moves¶
Bindings for protocols::moves namespace
- pyrosetta.rosetta.protocols.moves.AddPyMOLObserver(*args, **kwargs)¶
Overloaded function.
AddPyMOLObserver(p: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool, update_interval: float) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
- Helper function that create PyMOLObserver Object and add it to the give Pose.
This is the most likely the only function that you need to call…
C++: protocols::moves::AddPyMOLObserver(class core::pose::Pose &, bool, double) –> class std::shared_ptr<class protocols::moves::PyMOLObserver>
- pyrosetta.rosetta.protocols.moves.AddPyMOLObserver_to_conformation(*args, **kwargs)¶
Overloaded function.
AddPyMOLObserver_to_conformation(p: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_conformation(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_conformation(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool, update_interval: float) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
Helper function that create PyMOLObserver Object and add it to the give Pose conformation object so pymol only updates on conformation changes.
C++: protocols::moves::AddPyMOLObserver_to_conformation(class core::pose::Pose &, bool, double) –> class std::shared_ptr<class protocols::moves::PyMOLObserver>
- pyrosetta.rosetta.protocols.moves.AddPyMOLObserver_to_energies(*args, **kwargs)¶
Overloaded function.
AddPyMOLObserver_to_energies(p: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_energies(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_energies(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool, update_interval: float) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
Helper function that create PyMOLObserver Object and add it to the give Pose energies object so pymol only updates on energy changes.
C++: protocols::moves::AddPyMOLObserver_to_energies(class core::pose::Pose &, bool, double) –> class std::shared_ptr<class protocols::moves::PyMOLObserver>
- class pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the stored fold tree to the pose
C++: protocols::moves::ChangeFoldTreeMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover, : pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover) pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover ¶
C++: protocols::moves::ChangeFoldTreeMover::operator=(const class protocols::moves::ChangeFoldTreeMover &) –> class protocols::moves::ChangeFoldTreeMover &
- 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.moves.ChangeFoldTreeMover) str ¶
C++: protocols::moves::ChangeFoldTreeMover::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_foldtree(self: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::moves::ChangeFoldTreeMover::set_foldtree(class core::kinematics::FoldTree) –> 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.moves.CompositionMover¶
Bases:
Mover
- add_mover(self: pyrosetta.rosetta.protocols.moves.CompositionMover, m: pyrosetta.rosetta.protocols.moves.Mover) None ¶
C++: protocols::moves::CompositionMover::add_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.moves.CompositionMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::moves::CompositionMover::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.moves.CompositionMover, pose: pyrosetta.rosetta.core.pose.Pose, i: int, j: int) -> None
C++: protocols::moves::CompositionMover::apply(class core::pose::Pose &, const unsigned long, const unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.CompositionMover, : pyrosetta.rosetta.protocols.moves.CompositionMover) pyrosetta.rosetta.protocols.moves.CompositionMover ¶
C++: protocols::moves::CompositionMover::operator=(const class protocols::moves::CompositionMover &) –> class protocols::moves::CompositionMover &
- clear(self: pyrosetta.rosetta.protocols.moves.CompositionMover) None ¶
C++: protocols::moves::CompositionMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- 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_movers(self: pyrosetta.rosetta.protocols.moves.CompositionMover) pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::CompositionMover::get_movers() –> class utility::vector1<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > >
- get_name(self: pyrosetta.rosetta.protocols.moves.CompositionMover) str ¶
C++: protocols::moves::CompositionMover::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.moves.CycleMover¶
Bases:
MoverContainer
CycleMover iterates through its vector of Movers one at a time over many calls to apply().
- Each time CycleMover.apply() is called, it calls apply() on the next Mover in its sequence,
until reaching the end of the list and starting over. Useful for things like doing a full repack one out of every eight cycles, and a rotamer trials on the other seven.
- add_mover(*args, **kwargs)¶
Overloaded function.
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover) -> None
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover, weight_in: float) -> None
Adds a mover to the end of this container
C++: protocols::moves::MoverContainer::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void
- apply(self: pyrosetta.rosetta.protocols.moves.CycleMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::CycleMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.CycleMover, : pyrosetta.rosetta.protocols.moves.CycleMover) pyrosetta.rosetta.protocols.moves.CycleMover ¶
C++: protocols::moves::CycleMover::operator=(const class protocols::moves::CycleMover &) –> class protocols::moves::CycleMover &
- clear(self: pyrosetta.rosetta.protocols.moves.MoverContainer) None ¶
C++: protocols::moves::MoverContainer::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.CycleMover) pyrosetta.rosetta.protocols.moves.Mover ¶
Clone returns a new instance of CycleMover representing a deep copy of this mover.
C++: protocols::moves::CycleMover::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.CycleMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::CycleMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- front(self: pyrosetta.rosetta.protocols.moves.MoverContainer) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::MoverContainer::front() –> 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_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, index: int) str ¶
C++: protocols::moves::MoverContainer::get_mover(unsigned long) const –> std::string
- get_name(self: pyrosetta.rosetta.protocols.moves.CycleMover) str ¶
C++: protocols::moves::CycleMover::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
- movers(self: pyrosetta.rosetta.protocols.moves.MoverContainer) pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::MoverContainer::movers() const –> const class utility::vector0<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nr_moves(self: pyrosetta.rosetta.protocols.moves.MoverContainer) int ¶
C++: protocols::moves::MoverContainer::nr_moves() –> unsigned long
- 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.MoverContainer, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::moves::MoverContainer::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_cycle_index(self: pyrosetta.rosetta.protocols.moves.CycleMover) None ¶
C++: protocols::moves::CycleMover::reset_cycle_index() –> 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.MoverContainer, new_tag: str) None ¶
C++: protocols::moves::MoverContainer::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Sets the input Pose for both the container
and the contained movers, for rmsd
C++: protocols::moves::MoverContainer::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::MoverContainer::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
- size(self: pyrosetta.rosetta.protocols.moves.MoverContainer) int ¶
C++: protocols::moves::MoverContainer::size() const –> unsigned long
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*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 &
- weights(self: pyrosetta.rosetta.protocols.moves.MoverContainer) pyrosetta.rosetta.utility.vector0_double ¶
C++: protocols::moves::MoverContainer::weights() const –> const class utility::vector0<double, class std::allocator<double> > &
- class pyrosetta.rosetta.protocols.moves.CyclicMover¶
Bases:
Mover
A simple class for cycling between movers in consecutive calls to apply()
- apply(self: pyrosetta.rosetta.protocols.moves.CyclicMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::CyclicMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.CyclicMover, : pyrosetta.rosetta.protocols.moves.CyclicMover) pyrosetta.rosetta.protocols.moves.CyclicMover ¶
C++: protocols::moves::CyclicMover::operator=(const class protocols::moves::CyclicMover &) –> class protocols::moves::CyclicMover &
- 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.CyclicMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::CyclicMover::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>
- enqueue(self: pyrosetta.rosetta.protocols.moves.CyclicMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Enqueue the specified mover for execution
C++: protocols::moves::CyclicMover::enqueue(class std::shared_ptr<class protocols::moves::Mover>) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.CyclicMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::CyclicMover::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.moves.CyclicMover) str ¶
C++: protocols::moves::CyclicMover::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.moves.DsspMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.moves.DsspMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::DsspMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.DsspMover, : pyrosetta.rosetta.protocols.moves.DsspMover) pyrosetta.rosetta.protocols.moves.DsspMover ¶
C++: protocols::moves::DsspMover::operator=(const class protocols::moves::DsspMover &) –> class protocols::moves::DsspMover &
- 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.DsspMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone this object
C++: protocols::moves::DsspMover::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.DsspMover) pyrosetta.rosetta.protocols.moves.Mover ¶
create this type of object
C++: protocols::moves::DsspMover::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.moves.DsspMover) str ¶
C++: protocols::moves::DsspMover::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 mover_name() str ¶
C++: protocols::moves::DsspMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.DsspMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::moves::DsspMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::moves::DsspMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_asu_only(self: pyrosetta.rosetta.protocols.moves.DsspMover, asu_only: bool) None ¶
Select only the asymmetric unit residues or not.
C++: protocols::moves::DsspMover::set_asu_only(const bool) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_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.moves.DsspMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.moves.DsspMoverCreator, : pyrosetta.rosetta.protocols.moves.DsspMoverCreator) pyrosetta.rosetta.protocols.moves.DsspMoverCreator ¶
C++: protocols::moves::DsspMoverCreator::operator=(const class protocols::moves::DsspMoverCreator &) –> class protocols::moves::DsspMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.moves.DsspMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::DsspMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.moves.DsspMoverCreator) str ¶
C++: protocols::moves::DsspMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.moves.DualMonteCarlo¶
Bases:
pybind11_object
DualMonteCarlo is a wrapper class around MonteCarlo. Its original purpose is to allow for Boltzmann scoring a pose in centroid mode while simultaneously tracking a fullatom equivalent. It should work for any paired poses. Generally, “DMC_pose” refers to the pose this class tracks, whereas “MC_pose” refers to the one used by the underlying MC object. While this class contains a MonteCarlo object (by composition, not inheritance); you cannot pass in a MC object to it, nor can you get an OP to that object. const access to the underlying MC is provided at this time; if you want nonconst access you can write it in but beware that the user can then ruin the bookkeeping! Also note that I (SML) left the framework in place in comments for a lot of MC’s functions within DMC like checkpointing and counters. Flesh these out if you want them…
- MC(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
const access to MC object
C++: protocols::moves::DualMonteCarlo::MC() const –> const class protocols::moves::MonteCarlo &
- boltzmann(*args, **kwargs)¶
Overloaded function.
boltzmann(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
C++: protocols::moves::DualMonteCarlo::boltzmann(class core::pose::Pose &, class core::pose::Pose &, const std::string &) –> bool
- last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) pyrosetta.rosetta.core.pose.Pose ¶
this gets you only the DMC’s pose; call MC directly for its. Note that this pose is accepted based on the partner pose in the underlying MC.
C++: protocols::moves::DualMonteCarlo::last_accepted_pose() const –> const class core::pose::Pose &
- last_accepted_score(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) float ¶
C++: protocols::moves::DualMonteCarlo::last_accepted_score() const –> double
- lowest_score(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) float ¶
C++: protocols::moves::DualMonteCarlo::lowest_score() const –> double
- lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::DualMonteCarlo::lowest_score_pose() const –> const class core::pose::Pose &
- recover_low(*args, **kwargs)¶
Overloaded function.
recover_low(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose) -> None
- Copies the lowest_score_ pose into the input pose, as well as into
last_accepted_pose_. Copies action for underlying MC but does not return that pose.
C++: protocols::moves::DualMonteCarlo::recover_low(class core::pose::Pose &) –> void
recover_low(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose) -> None
- Copies the lowest_score_ pose into the input pose, as well as into
last_accepted_pose_. Always copies action for underlying MC. This version returns the MC’s pose.
C++: protocols::moves::DualMonteCarlo::recover_low(class core::pose::Pose &, class core::pose::Pose &) –> void
- reset(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
sets lowest and last_accepted poses to pose; calls MC’s reset too
C++: protocols::moves::DualMonteCarlo::reset(const class core::pose::Pose &, const class core::pose::Pose &) –> void
- score_function(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::moves::DualMonteCarlo::score_function() const –> const class core::scoring::ScoreFunction &
- show_scores(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) None ¶
C++: protocols::moves::DualMonteCarlo::show_scores() const –> void
- class pyrosetta.rosetta.protocols.moves.EXCN_Converged¶
Bases:
Exception
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.EXCN_Converged, : pyrosetta.rosetta.protocols.moves.EXCN_Converged) pyrosetta.rosetta.protocols.moves.EXCN_Converged ¶
C++: protocols::moves::EXCN_Converged::operator=(const class protocols::moves::EXCN_Converged &) –> class protocols::moves::EXCN_Converged &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.moves.FastLinearFunc¶
Bases:
RampingFunc
- assign(self: pyrosetta.rosetta.protocols.moves.FastLinearFunc, : pyrosetta.rosetta.protocols.moves.FastLinearFunc) pyrosetta.rosetta.protocols.moves.FastLinearFunc ¶
C++: protocols::moves::FastLinearFunc::operator=(const class protocols::moves::FastLinearFunc &) –> class protocols::moves::FastLinearFunc &
- func(self: pyrosetta.rosetta.protocols.moves.FastLinearFunc, x: float) float ¶
C++: protocols::moves::FastLinearFunc::func(double) const –> double
- class pyrosetta.rosetta.protocols.moves.FilterMover¶
Bases:
Mover
- add_filter(self: pyrosetta.rosetta.protocols.moves.FilterMover, my_filter: pyrosetta.rosetta.protocols.filters.Filter) None ¶
C++: protocols::moves::FilterMover::add_filter(const class std::shared_ptr<class protocols::filters::Filter> &) –> void
- apply(self: pyrosetta.rosetta.protocols.moves.FilterMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::FilterMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.FilterMover, : pyrosetta.rosetta.protocols.moves.FilterMover) pyrosetta.rosetta.protocols.moves.FilterMover ¶
C++: protocols::moves::FilterMover::operator=(const class protocols::moves::FilterMover &) –> class protocols::moves::FilterMover &
- 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.moves.FilterMover) str ¶
C++: protocols::moves::FilterMover::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
- max_tries(self: pyrosetta.rosetta.protocols.moves.FilterMover, mt: int) None ¶
set maximum tries of making a move with my_mover
C++: protocols::moves::FilterMover::max_tries(const unsigned long) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- 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_mover(self: pyrosetta.rosetta.protocols.moves.FilterMover, my_mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
set mover
C++: protocols::moves::FilterMover::set_mover(const class std::shared_ptr<class protocols::moves::Mover> &) –> 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.moves.FilterReportAsPoseExtraScoresMover¶
Bases:
Mover
This Mover runs a Filter and dumps the report_sm value to Pose’s extra scores (for later JD reporting) To do the same for all filters, use WriteFiltersToPose.
- apply(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, : pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover) pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::operator=(const class protocols::moves::FilterReportAsPoseExtraScoresMover &) –> class protocols::moves::FilterReportAsPoseExtraScoresMover &
- 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.FilterReportAsPoseExtraScoresMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::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.FilterReportAsPoseExtraScoresMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::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_filter(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::get_filter() const –> class std::shared_ptr<class protocols::filters::Filter>
- 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.moves.FilterReportAsPoseExtraScoresMover) str ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::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_report_as(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover) str ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::get_report_as() const –> const std::string &
- 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 mover_name() str ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None ¶
set filter we report from
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::set_filter(class std::shared_ptr<class protocols::filters::Filter>) –> 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_report_as(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, report_as: str) None ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::set_report_as(const std::string &) –> 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.FilterReportAsPoseExtraScoresMover) -> None
show(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::moves::FilterReportAsPoseExtraScoresMover::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.moves.FilterReportAsPoseExtraScoresMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator, : pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator) pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMoverCreator::operator=(const class protocols::moves::FilterReportAsPoseExtraScoresMoverCreator &) –> class protocols::moves::FilterReportAsPoseExtraScoresMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator) str ¶
C++: protocols::moves::FilterReportAsPoseExtraScoresMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.moves.FilterReporterMover¶
Bases:
Mover
A FilterMover that also calls report() on apply()
- apply(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::FilterReporterMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, rhs: pyrosetta.rosetta.protocols.moves.FilterReporterMover) pyrosetta.rosetta.protocols.moves.FilterReporterMover ¶
C++: protocols::moves::FilterReporterMover::operator=(const class protocols::moves::FilterReporterMover &) –> class protocols::moves::FilterReporterMover &
- 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.FilterReporterMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::FilterReporterMover::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.FilterReporterMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::FilterReporterMover::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_filter(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::moves::FilterReporterMover::get_filter() const –> class std::shared_ptr<class protocols::filters::Filter>
- 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_mover(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::FilterReporterMover::get_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_name(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover) str ¶
C++: protocols::moves::FilterReporterMover::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_out(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover) pyrosetta.rosetta.std.ostream ¶
C++: protocols::moves::FilterReporterMover::get_out() –> std::ostream &
- 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_filter(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None ¶
C++: protocols::moves::FilterReporterMover::set_filter(const class std::shared_ptr<class protocols::filters::Filter> &) –> 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_mover(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
C++: protocols::moves::FilterReporterMover::set_mover(const class std::shared_ptr<class protocols::moves::Mover> &) –> 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_out(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::moves::FilterReporterMover::set_out(const std::ostream &) –> 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.moves.GeometricFunc¶
Bases:
RampingFunc
Ramps rapidly from the starting value to the final value. Not 1 at x=1. Doesn’t really finish at (1,1). func(x) = 1 - exp( -1 * x * inv_xval_at_0p5 * 0.6931 );
- assign(self: pyrosetta.rosetta.protocols.moves.GeometricFunc, : pyrosetta.rosetta.protocols.moves.GeometricFunc) pyrosetta.rosetta.protocols.moves.GeometricFunc ¶
C++: protocols::moves::GeometricFunc::operator=(const class protocols::moves::GeometricFunc &) –> class protocols::moves::GeometricFunc &
- func(self: pyrosetta.rosetta.protocols.moves.GeometricFunc, x: float) float ¶
C++: protocols::moves::GeometricFunc::func(double) const –> double
- class pyrosetta.rosetta.protocols.moves.IfMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.moves.IfMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::IfMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.IfMover, : pyrosetta.rosetta.protocols.moves.IfMover) pyrosetta.rosetta.protocols.moves.IfMover ¶
C++: protocols::moves::IfMover::operator=(const class protocols::moves::IfMover &) –> class protocols::moves::IfMover &
- 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.IfMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::IfMover::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.IfMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::IfMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.IfMover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::IfMover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_additional_output_false_mover(self: pyrosetta.rosetta.protocols.moves.IfMover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::IfMover::get_additional_output_false_mover() –> class std::shared_ptr<class core::pose::Pose>
- get_additional_output_true_mover(self: pyrosetta.rosetta.protocols.moves.IfMover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::IfMover::get_additional_output_true_mover() –> 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.moves.IfMover) str ¶
C++: protocols::moves::IfMover::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 mover_name() str ¶
C++: protocols::moves::IfMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.IfMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::moves::IfMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::moves::IfMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.moves.IfMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.moves.IfMoverCreator, : pyrosetta.rosetta.protocols.moves.IfMoverCreator) pyrosetta.rosetta.protocols.moves.IfMoverCreator ¶
C++: protocols::moves::IfMoverCreator::operator=(const class protocols::moves::IfMoverCreator &) –> class protocols::moves::IfMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.moves.IfMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::IfMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.moves.IfMoverCreator) str ¶
C++: protocols::moves::IfMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.moves.InvGeometricFunc¶
Bases:
RampingFunc
Ramps slowly from the starting value to the final value Non-zero for x = 0. Doesn’t really start at (0,0). func(x) = exp( -1 * ( 1 - x ) / ( 1 - xval_at_0p5 ) * 0.6931 );
- assign(self: pyrosetta.rosetta.protocols.moves.InvGeometricFunc, : pyrosetta.rosetta.protocols.moves.InvGeometricFunc) pyrosetta.rosetta.protocols.moves.InvGeometricFunc ¶
C++: protocols::moves::InvGeometricFunc::operator=(const class protocols::moves::InvGeometricFunc &) –> class protocols::moves::InvGeometricFunc &
- func(self: pyrosetta.rosetta.protocols.moves.InvGeometricFunc, x: float) float ¶
C++: protocols::moves::InvGeometricFunc::func(double) const –> double
- class pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover¶
Bases:
Mover
A mover that repeatedly applies a sub-mover (up to a given maximum) until the given filter returns values within a certain delta for a given number of cycles.
- apply(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::IteratedConvergenceMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, : pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover ¶
C++: protocols::moves::IteratedConvergenceMover::operator=(const class protocols::moves::IteratedConvergenceMover &) –> class protocols::moves::IteratedConvergenceMover &
- 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.IteratedConvergenceMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::moves::IteratedConvergenceMover::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(*args, **kwargs)¶
Overloaded function.
cycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, cycles: int) -> None
C++: protocols::moves::IteratedConvergenceMover::cycles(unsigned long) –> void
cycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> int
C++: protocols::moves::IteratedConvergenceMover::cycles() const –> unsigned long
- delta(*args, **kwargs)¶
Overloaded function.
delta(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, delta: float) -> None
C++: protocols::moves::IteratedConvergenceMover::delta(double) –> void
delta(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> float
C++: protocols::moves::IteratedConvergenceMover::delta() const –> double
- filter(*args, **kwargs)¶
Overloaded function.
filter(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, filter: pyrosetta.rosetta.protocols.filters.Filter) -> None
C++: protocols::moves::IteratedConvergenceMover::filter(class std::shared_ptr<const class protocols::filters::Filter>) –> void
filter(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> pyrosetta.rosetta.protocols.filters.Filter
C++: protocols::moves::IteratedConvergenceMover::filter() const –> class std::shared_ptr<const class protocols::filters::Filter>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::moves::IteratedConvergenceMover::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.moves.IteratedConvergenceMover) str ¶
C++: protocols::moves::IteratedConvergenceMover::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
- maxcycles(*args, **kwargs)¶
Overloaded function.
maxcycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, maxcycles: int) -> None
C++: protocols::moves::IteratedConvergenceMover::maxcycles(unsigned long) –> void
maxcycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> int
C++: protocols::moves::IteratedConvergenceMover::maxcycles() const –> unsigned long
- static mover_name() str ¶
C++: protocols::moves::IteratedConvergenceMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML (specifically in the context of the parser/scripting scheme)
C++: protocols::moves::IteratedConvergenceMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::moves::IteratedConvergenceMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- submover(*args, **kwargs)¶
Overloaded function.
submover(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, mover: pyrosetta.rosetta.protocols.moves.Mover) -> None
C++: protocols::moves::IteratedConvergenceMover::submover(class std::shared_ptr<class protocols::moves::Mover>) –> void
submover(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> pyrosetta.rosetta.protocols.moves.Mover
C++: protocols::moves::IteratedConvergenceMover::submover() const –> class std::shared_ptr<class protocols::moves::Mover>
- 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.moves.IteratedConvergenceMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator, : pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator) pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator ¶
C++: protocols::moves::IteratedConvergenceMoverCreator::operator=(const class protocols::moves::IteratedConvergenceMoverCreator &) –> class protocols::moves::IteratedConvergenceMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::IteratedConvergenceMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator) str ¶
C++: protocols::moves::IteratedConvergenceMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.moves.JumpOutMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.moves.JumpOutMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Applies a move, and conditionally applies a second move.
This mover applies the first move, and checks if the score difference between the initial score and the score after the first move is within a tolerance. If the score after the first move is within the tolerance, the second move is applied.
C++: protocols::moves::JumpOutMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.JumpOutMover, : pyrosetta.rosetta.protocols.moves.JumpOutMover) pyrosetta.rosetta.protocols.moves.JumpOutMover ¶
C++: protocols::moves::JumpOutMover::operator=(const class protocols::moves::JumpOutMover &) –> class protocols::moves::JumpOutMover &
- 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.moves.JumpOutMover) str ¶
C++: protocols::moves::JumpOutMover::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.moves.LinearFunc¶
Bases:
RampingFunc
- assign(self: pyrosetta.rosetta.protocols.moves.LinearFunc, : pyrosetta.rosetta.protocols.moves.LinearFunc) pyrosetta.rosetta.protocols.moves.LinearFunc ¶
C++: protocols::moves::LinearFunc::operator=(const class protocols::moves::LinearFunc &) –> class protocols::moves::LinearFunc &
- func(self: pyrosetta.rosetta.protocols.moves.LinearFunc, x: float) float ¶
C++: protocols::moves::LinearFunc::func(double) const –> double
- class pyrosetta.rosetta.protocols.moves.MCA¶
Bases:
pybind11_object
Members:
MCA_accepted_score_beat_low
MCA_accepted_score_beat_last
MCA_accepted_thermally
MCA_rejected
- MCA_accepted_score_beat_last = <MCA.MCA_accepted_score_beat_last: 2>¶
- MCA_accepted_score_beat_low = <MCA.MCA_accepted_score_beat_low: 3>¶
- MCA_accepted_thermally = <MCA.MCA_accepted_thermally: 1>¶
- MCA_rejected = <MCA.MCA_rejected: 0>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.protocols.moves.MCShowMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.moves.MCShowMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::MCShowMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.MCShowMover, : pyrosetta.rosetta.protocols.moves.MCShowMover) pyrosetta.rosetta.protocols.moves.MCShowMover ¶
C++: protocols::moves::MCShowMover::operator=(const class protocols::moves::MCShowMover &) –> class protocols::moves::MCShowMover &
- 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.moves.MCShowMover) str ¶
C++: protocols::moves::MCShowMover::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.moves.MixedMonteCarlo¶
Bases:
pybind11_object
A wrapper class around MonteCarlo that uses both centroid and FA scorefxns.
A Hybrid Monte Carlo mover that employs both centroid and ful-atom score functions. The purpose of this object is to use a combination of centroid and full-atom scorefxn for Boltzmann scoring but only use only the full-atom pose for bookkeeping. This object is particularly important for Resolution Exchange MC based docking.
AmeyaHarmalkar (harmalkar.ameya24.com)
- MC(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
Const access to the MC object
C++: protocols::moves::MixedMonteCarlo::MC() const –> const class protocols::moves::MonteCarlo &
- boltzmann(*args, **kwargs)¶
Overloaded function.
boltzmann(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
This method should evaluate net score from CG and AA modes
C++: protocols::moves::MixedMonteCarlo::boltzmann(class core::pose::Pose &, class core::pose::Pose &, const std::string &) –> bool
- highres_score_function(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
Returns the highres scorefxn
C++: protocols::moves::MixedMonteCarlo::highres_score_function() const –> const class core::scoring::ScoreFunction &
- last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) pyrosetta.rosetta.core.pose.Pose ¶
this gets you only the low-res pose
C++: protocols::moves::MixedMonteCarlo::last_accepted_pose() const –> const class core::pose::Pose &
- last_accepted_score(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) float ¶
Returns the score value of the last accepted pose
C++: protocols::moves::MixedMonteCarlo::last_accepted_score() const –> double
- lowest_score(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) float ¶
Returns the score value of the lowest score pose encountered
C++: protocols::moves::MixedMonteCarlo::lowest_score() const –> double
- lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) pyrosetta.rosetta.core.pose.Pose ¶
this gets you only the low-res pose
C++: protocols::moves::MixedMonteCarlo::lowest_score_pose() const –> const class core::pose::Pose &
- lowres_score_function(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
Returns the lowres scorefxn
C++: protocols::moves::MixedMonteCarlo::lowres_score_function() const –> const class core::scoring::ScoreFunction &
- recover_low(*args, **kwargs)¶
Overloaded function.
recover_low(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, high_pose: pyrosetta.rosetta.core.pose.Pose) -> None
- Copies the lowest_score_ pose into the input pose as well as in the
last_accepted_ pose
C++: protocols::moves::MixedMonteCarlo::recover_low(class core::pose::Pose &) –> void
recover_low(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose) -> None
- Copies the lowest_score_ pose into the input pose as well as in the
last_accepted_ pose. Returns the highres pose
C++: protocols::moves::MixedMonteCarlo::recover_low(class core::pose::Pose &, class core::pose::Pose &) –> void
- reset(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Sets the lowest and last accepted poses to pose and calls MC reset
C++: protocols::moves::MixedMonteCarlo::reset(const class core::pose::Pose &, const class core::pose::Pose &) –> void
- show_scores(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) None ¶
Displays the last accepted and lowest scores
C++: protocols::moves::MixedMonteCarlo::show_scores() const –> void
- class pyrosetta.rosetta.protocols.moves.MonteCarlo¶
Bases:
pybind11_object
This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics.
- Output Methods:
MonteCarlo.show_counters() MonteCarlo.show_scores() MonteCarlo.show_state()
- Common Methods:
MonteCarlo.last_accepted_score MonteCarlo.last_accepted_pose MonteCarlo.lowest_score MonteCarlo.lowest_score_pose MonteCarlo.score_function MonteCarlo.set_temperature MonteCarlo.temperature
- boltzmann(*args, **kwargs)¶
Overloaded function.
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool
- Applies the Metropolis Criterion on pose based on
the ScoreFunction, temperature, and the last accepted pose. This method evaluates the change in score, compares the trial pose to the last accepted pose, and updates the pose structure and simulation statistics appropriately
- example(s):
mc.boltzmann( pose )
- See also:
MonteCarlo MonteCarlo.last_accepted_score MonteCarlo.lowest_score
C++: protocols::moves::MonteCarlo::boltzmann(class core::pose::Pose &, const std::string &, const double, const double) –> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str, proposal_density_ratio: float, inner_score_temperature_delta: float) -> bool
- Applies the Metropolis Criterion on pose based on
the externally computes score, temperature, and the last accepted pose. This method evaluates the change in score, compares the trial pose to the last accepted pose, and updates the pose structure and simulation statistics appropriately
- example(s):
mc.boltzmann( pose, score )
- See also:
MonteCarlo MonteCarlo.last_accepted_score MonteCarlo.lowest_score
C++: protocols::moves::MonteCarlo::boltzmann(class core::pose::Pose &, const double, const std::string &, const double, const double) –> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float, check_lowest_score: bool) -> bool
- Applies the Metropolis Criterion on the inputted
pose based on the supplied score delta
example(s):
- See also:
MonteCarlo
C++: protocols::moves::MonteCarlo::boltzmann(double, const std::string &, const double, const double, bool) –> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float, check_lowest_score: bool) -> bool
- Applies the Metropolis Criterion on the inputted
pose based on the supplied score delta. Updates the Pose Structure accordingly.
example(s):
- See also:
MonteCarlo
C++: protocols::moves::MonteCarlo::boltzmann(double, class core::pose::Pose &, const std::string &, const double, const double, bool) –> bool
- change_weight(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, t: pyrosetta.rosetta.core.scoring.ScoreType, setting: float) None ¶
Change the weight on a score term in the object’s scorefunction. Useful when we don’t want to reset the whole scorefunction during an annealing step.
C++: protocols::moves::MonteCarlo::change_weight(const enum core::scoring::ScoreType &, const double &) –> void
- check_frequency(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) int ¶
C++: protocols::moves::MonteCarlo::check_frequency() const –> unsigned long
- clear_poses(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) None ¶
Removes last accepted pose and lowest score pose
- example(s):
mc.clear_poses()
- See also:
MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.lowest_score_pose MonteCarlo.recover_low MonteCarlo.reset MonteCarlo.set_last_accepted_pose MonteCarlo.set_lowest_score_pose
C++: protocols::moves::MonteCarlo::clear_poses() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
C++: protocols::moves::MonteCarlo::clone() –> class std::shared_ptr<class protocols::moves::MonteCarlo>
- eval_lowest_score_pose(*args, **kwargs)¶
Overloaded function.
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool, update_stats: bool) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool, update_stats: bool, move_type: str) -> bool
- Compares score of <pose> to the lowest score found.
If lower, sets the current lowest score pose and lowest score. Use internal pose energies if score_pose is false. Used to evaluate lowest score without boltzmann. Does not change pose structure.
Does not update simulation statistics or last accepts by default.
- example(s):
mc.eval_lowest_score_pose( pose )
- See also:
MonteCarlo MonteCarlo.lowest_score MonteCarlo.lowest_score_pose MonteCarlo.recover_low
C++: protocols::moves::MonteCarlo::eval_lowest_score_pose(class core::pose::Pose &, bool, bool, const std::string &) –> bool
- get_update_boinc(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) bool ¶
C++: protocols::moves::MonteCarlo::get_update_boinc() const –> bool
- heat_after_cycles(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) int ¶
no brief for now
C++: protocols::moves::MonteCarlo::heat_after_cycles() const –> unsigned long
- last_accept(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) int ¶
Returns the number of trials since last acceptance
- example(s):
mc.last_accept()
- See also:
MonteCarlo MonteCarlo.show_counters MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score
C++: protocols::moves::MonteCarlo::last_accept() const –> unsigned long
- last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) pyrosetta.rosetta.core.pose.Pose ¶
Returns the last accepted pose
- example(s):
mc.last_accepted_pose()
- See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_score
C++: protocols::moves::MonteCarlo::last_accepted_pose() const –> const class core::pose::Pose &
- last_accepted_score(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) float ¶
Returns the score value of the last accepted pose
- example(s):
mc.last_accepted_score()
- See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::last_accepted_score() const –> double
- last_score(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) float ¶
Returns the score value of the last score
- example(s):
mc.last_accepted_score()
- See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::last_score() const –> double
- lowest_score(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) float ¶
Returns the score value of the lowest score pose encountered
- example(s):
mc.lowest_score()
- See also:
MonteCarlo MonteCarlo.lowest_score_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::lowest_score() const –> double
- lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) pyrosetta.rosetta.core.pose.Pose ¶
Returns the lowest score pose encountered
- example(s):
mc.lowest_score_pose()
- See also:
MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.lowest_score
C++: protocols::moves::MonteCarlo::lowest_score_pose() const –> const class core::pose::Pose &
- mc_accepted(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) pyrosetta.rosetta.protocols.moves.MCA ¶
Returns mc_accepted, informative of the last move applied
- Note: Returns true for an accept, false otherwise
3 = accepted:score beat low score and last_accepted score 2 = accepted:score beat last_accepted score 1 = thermally accepted: score worse than last_accepted score 0 = not accepted
- example(s):
mc.mc_accepted()
- See also:
MonteCarlo MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::mc_accepted() const –> enum protocols::moves::MCA
- mc_accepted_string(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) str ¶
Returns mc_accepted as a human-readable string, informative of the last move applied
C++: protocols::moves::MonteCarlo::mc_accepted_string() const –> std::string
- push_back(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, : protocols::moves::MonteCarloExceptionConverge) None ¶
no brief for now
C++: protocols::moves::MonteCarlo::push_back(class std::shared_ptr<class protocols::moves::MonteCarloExceptionConverge>) –> void
- recover_low(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Sets the input <pose> and last accepted pose to
the lowest score pose
- example(s):
mc.recover_low( pose )
- See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_score_pose
C++: protocols::moves::MonteCarlo::recover_low(class core::pose::Pose &) –> void
- reset(*args, **kwargs)¶
Overloaded function.
reset(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None
- Sets lowest score pose and last accepted pose to
the score of <pose>
(does not reset counters)
- example(s):
mc.reset(pose)
- See also:
MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_scored_pose
C++: protocols::moves::MonteCarlo::reset(const class core::pose::Pose &) –> void
reset(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None
- Sets lowest score pose and last accepted pose to
the score of <pose>
(does not reset counters)
- example(s):
mc.reset(pose, score)
- See also:
MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_scored_pose
C++: protocols::moves::MonteCarlo::reset(const class core::pose::Pose &, const double) –> void
- reset_counters(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) None ¶
Resets the mover counters
- example(s):
mc.reset_counters()
- See alse:
MonteCarlo MonteCarlo.show_counters
C++: protocols::moves::MonteCarlo::reset_counters() –> void
- reset_scorefxn(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, init_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Resets the ScoreFunction
C++: protocols::moves::MonteCarlo::reset_scorefxn(const class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void
- score_function(*args, **kwargs)¶
Overloaded function.
score_function(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the ScoreFunction to <scorefxn> , re-scores
last accepted pose and lowest score pose
- example(s):
mc.score_function( scorefxn )
- See also:
MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function
C++: protocols::moves::MonteCarlo::score_function(const class core::scoring::ScoreFunction &) –> void
score_function(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> pyrosetta.rosetta.core.scoring.ScoreFunction
Returns the MonteCarlo ScoreFunction
- example(s):
mc.score_function() mc.score_function()( pose )
- See also:
MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function
C++: protocols::moves::MonteCarlo::score_function() const –> const class core::scoring::ScoreFunction &
- set_autotemp(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: bool, quench_temp: float) None ¶
- Sets autotemp to quench_temp
example(s): See also:
MonteCarlo MonteCarlo.autotemp MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::set_autotemp(const bool, const double) –> void
- set_heat_after_cycles(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: int) None ¶
no brief for now
C++: protocols::moves::MonteCarlo::set_heat_after_cycles(unsigned long) –> void
- set_last_accepted(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) None ¶
C++: protocols::moves::MonteCarlo::set_last_accepted(double) –> void
- set_last_accepted_pose(*args, **kwargs)¶
Overloaded function.
set_last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Sets the last accepted pose to the score of <pose>
(does not reset counters)
C++: protocols::moves::MonteCarlo::set_last_accepted_pose(const class core::pose::Pose &) –> void
set_last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None
Sets the last accepted pose and last accepted score
(does not reset counters)
C++: protocols::moves::MonteCarlo::set_last_accepted_pose(const class core::pose::Pose &, double) –> void
- set_last_score(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) None ¶
Set the last score.
C++: protocols::moves::MonteCarlo::set_last_score(double) –> void
- set_lowest(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) None ¶
C++: protocols::moves::MonteCarlo::set_lowest(double) –> void
- set_lowest_score_pose(*args, **kwargs)¶
Overloaded function.
set_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::moves::MonteCarlo::set_lowest_score_pose(const class core::pose::Pose &) –> void
set_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None
C++: protocols::moves::MonteCarlo::set_lowest_score_pose(const class core::pose::Pose &, double) –> void
- set_temperature(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, temp: float) None ¶
Sets the temperature value used in the Metropolis Criterion to <temp>
- example(s):
mc.set_temperature( temp )
- See also:
MonteCarlo MonteCarlo.temperature MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::set_temperature(const double) –> void
- set_total_score_last_considered(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) None ¶
C++: protocols::moves::MonteCarlo::set_total_score_last_considered(double) –> void
- set_update_boinc(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: bool) None ¶
no brief for now
C++: protocols::moves::MonteCarlo::set_update_boinc(bool) –> void
- show_counters(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) None ¶
- Displays the number of trials performed, fraction
of trial moves accepted, and the average energy drop per accepted trial by mover types applied (unknown movers or perturbations are listed as “unktrials”)
- example(s):
mc.show_counters()
- Output as:
protocols.moves.MonteCarlo: unk trials= X; accepts= Y; energy_drop/trial= Z
- See also:
MonteCarlo MonteCarlo.show_scores MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::show_counters() const –> void
- show_scores(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) None ¶
Displays the last accepted score and the lowest score
- example(s):
mc.show_scores()
- Output as:
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: X Y
- See also:
MonteCarlo MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.show_counters MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::show_scores() const –> void
- show_state(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) None ¶
- Displays the entire MonteCarlo state
temperature, scores, annealing settings, move statistics, move counters (show_counters)
- example(s):
mc.show_state()
- Output as:
- protocols.moves.MonteCarlo: MC: t l1 l2 las lws la au qu mca
t= temperature l1= (*score_function_)(*last_accepted_pose_) l2= (*score_function_)(*lowest_score_pose_) las= last accepted score lws= lowest score la= last_accept_ au= autotemp_ qu= quench_temp_ mca= mc_accepted_
- See also:
MonteCarlo MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.temperature
C++: protocols::moves::MonteCarlo::show_state() const –> void
- temperature(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) float ¶
Returns the temperature value used in the Metropolis Criterion
- example(s):
mc.temperature()
- See also:
MonteCarlo MonteCarlo.set_temperature MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::temperature() const –> double
- total_score_of_last_considered_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) float ¶
C++: protocols::moves::MonteCarlo::total_score_of_last_considered_pose() const –> double
- total_trials(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) int ¶
Returns the total number of trials since the last reset
: MonteCarlo.boltzmann(pose) updates the number of trials
- example(s):
mc.total_trials()
- See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.show_counters MonteCarlo.show_state
C++: protocols::moves::MonteCarlo::total_trials() const –> unsigned long
- class pyrosetta.rosetta.protocols.moves.MonteCarloExceptionConverge¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.moves.MonteCarloExceptionConverge, : pyrosetta.rosetta.protocols.moves.MonteCarloExceptionConverge) pyrosetta.rosetta.protocols.moves.MonteCarloExceptionConverge ¶
C++: protocols::moves::MonteCarloExceptionConverge::operator=(const class protocols::moves::MonteCarloExceptionConverge &) –> class protocols::moves::MonteCarloExceptionConverge &
- class pyrosetta.rosetta.protocols.moves.MonteCarloUtil¶
Bases:
Mover
the MCResetMover applies a monte carlo reset
- apply(self: pyrosetta.rosetta.protocols.moves.MonteCarloUtil, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::MonteCarloUtil::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.MonteCarloUtil, : pyrosetta.rosetta.protocols.moves.MonteCarloUtil) pyrosetta.rosetta.protocols.moves.MonteCarloUtil ¶
C++: protocols::moves::MonteCarloUtil::operator=(const class protocols::moves::MonteCarloUtil &) –> class protocols::moves::MonteCarloUtil &
- 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.MonteCarloUtil) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::MonteCarloUtil::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.MonteCarloUtil) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::MonteCarloUtil::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.moves.MonteCarloUtil) str ¶
C++: protocols::moves::MonteCarloUtil::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.MonteCarloUtil, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::moves::MonteCarloUtil::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.moves.MoveMapMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.core.pose.Pose) None ¶
Main Method
C++: protocols::moves::Mover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.protocols.moves.MoveMapMover) pyrosetta.rosetta.protocols.moves.MoveMapMover ¶
C++: protocols::moves::MoveMapMover::operator=(const class protocols::moves::MoveMapMover &) –> class protocols::moves::MoveMapMover &
- 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.moves.Mover) str ¶
Each derived class must specify its name. The class name.
C++: protocols::moves::Mover::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 > > &
- initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movemap(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.MoveMap ¶
- Get a movemap for the given pose
(As the movemap may vary based on the Pose (e.g. MoveMapFactory), we need the Pose information)
C++: protocols::moves::MoveMapMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>
- 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_movemap(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::moves::MoveMapMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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.moves.Mover¶
Bases:
pybind11_object
- apply(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.core.pose.Pose) None ¶
Main Method
C++: protocols::moves::Mover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &
- 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.moves.Mover) str ¶
Each derived class must specify its name. The class name.
C++: protocols::moves::Mover::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.moves.MoverApplyingMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.core.pose.Pose) None ¶
Main Method
C++: protocols::moves::Mover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.MoverApplyingMover, : pyrosetta.rosetta.protocols.moves.MoverApplyingMover) pyrosetta.rosetta.protocols.moves.MoverApplyingMover ¶
C++: protocols::moves::MoverApplyingMover::operator=(const class protocols::moves::MoverApplyingMover &) –> class protocols::moves::MoverApplyingMover &
- 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.moves.Mover) str ¶
Each derived class must specify its name. The class name.
C++: protocols::moves::Mover::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
- mover(self: pyrosetta.rosetta.protocols.moves.MoverApplyingMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::MoverApplyingMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- 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_mover(self: pyrosetta.rosetta.protocols.moves.MoverApplyingMover, : pyrosetta.rosetta.protocols.moves.Mover) None ¶
C++: protocols::moves::MoverApplyingMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> 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.moves.MoverContainer¶
Bases:
Mover
- add_mover(*args, **kwargs)¶
Overloaded function.
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover) -> None
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover, weight_in: float) -> None
Adds a mover to the end of this container
C++: protocols::moves::MoverContainer::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void
- apply(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::MoverContainer::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.MoverContainer, : pyrosetta.rosetta.protocols.moves.MoverContainer) pyrosetta.rosetta.protocols.moves.MoverContainer ¶
C++: protocols::moves::MoverContainer::operator=(const class protocols::moves::MoverContainer &) –> class protocols::moves::MoverContainer &
- clear(self: pyrosetta.rosetta.protocols.moves.MoverContainer) None ¶
C++: protocols::moves::MoverContainer::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- 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>
- front(self: pyrosetta.rosetta.protocols.moves.MoverContainer) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::MoverContainer::front() –> 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_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, index: int) str ¶
C++: protocols::moves::MoverContainer::get_mover(unsigned long) const –> std::string
- get_name(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
Each derived class must specify its name. The class name.
C++: protocols::moves::Mover::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
- movers(self: pyrosetta.rosetta.protocols.moves.MoverContainer) pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::MoverContainer::movers() const –> const class utility::vector0<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nr_moves(self: pyrosetta.rosetta.protocols.moves.MoverContainer) int ¶
C++: protocols::moves::MoverContainer::nr_moves() –> unsigned long
- 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.MoverContainer, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::moves::MoverContainer::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.MoverContainer, new_tag: str) None ¶
C++: protocols::moves::MoverContainer::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Sets the input Pose for both the container
and the contained movers, for rmsd
C++: protocols::moves::MoverContainer::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::MoverContainer::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
- size(self: pyrosetta.rosetta.protocols.moves.MoverContainer) int ¶
C++: protocols::moves::MoverContainer::size() const –> unsigned long
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*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 &
- weights(self: pyrosetta.rosetta.protocols.moves.MoverContainer) pyrosetta.rosetta.utility.vector0_double ¶
C++: protocols::moves::MoverContainer::weights() const –> const class utility::vector0<double, class std::allocator<double> > &
- class pyrosetta.rosetta.protocols.moves.MoverCreator¶
Bases:
pybind11_object
Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class.
- assign(self: pyrosetta.rosetta.protocols.moves.MoverCreator, : pyrosetta.rosetta.protocols.moves.MoverCreator) pyrosetta.rosetta.protocols.moves.MoverCreator ¶
C++: protocols::moves::MoverCreator::operator=(const class protocols::moves::MoverCreator &) –> class protocols::moves::MoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.moves.MoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a new mover.
C++: protocols::moves::MoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.moves.MoverCreator) str ¶
Return the tag name associated with this factory.
C++: protocols::moves::MoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
Describe the schema for the Mover that this Creator is responsible for
C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.moves.MoverFactory¶
Bases:
SingletonBase_protocols_moves_MoverFactory_t
- define_mover_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverFactory, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::moves::MoverFactory::define_mover_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- factory_register(self: pyrosetta.rosetta.protocols.moves.MoverFactory, creator: pyrosetta.rosetta.protocols.moves.MoverCreator) None ¶
C++: protocols::moves::MoverFactory::factory_register(class std::shared_ptr<class protocols::moves::MoverCreator>) –> void
- get_citation_humanreadable(self: pyrosetta.rosetta.protocols.moves.MoverFactory, mover_name: str) str ¶
Get a human-readable listing of the citations for a given mover, by mover name.
Returns an empty string if there are no citations.
Vikram K. Mulligan (vmulligan.org).
C++: protocols::moves::MoverFactory::get_citation_humanreadable(const std::string &) const –> std::string
- static get_instance() protocols::moves::MoverFactory ¶
C++: utility::SingletonBase<protocols::moves::MoverFactory>::get_instance() –> class protocols::moves::MoverFactory *
- mover_creator_map(self: pyrosetta.rosetta.protocols.moves.MoverFactory) pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_moves_MoverCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_moves_MoverCreator_t ¶
Read access to the set of all MoverCreators; for unit testing purposes
C++: protocols::moves::MoverFactory::mover_creator_map() const –> const class std::map<std::string, class std::shared_ptr<class protocols::moves::MoverCreator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class protocols::moves::MoverCreator> > > > &
- mover_exists(self: pyrosetta.rosetta.protocols.moves.MoverFactory, mover_name: str) bool ¶
Is there a mover with the given name that’s known to Rosetta?
Vikram K. Mulligan (vmullig.edu)
C++: protocols::moves::MoverFactory::mover_exists(const std::string &) const –> bool
- static mover_xml_schema_group_name() str ¶
C++: protocols::moves::MoverFactory::mover_xml_schema_group_name() –> std::string
- newMover(*args, **kwargs)¶
Overloaded function.
newMover(self: pyrosetta.rosetta.protocols.moves.MoverFactory, : str) -> pyrosetta.rosetta.protocols.moves.Mover
Create a mover given its identifying string
C++: protocols::moves::MoverFactory::newMover(const std::string &) const –> class std::shared_ptr<class protocols::moves::Mover>
newMover(self: pyrosetta.rosetta.protocols.moves.MoverFactory, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.moves.Mover
return new Mover by Tag parsing; the identifying string for the Mover is in the Tag
C++: protocols::moves::MoverFactory::newMover(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> class std::shared_ptr<class protocols::moves::Mover>
- provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverFactory, mover_name: str, xsd: utility::tag::XMLSchemaDefinition) None ¶
Get the XML schema for a given mover.
Throws an error if the mover is unknown to Rosetta.
Vikram K. Mulligan (vmullig.edu)
C++: protocols::moves::MoverFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.moves.MoverForPoseList¶
Bases:
Mover
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, : pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::moves::MoverForPoseList::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None
C++: protocols::moves::MoverForPoseList::apply(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void
apply(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, viewer_pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::moves::MoverForPoseList::apply(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, : pyrosetta.rosetta.protocols.moves.MoverForPoseList) pyrosetta.rosetta.protocols.moves.MoverForPoseList ¶
C++: protocols::moves::MoverForPoseList::operator=(const class protocols::moves::MoverForPoseList &) –> class protocols::moves::MoverForPoseList &
- 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.moves.Mover) str ¶
Each derived class must specify its name. The class name.
C++: protocols::moves::Mover::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)