chemical::rings::RingConformerSet &) –> class core::chemical::rings::RingConformerSet &

get_all_nondegenerate_conformers(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer

Return a list of all nondegenerate conformers in the set.

C++: core::chemical::rings::RingConformerSet::get_all_nondegenerate_conformers() const –> const class utility::vector1<struct core::chemical::rings::RingConformer, class std::allocator<struct core::chemical::rings::RingConformer> > &

get_ideal_conformer_by_CP_parameters(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet, parameters: pyrosetta.rosetta.utility.vector1_double) pyrosetta.rosetta.core.chemical.rings.RingConformer

Return the conformer that is the best fit for the provided Cremer-Pople parameters.

C++: core::chemical::rings::RingConformerSet::get_ideal_conformer_by_CP_parameters(const class utility::vector1<double, class std::allocator<double> > &) const –> const struct core::chemical::rings::RingConformer &

get_ideal_conformer_by_name(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet, name: str) pyrosetta.rosetta.core.chemical.rings.RingConformer

Return the conformer corresponding to the requested name.

C++: core::chemical::rings::RingConformerSet::get_ideal_conformer_by_name(const std::string &) const –> const struct core::chemical::rings::RingConformer &

get_ideal_conformer_from_nus(*args, **kwargs)

Overloaded function.

  1. get_ideal_conformer_from_nus(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet, angles: pyrosetta.rosetta.utility.vector1_double) -> pyrosetta.rosetta.core.chemical.rings.RingConformer

  2. get_ideal_conformer_from_nus(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet, angles: pyrosetta.rosetta.utility.vector1_double, limit: float) -> pyrosetta.rosetta.core.chemical.rings.RingConformer

Return the conformer that is the best fit for the provided list of nu angles.

C++: core::chemical::rings::RingConformerSet::get_ideal_conformer_from_nus(const class utility::vector1<double, class std::allocator<double> > &, double) const –> const struct core::chemical::rings::RingConformer &

get_local_min_conformers(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer

C++: core::chemical::rings::RingConformerSet::get_local_min_conformers() const –> class utility::vector1<struct core::chemical::rings::RingConformer, class std::allocator<struct core::chemical::rings::RingConformer> >

get_lowest_energy_conformer(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) pyrosetta.rosetta.core.chemical.rings.RingConformer

Return the conformer that is known from studies (if available) to be the lowest energy ring conformer.

C++: core::chemical::rings::RingConformerSet::get_lowest_energy_conformer() const –> const struct core::chemical::rings::RingConformer &

get_random_conformer(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) pyrosetta.rosetta.core.chemical.rings.RingConformer

Return a random conformer from the set.

C++: core::chemical::rings::RingConformerSet::get_random_conformer() const –> const struct core::chemical::rings::RingConformer &

get_random_local_min_conformer(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) pyrosetta.rosetta.core.chemical.rings.RingConformer

Return a random conformer from the subset of conformers that are local minima.

C++: core::chemical::rings::RingConformerSet::get_random_local_min_conformer() const –> const struct core::chemical::rings::RingConformer &

low_energy_conformers_are_known(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) bool

Are the low-energy conformers known for this set?

C++: core::chemical::rings::RingConformerSet::low_energy_conformers_are_known() const –> bool

ring_size(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) int

Return the ring size of the conformers in this set.

C++: core::chemical::rings::RingConformerSet::ring_size() const –> unsigned long

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) -> None

  2. show(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of RingConformerSet for debugging purposes.

C++: core::chemical::rings::RingConformerSet::show(std::ostream &) const –> void

size(self: pyrosetta.rosetta.core.chemical.rings.RingConformerSet) int

Return the size of the conformer set.

C++: core::chemical::rings::RingConformerSet::size() const –> unsigned long

class pyrosetta.rosetta.core.chemical.rings.RingSaturationType

Bases: pybind11_builtins.pybind11_object

: An enumeration of saturation types for ring systems.

The value labels if a ring is aliphatic, aromatic, or some other saturation state.

Currently, the only options are ALIPHATIC and AROMATIC. In the future, other states will be added.

Members:

ALIPHATIC

AROMATIC

ALIPHATIC = <RingSaturationType.ALIPHATIC: 0>
AROMATIC = <RingSaturationType.AROMATIC: 1>
property name
pyrosetta.rosetta.core.chemical.rings.is_atom_axial_or_equatorial_to_ring(query_atom: pyrosetta.rosetta.numeric.xyzVector_double_t, attachment_atom: pyrosetta.rosetta.numeric.xyzVector_double_t, ring_atoms: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) pyrosetta.rosetta.core.chemical.rings.AxEqDesignation

Are the query atom coordinates axial or equatorial to the given ring or neither?

C++: core::chemical::rings::is_atom_axial_or_equatorial_to_ring(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> enum core::chemical::rings::AxEqDesignation

pyrosetta.rosetta.core.chemical.rings.opposite_designation(designation: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation) pyrosetta.rosetta.core.chemical.rings.AxEqDesignation

Return the opposite axial/equatorial designation.

C++: core::chemical::rings::opposite_designation(enum core::chemical::rings::AxEqDesignation) –> enum core::chemical::rings::AxEqDesignation

pyrosetta.rosetta.core.chemical.rings.read_conformers_from_database_file_for_ring_size(filename: str, ring_size: int) pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer

Return a list of ring conformers, read from a database file.

C++: core::chemical::rings::read_conformers_from_database_file_for_ring_size(const std::string &, unsigned long) –> class utility::vector1<struct core::chemical::rings::RingConformer, class std::allocator<struct core::chemical::rings::RingConformer> >