normalmode¶
Bindings for protocols::normalmode namespace
- class pyrosetta.rosetta.protocols.normalmode.ContactStruct¶
Bases:
pybind11_object
- property c21¶
- property d2¶
- property k¶
- property r21¶
- property tor1¶
- property tor2¶
- class pyrosetta.rosetta.protocols.normalmode.NormalMode¶
Bases:
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.
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> >
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.
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> > > > >
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.
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> > > >
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.
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> >
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.
set_harmonic_constants(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, k_uniform: float) -> None
C++: protocols::normalmode::NormalMode::set_harmonic_constants(const double &) –> void
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.
torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool) -> None
torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool, use_phi: bool) -> None
torsion(self: pyrosetta.rosetta.protocols.normalmode.NormalMode, bool_in: bool, use_phi: bool, use_psi: bool) -> None
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
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:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc¶
Bases:
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:
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_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.
set_harmonic_constants(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, k_uniform: float) -> None
Setters
C++: protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants(const double) –> void
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.
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
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.
set_random_mode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover) -> None
set_random_mode(self: pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover, select_option: str) -> None
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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