electron_density

Bindings for protocols::electron_density namespace

class pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover

Bases: pyrosetta.rosetta.protocols.moves.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_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.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_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

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

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

non-const accessor

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

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_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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.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

provide_xml_schema(self: pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc

Bases: pyrosetta.rosetta.core.optimization.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_builtins.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_builtins.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.DockFragmentsIntoDensityMover

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

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

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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover

Bases: pyrosetta.rosetta.protocols.moves.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>

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_std_allocator_std_string_t

non-const accessor

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

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

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

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

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

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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions

Bases: pybind11_builtins.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_builtins.pybind11_object

class pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions

Bases: pybind11_builtins.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_builtins.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_builtins.pybind11_object

class pyrosetta.rosetta.protocols.electron_density.RefinementResult

Bases: pybind11_builtins.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_builtins.pybind11_object

class pyrosetta.rosetta.protocols.electron_density.ReportFSC

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator

Bases: pyrosetta.rosetta.protocols.moves.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

provide_xml_schema(self: pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.electron_density.RevRefinementResultComparitor

Bases: pybind11_builtins.pybind11_object

class pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator

Bases: pyrosetta.rosetta.protocols.moves.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

provide_xml_schema(self: pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions

Bases: pybind11_builtins.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

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

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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.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

provide_xml_schema(self: pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc

Bases: pyrosetta.rosetta.core.optimization.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.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

provide_xml_schema(self: pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

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.

  1. dockPoseIntoMap(pose: pyrosetta.rosetta.core.pose.Pose) -> float

  2. 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.

  1. 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

  1. 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

  1. 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.

  1. remove_occupied_density_from_density(pose: pyrosetta.rosetta.core.pose.Pose, dens: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity) -> None

  2. remove_occupied_density_from_density(pose: pyrosetta.rosetta.core.pose.Pose, dens: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity, edge_trim: int) -> None

  3. 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