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.

static BOGUS_ATOM_ID() pyrosetta.rosetta.core.id.AtomID

C++: core::id::AtomID::BOGUS_ATOM_ID() –> class core::id::AtomID

static 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 &

deserialize(self: pyrosetta.rosetta.core.id.AtomID, 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 AtomID

C++: core::id::AtomID::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

rsd(self: pyrosetta.rosetta.core.id.AtomID) int

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

serialize(self: pyrosetta.rosetta.core.id.AtomID) pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize an AtomID to a json_spirit object

C++: core::id::AtomID::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

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.AtomID_Map_AtomID

Bases: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) bool

C++: core::id::AtomID_Map<core::id::AtomID>::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, : pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t

C++: core::id::AtomID_Map<core::id::AtomID>::operator=(const class core::id::AtomID_Map<class core::id::AtomID> &) –> class core::id::AtomID_Map<class core::id::AtomID> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::clear(const class core::id::AtomID &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> core::id::AtomID

C++: core::id::AtomID_Map<core::id::AtomID>::default_value() const –> const class core::id::AtomID &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::default_value(const class core::id::AtomID &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) bool

C++: core::id::AtomID_Map<core::id::AtomID>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, value: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::fill_with(const class core::id::AtomID &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, seqpos: int, value: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::fill_with(const unsigned long, const class core::id::AtomID &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, id: core::id::AtomID) core::id::AtomID

C++: core::id::AtomID_Map<core::id::AtomID>::get(const class core::id::AtomID &) const –> class core::id::AtomID

has(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<core::id::AtomID>::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res: int) int

C++: core::id::AtomID_Map<core::id::AtomID>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) int

C++: core::id::AtomID_Map<core::id::AtomID>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, n_res: int) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res: int, n_atom: int, value: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::resize(const unsigned long, const unsigned long, const class core::id::AtomID &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, id: core::id::AtomID, value: core::id::AtomID) None

C++: core::id::AtomID_Map<core::id::AtomID>::set(const class core::id::AtomID &, const class core::id::AtomID &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) int

C++: core::id::AtomID_Map<core::id::AtomID>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, s: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::swap(class core::id::AtomID_Map<class core::id::AtomID> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<core::id::AtomID>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_Real

Bases: pyrosetta.rosetta.core.id.AtomID_Map_double_t

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) bool

C++: core::id::AtomID_Map<double>::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, : pyrosetta.rosetta.core.id.AtomID_Map_double_t) pyrosetta.rosetta.core.id.AtomID_Map_double_t

C++: core::id::AtomID_Map<double>::operator=(const class core::id::AtomID_Map<double> &) –> class core::id::AtomID_Map<double> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) -> None

C++: core::id::AtomID_Map<double>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, default_value_a: float) -> None

C++: core::id::AtomID_Map<double>::clear(const double &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) -> float

C++: core::id::AtomID_Map<double>::default_value() const –> const double &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, default_value_a: float) -> None

C++: core::id::AtomID_Map<double>::default_value(const double &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) bool

C++: core::id::AtomID_Map<double>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, value: float) -> None

C++: core::id::AtomID_Map<double>::fill_with(const double &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, seqpos: int, value: float) -> None

C++: core::id::AtomID_Map<double>::fill_with(const unsigned long, const double &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, id: core::id::AtomID) float

C++: core::id::AtomID_Map<double>::get(const class core::id::AtomID &) const –> double

has(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<double>::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, i_res: int) int

C++: core::id::AtomID_Map<double>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) int

C++: core::id::AtomID_Map<double>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, n_res: int) -> None

C++: core::id::AtomID_Map<double>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<double>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, i_res: int, n_atom: int, value: float) -> None

C++: core::id::AtomID_Map<double>::resize(const unsigned long, const unsigned long, const double &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, id: core::id::AtomID, value: float) None

C++: core::id::AtomID_Map<double>::set(const class core::id::AtomID &, const double &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) int

C++: core::id::AtomID_Map<double>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, s: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::swap(class core::id::AtomID_Map<double> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<double>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_bool

Bases: pyrosetta.rosetta.core.id.AtomID_Map_bool_t

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) bool

C++: core::id::AtomID_Map<bool>::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, : pyrosetta.rosetta.core.id.AtomID_Map_bool_t) pyrosetta.rosetta.core.id.AtomID_Map_bool_t

C++: core::id::AtomID_Map<bool>::operator=(const class core::id::AtomID_Map<bool> &) –> class core::id::AtomID_Map<bool> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> None

C++: core::id::AtomID_Map<bool>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, default_value_a: bool) -> None

C++: core::id::AtomID_Map<bool>::clear(const bool &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> bool

C++: core::id::AtomID_Map<bool>::default_value() const –> const bool &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, default_value_a: bool) -> None

C++: core::id::AtomID_Map<bool>::default_value(const bool &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) bool

C++: core::id::AtomID_Map<bool>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, value: bool) -> None

C++: core::id::AtomID_Map<bool>::fill_with(const bool &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, seqpos: int, value: bool) -> None

C++: core::id::AtomID_Map<bool>::fill_with(const unsigned long, const bool &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<bool>::get(const class core::id::AtomID &) const –> bool

has(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<bool>::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, i_res: int) int

C++: core::id::AtomID_Map<bool>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) int

C++: core::id::AtomID_Map<bool>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, n_res: int) -> None

C++: core::id::AtomID_Map<bool>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<bool>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, i_res: int, n_atom: int, value: bool) -> None

C++: core::id::AtomID_Map<bool>::resize(const unsigned long, const unsigned long, const bool &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, id: core::id::AtomID, value: bool) None

C++: core::id::AtomID_Map<bool>::set(const class core::id::AtomID &, const bool &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) int

C++: core::id::AtomID_Map<bool>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, s: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::swap(class core::id::AtomID_Map<bool> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<bool>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_bool_t

Bases: pybind11_builtins.pybind11_object

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) bool

C++: core::id::AtomID_Map<bool>::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, : pyrosetta.rosetta.core.id.AtomID_Map_bool_t) pyrosetta.rosetta.core.id.AtomID_Map_bool_t

C++: core::id::AtomID_Map<bool>::operator=(const class core::id::AtomID_Map<bool> &) –> class core::id::AtomID_Map<bool> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> None

C++: core::id::AtomID_Map<bool>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, default_value_a: bool) -> None

C++: core::id::AtomID_Map<bool>::clear(const bool &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> bool

C++: core::id::AtomID_Map<bool>::default_value() const –> const bool &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, default_value_a: bool) -> None

C++: core::id::AtomID_Map<bool>::default_value(const bool &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) bool

C++: core::id::AtomID_Map<bool>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, value: bool) -> None

C++: core::id::AtomID_Map<bool>::fill_with(const bool &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, seqpos: int, value: bool) -> None

C++: core::id::AtomID_Map<bool>::fill_with(const unsigned long, const bool &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<bool>::get(const class core::id::AtomID &) const –> bool

has(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<bool>::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, i_res: int) int

C++: core::id::AtomID_Map<bool>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) int

C++: core::id::AtomID_Map<bool>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, n_res: int) -> None

C++: core::id::AtomID_Map<bool>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<bool>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, i_res: int, n_atom: int, value: bool) -> None

C++: core::id::AtomID_Map<bool>::resize(const unsigned long, const unsigned long, const bool &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, id: core::id::AtomID, value: bool) None

C++: core::id::AtomID_Map<bool>::set(const class core::id::AtomID &, const bool &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) int

C++: core::id::AtomID_Map<bool>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, s: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::id::AtomID_Map<bool>::swap(class core::id::AtomID_Map<bool> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<bool>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t

Bases: pybind11_builtins.pybind11_object

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) bool

C++: core::id::AtomID_Map<core::id::AtomID>::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, : pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t

C++: core::id::AtomID_Map<core::id::AtomID>::operator=(const class core::id::AtomID_Map<class core::id::AtomID> &) –> class core::id::AtomID_Map<class core::id::AtomID> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::clear(const class core::id::AtomID &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> core::id::AtomID

C++: core::id::AtomID_Map<core::id::AtomID>::default_value() const –> const class core::id::AtomID &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::default_value(const class core::id::AtomID &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) bool

C++: core::id::AtomID_Map<core::id::AtomID>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, value: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::fill_with(const class core::id::AtomID &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, seqpos: int, value: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::fill_with(const unsigned long, const class core::id::AtomID &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, id: core::id::AtomID) core::id::AtomID

C++: core::id::AtomID_Map<core::id::AtomID>::get(const class core::id::AtomID &) const –> class core::id::AtomID

has(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<core::id::AtomID>::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res: int) int

C++: core::id::AtomID_Map<core::id::AtomID>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) int

C++: core::id::AtomID_Map<core::id::AtomID>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, n_res: int) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res: int, n_atom: int, value: core::id::AtomID) -> None

C++: core::id::AtomID_Map<core::id::AtomID>::resize(const unsigned long, const unsigned long, const class core::id::AtomID &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, id: core::id::AtomID, value: core::id::AtomID) None

C++: core::id::AtomID_Map<core::id::AtomID>::set(const class core::id::AtomID &, const class core::id::AtomID &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) int

C++: core::id::AtomID_Map<core::id::AtomID>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, s: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) None

C++: core::id::AtomID_Map<core::id::AtomID>::swap(class core::id::AtomID_Map<class core::id::AtomID> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<core::id::AtomID>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t

Bases: pybind11_builtins.pybind11_object

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) bool

C++: core::id::AtomID_Map<core::id::TorsionID>::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, : pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t

C++: core::id::AtomID_Map<core::id::TorsionID>::operator=(const class core::id::AtomID_Map<class core::id::TorsionID> &) –> class core::id::AtomID_Map<class core::id::TorsionID> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, default_value_a: core::id::TorsionID) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::clear(const class core::id::TorsionID &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> core::id::TorsionID

C++: core::id::AtomID_Map<core::id::TorsionID>::default_value() const –> const class core::id::TorsionID &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, default_value_a: core::id::TorsionID) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::default_value(const class core::id::TorsionID &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) bool

C++: core::id::AtomID_Map<core::id::TorsionID>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) None

C++: core::id::AtomID_Map<core::id::TorsionID>::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, value: core::id::TorsionID) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::fill_with(const class core::id::TorsionID &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, seqpos: int, value: core::id::TorsionID) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::fill_with(const unsigned long, const class core::id::TorsionID &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) None

C++: core::id::AtomID_Map<core::id::TorsionID>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id: core::id::AtomID) core::id::TorsionID

C++: core::id::AtomID_Map<core::id::TorsionID>::get(const class core::id::AtomID &) const –> class core::id::TorsionID

has(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<core::id::TorsionID>::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res: int) int

C++: core::id::AtomID_Map<core::id::TorsionID>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) int

C++: core::id::AtomID_Map<core::id::TorsionID>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, n_res: int) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res: int, n_atom: int, value: core::id::TorsionID) -> None

C++: core::id::AtomID_Map<core::id::TorsionID>::resize(const unsigned long, const unsigned long, const class core::id::TorsionID &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id: core::id::AtomID, value: core::id::TorsionID) None

C++: core::id::AtomID_Map<core::id::TorsionID>::set(const class core::id::AtomID &, const class core::id::TorsionID &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) None

C++: core::id::AtomID_Map<core::id::TorsionID>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) int

C++: core::id::AtomID_Map<core::id::TorsionID>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, s: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t) None

C++: core::id::AtomID_Map<core::id::TorsionID>::swap(class core::id::AtomID_Map<class core::id::TorsionID> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<core::id::TorsionID>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_double_t

Bases: pybind11_builtins.pybind11_object

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) bool

C++: core::id::AtomID_Map<double>::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, : pyrosetta.rosetta.core.id.AtomID_Map_double_t) pyrosetta.rosetta.core.id.AtomID_Map_double_t

C++: core::id::AtomID_Map<double>::operator=(const class core::id::AtomID_Map<double> &) –> class core::id::AtomID_Map<double> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) -> None

C++: core::id::AtomID_Map<double>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, default_value_a: float) -> None

C++: core::id::AtomID_Map<double>::clear(const double &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) -> float

C++: core::id::AtomID_Map<double>::default_value() const –> const double &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, default_value_a: float) -> None

C++: core::id::AtomID_Map<double>::default_value(const double &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) bool

C++: core::id::AtomID_Map<double>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, value: float) -> None

C++: core::id::AtomID_Map<double>::fill_with(const double &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, seqpos: int, value: float) -> None

C++: core::id::AtomID_Map<double>::fill_with(const unsigned long, const double &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, id: core::id::AtomID) float

C++: core::id::AtomID_Map<double>::get(const class core::id::AtomID &) const –> double

has(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<double>::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, i_res: int) int

C++: core::id::AtomID_Map<double>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) int

C++: core::id::AtomID_Map<double>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, n_res: int) -> None

C++: core::id::AtomID_Map<double>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<double>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, i_res: int, n_atom: int, value: float) -> None

C++: core::id::AtomID_Map<double>::resize(const unsigned long, const unsigned long, const double &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, id: core::id::AtomID, value: float) None

C++: core::id::AtomID_Map<double>::set(const class core::id::AtomID &, const double &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t) int

C++: core::id::AtomID_Map<double>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, s: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None

C++: core::id::AtomID_Map<double>::swap(class core::id::AtomID_Map<double> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_double_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<double>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t

Bases: pybind11_builtins.pybind11_object

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) bool

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, : pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::operator=(const class core::id::AtomID_Map<class numeric::xyzVector<double> > &) –> class core::id::AtomID_Map<class numeric::xyzVector<double> > &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, default_value_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::clear(const class numeric::xyzVector<double> &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::default_value() const –> const class numeric::xyzVector<double> &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, default_value_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::default_value(const class numeric::xyzVector<double> &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) bool

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, value: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::fill_with(const class numeric::xyzVector<double> &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, seqpos: int, value: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::fill_with(const unsigned long, const class numeric::xyzVector<double> &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id: core::id::AtomID) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::get(const class core::id::AtomID &) const –> class numeric::xyzVector<double>

has(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res: int) int

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) int

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, n_res: int) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res: int, n_atom: int, value: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::resize(const unsigned long, const unsigned long, const class numeric::xyzVector<double> &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id: core::id::AtomID, value: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::set(const class core::id::AtomID &, const class numeric::xyzVector<double> &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) int

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, s: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::swap(class core::id::AtomID_Map<class numeric::xyzVector<double> > &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<numeric::xyzVector<double> >::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t

Bases: pybind11_builtins.pybind11_object

all_default(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) bool

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::all_default() –> bool

assign(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, : pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::operator=(const class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) –> class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, default_value_a: core::kinematics::tree::Atom) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::clear(const class std::shared_ptr<class core::kinematics::tree::Atom> &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> core::kinematics::tree::Atom

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::default_value() const –> const class std::shared_ptr<class core::kinematics::tree::Atom> &

  1. default_value(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, default_value_a: core::kinematics::tree::Atom) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::default_value(const class std::shared_ptr<class core::kinematics::tree::Atom> &) –> void

empty(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) bool

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::fill() –> void

fill_with(*args, **kwargs)

Overloaded function.

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, value: core::kinematics::tree::Atom) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::fill_with(const class std::shared_ptr<class core::kinematics::tree::Atom> &) –> void

  1. fill_with(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, seqpos: int, value: core::kinematics::tree::Atom) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::fill_with(const unsigned long, const class std::shared_ptr<class core::kinematics::tree::Atom> &) –> void

finalize(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::finalize() –> void

get(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id: core::id::AtomID) core::kinematics::tree::Atom

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::get(const class core::id::AtomID &) const –> class std::shared_ptr<class core::kinematics::tree::Atom>

has(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id: core::id::AtomID) bool

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::has(const class core::id::AtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res: int) int

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) int

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, n_res: int) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res: int, n_atom: int) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res: int, n_atom: int, value: core::kinematics::tree::Atom) -> None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::resize(const unsigned long, const unsigned long, const class std::shared_ptr<class core::kinematics::tree::Atom> &) –> void

set(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id: core::id::AtomID, value: core::kinematics::tree::Atom) None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::set(const class core::id::AtomID &, const class std::shared_ptr<class core::kinematics::tree::Atom> &) –> void

shrink(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::shrink() –> void

size(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) int

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, s: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::swap(class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::AtomID_Map<std::shared_ptr<core::kinematics::tree::Atom> >::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.BondID

Bases: pybind11_builtins.pybind11_object

two more classes, temporary for testing purposes

property atom1
property atom2
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

static 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_Map_bool_t

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, : pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t

C++: core::id::DOF_ID_Map<bool>::operator=(const class core::id::DOF_ID_Map<bool> &) –> class core::id::DOF_ID_Map<bool> &

clear(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) None

C++: core::id::DOF_ID_Map<bool>::clear() –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, dof: pyrosetta.rosetta.core.id.DOF_Type) -> bool

C++: core::id::DOF_ID_Map<bool>::default_value(const enum core::id::DOF_Type) const –> const bool &

  1. default_value(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, dof: pyrosetta.rosetta.core.id.DOF_Type, default_value_a: bool) -> None

C++: core::id::DOF_ID_Map<bool>::default_value(const enum core::id::DOF_Type, const bool &) –> void

  1. default_value(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, default_value_a: bool) -> None

C++: core::id::DOF_ID_Map<bool>::default_value(const bool &) –> void

empty(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) bool

C++: core::id::DOF_ID_Map<bool>::empty() const –> bool

finalize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) None

C++: core::id::DOF_ID_Map<bool>::finalize() –> void

n_atom(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, i_res: int) int

C++: core::id::DOF_ID_Map<bool>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) int

C++: core::id::DOF_ID_Map<bool>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, n_res: int) -> None

C++: core::id::DOF_ID_Map<bool>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, i_res: int, n_atom: int) -> None

C++: core::id::DOF_ID_Map<bool>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, i_res: int, n_atom: int, value: bool) -> None

C++: core::id::DOF_ID_Map<bool>::resize(const unsigned long, const unsigned long, const bool &) –> void

set(*args, **kwargs)

Overloaded function.

  1. set(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, dof: pyrosetta.rosetta.core.id.DOF_Type) -> None

C++: core::id::DOF_ID_Map<bool>::set(const enum core::id::DOF_Type) –> void

  1. set(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, dof: pyrosetta.rosetta.core.id.DOF_Type, value: bool) -> None

C++: core::id::DOF_ID_Map<bool>::set(const enum core::id::DOF_Type, const bool &) –> void

shrink(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) None

C++: core::id::DOF_ID_Map<bool>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) int

C++: core::id::DOF_ID_Map<bool>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, s: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) None

C++: core::id::DOF_ID_Map<bool>::swap(class core::id::DOF_ID_Map<bool> &) –> void

class pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t

Bases: pybind11_builtins.pybind11_object

clear(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::clear() –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof: pyrosetta.rosetta.core.id.DOF_Type) -> core::id::TorsionID

C++: core::id::DOF_ID_Map<core::id::TorsionID>::default_value(const enum core::id::DOF_Type) const –> const class core::id::TorsionID &

  1. default_value(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof: pyrosetta.rosetta.core.id.DOF_Type, default_value_a: core::id::TorsionID) -> None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::default_value(const enum core::id::DOF_Type, const class core::id::TorsionID &) –> void

  1. default_value(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, default_value_a: core::id::TorsionID) -> None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::default_value(const class core::id::TorsionID &) –> void

empty(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) bool

C++: core::id::DOF_ID_Map<core::id::TorsionID>::empty() const –> bool

finalize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::finalize() –> void

n_atom(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res: int) int

C++: core::id::DOF_ID_Map<core::id::TorsionID>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) int

C++: core::id::DOF_ID_Map<core::id::TorsionID>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, n_res: int) -> None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res: int, n_atom: int) -> None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res: int, n_atom: int, value: core::id::TorsionID) -> None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::resize(const unsigned long, const unsigned long, const class core::id::TorsionID &) –> void

set(*args, **kwargs)

Overloaded function.

  1. set(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof: pyrosetta.rosetta.core.id.DOF_Type) -> None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::set(const enum core::id::DOF_Type) –> void

  1. set(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof: pyrosetta.rosetta.core.id.DOF_Type, value: core::id::TorsionID) -> None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::set(const enum core::id::DOF_Type, const class core::id::TorsionID &) –> void

shrink(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) int

C++: core::id::DOF_ID_Map<core::id::TorsionID>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, s: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) None

C++: core::id::DOF_ID_Map<core::id::TorsionID>::swap(class core::id::DOF_ID_Map<class core::id::TorsionID> &) –> void

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

D = <DOF_Type.D: 3>
INVALID_DOF = <DOF_Type.INVALID_DOF: 0>
PHI = <DOF_Type.PHI: 1>
RB1 = <DOF_Type.RB1: 4>
RB2 = <DOF_Type.RB2: 5>
RB3 = <DOF_Type.RB3: 6>
RB4 = <DOF_Type.RB4: 7>
RB5 = <DOF_Type.RB5: 8>
RB6 = <DOF_Type.RB6: 9>
THETA = <DOF_Type.THETA: 2>
property name
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.EXCN_AtomNotFound

Bases: pyrosetta.rosetta.utility.excn.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.core.id.EXCN_AtomNotFound, : pyrosetta.rosetta.core.id.EXCN_AtomNotFound) pyrosetta.rosetta.core.id.EXCN_AtomNotFound

C++: core::id::EXCN_AtomNotFound::operator=(const class core::id::EXCN_AtomNotFound &) –> class core::id::EXCN_AtomNotFound &

atom(self: pyrosetta.rosetta.core.id.EXCN_AtomNotFound) pyrosetta.rosetta.core.id.NamedAtomID

C++: core::id::EXCN_AtomNotFound::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.

  1. 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

  1. 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.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

property name
omega2_dihedral = <MainchainTorsionType.omega2_dihedral: 4>
omega3_dihedral = <MainchainTorsionType.omega3_dihedral: 5>
omega_dihedral = <MainchainTorsionType.omega_dihedral: 3>
phi_dihedral = <MainchainTorsionType.phi_dihedral: 1>
psi_dihedral = <MainchainTorsionType.psi_dihedral: 2>
class pyrosetta.rosetta.core.id.NamedAtomID

Bases: pybind11_builtins.pybind11_object

Atom identifier class

static BOGUS_NAMED_ATOM_ID() pyrosetta.rosetta.core.id.NamedAtomID

C++: core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID() –> const class core::id::NamedAtomID

static 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.NamedAtomID_Map_NamedAtomID

Bases: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t

assign(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID, : pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID) pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID

C++: core::id::NamedAtomID_Map_NamedAtomID::operator=(const class core::id::NamedAtomID_Map_NamedAtomID &) –> class core::id::NamedAtomID_Map_NamedAtomID &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a: pyrosetta.rosetta.core.id.NamedAtomID) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::clear(const class core::id::NamedAtomID &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> pyrosetta.rosetta.core.id.NamedAtomID

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::default_value() const –> const class core::id::NamedAtomID &

  1. default_value(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a: pyrosetta.rosetta.core.id.NamedAtomID) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::default_value(const class core::id::NamedAtomID &) –> void

empty(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) bool

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::fill() –> void

finalize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id: pyrosetta.rosetta.core.id.NamedAtomID) pyrosetta.rosetta.core.id.NamedAtomID

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::get(const class core::id::NamedAtomID &) const –> const class core::id::NamedAtomID

has(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id: pyrosetta.rosetta.core.id.NamedAtomID) bool

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::has(const class core::id::NamedAtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res: int) int

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) int

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, n_res: int) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, : int, : int) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, : int, : int, : pyrosetta.rosetta.core.id.NamedAtomID) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::resize(const unsigned long, const unsigned long, const class core::id::NamedAtomID &) –> void

set(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id: pyrosetta.rosetta.core.id.NamedAtomID, value: pyrosetta.rosetta.core.id.NamedAtomID) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::set(const class core::id::NamedAtomID &, const class core::id::NamedAtomID &) –> void

shrink(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) int

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, s: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::swap(class core::id::NamedAtomID_Map<class core::id::NamedAtomID> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, : pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::operator=(const class core::id::NamedAtomID_Map<class core::id::NamedAtomID> &) –> class core::id::NamedAtomID_Map<class core::id::NamedAtomID> &

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::clear() –> void

  1. clear(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a: pyrosetta.rosetta.core.id.NamedAtomID) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::clear(const class core::id::NamedAtomID &) –> void

default_value(*args, **kwargs)

Overloaded function.

  1. default_value(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> pyrosetta.rosetta.core.id.NamedAtomID

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::default_value() const –> const class core::id::NamedAtomID &

  1. default_value(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a: pyrosetta.rosetta.core.id.NamedAtomID) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::default_value(const class core::id::NamedAtomID &) –> void

empty(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) bool

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::empty() const –> bool

fill(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::fill() –> void

finalize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::finalize() –> void

get(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id: pyrosetta.rosetta.core.id.NamedAtomID) pyrosetta.rosetta.core.id.NamedAtomID

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::get(const class core::id::NamedAtomID &) const –> const class core::id::NamedAtomID

has(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id: pyrosetta.rosetta.core.id.NamedAtomID) bool

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::has(const class core::id::NamedAtomID &) const –> bool

n_atom(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res: int) int

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::n_atom(const unsigned long) const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) int

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::n_residue() const –> unsigned long

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, n_res: int) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::resize(const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, : int, : int) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::resize(const unsigned long, const unsigned long) –> void

  1. resize(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, : int, : int, : pyrosetta.rosetta.core.id.NamedAtomID) -> None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::resize(const unsigned long, const unsigned long, const class core::id::NamedAtomID &) –> void

set(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id: pyrosetta.rosetta.core.id.NamedAtomID, value: pyrosetta.rosetta.core.id.NamedAtomID) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::set(const class core::id::NamedAtomID &, const class core::id::NamedAtomID &) –> void

shrink(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::shrink() –> void

size(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) int

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, s: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::swap(class core::id::NamedAtomID_Map<class core::id::NamedAtomID> &) –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, new_size: int, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::id::NamedAtomID_Map<core::id::NamedAtomID>::update_sequence_numbering(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

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 &

property atom1
property atom2
property atom3
center(self: pyrosetta.rosetta.core.id.NamedStubID) pyrosetta.rosetta.core.id.NamedAtomID

C++: core::id::NamedStubID::center() const –> const class core::id::NamedAtomID &

property center_
valid(self: pyrosetta.rosetta.core.id.NamedStubID) bool

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

class pyrosetta.rosetta.core.id.PartialAtomID

Bases: pybind11_builtins.pybind11_object

Partial atom identifier class. Defined by an atom index and a residue number, or by an inter-residue-connection index, the number of bonds away from the inter-residue-connection atom, and a residue number.

static BOGUS_PARTIAL_ATOM_ID() pyrosetta.rosetta.core.id.PartialAtomID

C++: core::id::PartialAtomID::BOGUS_PARTIAL_ATOM_ID() –> class core::id::PartialAtomID

static CHAINBREAK_BOGUS_PARTIAL_ATOM_ID() pyrosetta.rosetta.core.id.PartialAtomID

C++: core::id::PartialAtomID::CHAINBREAK_BOGUS_PARTIAL_ATOM_ID() –> class core::id::PartialAtomID

assign(self: pyrosetta.rosetta.core.id.PartialAtomID, : pyrosetta.rosetta.core.id.PartialAtomID) pyrosetta.rosetta.core.id.PartialAtomID

C++: core::id::PartialAtomID::operator=(const class core::id::PartialAtomID &) –> class core::id::PartialAtomID &

atomno(self: pyrosetta.rosetta.core.id.PartialAtomID) int

Returns the atom index

C++: core::id::PartialAtomID::atomno() const –> unsigned long

bonds_from_resconn(self: pyrosetta.rosetta.core.id.PartialAtomID) int
Returns the number of chemical bonds away from the

residue-connection atom the target atom is located

C++: core::id::PartialAtomID::bonds_from_resconn() const –> unsigned long

complete(self: pyrosetta.rosetta.core.id.PartialAtomID) bool

C++: core::id::PartialAtomID::complete() const –> bool

deserialize(self: pyrosetta.rosetta.core.id.PartialAtomID, 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 AtomID

C++: core::id::PartialAtomID::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

partial(self: pyrosetta.rosetta.core.id.PartialAtomID) bool

C++: core::id::PartialAtomID::partial() const –> bool

resconnid(self: pyrosetta.rosetta.core.id.PartialAtomID) int

Returns the inter-residue connection index

C++: core::id::PartialAtomID::resconnid() const –> unsigned long

rsd(self: pyrosetta.rosetta.core.id.PartialAtomID) int

Returns the residue number

C++: core::id::PartialAtomID::rsd() const –> unsigned long

serialize(self: pyrosetta.rosetta.core.id.PartialAtomID) pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize an AtomID to a json_spirit object

C++: core::id::PartialAtomID::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_complete(self: pyrosetta.rosetta.core.id.PartialAtomID, atomno_in: int, rsd_in: int) None

Set the value of atom and residue.

C++: core::id::PartialAtomID::set_complete(unsigned long, unsigned long) –> void

set_partial(self: pyrosetta.rosetta.core.id.PartialAtomID, resconnid_in: int, bonds_from_resconn_in: int, rsd_in: int) None

Set the value of the inter-residue connection index and residue.

C++: core::id::PartialAtomID::set_partial(unsigned long, unsigned long, unsigned long) –> void

valid(self: pyrosetta.rosetta.core.id.PartialAtomID) bool

Returns true if the PartialAtomID is valid

must return false for BOGUS_ATOM_ID

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

class pyrosetta.rosetta.core.id.SequenceMapping

Bases: pybind11_builtins.pybind11_object

all_aligned(self: pyrosetta.rosetta.core.id.SequenceMapping) bool

C++: core::id::SequenceMapping::all_aligned() const –> bool

assign(self: pyrosetta.rosetta.core.id.SequenceMapping, src: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.id.SequenceMapping

C++: core::id::SequenceMapping::operator=(const class core::id::SequenceMapping &) –> class core::id::SequenceMapping &

clear(self: pyrosetta.rosetta.core.id.SequenceMapping) None

C++: core::id::SequenceMapping::clear() –> void

delete_source_residue(self: pyrosetta.rosetta.core.id.SequenceMapping, pos1: int) None

C++: core::id::SequenceMapping::delete_source_residue(const unsigned long) –> void

delete_target_residue(self: pyrosetta.rosetta.core.id.SequenceMapping, pos: int) None

C++: core::id::SequenceMapping::delete_target_residue(const unsigned long) –> void

downstream_combine(self: pyrosetta.rosetta.core.id.SequenceMapping, smap_to_add: pyrosetta.rosetta.core.id.SequenceMapping) None
Apply a B->C mapping to the current A->B mapping to get an A->C mapping

i.e. smap[j] becomes smap_to_add[ smap[j] ]

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

get_corresponding_residue_in_current(self: pyrosetta.rosetta.core.id.SequenceMapping, original_resnum: int) int

A->B; Get the corresponding (new) resnum (B) from the old (A).

C++: core::id::SequenceMapping::get_corresponding_residue_in_current(unsigned long) const –> unsigned long

static identity(size: int) pyrosetta.rosetta.core.id.SequenceMapping
Construct an identity mapping, which means that for all positions,

i in seq1 maps to i in seq2.

C++: core::id::SequenceMapping::identity(const unsigned long) –> class core::id::SequenceMapping

insert_aligned_residue(self: pyrosetta.rosetta.core.id.SequenceMapping, pos1: int, pos2: int) None

C++: core::id::SequenceMapping::insert_aligned_residue(const unsigned long, const unsigned long) –> void

insert_aligned_residue_safe(self: pyrosetta.rosetta.core.id.SequenceMapping, pos1: int, pos2: int) None

same as insert_aligned_residue, but a couple of extra checks on size1 and size2.

C++: core::id::SequenceMapping::insert_aligned_residue_safe(const unsigned long, const unsigned long) –> void

insert_source_residue(self: pyrosetta.rosetta.core.id.SequenceMapping, pos1: int) None

C++: core::id::SequenceMapping::insert_source_residue(const unsigned long) –> void

insert_target_residue(self: pyrosetta.rosetta.core.id.SequenceMapping, pos: int) None

C++: core::id::SequenceMapping::insert_target_residue(const unsigned long) –> void

is_identity(self: pyrosetta.rosetta.core.id.SequenceMapping) bool

C++: core::id::SequenceMapping::is_identity() const –> bool

is_identity_ignore_gaps(self: pyrosetta.rosetta.core.id.SequenceMapping) bool

C++: core::id::SequenceMapping::is_identity_ignore_gaps() const –> bool

mapping(*args, **kwargs)

Overloaded function.

  1. mapping(self: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::id::SequenceMapping::mapping() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. mapping(self: pyrosetta.rosetta.core.id.SequenceMapping, mapping: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::id::SequenceMapping::mapping(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

push_back(self: pyrosetta.rosetta.core.id.SequenceMapping, al: int) None

C++: core::id::SequenceMapping::push_back(const unsigned long) –> void

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.core.id.SequenceMapping, s1: int, s2: int) -> None

  2. resize(self: pyrosetta.rosetta.core.id.SequenceMapping, s1: int, s2: int, clear_values: bool) -> None

resize

new size of the target sequence

new size of the aligned sequence

optional parameter, defaults to true. By default, reset mapping to empty. Cases where passing clear_values as false is desired should be rare.

C++: core::id::SequenceMapping::resize(const unsigned long, const unsigned long, bool) –> void

reverse(self: pyrosetta.rosetta.core.id.SequenceMapping) None

go from an A->B mapping to a B->A mapping

C++: core::id::SequenceMapping::reverse() –> void

same_type_as_me(self: pyrosetta.rosetta.core.id.SequenceMapping, other: pyrosetta.rosetta.core.id.SequenceMapping) bool
virtual function for ensuring both sequence mappings are the same type;

essential for a valid equality operator.

C++: core::id::SequenceMapping::same_type_as_me(const class core::id::SequenceMapping &) const –> bool

set_offset(self: pyrosetta.rosetta.core.id.SequenceMapping, setting: int) None

C++: core::id::SequenceMapping::set_offset(int) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.id.SequenceMapping) -> None

C++: core::id::SequenceMapping::show() const –> void

  1. show(self: pyrosetta.rosetta.core.id.SequenceMapping, output: pyrosetta.rosetta.std.ostream) -> None

C++: core::id::SequenceMapping::show(std::ostream &) const –> void

size1(self: pyrosetta.rosetta.core.id.SequenceMapping) int

size of target sequence

C++: core::id::SequenceMapping::size1() const –> unsigned long

size2(*args, **kwargs)

Overloaded function.

  1. size2(self: pyrosetta.rosetta.core.id.SequenceMapping) -> int

size of aligned sequence ???

C++: core::id::SequenceMapping::size2() const –> unsigned long

  1. size2(self: pyrosetta.rosetta.core.id.SequenceMapping, s2: int) -> None

C++: core::id::SequenceMapping::size2(const unsigned long) –> void

to_string(self: pyrosetta.rosetta.core.id.SequenceMapping) str

C++: core::id::SequenceMapping::to_string() const –> std::string

upstream_combine(self: pyrosetta.rosetta.core.id.SequenceMapping, smap_to_add: pyrosetta.rosetta.core.id.SequenceMapping) None
Apply a C->A mapping to the current A->B mapping to get a C->B mapping

i.e. smap[j] becomes smap[ smap_to_add[ j ] ]

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

class pyrosetta.rosetta.core.id.StubID

Bases: pybind11_builtins.pybind11_object

static 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 &

property atom1
property atom2
property atom3
center(self: pyrosetta.rosetta.core.id.StubID) pyrosetta.rosetta.core.id.AtomID

C++: core::id::StubID::center() const –> const class core::id::AtomID &

property center_
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.

static 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 &

str(self: pyrosetta.rosetta.core.id.TorsionID) str

C++: core::id::TorsionID::str() const –> std::string

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

BB = <TorsionType.BB: 1>
BRANCH = <TorsionType.BRANCH: 4>
CHI = <TorsionType.CHI: 2>
JUMP = <TorsionType.JUMP: 5>
NU = <TorsionType.NU: 3>
property name
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.

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

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

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

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