electron_density¶
Bindings for protocols::electron_density namespace
- class pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover¶
Bases:
Mover
mover to fit B factors
- apply(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::BfactorFittingMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, : pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover ¶
C++: protocols::electron_density::BfactorFittingMover::operator=(const class protocols::electron_density::BfactorFittingMover &) –> class protocols::electron_density::BfactorFittingMover &
- 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.electron_density.BfactorFittingMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::BfactorFittingMover::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>
- fresh_instance(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::BfactorFittingMover::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_exact(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) bool ¶
C++: protocols::electron_density::BfactorFittingMover::get_exact() –> bool
- get_init(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) bool ¶
C++: protocols::electron_density::BfactorFittingMover::get_init() –> bool
- 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_max_iter(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) int ¶
C++: protocols::electron_density::BfactorFittingMover::get_max_iter() –> unsigned long
- get_minimizer(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) str ¶
C++: protocols::electron_density::BfactorFittingMover::get_minimizer() –> std::string
- get_name(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) str ¶
C++: protocols::electron_density::BfactorFittingMover::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_radius_exp(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) int ¶
C++: protocols::electron_density::BfactorFittingMover::get_radius_exp() –> unsigned long
- get_rmax(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) float ¶
C++: protocols::electron_density::BfactorFittingMover::get_rmax() –> double
- get_scorescale(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) float ¶
C++: protocols::electron_density::BfactorFittingMover::get_scorescale() –> double
- 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
- get_wt_adp(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) float ¶
C++: protocols::electron_density::BfactorFittingMover::get_wt_adp() –> double
- get_wt_dens(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover) float ¶
C++: protocols::electron_density::BfactorFittingMover::get_wt_dens() –> double
- 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.electron_density.BfactorFittingMover) None ¶
C++: protocols::electron_density::BfactorFittingMover::init() –> 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::electron_density::BfactorFittingMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::electron_density::BfactorFittingMover::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::electron_density::BfactorFittingMover::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_exact(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, exact: bool) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_exact(bool) –> void
- set_init(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, init: bool) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_init(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_iter(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, max_iter: int) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_max_iter(unsigned long) –> void
- set_minimizer(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, minimizer: str) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_minimizer(std::string) –> 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_radius_exp(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, radius_exp: int) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_radius_exp(unsigned long) –> void
- set_rmax(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, rmax: float) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_rmax(double) –> void
- set_scorescale(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, scorescale: float) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_scorescale(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_wt_adp(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, wt_adp: float) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_wt_adp(double) –> void
- set_wt_dens(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover, wt_dens: float) None ¶
C++: protocols::electron_density::BfactorFittingMover::set_wt_dens(double) –> 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.electron_density.BfactorFittingMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator, : pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator) pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator ¶
C++: protocols::electron_density::BfactorFittingMoverCreator::operator=(const class protocols::electron_density::BfactorFittingMoverCreator &) –> class protocols::electron_density::BfactorFittingMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::BfactorFittingMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator) str ¶
C++: protocols::electron_density::BfactorFittingMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc¶
Bases:
Multifunc
Bfactor multifunc
- 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.electron_density.BfactorMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::electron_density::BfactorMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void
- dump(self: pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc, x1: pyrosetta.rosetta.utility.vector1_double, x2: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::electron_density::BfactorMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void
- multivec2poseBfacts(self: pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::BfactorMultifunc::multivec2poseBfacts(const class utility::vector1<double, class std::allocator<double> > &, class core::pose::Pose &) const –> void
- poseBfacts2multivec(self: pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc, pose: pyrosetta.rosetta.core.pose.Pose, y: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::electron_density::BfactorMultifunc::poseBfacts2multivec(class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &) const –> void
- class pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions¶
Bases:
pybind11_object
- property B_¶
- assign(self: pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions, : pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions) pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions ¶
C++: protocols::electron_density::DensityGridSearchOptions::operator=(const struct protocols::electron_density::DensityGridSearchOptions &) –> struct protocols::electron_density::DensityGridSearchOptions &
- property center_on_middle_ca_¶
- property cluster_radius_¶
- property convolute_single_residue_¶
- property delRSteps_¶
- property include_distance_during_fast_cluster_¶
- property laplacian_offset_¶
- property max_rot_per_trans_¶
- property nRsteps_¶
- property native_coms_¶
- property native_middle_cas_¶
- property natives_¶
- property output_fn_¶
- property point_search_end_¶
- property point_search_start_¶
- property rms_cutoff_¶
- property symminfo_¶
- class pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo¶
Bases:
pybind11_object
scale density map intensities to match a pose’s
- assign(self: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo, : pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo) pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo ¶
C++: protocols::electron_density::DensitySymmInfo::operator=(const class protocols::electron_density::DensitySymmInfo &) –> class protocols::electron_density::DensitySymmInfo &
- detect_axes(self: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo, e: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity) None ¶
C++: protocols::electron_density::DensitySymmInfo::detect_axes(const class core::scoring::electron_density::ElectronDensity &) –> void
- enabled(self: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo) bool ¶
C++: protocols::electron_density::DensitySymmInfo::enabled() const –> bool
- mask_asu(self: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo, vol: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, e: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity, value: float) None ¶
C++: protocols::electron_density::DensitySymmInfo::mask_asu(class ObjexxFCL::FArray3D<double> &, const class core::scoring::electron_density::ElectronDensity &, double) const –> void
- min_symm_dist2(self: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo, X: pyrosetta.rosetta.numeric.xyzVector_double_t, Y: pyrosetta.rosetta.numeric.xyzVector_double_t) float ¶
C++: protocols::electron_density::DensitySymmInfo::min_symm_dist2(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double
- class pyrosetta.rosetta.protocols.electron_density.DensityZscores¶
Bases:
Mover
protocol to score local density-fit
- apply(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the mover
C++: protocols::electron_density::DensityZscores::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &
- calc_avg_nbrhood_bfac(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores, pose: pyrosetta.rosetta.core.pose.Pose, x: pyrosetta.rosetta.numeric.xyzVector_double_t) float ¶
C++: protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac(const class core::pose::Pose &, const class numeric::xyzVector<double>) const –> double
- calc_avg_residue_bfac(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores, resi: int, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
Mover Methods ///
C++: protocols::electron_density::DensityZscores::calc_avg_residue_bfac(const unsigned long, const class core::pose::Pose &) const –> double
- 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.electron_density.DensityZscores) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::electron_density::DensityZscores::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>
- fresh_instance(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::electron_density::DensityZscores::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.electron_density.DensityZscores) str ¶
C++: protocols::electron_density::DensityZscores::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_nbrhood_bfacs(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::electron_density::DensityZscores::get_nbrhood_bfacs() const –> class utility::vector1<double, class std::allocator<double> >
- get_res_bfacs(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::electron_density::DensityZscores::get_res_bfacs() const –> class utility::vector1<double, class std::allocator<double> >
- 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
- get_win1_dens_zscore(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::electron_density::DensityZscores::get_win1_dens_zscore() const –> class utility::vector1<double, class std::allocator<double> >
- get_win1_denscc(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::electron_density::DensityZscores::get_win1_denscc() const –> class utility::vector1<double, class std::allocator<double> >
- get_win3_dens_zscore(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::electron_density::DensityZscores::get_win3_dens_zscore() const –> class utility::vector1<double, class std::allocator<double> >
- get_win3_denscc(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::electron_density::DensityZscores::get_win3_denscc() const –> class utility::vector1<double, class std::allocator<double> >
- 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::electron_density::DensityZscores::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::electron_density::DensityZscores::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
This mover is unpublished. It returns Gabriella Reggiano as its author.
C++: protocols::electron_density::DensityZscores::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::electron_density::DensityZscores::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_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.electron_density.DensityZscores) -> None
show(self: pyrosetta.rosetta.protocols.electron_density.DensityZscores, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::electron_density::DensityZscores::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.electron_density.DensityZscoresCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator, : pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator) pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator ¶
C++: protocols::electron_density::DensityZscoresCreator::operator=(const class protocols::electron_density::DensityZscoresCreator &) –> class protocols::electron_density::DensityZscoresCreator &
- create_mover(self: pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::DensityZscoresCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator) str ¶
C++: protocols::electron_density::DensityZscoresCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover¶
Bases:
Mover
The workhorse
- apply(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::apply(class core::pose::Pose &) –> void
- apply_multi(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void
- assign(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, : pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover) pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::operator=(const class protocols::electron_density::DockFragmentsIntoDensityMover &) –> class protocols::electron_density::DockFragmentsIntoDensityMover &
- 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>
- 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_multi_native(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::get_multi_native() const –> class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > >
- get_multi_native_com(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::get_multi_native_com() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >
- get_multi_native_mca(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::get_multi_native_mca() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >
- get_name(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover) str ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::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
- map_from_spectrum(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, pose_1dspec: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::map_from_spectrum(const class utility::vector1<double, class std::allocator<double> > &, class ObjexxFCL::FArray3D<double> &) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- 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
- predefine_search(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, pts_in: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::predefine_search(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> 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 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
- setB(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, B: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setB(double) –> void
- setCenterOnMiddleCA(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, val: bool) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setCenterOnMiddleCA(bool) –> void
- setClusterOversamp(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, cluster_oversample: int) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setClusterOversamp(unsigned long) –> void
- setClusterRadius(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, cluster_radius: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setClusterRadius(double) –> void
- setConvoluteSingleR(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, convolute_single_residue: bool) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setConvoluteSingleR(bool) –> void
- setDelR(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, delR: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setDelR(double) –> void
- setDoRefine(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, do_refine: bool) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setDoRefine(bool) –> void
- setFragDens(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, fragDens: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setFragDens(double) –> void
- setGridStep(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, gridStep: int) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setGridStep(unsigned long) –> void
- setLaplacianOffset(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, laplacian_offset: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setLaplacianOffset(double) –> void
- setMaxRotPerTrans(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, max_rot_per_trans: int) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setMaxRotPerTrans(unsigned long) –> void
- setMinBackbone(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, min_backbone: bool) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setMinBackbone(bool) –> void
- setMinDist(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, mindist: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setMinDist(double) –> void
- setNCyc(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, ncyc: int) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setNCyc(unsigned long) –> void
- setNRsteps(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, nRsteps: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setNRsteps(double) –> void
- setNative(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, native: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setNative(class std::shared_ptr<class core::pose::Pose>) –> void
- setOutputSilent(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, silent_out: str) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setOutputSilent(std::string) –> void
- setPassThrough(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, passthrough: bool) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setPassThrough(bool) –> void
- setPointRadius(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, point_radius: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setPointRadius(double) –> void
- setSymminfo(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, symminfo: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setSymminfo(const class protocols::electron_density::DensitySymmInfo &) –> void
- setTag(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, tag: str) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setTag(std::string) –> void
- setTopN(self: pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover, topNtrans: float, topNfilter: float, topNfinal: float) None ¶
C++: protocols::electron_density::DockFragmentsIntoDensityMover::setTopN(double, double, 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_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_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.electron_density.DockPDBIntoDensityMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover) pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::operator=(const class protocols::electron_density::DockPDBIntoDensityMover &) –> class protocols::electron_density::DockPDBIntoDensityMover &
- check_for_existing_output_file(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::check_for_existing_output_file(const std::string &) const –> void
- 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>
- cluster_silent(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.utility.vector1_std_string) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::cluster_silent(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void
- compare_and_align_poses(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(class core::pose::Pose &, const class core::pose::Pose &) –> double
- 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.electron_density.DockPDBIntoDensityMover) str ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::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_points_to_search(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::get_points_to_search(const class std::shared_ptr<class core::pose::Pose>) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >
- get_radius(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::get_radius(const class core::pose::Pose &) –> double
- 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_top_N_filter(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover) int ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::get_top_N_filter() const –> unsigned long
- 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
- manual_refine_pdb(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::manual_refine_pdb(const class std::shared_ptr<class core::pose::Pose> &) –> void
- minimize_poseOP_into_density(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.core.pose.Pose, params: pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions, : pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::minimize_poseOP_into_density(const class std::shared_ptr<class core::pose::Pose>, const struct protocols::electron_density::MinimizePoseIntoDensityOptions &, class utility::vector1<double, class std::allocator<double> > &) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- 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
- predefine_search(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, pts_in: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::predefine_search(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> 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
- read_in_points_to_search(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover) None ¶
Read in points to search
C++: protocols::electron_density::DockPDBIntoDensityMover::read_in_points_to_search() –> 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
- run_aio(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::run_aio(const class std::shared_ptr<class core::pose::Pose>) –> void
- score_and_dump_natives(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::score_and_dump_natives() –> void
- search_results_to_pdb(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.utility.vector1_std_string, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::search_results_to_pdb(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class std::shared_ptr<class core::pose::Pose> &) –> void
- setB(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, B: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setB(double) –> void
- setCartRef(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, cart_ref: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setCartRef(double) –> void
- setCentroidSilentOut(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, centroid_silent_out: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setCentroidSilentOut(bool) –> void
- setCheatNativeCOM(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, cheat_native_com: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setCheatNativeCOM(bool) –> void
- setCheatNativeMCA(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, cheat_native_mca: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setCheatNativeMCA(bool) –> void
- setClusterOversamp(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, cluster_oversample: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setClusterOversamp(unsigned long) –> void
- setClusterRadius(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, cluster_radius: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setClusterRadius(double) –> void
- setCombinedSearchResultsFname(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, combined_search_results_fname: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setCombinedSearchResultsFname(const std::string &) –> void
- setConstrainRefinement(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, constrain_refinement: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setConstrainRefinement(double) –> void
- setConvoluteSingleR(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, convolute_single_residue: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setConvoluteSingleR(bool) –> void
- setCoreIdx(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, core_idx: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setCoreIdx(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void
- setDelR(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, delR: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setDelR(double) –> void
- setDoRefine(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, do_refine: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setDoRefine(bool) –> void
- setDumpInter(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, dump_inter: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setDumpInter(bool) –> void
- setDumpInterSilent(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, dump_inter_silent: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setDumpInterSilent(bool) –> void
- setFinalChain(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, final_chain: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setFinalChain(const std::string &) –> void
- setFragDens(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, fragDens: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setFragDens(double) –> void
- setGaussianBlur(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, gaussian_blur: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setGaussianBlur(bool) –> void
- setGridStep(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, gridStep: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setGridStep(unsigned long) –> void
- setLaplacianOffset(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, laplacian_offset: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setLaplacianOffset(double) –> void
- setMaxRotPerTrans(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, max_rot_per_trans: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setMaxRotPerTrans(unsigned long) –> void
- setMinBackbone(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, min_backbone: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setMinBackbone(bool) –> void
- setMultiNative(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setMultiNative(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void
- setNCyc(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, ncyc: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setNCyc(unsigned long) –> void
- setNRsteps(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, nRsteps: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setNRsteps(double) –> void
- setOutputSilent(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, silent_out: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setOutputSilent(std::string) –> void
- setOverwrite(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, overwrite: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setOverwrite(bool) –> void
- setPassThrough(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, passthrough: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setPassThrough(bool) –> void
- setPointRadius(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, point_radius: float) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setPointRadius(double) –> void
- setPointSearchResultsFname(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, point_search_results_fname: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setPointSearchResultsFname(const std::string &) –> void
- setPointsToSearchFname(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, pts_fname: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setPointsToSearchFname(const std::string &) –> void
- setPointsToSearchPDBFname(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, pts_fname: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setPointsToSearchPDBFname(const std::string &) –> void
- setRefineEnd(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, refine_end: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setRefineEnd(unsigned long) –> void
- setRefineStart(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, refine_start: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setRefineStart(unsigned long) –> void
- setRotateMiddleCA(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, rot_middle_ca: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setRotateMiddleCA(bool) –> void
- setRotateOnSeqCenter(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, val: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setRotateOnSeqCenter(bool) –> void
- setRotateSeqCenter(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, rot_seq_center: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setRotateSeqCenter(bool) –> void
- setScoreNatives(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, score_natives: bool) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setScoreNatives(bool) –> void
- setSearchEnd(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, point_search_end: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setSearchEnd(unsigned long) –> void
- setSearchStart(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, point_search_start: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setSearchStart(unsigned long) –> void
- setStartModel(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, startmodel: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setStartModel(const std::string &) –> void
- setSymminfo(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, symminfo: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setSymminfo(const class protocols::electron_density::DensitySymmInfo &) –> void
- setTag(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, tag: str) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setTag(std::string) –> void
- setTopN(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, topNtrans: int, topNfilter: int, topNfinal: int) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::setTopN(const unsigned long, const unsigned long, const unsigned long) –> 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_nRsteps_from_pose(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(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_search_responsibilities(self: pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover) None ¶
C++: protocols::electron_density::DockPDBIntoDensityMover::set_search_responsibilities() –> 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.electron_density.MinimizePoseIntoDensityOptions¶
Bases:
pybind11_object
- property bbmin¶
- property packer¶
- property rbmin¶
- property scorefxn_dens¶
- property scorefxn_refine¶
- property scorefxn_refine_rb¶
- class pyrosetta.rosetta.protocols.electron_density.PointScoreComparator¶
Bases:
pybind11_object
- class pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions¶
Bases:
pybind11_object
- property B_¶
- property center_on_middle_ca_¶
- property delRsteps_¶
- property laplacian_offset_¶
- property nRsteps_¶
- class pyrosetta.rosetta.protocols.electron_density.RBfitResult¶
Bases:
pybind11_object
CLASSES
- property pose_idx_¶
- property post_trans_¶
- property pre_trans_¶
- property rotation_¶
- property score_¶
- class pyrosetta.rosetta.protocols.electron_density.RBfitResultComparitor¶
Bases:
pybind11_object
- class pyrosetta.rosetta.protocols.electron_density.RefinementResult¶
Bases:
pybind11_object
- center(self: pyrosetta.rosetta.protocols.electron_density.RefinementResult) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: protocols::electron_density::RefinementResult::center() –> class numeric::xyzVector<double>
- property pose_¶
- property prerefine_score_¶
- property score_¶
- property spharm_score_¶
- class pyrosetta.rosetta.protocols.electron_density.RefinementResultComparitor¶
Bases:
pybind11_object
- class pyrosetta.rosetta.protocols.electron_density.ReportFSC¶
Bases:
Mover
scale density map intensities to match a pose’s
- apply(self: pyrosetta.rosetta.protocols.electron_density.ReportFSC, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::ReportFSC::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.electron_density.ReportFSC, : pyrosetta.rosetta.protocols.electron_density.ReportFSC) pyrosetta.rosetta.protocols.electron_density.ReportFSC ¶
C++: protocols::electron_density::ReportFSC::operator=(const class protocols::electron_density::ReportFSC &) –> class protocols::electron_density::ReportFSC &
- 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.electron_density.ReportFSC) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::ReportFSC::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>
- fresh_instance(self: pyrosetta.rosetta.protocols.electron_density.ReportFSC) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::ReportFSC::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.electron_density.ReportFSC) str ¶
C++: protocols::electron_density::ReportFSC::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.electron_density.ReportFSC) None ¶
C++: protocols::electron_density::ReportFSC::init() –> 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::electron_density::ReportFSC::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.electron_density.ReportFSC, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::electron_density::ReportFSC::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::electron_density::ReportFSC::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_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.electron_density.ReportFSCCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator, : pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator) pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator ¶
C++: protocols::electron_density::ReportFSCCreator::operator=(const class protocols::electron_density::ReportFSCCreator &) –> class protocols::electron_density::ReportFSCCreator &
- create_mover(self: pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::ReportFSCCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator) str ¶
C++: protocols::electron_density::ReportFSCCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.electron_density.RevRefinementResultComparitor¶
Bases:
pybind11_object
- class pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities¶
Bases:
Mover
scale density map intensities to match a pose’s
- apply(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::ScaleMapIntensities::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities, : pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities) pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities ¶
C++: protocols::electron_density::ScaleMapIntensities::operator=(const class protocols::electron_density::ScaleMapIntensities &) –> class protocols::electron_density::ScaleMapIntensities &
- 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.electron_density.ScaleMapIntensities) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::ScaleMapIntensities::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>
- fresh_instance(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::ScaleMapIntensities::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.electron_density.ScaleMapIntensities) str ¶
C++: protocols::electron_density::ScaleMapIntensities::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.electron_density.ScaleMapIntensities) None ¶
C++: protocols::electron_density::ScaleMapIntensities::init() –> 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::electron_density::ScaleMapIntensities::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::electron_density::ScaleMapIntensities::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::electron_density::ScaleMapIntensities::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_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.electron_density.ScaleMapIntensitiesCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator, : pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator) pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator ¶
C++: protocols::electron_density::ScaleMapIntensitiesCreator::operator=(const class protocols::electron_density::ScaleMapIntensitiesCreator &) –> class protocols::electron_density::ScaleMapIntensitiesCreator &
- create_mover(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::ScaleMapIntensitiesCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator) str ¶
C++: protocols::electron_density::ScaleMapIntensitiesCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions¶
Bases:
pybind11_object
- property B_¶
- property center_on_middle_ca_¶
- property convolute_single_residue_¶
- property delRsteps_¶
- property fragDens_¶
- property gridStep_¶
- property laplacian_offset_¶
- property nRsteps_¶
- property native_coms_¶
- property native_middle_cas_¶
- property natives_¶
- property point_radius_¶
- property symminfo_¶
- property topNtrans_¶
- class pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::SetupForDensityScoringMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover, : pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover) pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover ¶
C++: protocols::electron_density::SetupForDensityScoringMover::operator=(const class protocols::electron_density::SetupForDensityScoringMover &) –> class protocols::electron_density::SetupForDensityScoringMover &
- 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.electron_density.SetupForDensityScoringMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::SetupForDensityScoringMover::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>
- 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>
- getScore(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover) float ¶
C++: protocols::electron_density::SetupForDensityScoringMover::getScore() –> double
- 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.electron_density.SetupForDensityScoringMover) str ¶
C++: protocols::electron_density::SetupForDensityScoringMover::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
- mask(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover, loops: pyrosetta.rosetta.protocols.loops.Loops) None ¶
C++: protocols::electron_density::SetupForDensityScoringMover::mask(const class protocols::loops::Loops &) –> void
- static mover_name() str ¶
C++: protocols::electron_density::SetupForDensityScoringMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- static options_read_in_ctor(opts: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) None ¶
C++: protocols::electron_density::SetupForDensityScoringMover::options_read_in_ctor(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::electron_density::SetupForDensityScoringMover::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::electron_density::SetupForDensityScoringMover::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_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.electron_density.SetupForDensityScoringMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator, : pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator) pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator ¶
C++: protocols::electron_density::SetupForDensityScoringMoverCreator::operator=(const class protocols::electron_density::SetupForDensityScoringMoverCreator &) –> class protocols::electron_density::SetupForDensityScoringMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::SetupForDensityScoringMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator) str ¶
C++: protocols::electron_density::SetupForDensityScoringMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc¶
Bases:
Multifunc
Bfactor multifunc
- 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
- assign(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc, : pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc) pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc ¶
C++: protocols::electron_density::VoxelSpacingMultifunc::operator=(const class protocols::electron_density::VoxelSpacingMultifunc &) –> class protocols::electron_density::VoxelSpacingMultifunc &
- dfunc(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::electron_density::VoxelSpacingMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void
- dump(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc, x1: pyrosetta.rosetta.utility.vector1_double, x2: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::electron_density::VoxelSpacingMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void
- foldInChanges(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc, pose: pyrosetta.rosetta.core.pose.Pose, y: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::electron_density::VoxelSpacingMultifunc::foldInChanges(class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &) –> void
- getMapSpacingAndOrigin(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc, x1: pyrosetta.rosetta.utility.vector1_double, aniso: bool) None ¶
C++: protocols::electron_density::VoxelSpacingMultifunc::getMapSpacingAndOrigin(class utility::vector1<double, class std::allocator<double> > &, bool) –> void
- class pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover¶
Bases:
Mover
mover to fit B factors
- apply(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::electron_density::VoxelSpacingRefinementMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover, : pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover) pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover ¶
C++: protocols::electron_density::VoxelSpacingRefinementMover::operator=(const class protocols::electron_density::VoxelSpacingRefinementMover &) –> class protocols::electron_density::VoxelSpacingRefinementMover &
- 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.electron_density.VoxelSpacingRefinementMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::VoxelSpacingRefinementMover::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>
- fresh_instance(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::VoxelSpacingRefinementMover::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.electron_density.VoxelSpacingRefinementMover) str ¶
C++: protocols::electron_density::VoxelSpacingRefinementMover::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.electron_density.VoxelSpacingRefinementMover) None ¶
C++: protocols::electron_density::VoxelSpacingRefinementMover::init() –> 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::electron_density::VoxelSpacingRefinementMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::electron_density::VoxelSpacingRefinementMover::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::electron_density::VoxelSpacingRefinementMover::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_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.electron_density.VoxelSpacingRefinementMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator, : pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator) pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator ¶
C++: protocols::electron_density::VoxelSpacingRefinementMoverCreator::operator=(const class protocols::electron_density::VoxelSpacingRefinementMoverCreator &) –> class protocols::electron_density::VoxelSpacingRefinementMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::electron_density::VoxelSpacingRefinementMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator) str ¶
C++: protocols::electron_density::VoxelSpacingRefinementMoverCreator::keyname() const –> std::string
- pyrosetta.rosetta.protocols.electron_density.apply_transform(pose: pyrosetta.rosetta.core.pose.Pose, transform: pyrosetta.rosetta.protocols.electron_density.RBfitResult) None ¶
C++: protocols::electron_density::apply_transform(class core::pose::Pose &, const class protocols::electron_density::RBfitResult &) –> void
- pyrosetta.rosetta.protocols.electron_density.dockPoseIntoMap(*args, **kwargs)¶
Overloaded function.
dockPoseIntoMap(pose: pyrosetta.rosetta.core.pose.Pose) -> float
dockPoseIntoMap(pose: pyrosetta.rosetta.core.pose.Pose, align_in: str) -> float
C++: protocols::electron_density::dockPoseIntoMap(class core::pose::Pose &, const std::string &) –> double
- pyrosetta.rosetta.protocols.electron_density.dump_points_to_search_to_pdb_or_txt(points_to_search: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, pdb_filename: str, txt_filename: str) None ¶
C++: protocols::electron_density::dump_points_to_search_to_pdb_or_txt(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const std::string &, const std::string &) –> void
- pyrosetta.rosetta.protocols.electron_density.findLoopFromDensity(pose: pyrosetta.rosetta.core.pose.Pose, frac: float, max_helix: int, max_strand: int) pyrosetta.rosetta.protocols.loops.Loops ¶
C++: protocols::electron_density::findLoopFromDensity(class core::pose::Pose &, double, int, int) –> class protocols::loops::Loops
- pyrosetta.rosetta.protocols.electron_density.get_gdt(r1: pyrosetta.rosetta.core.pose.Pose, r2: pyrosetta.rosetta.core.pose.Pose, d: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo, native: bool) float ¶
C++: protocols::electron_density::get_gdt(const class core::pose::Pose &, const class core::pose::Pose &, const class protocols::electron_density::DensitySymmInfo &, const bool) –> double
- pyrosetta.rosetta.protocols.electron_density.get_radius(pose: pyrosetta.rosetta.core.pose.Pose, com: pyrosetta.rosetta.numeric.xyzVector_double_t, center_on_middle_ca: bool) float ¶
Get max extent of pose
C++: protocols::electron_density::get_radius(const class core::pose::Pose &, class numeric::xyzVector<double> &, const bool) –> double
- pyrosetta.rosetta.protocols.electron_density.get_rms(*args, **kwargs)¶
Overloaded function.
get_rms(r1: pyrosetta.rosetta.core.pose.Pose, r2: pyrosetta.rosetta.core.pose.Pose, d: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo) -> float
C++: protocols::electron_density::get_rms(const class core::pose::Pose &, const class core::pose::Pose &, const class protocols::electron_density::DensitySymmInfo &) –> double
get_rms(r1: pyrosetta.rosetta.protocols.electron_density.RefinementResult, r2: pyrosetta.rosetta.protocols.electron_density.RefinementResult, d: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo) -> float
C++: protocols::electron_density::get_rms(const class protocols::electron_density::RefinementResult &, const class protocols::electron_density::RefinementResult &, const class protocols::electron_density::DensitySymmInfo &) –> double
get_rms(r1: pyrosetta.rosetta.core.pose.Pose, r2: pyrosetta.rosetta.core.pose.Pose, d: pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo, native: bool) -> float
C++: protocols::electron_density::get_rms(const class core::pose::Pose &, const class core::pose::Pose &, const class protocols::electron_density::DensitySymmInfo &, const bool) –> double
- pyrosetta.rosetta.protocols.electron_density.get_rot_angle(R: pyrosetta.rosetta.numeric.xyzMatrix_double_t) float ¶
C++: protocols::electron_density::get_rot_angle(const class numeric::xyzMatrix<double> &) –> double
- pyrosetta.rosetta.protocols.electron_density.get_spectrum(pose: pyrosetta.rosetta.core.pose.Pose, pose_1dspec: pyrosetta.rosetta.utility.vector1_double, delR: float, fragDens: float, convolute_single_residue: bool, center_on_middle_ca: bool) float ¶
Get 1d power spectrum of a pose
C++: protocols::electron_density::get_spectrum(const class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &, const double, const double, const bool, const bool) –> double
- pyrosetta.rosetta.protocols.electron_density.map_from_spectrum(pose_1dspec: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, delR: float) None ¶
C++: protocols::electron_density::map_from_spectrum(const class utility::vector1<double, class std::allocator<double> > &, class ObjexxFCL::FArray3D<double> &, const double) –> void
- pyrosetta.rosetta.protocols.electron_density.pose_spherical_samples(pose: pyrosetta.rosetta.core.pose.Pose, sigR: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, epsR: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, params: pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions) None ¶
Step 0: map pose to spherically sampled density + mask
C++: protocols::electron_density::pose_spherical_samples(const class core::pose::Pose &, class ObjexxFCL::FArray3D<double> &, class ObjexxFCL::FArray3D<double> &, const struct protocols::electron_density::PoseSphericalSamplesOptions &) –> void
- pyrosetta.rosetta.protocols.electron_density.remove_occupied_density_from_density(*args, **kwargs)¶
Overloaded function.
remove_occupied_density_from_density(pose: pyrosetta.rosetta.core.pose.Pose, dens: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity) -> None
remove_occupied_density_from_density(pose: pyrosetta.rosetta.core.pose.Pose, dens: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity, edge_trim: int) -> None
remove_occupied_density_from_density(pose: pyrosetta.rosetta.core.pose.Pose, dens: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity, edge_trim: int, mask_radius: float) -> None
C++: protocols::electron_density::remove_occupied_density_from_density(const class core::pose::Pose &, class core::scoring::electron_density::ElectronDensity &, const unsigned long, const double) –> void
- pyrosetta.rosetta.protocols.electron_density.select_density_points(pose: pyrosetta.rosetta.core.pose.Pose, params: pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions, nRsteps: int) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t ¶
C++: protocols::electron_density::select_density_points(const class core::pose::Pose &, const struct protocols::electron_density::SelectDensityPointsOptions &, unsigned long &) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >
- pyrosetta.rosetta.protocols.electron_density.set_pose_and_scorefxn_for_edens_scoring(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::electron_density::set_pose_and_scorefxn_for_edens_scoring(class core::pose::Pose &, class core::scoring::ScoreFunction &) –> void