magnesium

Classes:

• pyrosetta.rosetta.protocols.magnesium.MgHydrater
• pyrosetta.rosetta.protocols.magnesium.MgMinimizer
• pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo
• pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder
• pyrosetta.rosetta.protocols.magnesium.MgScanner
• pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker
• pyrosetta.rosetta.protocols.magnesium.SampleGrid

Functions:

• pyrosetta.rosetta.protocols.magnesium.add_single_magnesium
• pyrosetta.rosetta.protocols.magnesium.append_mg_bound_water
• pyrosetta.rosetta.protocols.magnesium.define_mg_water_map
• pyrosetta.rosetta.protocols.magnesium.filter_acceptor_ligands
• pyrosetta.rosetta.protocols.magnesium.find_bound_waters_that_are_daughters_in_fold_tree
• pyrosetta.rosetta.protocols.magnesium.fixup_magnesiums
• pyrosetta.rosetta.protocols.magnesium.get_closest_non_hoh_contact
• pyrosetta.rosetta.protocols.magnesium.get_hydration_stats
• pyrosetta.rosetta.protocols.magnesium.get_mg_ligands
• pyrosetta.rosetta.protocols.magnesium.get_mg_res
• pyrosetta.rosetta.protocols.magnesium.get_mg_rsd
• pyrosetta.rosetta.protocols.magnesium.get_mg_scorefxn
• pyrosetta.rosetta.protocols.magnesium.get_mg_water_pairs
• pyrosetta.rosetta.protocols.magnesium.get_octahedral_uniform_rotation_sampler
• pyrosetta.rosetta.protocols.magnesium.get_useful_HOH_coords
• pyrosetta.rosetta.protocols.magnesium.get_water_res
• pyrosetta.rosetta.protocols.magnesium.get_water_uniform_rotation_sampler
• pyrosetta.rosetta.protocols.magnesium.hydrate_magnesiums
• pyrosetta.rosetta.protocols.magnesium.instantiate_water_at_octahedral_vertex
• pyrosetta.rosetta.protocols.magnesium.minimize_magnesium_and_hydration_shell
• pyrosetta.rosetta.protocols.magnesium.pdbslice
• pyrosetta.rosetta.protocols.magnesium.remove_mg_bound_waters
• pyrosetta.rosetta.protocols.magnesium.remove_waters_except_mg_bound
• pyrosetta.rosetta.protocols.magnesium.strip_out_magnesiums
• pyrosetta.rosetta.protocols.magnesium.update_jump_atoms_for_mg_bound_water
• pyrosetta.rosetta.protocols.magnesium.update_mg_hoh_fold_tree
• pyrosetta.rosetta.protocols.magnesium.update_numbers_in_pdb_info

Bindings for protocols::magnesium namespace

class pyrosetta.rosetta.protocols.magnesium.MgHydrater

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::MgHydrater::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater, : pyrosetta.rosetta.protocols.magnesium.MgHydrater) → pyrosetta.rosetta.protocols.magnesium.MgHydrater

C++: protocols::magnesium::MgHydrater::operator=(const class protocols::magnesium::MgHydrater &) –> class protocols::magnesium::MgHydrater &

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>

excise_mini_pose(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater) → bool

C++: protocols::magnesium::MgHydrater::excise_mini_pose() const –> bool

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.magnesium.MgHydrater) → str

C++: protocols::magnesium::MgHydrater::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static 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

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

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_excise_mini_pose(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater, setting: bool) → None

C++: protocols::magnesium::MgHydrater::set_excise_mini_pose(const bool &) –> void

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

set_use_fast_frame_heuristic(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater, setting: bool) → None

C++: protocols::magnesium::MgHydrater::set_use_fast_frame_heuristic(const bool &) –> void

set_use_virtual_waters_as_placeholders(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater, setting: bool) → None

C++: protocols::magnesium::MgHydrater::set_use_virtual_waters_as_placeholders(const bool &) –> void

set_verbose(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater, setting: bool) → None

C++: protocols::magnesium::MgHydrater::set_verbose(const bool &) –> 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

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

Get the set ‘type’ string

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

use_fast_frame_heuristic(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater) → bool

C++: protocols::magnesium::MgHydrater::use_fast_frame_heuristic() const –> bool

use_virtual_waters_as_placeholders(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater) → bool

C++: protocols::magnesium::MgHydrater::use_virtual_waters_as_placeholders() const –> bool

verbose(self: pyrosetta.rosetta.protocols.magnesium.MgHydrater) → bool

C++: protocols::magnesium::MgHydrater::verbose() const –> bool

class pyrosetta.rosetta.protocols.magnesium.MgMinimizer

Bases: MoverForPoseList

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, viewer_pose: pyrosetta.rosetta.core.pose.Pose) -> None

2. apply(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None

3. apply(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::magnesium::MgMinimizer::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, : pyrosetta.rosetta.protocols.magnesium.MgMinimizer) → pyrosetta.rosetta.protocols.magnesium.MgMinimizer

C++: protocols::magnesium::MgMinimizer::operator=(const class protocols::magnesium::MgMinimizer &) –> class protocols::magnesium::MgMinimizer &

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_name(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer) → str

C++: protocols::magnesium::MgMinimizer::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

mg_coord_cst_dist(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer) → float

C++: protocols::magnesium::MgMinimizer::mg_coord_cst_dist() const –> double

mg_res(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::MgMinimizer::mg_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

minimize_scorefxn(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::magnesium::MgMinimizer::minimize_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

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_mg_coord_cst_dist(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, setting: float) → None

C++: protocols::magnesium::MgMinimizer::set_mg_coord_cst_dist(const double &) –> void

set_mg_res(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::magnesium::MgMinimizer::set_mg_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_minimize_scorefxn(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::magnesium::MgMinimizer::set_minimize_scorefxn(const class std::shared_ptr<const class core::scoring::ScoreFunction> &) –> 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

2. 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.magnesium.MgMonteCarlo

Bases: Mover

add_delete_frequency(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo) → float

C++: protocols::magnesium::MgMonteCarlo::add_delete_frequency() const –> double

apply(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::MgMonteCarlo::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo, : pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo) → pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo

C++: protocols::magnesium::MgMonteCarlo::operator=(const class protocols::magnesium::MgMonteCarlo &) –> class protocols::magnesium::MgMonteCarlo &

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>

cycles(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo) → int

C++: protocols::magnesium::MgMonteCarlo::cycles() const –> unsigned long

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.magnesium.MgMonteCarlo) → str

C++: protocols::magnesium::MgMonteCarlo::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() → str

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

output_pdb(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo) → bool

C++: protocols::magnesium::MgMonteCarlo::output_pdb() const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

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

set_add_delete_frequency(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo, setting: float) → None

C++: protocols::magnesium::MgMonteCarlo::set_add_delete_frequency(const double &) –> void

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

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

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

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

set_cycles(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo, setting: int) → None

C++: protocols::magnesium::MgMonteCarlo::set_cycles(const unsigned long &) –> void

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

setter for poses contained for rms

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

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

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

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

set_output_pdb(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo, setting: bool) → None

C++: protocols::magnesium::MgMonteCarlo::set_output_pdb(const bool &) –> void

set_temperature(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo, setting: float) → None

C++: protocols::magnesium::MgMonteCarlo::set_temperature(const double &) –> void

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

Set the ‘type’ string

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

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

temperature(self: pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo) → float

C++: protocols::magnesium::MgMonteCarlo::temperature() const –> double

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

2. 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.magnesium.MgOrbitalFrameFinder

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::MgOrbitalFrameFinder::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder, : pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder) → pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder

C++: protocols::magnesium::MgOrbitalFrameFinder::operator=(const class protocols::magnesium::MgOrbitalFrameFinder &) –> class protocols::magnesium::MgOrbitalFrameFinder &

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_name(self: pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder) → str

C++: protocols::magnesium::MgOrbitalFrameFinder::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static 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

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

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

2. 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.magnesium.MgScanner

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::MgScanner::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, : pyrosetta.rosetta.protocols.magnesium.MgScanner) → pyrosetta.rosetta.protocols.magnesium.MgScanner

C++: protocols::magnesium::MgScanner::operator=(const class protocols::magnesium::MgScanner &) –> class protocols::magnesium::MgScanner &

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_name(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → str

C++: protocols::magnesium::MgScanner::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

hydrate(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → bool

C++: protocols::magnesium::MgScanner::hydrate() const –> bool

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

non-const accessor

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

input_scan_res(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::MgScanner::input_scan_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

integration_test(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → bool

C++: protocols::magnesium::MgScanner::integration_test() const –> bool

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

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

minimize(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → bool

C++: protocols::magnesium::MgScanner::minimize() const –> bool

minimize_during_scoring(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → bool

C++: protocols::magnesium::MgScanner::minimize_during_scoring() const –> bool

minimize_mg_coord_constraint_distance(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → float

C++: protocols::magnesium::MgScanner::minimize_mg_coord_constraint_distance() const –> double

static name() → str

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

output_pdb(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → str

C++: protocols::magnesium::MgScanner::output_pdb() const –> 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

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

score_cut(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → float

C++: protocols::magnesium::MgScanner::score_cut() const –> double

score_cut_PDB(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → float

C++: protocols::magnesium::MgScanner::score_cut_PDB() const –> double

scorefxn(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::magnesium::MgScanner::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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_hydrate(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: bool) → None

C++: protocols::magnesium::MgScanner::set_hydrate(const bool &) –> void

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

setter for poses contained for rms

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

set_input_scan_res(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::magnesium::MgScanner::set_input_scan_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_integration_test(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: bool) → None

C++: protocols::magnesium::MgScanner::set_integration_test(const bool &) –> void

set_minimize(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: bool) → None

C++: protocols::magnesium::MgScanner::set_minimize(const bool &) –> void

set_minimize_during_scoring(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: bool) → None

C++: protocols::magnesium::MgScanner::set_minimize_during_scoring(const bool &) –> void

set_minimize_mg_coord_constraint_distance(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: float) → None

C++: protocols::magnesium::MgScanner::set_minimize_mg_coord_constraint_distance(const double &) –> void

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

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

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

set_output_pdb(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: str) → None

C++: protocols::magnesium::MgScanner::set_output_pdb(const std::string &) –> void

set_score_cut(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: float) → None

C++: protocols::magnesium::MgScanner::set_score_cut(const double &) –> void

set_score_cut_PDB(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: float) → None

C++: protocols::magnesium::MgScanner::set_score_cut_PDB(const double &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::magnesium::MgScanner::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_silent_file(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: str) → None

C++: protocols::magnesium::MgScanner::set_silent_file(const std::string &) –> void

set_tether_to_closest_res(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: bool) → None

C++: protocols::magnesium::MgScanner::set_tether_to_closest_res(const bool &) –> void

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

Set the ‘type’ string

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

set_xyz_step(self: pyrosetta.rosetta.protocols.magnesium.MgScanner, setting: float) → None

C++: protocols::magnesium::MgScanner::set_xyz_step(const double &) –> 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

silent_file(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → str

C++: protocols::magnesium::MgScanner::silent_file() const –> std::string

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

tether_to_closest_res(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → bool

C++: protocols::magnesium::MgScanner::tether_to_closest_res() const –> bool

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

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

Get the set ‘type’ string

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

xyz_step(self: pyrosetta.rosetta.protocols.magnesium.MgScanner) → float

C++: protocols::magnesium::MgScanner::xyz_step() const –> double

class pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker

Bases: Mover

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::magnesium::MgWaterHydrogenPacker::apply(class core::pose::Pose &) –> void

2. apply(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker, pose: pyrosetta.rosetta.core.pose.Pose, mg_water: Tuple[int, int]) -> None

C++: protocols::magnesium::MgWaterHydrogenPacker::apply(class core::pose::Pose &, const struct std::pair<unsigned long, unsigned long> &) –> void

assign(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker, : pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker) → pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker

C++: protocols::magnesium::MgWaterHydrogenPacker::operator=(const class protocols::magnesium::MgWaterHydrogenPacker &) –> class protocols::magnesium::MgWaterHydrogenPacker &

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>

excise_mini_pose(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker) → bool

C++: protocols::magnesium::MgWaterHydrogenPacker::excise_mini_pose() const –> bool

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.magnesium.MgWaterHydrogenPacker) → str

C++: protocols::magnesium::MgWaterHydrogenPacker::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static 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

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

remove_waters_except_mg_bound(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::MgWaterHydrogenPacker::remove_waters_except_mg_bound(class core::pose::Pose &) const –> void

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

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

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

set_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_excise_mini_pose(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker, setting: bool) → None

C++: protocols::magnesium::MgWaterHydrogenPacker::set_excise_mini_pose(const bool &) –> void

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

set_use_fast_heuristic(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker, setting: bool) → None

C++: protocols::magnesium::MgWaterHydrogenPacker::set_use_fast_heuristic(const bool &) –> 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

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

Get the set ‘type’ string

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

use_fast_heuristic(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker) → bool

C++: protocols::magnesium::MgWaterHydrogenPacker::use_fast_heuristic() const –> bool

class pyrosetta.rosetta.protocols.magnesium.SampleGrid

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid, : pyrosetta.rosetta.protocols.magnesium.SampleGrid) → pyrosetta.rosetta.protocols.magnesium.SampleGrid

C++: protocols::magnesium::SampleGrid::operator=(const class protocols::magnesium::SampleGrid &) –> class protocols::magnesium::SampleGrid &

get_mg_positions(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::magnesium::SampleGrid::get_mg_positions(const class core::pose::Pose &) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

input_scan_res(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::SampleGrid::input_scan_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_input_scan_res(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::magnesium::SampleGrid::set_input_scan_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_tether_to_closest_res(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid, setting: bool) → None

C++: protocols::magnesium::SampleGrid::set_tether_to_closest_res(const bool &) –> void

set_xyz_step(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid, setting: float) → None

C++: protocols::magnesium::SampleGrid::set_xyz_step(const double &) –> void

tether_to_closest_res(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → bool

C++: protocols::magnesium::SampleGrid::tether_to_closest_res() const –> bool

xmax(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → float

C++: protocols::magnesium::SampleGrid::xmax() const –> double

xmin(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → float

C++: protocols::magnesium::SampleGrid::xmin() const –> double

xyz_step(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → float

C++: protocols::magnesium::SampleGrid::xyz_step() const –> double

ymax(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → float

C++: protocols::magnesium::SampleGrid::ymax() const –> double

ymin(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → float

C++: protocols::magnesium::SampleGrid::ymin() const –> double

zmax(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → float

C++: protocols::magnesium::SampleGrid::zmax() const –> double

zmin(self: pyrosetta.rosetta.protocols.magnesium.SampleGrid) → float

C++: protocols::magnesium::SampleGrid::zmin() const –> double

pyrosetta.rosetta.protocols.magnesium.add_single_magnesium(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::add_single_magnesium(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.append_mg_bound_water(pose: pyrosetta.rosetta.core.pose.Pose, rsd: pyrosetta.rosetta.core.conformation.Residue, mg_res: int) → int

C++: protocols::magnesium::append_mg_bound_water(class core::pose::Pose &, const class core::conformation::Residue &, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.magnesium.define_mg_water_map(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: protocols::magnesium::define_mg_water_map(const class core::pose::Pose &) –> class std::map<unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > >

pyrosetta.rosetta.protocols.magnesium.filter_acceptor_ligands(pose: pyrosetta.rosetta.core.pose.Pose, ligands: pyrosetta.rosetta.utility.vector1_core_id_AtomID) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

C++: protocols::magnesium::filter_acceptor_ligands(const class core::pose::Pose &, const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.protocols.magnesium.find_bound_waters_that_are_daughters_in_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(const class core::pose::Pose &, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.fixup_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::fixup_magnesiums(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.get_closest_non_hoh_contact(*args, **kwargs)

Overloaded function.

1. get_closest_non_hoh_contact(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> pyrosetta.rosetta.core.id.AtomID

2. get_closest_non_hoh_contact(pose: pyrosetta.rosetta.core.pose.Pose, i: int, exclude_rsd: str) -> pyrosetta.rosetta.core.id.AtomID

C++: protocols::magnesium::get_closest_non_hoh_contact(const class core::pose::Pose &, const unsigned long, const std::string &) –> class core::id::AtomID

pyrosetta.rosetta.protocols.magnesium.get_hydration_stats(pose: pyrosetta.rosetta.core.pose.Pose, reference_pose: pyrosetta.rosetta.core.pose.Pose, pdb_mg_res_list_in: pyrosetta.rosetta.utility.vector1_unsigned_long, outfile: str) → None

C++: protocols::magnesium::get_hydration_stats(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const std::string &) –> void

pyrosetta.rosetta.protocols.magnesium.get_mg_ligands(*args, **kwargs)

Overloaded function.

1. get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

2. get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int, filter_for_acceptors: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

3. get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int, filter_for_acceptors: bool, exclude_virtual_waters: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

C++: protocols::magnesium::get_mg_ligands(const class core::pose::Pose &, const unsigned long, const bool, const bool) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.protocols.magnesium.get_mg_res(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::get_mg_res(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.get_mg_rsd() → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::magnesium::get_mg_rsd() –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.protocols.magnesium.get_mg_scorefxn() → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::magnesium::get_mg_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.magnesium.get_mg_water_pairs(*args, **kwargs)

Overloaded function.

1. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

2. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose, exclude_virtual_waters: bool) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::magnesium::get_mg_water_pairs(const class core::pose::Pose &, const bool) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

3. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

4. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, exclude_virtual_waters: bool) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::magnesium::get_mg_water_pairs(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

pyrosetta.rosetta.protocols.magnesium.get_octahedral_uniform_rotation_sampler(*args, **kwargs)

Overloaded function.

1. get_octahedral_uniform_rotation_sampler() -> pyrosetta.rosetta.numeric.UniformRotationSampler

2. get_octahedral_uniform_rotation_sampler(rotstep: float) -> pyrosetta.rosetta.numeric.UniformRotationSampler

3. get_octahedral_uniform_rotation_sampler(rotstep: float, remove_redundant: bool) -> pyrosetta.rosetta.numeric.UniformRotationSampler

C++: protocols::magnesium::get_octahedral_uniform_rotation_sampler(const double, const bool) –> class std::shared_ptr<const class numeric::UniformRotationSampler>

pyrosetta.rosetta.protocols.magnesium.get_useful_HOH_coords(Oc: pyrosetta.rosetta.numeric.xyzVector_double_t, OH1c: pyrosetta.rosetta.numeric.xyzVector_double_t, OH2c: pyrosetta.rosetta.numeric.xyzVector_double_t, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::magnesium::get_useful_HOH_coords(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::chemical::ResidueTypeSet &) –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.protocols.magnesium.get_water_res(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::get_water_res(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.get_water_uniform_rotation_sampler() → pyrosetta.rosetta.numeric.UniformRotationSampler

C++: protocols::magnesium::get_water_uniform_rotation_sampler() –> class std::shared_ptr<const class numeric::UniformRotationSampler>

pyrosetta.rosetta.protocols.magnesium.hydrate_magnesiums(*args, **kwargs)

Overloaded function.

1. hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose) -> None

2. hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose, use_virtual_waters_as_placeholders: bool) -> None

3. hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose, use_virtual_waters_as_placeholders: bool, test_all_mg_hydration_frames: bool) -> None

C++: protocols::magnesium::hydrate_magnesiums(class core::pose::Pose &, bool, bool) –> void

pyrosetta.rosetta.protocols.magnesium.instantiate_water_at_octahedral_vertex(*args, **kwargs)

Overloaded function.

1. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int) -> int

2. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float) -> int

3. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float, replace_residue: bool) -> int

4. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float, replace_residue: bool, virtual_water: bool) -> int

C++: protocols::magnesium::instantiate_water_at_octahedral_vertex(class core::pose::Pose &, const unsigned long, const unsigned long, const double, const bool, const bool) –> unsigned long

pyrosetta.rosetta.protocols.magnesium.minimize_magnesium_and_hydration_shell(*args, **kwargs)

Overloaded function.

1. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

3. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mg_coord_cst_dist: float) -> None

C++: protocols::magnesium::minimize_magnesium_and_hydration_shell(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const double) –> void

4. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

5. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

6. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mg_coord_cst_dist: float) -> None

C++: protocols::magnesium::minimize_magnesium_and_hydration_shell(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const double) –> void

pyrosetta.rosetta.protocols.magnesium.pdbslice(*args, **kwargs)

Overloaded function.

1. pdbslice(pose: pyrosetta.rosetta.core.pose.Pose, center_res: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

2. pdbslice(pose: pyrosetta.rosetta.core.pose.Pose, center_res: int, distance_cutoff: float) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::pdbslice(class core::pose::Pose &, const unsigned long, double) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.remove_mg_bound_waters(*args, **kwargs)

Overloaded function.

1. remove_mg_bound_waters(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. remove_mg_bound_waters(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, leave_other_waters: bool) -> None

C++: protocols::magnesium::remove_mg_bound_waters(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.protocols.magnesium.remove_waters_except_mg_bound(pose: pyrosetta.rosetta.core.pose.Pose, mg_water_pairs: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

C++: protocols::magnesium::remove_waters_except_mg_bound(class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

pyrosetta.rosetta.protocols.magnesium.strip_out_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::strip_out_magnesiums(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.update_jump_atoms_for_mg_bound_water(pose: pyrosetta.rosetta.core.pose.Pose, n: int) → None

C++: protocols::magnesium::update_jump_atoms_for_mg_bound_water(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.magnesium.update_mg_hoh_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::update_mg_hoh_fold_tree(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.update_numbers_in_pdb_info(*args, **kwargs)

Overloaded function.

1. update_numbers_in_pdb_info(pose: pyrosetta.rosetta.core.pose.Pose) -> None

2. update_numbers_in_pdb_info(pose: pyrosetta.rosetta.core.pose.Pose, reset_waters: bool) -> None

C++: protocols::magnesium::update_numbers_in_pdb_info(class core::pose::Pose &, const bool) –> void