rna¶
Bindings for protocols::stepwise::sampler::rna namespace
- class pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler¶
Bases:
StepWiseSamplerOneTorsion
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Apply the current rotamer to pose
C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> None
Apply the i-th rotamer to pose
C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::apply(class core::pose::Pose &, const unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, : pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::operator=(const class protocols::stepwise::sampler::StepWiseSamplerSized &) –> class protocols::stepwise::sampler::StepWiseSamplerSized &
- base_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler) pyrosetta.rosetta.core.chemical.rna.ChiState ¶
Get the base state (WHATEVER / ANTI / SYN)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::base_state() –> enum core::chemical::rna::ChiState
- 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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::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>
- fast_forward(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward() –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::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.stepwise.sampler.rna.RNA_ChiStepWiseSampler) str ¶
Name of the class
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::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
- id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) int ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::id() const –> const unsigned long &
- 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 > > &
- init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler) None ¶
Initialization
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::init() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) bool ¶
Check if reach the end of rotamer list
C++: protocols::stepwise::sampler::StepWiseSamplerSized::not_end() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pre_increment(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Move to next rotamer
C++: protocols::stepwise::sampler::StepWiseSamplerSized::operator++() –> 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
- pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler) pyrosetta.rosetta.core.chemical.rna.PuckerState ¶
Get the pucker state (NORTH / SOUTH)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::pucker_state() –> enum core::chemical::rna::PuckerState
- random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) bool ¶
Check if is random modeler
C++: protocols::stepwise::sampler::StepWiseSampler::random() const –> bool
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Reset to the first (or random if random()) rotamer.
C++: protocols::stepwise::sampler::StepWiseSamplerSized::reset() –> void
- 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_base_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: pyrosetta.rosetta.core.chemical.rna.ChiState) None ¶
Set the base state (WHATEVER / ANTI / SYN)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_base_state(const enum core::chemical::rna::ChiState) –> void
- set_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: float) None ¶
Set the bin_size (default: 20)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_bin_size(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_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: bool) None ¶
Set use extra chi (+-60)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_extra_chi(const bool) –> void
- set_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, setting: int) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::set_id(const unsigned long) –> 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_max_range(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: float) None ¶
Set the max_range of modeler (default: +-20)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_max_range(const double) –> 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_pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: pyrosetta.rosetta.core.chemical.rna.PuckerState) None ¶
Set the pucker state (NORTH / SOUTH)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_pucker_state(const enum core::chemical::rna::PuckerState) –> void
- set_random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler, setting: bool) None ¶
Set the random modeler state
C++: protocols::stepwise::sampler::StepWiseSampler::set_random(const bool) –> void
- set_rsd_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: int) None ¶
Set the residue id
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_rsd_id(const unsigned long) –> void
- set_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_sample_all_chi(const bool &) –> void
- set_torsion_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, setting: pyrosetta.rosetta.core.id.TorsionID) None ¶
Set the TorsionID of the sampler
C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::set_torsion_id(const class core::id::TorsionID &) –> void
- set_torsions(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, setting: pyrosetta.rosetta.utility.vector1_double) None ¶
Set the allowed torsions in sampler
C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::set_torsions(const class utility::vector1<double, class std::allocator<double> > &) –> 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
- set_values(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue, setting: pyrosetta.rosetta.utility.vector1_double) None ¶
Set the allowed values in sampler
C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::set_values(const class utility::vector1<double, class std::allocator<double> > &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream, indent: int) -> None
output summary of class
C++: protocols::stepwise::sampler::StepWiseSamplerSized::show(std::ostream &, const unsigned long) const –> void
- size(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue) int ¶
Get the total number of rotamers in sampler
C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::size() const –> unsigned long
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType ¶
Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)
C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::type() const –> enum protocols::toolbox::SamplerPlusPlusType
- value(*args, **kwargs)¶
Overloaded function.
value(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue) -> float
Get the value of current value
C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::value() const –> double
value(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue, i: int) -> float
Get the value of i-th value
C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::value(const unsigned long) const –> double
- class pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler¶
Bases:
StepWiseSampler
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Apply the current rotamer to pose
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) -> None
Apply the current rotamer to ref_pose_
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply() –> void
- assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler, : pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler ¶
C++: protocols::stepwise::sampler::StepWiseSampler::operator=(const class protocols::stepwise::sampler::StepWiseSampler &) –> class protocols::stepwise::sampler::StepWiseSampler &
- 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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- closable(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) bool ¶
If the chain is closable (random modeler only)
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::closable() const –> bool
- 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>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::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.stepwise.sampler.rna.RNA_KIC_Sampler) str ¶
Name of the class
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::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 > > &
- init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) None ¶
Initialization
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::init() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) bool ¶
Check if reach the end of rotamer list
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::not_end() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pre_increment(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) None ¶
Move to next rotamer
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator++() –> 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
- random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) bool ¶
Check if is random modeler
C++: protocols::stepwise::sampler::StepWiseSampler::random() const –> bool
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) None ¶
Reset to the first (or random if is_random()) rotamer.
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::reset() –> void
- 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_base_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: pyrosetta.rosetta.core.chemical.rna.ChiState) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_base_state(const enum core::chemical::rna::ChiState) –> void
- set_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: float) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_bin_size(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_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_chi(const bool) –> void
- set_extra_epsilon(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_epsilon(const bool) –> void
- set_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: float) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_fast(const double) –> void
- set_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_idealize_coord(const bool) –> 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_max_tries(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: int) None ¶
Max # of step for trying in random sampling
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_max_tries(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_pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: pyrosetta.rosetta.core.chemical.rna.PuckerState) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_pucker_state(const enum core::chemical::rna::PuckerState) –> void
- set_random(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
Set the random modeler state
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_random(const bool) –> void
- set_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_all_chi(const bool) –> void
- set_sample_nucleoside(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: int) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_nucleoside(const unsigned long) –> void
- set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_skip_same_pucker(const bool) –> void
- set_torsion_screen(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_torsion_screen(const bool) –> 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
- set_verbose(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_verbose(const bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) -> None
show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, output: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, out: pyrosetta.rosetta.std.ostream, indent: int) -> None
output summary of class
C++: protocols::toolbox::SamplerPlusPlus::show(std::ostream &, const unsigned long) 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType ¶
Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)
C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::type() const –> enum protocols::toolbox::SamplerPlusPlusType
- class pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser¶
Bases:
StepWiseSamplerSized
The RNA de novo structure modeling protocol
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose: pyrosetta.rosetta.core.pose.Pose, id: int) -> None
Apply the i-th rotamer to pose
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::apply(class core::pose::Pose &, const unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, : pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::operator=(const class protocols::stepwise::sampler::StepWiseSamplerSized &) –> class protocols::stepwise::sampler::StepWiseSamplerSized &
- calculate_jacobians(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) bool ¶
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::calculate_jacobians() const –> bool
- 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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::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>
- fast_forward(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward() –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::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_all_jacobians(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_all_jacobians() const –> class utility::vector1<double, class std::allocator<double> >
- 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_jacobian(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
Calculate the jacobian
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_jacobian(class core::pose::Pose &) const –> double
- 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.stepwise.sampler.rna.RNA_KinematicCloser) str ¶
Class name
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::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
- id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) int ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::id() const –> const unsigned long &
- 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 > > &
- init(*args, **kwargs)¶
Overloaded function.
init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) -> None
Initialization
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::init() –> void
init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose_current: pyrosetta.rosetta.core.pose.Pose, pose_closed: pyrosetta.rosetta.core.pose.Pose) -> None
init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose_current: pyrosetta.rosetta.core.pose.Pose, pose_closed: pyrosetta.rosetta.core.pose.Pose, use_pose_closed: bool) -> None
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::init(const class core::pose::Pose &, const class core::pose::Pose &, bool) –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) bool ¶
Check if reach the end of rotamer list
C++: protocols::stepwise::sampler::StepWiseSamplerSized::not_end() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pre_increment(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Move to next rotamer
C++: protocols::stepwise::sampler::StepWiseSamplerSized::operator++() –> 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
- random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) bool ¶
Check if is random modeler
C++: protocols::stepwise::sampler::StepWiseSampler::random() const –> bool
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Reset to the first (or random if random()) rotamer.
C++: protocols::stepwise::sampler::StepWiseSamplerSized::reset() –> void
- 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_calculate_jacobians(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_calculate_jacobians(const bool &) –> 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_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, setting: int) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::set_id(const unsigned long) –> 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_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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler, setting: bool) None ¶
Set the random modeler state
C++: protocols::stepwise::sampler::StepWiseSampler::set_random(const bool) –> 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
- set_verbose(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, setting: bool) None ¶
Set verbose
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_verbose(const bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream, indent: int) -> None
output summary of class
C++: protocols::stepwise::sampler::StepWiseSamplerSized::show(std::ostream &, const unsigned long) const –> void
- size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) int ¶
Get the total number of rotamers in sampler
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::size() const –> unsigned long
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType ¶
Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)
C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::type() const –> enum protocols::toolbox::SamplerPlusPlusType
- class pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler¶
Bases:
StepWiseSamplerSizedAny
- add_external_loop_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, rotamer: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Add one more rotamer sampler to this sampler
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::add_external_loop_rotamer(const class std::shared_ptr<class protocols::stepwise::sampler::StepWiseSamplerSized> &) –> void
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Apply the current rotamer to pose
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> None
Apply the i-th rotamer to pose
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::apply(class core::pose::Pose &, const unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, : pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::operator=(const class protocols::stepwise::sampler::StepWiseSamplerSizedAny &) –> class protocols::stepwise::sampler::StepWiseSamplerSizedAny &
- 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
- clear_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None ¶
Clear all rotamer samplers stored in this sampler
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::clear_rotamer() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::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>
- fast_forward(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward() –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::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.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler) str ¶
Name of the class
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::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
- id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) int ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::id() const –> const unsigned long &
- 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 > > &
- init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler) None ¶
Initialization wrapper
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::init() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) bool ¶
Check if reach the end of rotamer list
C++: protocols::stepwise::sampler::StepWiseSamplerSized::not_end() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pre_increment(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None ¶
Move to next rotamer
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::operator++() –> 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
- random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) bool ¶
Check if is random modeler
C++: protocols::stepwise::sampler::StepWiseSampler::random() const –> bool
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None ¶
Reset to the first (or random if random()) rotamer
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::reset() –> void
- 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_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: float) None ¶
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_bin_size(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_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None ¶
Set functions
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_extra_chi(const bool) –> void
- set_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None ¶
Just sample the center chi torsion.
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_fast(const bool) –> void
- set_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, setting: int) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::set_id(const unsigned long) –> void
- set_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_idealize_coord(const bool) –> 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_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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler, setting: bool) None ¶
Set the random modeler state
C++: protocols::stepwise::sampler::StepWiseSampler::set_random(const bool) –> void
- set_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_sample_all_chi(const bool) –> void
- set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_skip_same_pucker(const bool) –> 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.stepwise.sampler.StepWiseSamplerSizedAny, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, out: pyrosetta.rosetta.std.ostream, indent: int) -> None
output summary of class
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::show(std::ostream &, const unsigned long) const –> void
- size(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) int ¶
Get the total number of rotamers in sampler
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::size() const –> unsigned long
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType ¶
Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)
C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::type() const –> enum protocols::toolbox::SamplerPlusPlusType
- class pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler¶
Bases:
StepWiseSamplerSized
- apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, pose: pyrosetta.rosetta.core.pose.Pose, i: int) None ¶
Apply the i-th rotamer to pose
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply(class core::pose::Pose &, const unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, : pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler ¶
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::operator=(const class protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler &) –> class protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler &
- 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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::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>
- fast_forward(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward() –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::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.stepwise.sampler.rna.RNA_SugarStepWiseSampler) str ¶
Name of the class
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::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
- id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) int ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::id() const –> const unsigned long &
- 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 > > &
- init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) None ¶
Initialization
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::init() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) bool ¶
Check if reach the end of rotamer list
C++: protocols::stepwise::sampler::StepWiseSamplerSized::not_end() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pre_increment(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Move to next rotamer
C++: protocols::stepwise::sampler::StepWiseSamplerSized::operator++() –> 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
- pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) pyrosetta.rosetta.core.chemical.rna.PuckerState ¶
Get the current pucker state.
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker() const –> enum core::chemical::rna::PuckerState
- random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) bool ¶
Check if is random modeler
C++: protocols::stepwise::sampler::StepWiseSampler::random() const –> bool
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Reset to the first (or random if random()) rotamer.
C++: protocols::stepwise::sampler::StepWiseSamplerSized::reset() –> void
- 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
- rsd_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) int ¶
Get the residue id being sampled
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::rsd_id() const –> const unsigned long &
- 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_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, setting: int) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::set_id(const unsigned long) –> void
- set_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: bool) None ¶
Set if using RNA_IdealCoord to sample puckers
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_idealize_coord(const bool) –> 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_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_pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: pyrosetta.rosetta.core.chemical.rna.PuckerState) None ¶
Set the pucker_state (WHATEVER / NORTH / SOUTH)
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_pucker_state(const enum core::chemical::rna::PuckerState) –> void
- set_random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler, setting: bool) None ¶
Set the random modeler state
C++: protocols::stepwise::sampler::StepWiseSampler::set_random(const bool) –> void
- set_rsd_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: int) None ¶
Set the residue id being sampled
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_rsd_id(const unsigned long) –> void
- set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: bool) None ¶
Set if the sampler will skip pucker applying when input pose has
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_skip_same_pucker(const bool) –> 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.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream, indent: int) -> None
output summary of class
C++: protocols::stepwise::sampler::StepWiseSamplerSized::show(std::ostream &, const unsigned long) const –> void
- size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) int ¶
Get the total number of rotamers in sampler
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::size() const –> unsigned long
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType ¶
Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)
C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::type() const –> enum protocols::toolbox::SamplerPlusPlusType
- class pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler¶
Bases:
StepWiseSamplerSizedAny
- add_external_loop_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, rotamer: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
Add one more rotamer sampler to this sampler
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::add_external_loop_rotamer(const class std::shared_ptr<class protocols::stepwise::sampler::StepWiseSamplerSized> &) –> void
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Apply the current rotamer to pose
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> None
Apply the i-th rotamer to pose
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::apply(class core::pose::Pose &, const unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, : pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::operator=(const class protocols::stepwise::sampler::StepWiseSamplerSizedAny &) –> class protocols::stepwise::sampler::StepWiseSamplerSizedAny &
- 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
- clear_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None ¶
Clear all rotamer samplers stored in this sampler
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::clear_rotamer() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::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>
- fast_forward(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward() –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::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.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) str ¶
Name of the class
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::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
- id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) int ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::id() const –> const unsigned long &
- 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 > > &
- init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) None ¶
Initialization wrapper
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init() –> void
- init_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) None ¶
Initialization for fast mode
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_fast() –> void
- init_standard(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) None ¶
Initialization for standard modeler
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) bool ¶
Check if reach the end of rotamer list
C++: protocols::stepwise::sampler::StepWiseSamplerSized::not_end() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pre_increment(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None ¶
Move to next rotamer
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::operator++() –> 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
- random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) bool ¶
Check if is random modeler
C++: protocols::stepwise::sampler::StepWiseSampler::random() const –> bool
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None ¶
Reset to the first (or random if random()) rotamer
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::reset() –> void
- 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_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: float) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_bin_size(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_extra_beta(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_beta(const bool) –> void
- set_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_chi(const bool) –> void
- set_extra_epsilon(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_epsilon(const bool) –> void
- set_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
Fast mode: just sample popular center torsions
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_fast(const bool) –> void
- set_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, setting: int) None ¶
C++: protocols::stepwise::sampler::StepWiseSamplerSized::set_id(const unsigned long) –> void
- set_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_idealize_coord(const bool) –> 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_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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler, setting: bool) None ¶
Set the random modeler state
C++: protocols::stepwise::sampler::StepWiseSampler::set_random(const bool) –> void
- set_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_all_chi(const bool) –> void
- set_sample_nucleoside_lower(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
Set functions
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_nucleoside_lower(const bool) –> void
- set_sample_nucleoside_upper(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_nucleoside_upper(const bool) –> void
- set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None ¶
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_skip_same_pucker(const bool) –> 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.stepwise.sampler.StepWiseSamplerSizedAny, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, out: pyrosetta.rosetta.std.ostream, indent: int) -> None
output summary of class
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::show(std::ostream &, const unsigned long) const –> void
- size(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) int ¶
Get the total number of rotamers in sampler
C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::size() const –> unsigned long
- 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType ¶
Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)
C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::type() const –> enum protocols::toolbox::SamplerPlusPlusType
- pyrosetta.rosetta.protocols.stepwise.sampler.rna.modeler_sugar_at_five_prime(pose: pyrosetta.rosetta.core.pose.Pose, moving_suite: int) bool ¶
C++: protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(const class core::pose::Pose &, const unsigned long) –> bool
- pyrosetta.rosetta.protocols.stepwise.sampler.rna.modeler_sugar_at_three_prime(pose: pyrosetta.rosetta.core.pose.Pose, moving_suite: int) bool ¶
C++: protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(const class core::pose::Pose &, const unsigned long) –> bool
- pyrosetta.rosetta.protocols.stepwise.sampler.rna.setup_sampler(pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions, working_parameters: pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters, build_pose_from_scratch: bool, kic_modeler: bool, close_chain: bool) pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler ¶
C++: protocols::stepwise::sampler::rna::setup_sampler(const class core::pose::Pose &, class std::shared_ptr<const class protocols::stepwise::modeler::options::StepWiseModelerOptions>, class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>, const bool, const bool, const bool) –> class std::shared_ptr<class protocols::stepwise::sampler::StepWiseSampler>