magnesium¶
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- 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.
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
apply(self: pyrosetta.rosetta.protocols.magnesium.MgMinimizer, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- 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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- 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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- 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.
apply(self: pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker, pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::magnesium::MgWaterHydrogenPacker::apply(class core::pose::Pose &) –> void
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- 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.
get_closest_non_hoh_contact(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> pyrosetta.rosetta.core.id.AtomID
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.
get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID
get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int, filter_for_acceptors: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID
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.
get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
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> > >
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
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.
get_octahedral_uniform_rotation_sampler() -> pyrosetta.rosetta.numeric.UniformRotationSampler
get_octahedral_uniform_rotation_sampler(rotstep: float) -> pyrosetta.rosetta.numeric.UniformRotationSampler
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.
hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose) -> None
hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose, use_virtual_waters_as_placeholders: bool) -> None
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.
instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int) -> int
instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float) -> int
instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float, replace_residue: bool) -> int
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.
minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
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
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
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
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
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.
pdbslice(pose: pyrosetta.rosetta.core.pose.Pose, center_res: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long
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.
remove_mg_bound_waters(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
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.
update_numbers_in_pdb_info(pose: pyrosetta.rosetta.core.pose.Pose) -> None
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