normalmode

Bindings for protocols::normalmode namespace

class pyrosetta.rosetta.protocols.normalmode.ContactStruct

Bases: pybind11_builtins.pybind11_object

property c21
property d2
property k
property r21
property tor1
property tor2
class pyrosetta.rosetta.protocols.normalmode.NormalMode

Bases: pybind11_builtins.pybind11_object

a_to_i(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, a: int) int

C++: protocols::normalmode::NormalMode::a_to_i(const unsigned long) const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, : pyrosetta.rosetta.protocols.normalmode.NormalMode) pyrosetta.rosetta.protocols.normalmode.NormalMode

C++: protocols::normalmode::NormalMode::operator=(const class protocols::normalmode::NormalMode &) –> class protocols::normalmode::NormalMode &

clear_torsions_using(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) None

C++: protocols::normalmode::NormalMode::clear_torsions_using() –> void

dist2_cut(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) float

C++: protocols::normalmode::NormalMode::dist2_cut() const –> double

eckart_correction(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool) None

C++: protocols::normalmode::NormalMode::eckart_correction(const bool) –> void

get_atomID(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) pyrosetta.rosetta.utility.vector1_core_id_AtomID

C++: protocols::normalmode::NormalMode::get_atomID() const –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

get_eigval(*args, **kwargs)

Overloaded function.

  1. get_eigval(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::normalmode::NormalMode::get_eigval() const –> class utility::vector1<double, class std::allocator<double> >

  1. get_eigval(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, imode: int) -> float

C++: protocols::normalmode::NormalMode::get_eigval(const unsigned long) const –> double

get_eigvec_cart(*args, **kwargs)

Overloaded function.

  1. get_eigvec_cart(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) -> pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t

C++: protocols::normalmode::NormalMode::get_eigvec_cart() const –> class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > >

  1. get_eigvec_cart(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, imode: int) -> pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::normalmode::NormalMode::get_eigvec_cart(const unsigned long) const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_eigvec_tor(*args, **kwargs)

Overloaded function.

  1. get_eigvec_tor(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) -> pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: protocols::normalmode::NormalMode::get_eigvec_tor() const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

  1. get_eigvec_tor(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, imode: int) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::normalmode::NormalMode::get_eigvec_tor(const unsigned long) const –> class utility::vector1<double, class std::allocator<double> >

get_importance(*args, **kwargs)

Overloaded function.

  1. get_importance(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::normalmode::NormalMode::get_importance() const –> class utility::vector1<double, class std::allocator<double> >

  1. get_importance(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, imode: int) -> float

C++: protocols::normalmode::NormalMode::get_importance(const unsigned long) const –> double

get_k(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, i: int, j: int) float

C++: protocols::normalmode::NormalMode::get_k(const unsigned long, const unsigned long) const –> double

get_torID(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) pyrosetta.rosetta.utility.vector1_core_id_TorsionID

C++: protocols::normalmode::NormalMode::get_torID() const –> class utility::vector1<class core::id::TorsionID, class std::allocator<class core::id::TorsionID> >

i_to_a(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, i: int) int

C++: protocols::normalmode::NormalMode::i_to_a(const unsigned long) const –> unsigned long

mode(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) str

C++: protocols::normalmode::NormalMode::mode() const –> std::string

natm(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) int

C++: protocols::normalmode::NormalMode::natm() const –> unsigned long

nmode(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) int

C++: protocols::normalmode::NormalMode::nmode() const –> unsigned long

ntor(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) int

C++: protocols::normalmode::NormalMode::ntor() const –> unsigned long

set_harmonic_constants(*args, **kwargs)

Overloaded function.

  1. set_harmonic_constants(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, k_uniform: float) -> None

C++: protocols::normalmode::NormalMode::set_harmonic_constants(const double &) –> void

  1. set_harmonic_constants(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, k_short: float, k_SS: float, k_long: float) -> None

C++: protocols::normalmode::NormalMode::set_harmonic_constants(const double &, const double &, const double &) –> void

set_torsions_using(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, seqpos: int) None

C++: protocols::normalmode::NormalMode::set_torsions_using(const unsigned long) –> void

solve(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::normalmode::NormalMode::solve(const class core::pose::Pose &) –> void

torsion(*args, **kwargs)

Overloaded function.

  1. torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool) -> None

  2. torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool, use_phi: bool) -> None

  3. torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool, use_phi: bool, use_psi: bool) -> None

  4. torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool, use_phi: bool, use_psi: bool, eckart_correction: bool) -> None

C++: protocols::normalmode::NormalMode::torsion(const bool, const bool, const bool, const bool) –> void

  1. torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode) -> bool

C++: protocols::normalmode::NormalMode::torsion() const –> bool

xyz(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, i: int) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::normalmode::NormalMode::xyz(const unsigned long) const –> class numeric::xyzVector<double>

class pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer

Bases: pyrosetta.rosetta.protocols.moves.Mover

High-level atom tree minimizer class

apply(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::normalmode::NormalModeMinimizer::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer, : pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer) pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer

C++: protocols::normalmode::NormalModeMinimizer::operator=(const class protocols::normalmode::NormalModeMinimizer &) –> class protocols::normalmode::NormalModeMinimizer &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::normalmode::NormalModeMinimizer::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

deriv_check_result(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer) pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult
After minimization has concluded, the user may access the deriv-check result,

assuming that they have run the NormalModeMinimizer with deriv_check = true;

C++: protocols::normalmode::NormalModeMinimizer::deriv_check_result() const –> class std::shared_ptr<class core::optimization::NumericalDerivCheckResult>

fresh_instance(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::normalmode::NormalModeMinimizer::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer) str

C++: protocols::normalmode::NormalModeMinimizer::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::normalmode::NormalModeMinimizer::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::normalmode::NormalModeMinimizer::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::normalmode::NormalModeMinimizer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_modes(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer, modes_using_in: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::normalmode::NormalModeMinimizer::set_modes(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator, : pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator) pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator

C++: protocols::normalmode::NormalModeMinimizerCreator::operator=(const class protocols::normalmode::NormalModeMinimizerCreator &) –> class protocols::normalmode::NormalModeMinimizerCreator &

create_mover(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::normalmode::NormalModeMinimizerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator) str

C++: protocols::normalmode::NormalModeMinimizerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::normalmode::NormalModeMinimizerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc

Bases: pyrosetta.rosetta.core.optimization.Multifunc

Atom tree multifunction class

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) bool
Christophe added the following to allow premature end of minimization

If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::normalmode::NormalModeMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dofs_to_vars(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc, dofs: pyrosetta.rosetta.utility.vector1_double) pyrosetta.rosetta.utility.vector1_double

C++: protocols::normalmode::NormalModeMultifunc::dofs_to_vars(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >

dump(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, vars2: pyrosetta.rosetta.utility.vector1_double) None

Error state reached – derivative does not match gradient

C++: protocols::normalmode::NormalModeMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

nmodes(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc) int

C++: protocols::normalmode::NormalModeMultifunc::nmodes() const –> unsigned long

nvar(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc) int

C++: protocols::normalmode::NormalModeMultifunc::nvar() const –> unsigned long

set_deriv_check_result(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc, deriv_check_result: pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult) None

C++: protocols::normalmode::NormalModeMultifunc::set_deriv_check_result(class std::shared_ptr<class core::optimization::NumericalDerivCheckResult>) –> void

set_modes(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc, : pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::normalmode::NormalModeMultifunc::set_modes(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

vars_to_dofs(self: pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) pyrosetta.rosetta.utility.vector1_double

C++: protocols::normalmode::NormalModeMultifunc::vars_to_dofs(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >

class pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

NM(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) pyrosetta.rosetta.protocols.normalmode.NormalMode

C++: protocols::normalmode::NormalModeRelaxMover::NM() const –> const class protocols::normalmode::NormalMode

apply(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::normalmode::NormalModeRelaxMover::apply(class core::pose::Pose &) –> void

apply_on_pose(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, pose: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::normalmode::NormalModeRelaxMover::apply_on_pose(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

assign(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, : pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover

C++: protocols::normalmode::NormalModeRelaxMover::operator=(const class protocols::normalmode::NormalModeRelaxMover &) –> class protocols::normalmode::NormalModeRelaxMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::normalmode::NormalModeRelaxMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cst_sdev(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) float

C++: protocols::normalmode::NormalModeRelaxMover::cst_sdev() const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) pyrosetta.rosetta.protocols.moves.Mover

Virtual functions from Mover

C++: protocols::normalmode::NormalModeRelaxMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) pyrosetta.rosetta.core.pose.Pose

used by the job distributor and MultiplePoseMover (MPM) to return as many of the potential poses as possible.

C++: protocols::normalmode::NormalModeRelaxMover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_dynamic_scale(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) float

C++: protocols::normalmode::NormalModeRelaxMover::get_dynamic_scale() const –> double

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) str

C++: protocols::normalmode::NormalModeRelaxMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

invert_direction(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) None

C++: protocols::normalmode::NormalModeRelaxMover::invert_direction() –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::normalmode::NormalModeRelaxMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::normalmode::NormalModeRelaxMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::normalmode::NormalModeRelaxMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh_normalmode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) None

C++: protocols::normalmode::NormalModeRelaxMover::refresh_normalmode() –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

relaxmode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) str

C++: protocols::normalmode::NormalModeRelaxMover::relaxmode() const –> std::string

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_cartesian_minimize(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, value: bool) None

C++: protocols::normalmode::NormalModeRelaxMover::set_cartesian_minimize(const bool) –> void

set_cst_sdev(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, cst_sdev: float) None

C++: protocols::normalmode::NormalModeRelaxMover::set_cst_sdev(const double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_default(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) None

C++: protocols::normalmode::NormalModeRelaxMover::set_default() –> void

set_extrapolate_scale(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, scale: float) None

C++: protocols::normalmode::NormalModeRelaxMover::set_extrapolate_scale(const double) –> void

set_harmonic_constants(*args, **kwargs)

Overloaded function.

  1. set_harmonic_constants(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, k_uniform: float) -> None

Setters

C++: protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants(const double) –> void

  1. set_harmonic_constants(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, k_connected: float, k_segment: float, k_long: float) -> None

C++: protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants(const double, const double, const double) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_minoption(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, minoption: pyrosetta.rosetta.core.optimization.MinimizerOptions) None

C++: protocols::normalmode::NormalModeRelaxMover::set_minoption(class std::shared_ptr<const class core::optimization::MinimizerOptions>) –> void

set_mode(*args, **kwargs)

Overloaded function.

  1. set_mode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, mode_using: pyrosetta.rosetta.utility.vector1_unsigned_long, mode_scales: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::normalmode::NormalModeRelaxMover::set_mode(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >, const class utility::vector1<double, class std::allocator<double> >) –> void

  1. set_mode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, i_mode: int) -> None

C++: protocols::normalmode::NormalModeRelaxMover::set_mode(const unsigned long) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_random_mode(*args, **kwargs)

Overloaded function.

  1. set_random_mode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) -> None

  2. set_random_mode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, select_option: str) -> None

  3. set_random_mode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, select_option: str, importance_portion: float) -> None

C++: protocols::normalmode::NormalModeRelaxMover::set_random_mode(const std::string, const double) –> void

set_relaxmode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, mode: str) None

C++: protocols::normalmode::NormalModeRelaxMover::set_relaxmode(const std::string) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator, : pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator) pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator

C++: protocols::normalmode::NormalModeRelaxMoverCreator::operator=(const class protocols::normalmode::NormalModeRelaxMoverCreator &) –> class protocols::normalmode::NormalModeRelaxMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::normalmode::NormalModeRelaxMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator) str

C++: protocols::normalmode::NormalModeRelaxMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::normalmode::NormalModeRelaxMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void