environment

Bindings for core::environment namespace

class pyrosetta.rosetta.core.environment.DofPassport

Bases: pybind11_object

active_dofs(self: pyrosetta.rosetta.core.environment.DofPassport) → pyrosetta.rosetta.std.set_core_id_DOF_ID_t

C++: core::environment::DofPassport::active_dofs() const –> const class std::set<class core::id::DOF_ID, struct std::less<class core::id::DOF_ID>, class std::allocator<class core::id::DOF_ID> > &

active_jumps(self: pyrosetta.rosetta.core.environment.DofPassport) → pyrosetta.rosetta.utility.vector1_int

C++: core::environment::DofPassport::active_jumps() const –> class utility::vector1<int, class std::allocator<int> >

add_dof_access(self: pyrosetta.rosetta.core.environment.DofPassport, id: pyrosetta.rosetta.core.id.DOF_ID) → None

configure passport to allow access to a bond length or angle dof_id

the DOF_ID to allow access to

C++: core::environment::DofPassport::add_dof_access(const class core::id::DOF_ID &) –> void

assign(self: pyrosetta.rosetta.core.environment.DofPassport, : pyrosetta.rosetta.core.environment.DofPassport) → pyrosetta.rosetta.core.environment.DofPassport

C++: core::environment::DofPassport::operator=(const class core::environment::DofPassport &) –> class core::environment::DofPassport &

dof_access(*args, **kwargs)

Overloaded function.

  1. dof_access(self: pyrosetta.rosetta.core.environment.DofPassport, id: pyrosetta.rosetta.core.id.DOF_ID) -> bool

C++: core::environment::DofPassport::dof_access(const class core::id::DOF_ID &) const –> bool

  1. dof_access(self: pyrosetta.rosetta.core.environment.DofPassport, : core::environment::EnvCore, id: pyrosetta.rosetta.core.id.DOF_ID) -> bool

C++: core::environment::DofPassport::dof_access(const class core::environment::EnvCore &, const class core::id::DOF_ID &) const –> bool

env_id(self: pyrosetta.rosetta.core.environment.DofPassport) → int

C++: core::environment::DofPassport::env_id() const –> const unsigned long &

has_jump_access(self: pyrosetta.rosetta.core.environment.DofPassport, jump_num: int) → bool

C++: core::environment::DofPassport::has_jump_access(int) const –> bool

mover(self: pyrosetta.rosetta.core.environment.DofPassport) → str

C++: core::environment::DofPassport::mover() const –> const std::string &

reference_conformation(*args, **kwargs)

Overloaded function.

  1. reference_conformation(self: pyrosetta.rosetta.core.environment.DofPassport) -> pyrosetta.rosetta.core.conformation.Conformation

C++: core::environment::DofPassport::reference_conformation() const –> class std::shared_ptr<const class core::conformation::Conformation>

  1. reference_conformation(self: pyrosetta.rosetta.core.environment.DofPassport, conf: pyrosetta.rosetta.core.conformation.Conformation) -> None

C++: core::environment::DofPassport::reference_conformation(class std::shared_ptr<const class core::conformation::Conformation>) –> void

render_movemap(*args, **kwargs)

Overloaded function.

  1. render_movemap(self: pyrosetta.rosetta.core.environment.DofPassport) -> core::kinematics::MoveMap

C++: core::environment::DofPassport::render_movemap() const –> class std::shared_ptr<class core::kinematics::MoveMap>

  1. render_movemap(self: pyrosetta.rosetta.core.environment.DofPassport, : core::kinematics::MoveMap) -> None

C++: core::environment::DofPassport::render_movemap(class std::shared_ptr<class core::kinematics::MoveMap>) const –> void

revoke_all_access(self: pyrosetta.rosetta.core.environment.DofPassport) → None

C++: core::environment::DofPassport::revoke_all_access() –> void

show(self: pyrosetta.rosetta.core.environment.DofPassport, : pyrosetta.rosetta.std.ostream) → None

C++: core::environment::DofPassport::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.environment.EXCN_Env_Exception

Bases: 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.environment.EXCN_Env_Exception, : pyrosetta.rosetta.core.environment.EXCN_Env_Exception) → pyrosetta.rosetta.core.environment.EXCN_Env_Exception

C++: core::environment::EXCN_Env_Exception::operator=(const class core::environment::EXCN_Env_Exception &) –> class core::environment::EXCN_Env_Exception &

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.environment.EXCN_FTSketchGraph

Bases: 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.environment.EXCN_FTSketchGraph, : pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph) → pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph

C++: core::environment::EXCN_FTSketchGraph::operator=(const class core::environment::EXCN_FTSketchGraph &) –> class core::environment::EXCN_FTSketchGraph &

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.environment.EnvCore

Bases: pybind11_object

id(self: pyrosetta.rosetta.core.environment.EnvCore) → int

C++: core::environment::EnvCore::id() const –> const unsigned long &

name(self: pyrosetta.rosetta.core.environment.EnvCore) → str

C++: core::environment::EnvCore::name() const –> const std::string &

superenv(self: pyrosetta.rosetta.core.environment.EnvCore) → pyrosetta.rosetta.std.weak_ptr_const_core_environment_EnvCore_t

C++: core::environment::EnvCore::superenv() const –> class std::weak_ptr<const class core::environment::EnvCore>

class pyrosetta.rosetta.core.environment.FoldTreeSketch

Bases: pybind11_object

class Node

Bases: pybind11_object

add_jump_neighbor(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, n: pyrosetta.rosetta.std.weak_ptr_core_environment_FoldTreeSketch_Node_t) → None

C++: core::environment::FoldTreeSketch::Node::add_jump_neighbor(class std::weak_ptr<class core::environment::FoldTreeSketch::Node>) –> void

add_peptide_neighbor(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, n: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node) → None

C++: core::environment::FoldTreeSketch::Node::add_peptide_neighbor(class std::shared_ptr<class core::environment::FoldTreeSketch::Node>) –> void

assign(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, : pyrosetta.rosetta.core.environment.FoldTreeSketch.Node) → pyrosetta.rosetta.core.environment.FoldTreeSketch.Node

C++: core::environment::FoldTreeSketch::Node::operator=(const class core::environment::FoldTreeSketch::Node &) –> class core::environment::FoldTreeSketch::Node &

collect_jumps(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, v: pyrosetta.rosetta.std.set_std_pair_unsigned_long_unsigned_long_t) → None

C++: core::environment::FoldTreeSketch::Node::collect_jumps(class std::set<struct std::pair<unsigned long, unsigned long>, struct std::less<struct std::pair<unsigned long, unsigned long> >, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> void

has_jump_neighbor(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, n: pyrosetta.rosetta.std.weak_ptr_const_core_environment_FoldTreeSketch_Node_t) → bool

C++: core::environment::FoldTreeSketch::Node::has_jump_neighbor(class std::weak_ptr<const class core::environment::FoldTreeSketch::Node>) const –> bool

has_neighbor(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, n: pyrosetta.rosetta.std.weak_ptr_const_core_environment_FoldTreeSketch_Node_t) → bool

C++: core::environment::FoldTreeSketch::Node::has_neighbor(class std::weak_ptr<const class core::environment::FoldTreeSketch::Node>) const –> bool

has_peptide_neighbor(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, n: pyrosetta.rosetta.std.weak_ptr_const_core_environment_FoldTreeSketch_Node_t) → bool

C++: core::environment::FoldTreeSketch::Node::has_peptide_neighbor(class std::weak_ptr<const class core::environment::FoldTreeSketch::Node>) const –> bool

static newNode(i: int) → pyrosetta.rosetta.core.environment.FoldTreeSketch.Node

C++: core::environment::FoldTreeSketch::Node::newNode(unsigned long) –> class std::shared_ptr<class core::environment::FoldTreeSketch::Node>

rm_jump_neighbor(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, n: pyrosetta.rosetta.std.weak_ptr_core_environment_FoldTreeSketch_Node_t) → None

C++: core::environment::FoldTreeSketch::Node::rm_jump_neighbor(class std::weak_ptr<class core::environment::FoldTreeSketch::Node>) –> void

rm_peptide_neighbor(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node, n: pyrosetta.rosetta.std.weak_ptr_core_environment_FoldTreeSketch_Node_t) → None

C++: core::environment::FoldTreeSketch::Node::rm_peptide_neighbor(class std::weak_ptr<class core::environment::FoldTreeSketch::Node>) –> void

seqid(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node) → int

C++: core::environment::FoldTreeSketch::Node::seqid() const –> unsigned long

unvisit(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node) → None

C++: core::environment::FoldTreeSketch::Node::unvisit() const –> void

visited(self: pyrosetta.rosetta.core.environment.FoldTreeSketch.Node) → bool

C++: core::environment::FoldTreeSketch::Node::visited() const –> bool

append_peptide(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, l: int) → None

add a new (graph-detached) peptide-bonded strech of length l at the end of the sequence

C++: core::environment::FoldTreeSketch::append_peptide(const unsigned long) –> void

append_residue(self: pyrosetta.rosetta.core.environment.FoldTreeSketch) → None

C++: core::environment::FoldTreeSketch::append_residue() –> void

cycle(*args, **kwargs)

Overloaded function.

  1. cycle(self: pyrosetta.rosetta.core.environment.FoldTreeSketch) -> pyrosetta.rosetta.utility.vector1_unsigned_long

  2. cycle(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, start: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::environment::FoldTreeSketch::cycle(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> >

has_cut(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, : int) → bool

C++: core::environment::FoldTreeSketch::has_cut(const unsigned long) const –> bool

has_jump(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, p1: int, p2: int) → bool

C++: core::environment::FoldTreeSketch::has_jump(const unsigned long, const unsigned long) const –> bool

insert_cut(*args, **kwargs)

Overloaded function.

  1. insert_cut(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, l: int) -> None

insert a cut after position l (i.e. between position l and l+1)

C++: core::environment::FoldTreeSketch::insert_cut(const unsigned long) –> void

  1. insert_cut(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, bias: pyrosetta.rosetta.utility.vector1_double) -> int

randomly insert a cut using the bias passed in.

C++: core::environment::FoldTreeSketch::insert_cut(class utility::vector1<double, class std::allocator<double> >) –> unsigned long

insert_jump(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, p1: int, p2: int) → None

insert a jump between positions p1 and p2 in the graph

C++: core::environment::FoldTreeSketch::insert_jump(const unsigned long, const unsigned long) –> void

nres(self: pyrosetta.rosetta.core.environment.FoldTreeSketch) → int

C++: core::environment::FoldTreeSketch::nres() const –> unsigned long

num_cuts(self: pyrosetta.rosetta.core.environment.FoldTreeSketch) → int

C++: core::environment::FoldTreeSketch::num_cuts() const –> int

num_jumps(self: pyrosetta.rosetta.core.environment.FoldTreeSketch) → int

C++: core::environment::FoldTreeSketch::num_jumps() const –> unsigned long

remove_cycles(*args, **kwargs)

Overloaded function.

  1. remove_cycles(self: pyrosetta.rosetta.core.environment.FoldTreeSketch) -> pyrosetta.rosetta.std.set_unsigned_long_t

C++: core::environment::FoldTreeSketch::remove_cycles() –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

  1. remove_cycles(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, bias: pyrosetta.rosetta.utility.vector1_double) -> pyrosetta.rosetta.std.set_unsigned_long_t

C++: core::environment::FoldTreeSketch::remove_cycles(const class utility::vector1<double, class std::allocator<double> > &) –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

render(*args, **kwargs)

Overloaded function.

  1. render(self: pyrosetta.rosetta.core.environment.FoldTreeSketch) -> pyrosetta.rosetta.core.kinematics.FoldTree

wrapper for the other render()

C++: core::environment::FoldTreeSketch::render() const –> class std::shared_ptr<class core::kinematics::FoldTree>

  1. render(self: pyrosetta.rosetta.core.environment.FoldTreeSketch, ft: pyrosetta.rosetta.core.kinematics.FoldTree) -> None

build this graph into the FoldTree ft. The state of the graph must be valid here.

C++: core::environment::FoldTreeSketch::render(class core::kinematics::FoldTree &) const –> void

class pyrosetta.rosetta.core.environment.LocalPosition

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.environment.LocalPosition, : pyrosetta.rosetta.core.environment.LocalPosition) → pyrosetta.rosetta.core.environment.LocalPosition

C++: core::environment::LocalPosition::operator=(const class core::environment::LocalPosition &) –> class core::environment::LocalPosition &

label(self: pyrosetta.rosetta.core.environment.LocalPosition) → str

C++: core::environment::LocalPosition::label() const –> const std::string &

position(self: pyrosetta.rosetta.core.environment.LocalPosition) → int

C++: core::environment::LocalPosition::position() const –> const unsigned long &

class pyrosetta.rosetta.core.environment.SequenceAnnotation

Bases: pybind11_object

add_jump_label(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, : str, : int) → None

C++: core::environment::SequenceAnnotation::add_jump_label(const std::string &, unsigned long) –> void

add_seq_label(*args, **kwargs)

Overloaded function.

  1. add_seq_label(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, : str, : pyrosetta.rosetta.std.vector_unsigned_long) -> None

C++: core::environment::SequenceAnnotation::add_seq_label(const std::string &, const class std::vector<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. add_seq_label(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, : str, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::environment::SequenceAnnotation::add_seq_label(const std::string &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

append_seq(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, label: str) → None

append a single residue with the given label to the end of the Annotation

C++: core::environment::SequenceAnnotation::append_seq(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, : pyrosetta.rosetta.core.environment.SequenceAnnotation) → pyrosetta.rosetta.core.environment.SequenceAnnotation

C++: core::environment::SequenceAnnotation::operator=(const class core::environment::SequenceAnnotation &) –> class core::environment::SequenceAnnotation &

has_seq_label(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, : str) → bool

C++: core::environment::SequenceAnnotation::has_seq_label(const std::string &) const –> bool

length(*args, **kwargs)

Overloaded function.

  1. length(self: pyrosetta.rosetta.core.environment.SequenceAnnotation) -> int

C++: core::environment::SequenceAnnotation::length() const –> const unsigned long &

  1. length(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, label: str) -> int

C++: core::environment::SequenceAnnotation::length(const std::string &) const –> unsigned long

resolve_jump(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, label: str) → int

C++: core::environment::SequenceAnnotation::resolve_jump(const std::string &) const –> unsigned long

resolve_seq(*args, **kwargs)

Overloaded function.

  1. resolve_seq(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, : pyrosetta.rosetta.core.environment.LocalPosition) -> int

C++: core::environment::SequenceAnnotation::resolve_seq(const class core::environment::LocalPosition &) const –> unsigned long

  1. resolve_seq(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, label: str) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::environment::SequenceAnnotation::resolve_seq(const std::string &) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

rm_seq_label(self: pyrosetta.rosetta.core.environment.SequenceAnnotation, : str) → None

C++: core::environment::SequenceAnnotation::rm_seq_label(const std::string &) –> void