id¶

Bindings for core::id namespace

class pyrosetta.rosetta.core.id.AtomID¶

Bases: pybind11_builtins.pybind11_object

Atom identifier class. Defined by the atom number and the residue number.

BOGUS_ATOM_ID() → pyrosetta.rosetta.core.id.AtomID¶: C++: core::id::AtomID::BOGUS_ATOM_ID() –> class core::id::AtomID

CHAINBREAK_BOGUS_ATOM_ID() → pyrosetta.rosetta.core.id.AtomID¶: C++: core::id::AtomID::CHAINBREAK_BOGUS_ATOM_ID() –> class core::id::AtomID

assign(self: pyrosetta.rosetta.core.id.AtomID, : pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::id::AtomID::operator=(const class core::id::AtomID &) –> class core::id::AtomID &

atomno(self: pyrosetta.rosetta.core.id.AtomID) → int¶: C++: core::id::AtomID::atomno() –> unsigned long &

rsd(self: pyrosetta.rosetta.core.id.AtomID) → int¶: C++: core::id::AtomID::rsd() –> unsigned long &

set(self: pyrosetta.rosetta.core.id.AtomID, atomno_in: int, rsd_in: int) → None¶

Set the value of atom and residue.

C++: core::id::AtomID::set(unsigned long, unsigned long) –> void

valid(self: pyrosetta.rosetta.core.id.AtomID) → bool¶

Returns true if the AtomID is valid

must return false for BOGUS_ATOM_ID

C++: core::id::AtomID::valid() const –> bool

class pyrosetta.rosetta.core.id.BondID¶

Bases: pybind11_builtins.pybind11_object

two more classes, temporary for testing purposes

has(self: pyrosetta.rosetta.core.id.BondID, id: pyrosetta.rosetta.core.id.AtomID) → bool¶: C++: core::id::BondID::has(const class core::id::AtomID &) const –> bool

other_atom(self: pyrosetta.rosetta.core.id.BondID, id: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::id::BondID::other_atom(const class core::id::AtomID &) const –> const class core::id::AtomID &

reverse(self: pyrosetta.rosetta.core.id.BondID) → None¶: C++: core::id::BondID::reverse() –> void

reversed(self: pyrosetta.rosetta.core.id.BondID) → pyrosetta.rosetta.core.id.BondID¶: C++: core::id::BondID::reversed() const –> class core::id::BondID

class pyrosetta.rosetta.core.id.CacheableAtomID_MapVector¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

AtomID_Map< xyzVector< Real > >

assign(self: pyrosetta.rosetta.core.id.CacheableAtomID_MapVector, : pyrosetta.rosetta.core.id.CacheableAtomID_MapVector) → pyrosetta.rosetta.core.id.CacheableAtomID_MapVector¶: C++: core::id::CacheableAtomID_MapVector::operator=(const class core::id::CacheableAtomID_MapVector &) –> class core::id::CacheableAtomID_MapVector &

clone(self: pyrosetta.rosetta.core.id.CacheableAtomID_MapVector) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::id::CacheableAtomID_MapVector::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>

map(self: pyrosetta.rosetta.core.id.CacheableAtomID_MapVector) → pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t¶: C++: core::id::CacheableAtomID_MapVector::map() –> class core::id::AtomID_Map<class numeric::xyzVector<double> > &

class pyrosetta.rosetta.core.id.DOF_ID¶

Bases: pybind11_builtins.pybind11_object

Kinematics DOF identifier class

BOGUS_DOF_ID() → pyrosetta.rosetta.core.id.DOF_ID¶: C++: core::id::DOF_ID::BOGUS_DOF_ID() –> class core::id::DOF_ID

assign(self: pyrosetta.rosetta.core.id.DOF_ID, : pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.id.DOF_ID¶: C++: core::id::DOF_ID::operator=(const class core::id::DOF_ID &) –> class core::id::DOF_ID &

atom_id(self: pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::id::DOF_ID::atom_id() const –> const class core::id::AtomID &

atomno(self: pyrosetta.rosetta.core.id.DOF_ID) → int¶: C++: core::id::DOF_ID::atomno() const –> unsigned long

rsd(self: pyrosetta.rosetta.core.id.DOF_ID) → int¶: C++: core::id::DOF_ID::rsd() const –> unsigned long

type(self: pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.id.DOF_Type¶: C++: core::id::DOF_ID::type() const –> enum core::id::DOF_Type

valid(self: pyrosetta.rosetta.core.id.DOF_ID) → bool¶

Is this DOF_ID valid?

Must return false for BOGUS_TORSION_ID.

C++: core::id::DOF_ID::valid() const –> bool

class pyrosetta.rosetta.core.id.DOF_ID_Range¶

Bases: pybind11_builtins.pybind11_object

Kinematics DOF identifier (with range) class

dof_id(self: pyrosetta.rosetta.core.id.DOF_ID_Range) → pyrosetta.rosetta.core.id.DOF_ID¶: C++: core::id::DOF_ID_Range::dof_id() const –> const class core::id::DOF_ID &

max(self: pyrosetta.rosetta.core.id.DOF_ID_Range) → float¶: C++: core::id::DOF_ID_Range::max() const –> double

min(self: pyrosetta.rosetta.core.id.DOF_ID_Range) → float¶: C++: core::id::DOF_ID_Range::min() const –> double

class pyrosetta.rosetta.core.id.DOF_Type¶

Bases: pybind11_builtins.pybind11_object

DOF (degrees of freedom) type

PHI : torsion or improper angle

THETA : bond angle

D : distance

RB1-RB6 : rigid-body jump translation and rotation

Members:

INVALID_DOF

PHI

THETA

D

RB1

RB2

RB3

RB4

RB5

RB6

pyrosetta.rosetta.core.id.DOF_type_is_rb(t: pyrosetta.rosetta.core.id.DOF_Type) → bool¶: C++: core::id::DOF_type_is_rb(const enum core::id::DOF_Type) –> bool

class pyrosetta.rosetta.core.id.JumpID¶

Bases: pybind11_builtins.pybind11_object

/brief

Torsion identifier class

Note the order of the elements in construction calls:

( residue, type, torsion )

sort of from least to most specific

rsd1(self: pyrosetta.rosetta.core.id.JumpID) → int¶: C++: core::id::JumpID::rsd1() const –> unsigned long

rsd2(self: pyrosetta.rosetta.core.id.JumpID) → int¶: C++: core::id::JumpID::rsd2() –> unsigned long &

valid(self: pyrosetta.rosetta.core.id.JumpID) → bool¶

Is this id valid?

Must return false for BOGUS_TORSION_ID

C++: core::id::JumpID::valid() const –> bool

class pyrosetta.rosetta.core.id.MainchainTorsionType¶

Bases: pybind11_builtins.pybind11_object

Members:

phi_dihedral

psi_dihedral

omega_dihedral

omega2_dihedral

omega3_dihedral

class pyrosetta.rosetta.core.id.NamedAtomID¶

Bases: pybind11_builtins.pybind11_object

Atom identifier class

BOGUS_NAMED_ATOM_ID() → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID() –> const class core::id::NamedAtomID

CHAINBREAK_BOGUS_NAMED_ATOM_ID() → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: core::id::NamedAtomID::CHAINBREAK_BOGUS_NAMED_ATOM_ID() –> const class core::id::NamedAtomID

assign(self: pyrosetta.rosetta.core.id.NamedAtomID, : pyrosetta.rosetta.core.id.NamedAtomID) → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: core::id::NamedAtomID::operator=(const class core::id::NamedAtomID &) –> class core::id::NamedAtomID &

atom(self: pyrosetta.rosetta.core.id.NamedAtomID) → str¶: C++: core::id::NamedAtomID::atom() –> std::string &

rsd(self: pyrosetta.rosetta.core.id.NamedAtomID) → int¶: C++: core::id::NamedAtomID::rsd() –> unsigned long &

to_string(self: pyrosetta.rosetta.core.id.NamedAtomID) → str¶: C++: core::id::NamedAtomID::to_string() const –> std::string

valid(self: pyrosetta.rosetta.core.id.NamedAtomID) → bool¶

Is this id valid?

Must return false for BOGUS_ATOM_ID

C++: core::id::NamedAtomID::valid() const –> bool

class pyrosetta.rosetta.core.id.NamedStubID¶

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.id.NamedStubID, : pyrosetta.rosetta.core.id.NamedStubID) → pyrosetta.rosetta.core.id.NamedStubID¶: C++: core::id::NamedStubID::operator=(const class core::id::NamedStubID &) –> class core::id::NamedStubID &

atom(self: pyrosetta.rosetta.core.id.NamedStubID, index: int) → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: core::id::NamedStubID::atom(const unsigned long) const –> const class core::id::NamedAtomID &

center(self: pyrosetta.rosetta.core.id.NamedStubID) → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: core::id::NamedStubID::center() const –> const class core::id::NamedAtomID &

valid(self: pyrosetta.rosetta.core.id.NamedStubID) → bool¶: C++: core::id::NamedStubID::valid() const –> bool

class pyrosetta.rosetta.core.id.StubID¶

Bases: pybind11_builtins.pybind11_object

BOGUS_STUB_ID() → pyrosetta.rosetta.core.id.StubID¶: C++: core::id::StubID::BOGUS_STUB_ID() –> const class core::id::StubID

assign(self: pyrosetta.rosetta.core.id.StubID, : pyrosetta.rosetta.core.id.StubID) → pyrosetta.rosetta.core.id.StubID¶: C++: core::id::StubID::operator=(const class core::id::StubID &) –> class core::id::StubID &

atom(self: pyrosetta.rosetta.core.id.StubID, index: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::id::StubID::atom(const unsigned long) const –> const class core::id::AtomID &

center(self: pyrosetta.rosetta.core.id.StubID) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::id::StubID::center() const –> const class core::id::AtomID &

valid(self: pyrosetta.rosetta.core.id.StubID) → bool¶: C++: core::id::StubID::valid() const –> bool

class pyrosetta.rosetta.core.id.TorsionID¶

Bases: pybind11_builtins.pybind11_object

Torsion identifier class

Consider a few examples to get a better picture for how torsions are uniquely identified:

Note the order of the elements in construction calls (residue, type, torsion) go from least to most specific.

TorsionIDs are very different for JUMP TorsionTypes. In such a case, they are interpreted as follows: TorsionID(1, JUMP, 2) // RB2 of jump #1 for the Pose.

BOGUS_TORSION_ID() → pyrosetta.rosetta.core.id.TorsionID¶: C++: core::id::TorsionID::BOGUS_TORSION_ID() –> class core::id::TorsionID

assign(self: pyrosetta.rosetta.core.id.TorsionID, : pyrosetta.rosetta.core.id.TorsionID) → pyrosetta.rosetta.core.id.TorsionID¶: C++: core::id::TorsionID::operator=(const class core::id::TorsionID &) –> class core::id::TorsionID &

rsd(self: pyrosetta.rosetta.core.id.TorsionID) → int¶

For this TorsionID, set the Residue number within the complex OR the Jump number for the Pose.

C++: core::id::TorsionID::rsd() –> unsigned long &

torsion(self: pyrosetta.rosetta.core.id.TorsionID) → int¶

Set the torsion number of the given type within the residue OR: the rigid-body identifier for a JUMP TorsionType.

C++: core::id::TorsionID::torsion() –> unsigned long &

type(self: pyrosetta.rosetta.core.id.TorsionID) → pyrosetta.rosetta.core.id.TorsionType¶

Set the type (BB, CHI,NU, BRANCH, JUMP) of this torsion.

C++: core::id::TorsionID::type() –> enum core::id::TorsionType &

valid(self: pyrosetta.rosetta.core.id.TorsionID) → bool¶

Is this id valid?

Must return false for BOGUS_TORSION_ID

C++: core::id::TorsionID::valid() const –> bool

class pyrosetta.rosetta.core.id.TorsionID_Range¶

Bases: pybind11_builtins.pybind11_object

Kinematics DOF identifier (with range) class

max(self: pyrosetta.rosetta.core.id.TorsionID_Range) → float¶: C++: core::id::TorsionID_Range::max() const –> double

min(self: pyrosetta.rosetta.core.id.TorsionID_Range) → float¶: C++: core::id::TorsionID_Range::min() const –> double

torsion_id(self: pyrosetta.rosetta.core.id.TorsionID_Range) → pyrosetta.rosetta.core.id.TorsionID¶: C++: core::id::TorsionID_Range::torsion_id() const –> const class core::id::TorsionID &

class pyrosetta.rosetta.core.id.TorsionType¶

Bases: pybind11_builtins.pybind11_object

Torsion type – used in the TorsionID class

BB : “backbone” torsion (Actually, this is a main-chain torsion.)

CHI : sidechain torsion

NU : internal ring torsion

BRANCH : torsions at branch connection points which are CHEMICAL edges of the FoldTree

JUMP : rigid-body transformation

Members:

BB

CHI

NU

BRANCH

JUMP

pyrosetta.rosetta.core.id.combine_sequence_mappings(smap: pyrosetta.rosetta.core.id.SequenceMapping, smap_to_add: pyrosetta.rosetta.core.id.SequenceMapping) → None¶

combine the input sequence mappings into one: utility function added by flo, feb 2011

C++: core::id::combine_sequence_mappings(class core::id::SequenceMapping &, const class core::id::SequenceMapping &) –> void

pyrosetta.rosetta.core.id.get_rb_number(t: pyrosetta.rosetta.core.id.DOF_Type) → int¶: C++: core::id::get_rb_number(const enum core::id::DOF_Type) –> unsigned long

pyrosetta.rosetta.core.id.get_rb_type(k: int) → pyrosetta.rosetta.core.id.DOF_Type¶: C++: core::id::get_rb_type(const unsigned long) –> enum core::id::DOF_Type

pyrosetta.rosetta.core.id.initialize_core_id_globals() → None¶

Calling this function ensures that all of the global variables in core::id are initialize: before they are needed

C++: core::id::initialize_core_id_globals() –> void

pyrosetta.rosetta.core.id.to_string(*args, **kwargs)¶

Overloaded function.

to_string(type: pyrosetta.rosetta.core.id.DOF_Type) -> str

C++: core::id::to_string(const enum core::id::DOF_Type &) –> std::string

to_string(type: pyrosetta.rosetta.core.id.TorsionType) -> str

C++: core::id::to_string(const enum core::id::TorsionType &) –> std::string