dna

Bindings for core::scoring::dna namespace

class pyrosetta.rosetta.core.scoring.dna.BasePartner

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

silly vector1 wrapper class so we can derive from PoseCachedData

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(self: pyrosetta.rosetta.core.scoring.dna.BasePartner, pos: int) → int

C++: core::scoring::dna::BasePartner::operator[](const unsigned long) –> unsigned long &

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.dna.BasePartner, partner_in: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.dna.BasePartner, arg0: pyrosetta.rosetta.core.scoring.dna.BasePartner) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.core.scoring.dna.BasePartner, : pyrosetta.rosetta.core.scoring.dna.BasePartner) → pyrosetta.rosetta.core.scoring.dna.BasePartner

C++: core::scoring::dna::BasePartner::operator=(const class core::scoring::dna::BasePartner &) –> class core::scoring::dna::BasePartner &

clone(self: pyrosetta.rosetta.core.scoring.dna.BasePartner) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::scoring::dna::BasePartner::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

resize(self: pyrosetta.rosetta.core.scoring.dna.BasePartner, size_: int) → None

C++: core::scoring::dna::BasePartner::resize(const unsigned long) –> void

size(self: pyrosetta.rosetta.core.scoring.dna.BasePartner) → int

C++: core::scoring::dna::BasePartner::size() const –> unsigned long

class pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential

Bases: pybind11_builtins.pybind11_object

1st pass implementation of Kono + Sarai’s protein-DNA interaction potential

Needs polishing, converting to mini standards in some respects, but still in trial stage.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential, arg0: pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

rsd_rsd_energy(self: pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

pyrosetta.rosetta.core.scoring.dna.find_basepairs(pose: pyrosetta.rosetta.core.pose.Pose, partner: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: core::scoring::dna::find_basepairs(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_base_pair_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, params: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::scoring::dna::get_base_pair_params(const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_base_pair_stub_slow(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.kinematics.Stub

C++: core::scoring::dna::get_base_pair_stub_slow(const class core::conformation::Residue &, const class core::conformation::Residue &) –> class core::kinematics::Stub

pyrosetta.rosetta.core.scoring.dna.get_base_step_params(*args, **kwargs)

Overloaded function.

1. get_base_step_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, params: pyrosetta.rosetta.utility.vector1_double) -> None

C++: core::scoring::dna::get_base_step_params(const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

2. get_base_step_params(rsd11: pyrosetta.rosetta.core.conformation.Residue, rsd12: pyrosetta.rosetta.core.conformation.Residue, rsd21: pyrosetta.rosetta.core.conformation.Residue, rsd22: pyrosetta.rosetta.core.conformation.Residue, params: pyrosetta.rosetta.utility.vector1_double) -> None

C++: core::scoring::dna::get_base_step_params(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_base_stub(rsd: pyrosetta.rosetta.core.conformation.Residue, strand: int) → pyrosetta.rosetta.core.kinematics.Stub

C++: core::scoring::dna::get_base_stub(const class core::conformation::Residue &, const int) –> class core::kinematics::Stub

pyrosetta.rosetta.core.scoring.dna.get_sugar_torsions(rsd: pyrosetta.rosetta.core.conformation.Residue, torsions: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::scoring::dna::get_sugar_torsions(const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_y_axis(rsd: pyrosetta.rosetta.core.conformation.Residue, strand: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::dna::get_y_axis(const class core::conformation::Residue &, const int) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.dna.get_y_axis_atoms(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, strand: int, a1: str, a2: str) → None

C++: core::scoring::dna::get_y_axis_atoms(const class core::chemical::ResidueType &, const int, class std::basic_string<char> &, class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.scoring.dna.get_z_axis(rsd: pyrosetta.rosetta.core.conformation.Residue, y_axis: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::dna::get_z_axis(const class core::conformation::Residue &, const class numeric::xyzVector<double> &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.dna.is_orthonormal(M: pyrosetta.rosetta.numeric.xyzMatrix_double_t, tol: float) → bool

C++: core::scoring::dna::is_orthonormal(const class numeric::xyzMatrix<double> &, const double) –> bool

pyrosetta.rosetta.core.scoring.dna.retrieve_base_partner_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.scoring.dna.BasePartner

helper fcn

C++: core::scoring::dna::retrieve_base_partner_from_pose(const class core::pose::Pose &) –> const class core::scoring::dna::BasePartner &

pyrosetta.rosetta.core.scoring.dna.set_base_partner(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::scoring::dna::set_base_partner(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.dna.show_base_pair_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::scoring::dna::show_base_pair_params(const class core::conformation::Residue &, const class core::conformation::Residue &) –> void

pyrosetta.rosetta.core.scoring.dna.show_dna_geometry(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) → None

C++: core::scoring::dna::show_dna_geometry(const class core::pose::Pose &, class std::basic_ostream<char> &) –> void

pyrosetta.rosetta.core.scoring.dna.show_new_base_step_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::scoring::dna::show_new_base_step_params(const class core::conformation::Residue &, const class core::conformation::Residue &) –> void