symmetric_docking¶
Bindings for protocols::symmetric_docking namespace
- class pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockBaseProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol ¶
C++: protocols::symmetric_docking::SymDockBaseProtocol::operator=(const class protocols::symmetric_docking::SymDockBaseProtocol &) –> class protocols::symmetric_docking::SymDockBaseProtocol &
- 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_highres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::symmetric_docking::SymDockBaseProtocol::get_highres_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>
- 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_lowres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::symmetric_docking::SymDockBaseProtocol::get_lowres_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>
- get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) str ¶
C++: protocols::symmetric_docking::SymDockBaseProtocol::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.symmetric_docking.SymDockProtocol¶
Bases:
Mover
Main Symmetric Docking protocol class
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Mover Methods /////////
C++: protocols::symmetric_docking::SymDockProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol ¶
C++: protocols::symmetric_docking::SymDockProtocol::operator=(const class protocols::symmetric_docking::SymDockProtocol &) –> class protocols::symmetric_docking::SymDockProtocol &
- calc_CAPRI_rank(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, Irmsd: float, Lrmsd: float, Fnat: float) float ¶
Calculate fraction of native contacts recovered for one chain assuming correct native chain order
C++: protocols::symmetric_docking::SymDockProtocol::calc_CAPRI_rank(const double, const double, const double) –> double
- calc_Irms(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
Calculate interface RMSD of one chain to symmetric starting structure assuming correct native chain order
C++: protocols::symmetric_docking::SymDockProtocol::calc_Irms(class core::pose::Pose &) –> double
- calc_fnat(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) float ¶
Calculate fraction of native contacts recovered for one chain assuming correct native chain order
C++: protocols::symmetric_docking::SymDockProtocol::calc_fnat(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>) –> double
- calc_interaction_energy(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
Calculate Interaction energy between partners
C++: protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(class core::pose::Pose &) –> double
- calc_res_contact(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, dist_cutoff: float) bool ¶
Calculate whether two residues are within a distance cutoff of each other
C++: protocols::symmetric_docking::SymDockProtocol::calc_res_contact(const class std::shared_ptr<class core::conformation::Residue>, const class std::shared_ptr<class core::conformation::Residue>, const double) –> bool
- calc_rms(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
Calculate RMSD from partner to symmetric starting structure
C++: protocols::symmetric_docking::SymDockProtocol::calc_rms(class core::pose::Pose &) –> double
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::symmetric_docking::SymDockProtocol::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>
- design(*args, **kwargs)¶
Overloaded function.
design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, des: bool) -> None
Turn on Design of partner 2 during docking - not thoroughly tested
I think this is just copied over from regular docking protocol?
C++: protocols::symmetric_docking::SymDockProtocol::design(const bool) –> void
design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) -> bool
C++: protocols::symmetric_docking::SymDockProtocol::design() const –> bool
- docking_highres_filter(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::symmetric_docking::SymDockProtocol::docking_highres_filter(class core::pose::Pose &) –> bool
- docking_lowres_filter(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(class core::pose::Pose &) –> bool
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
- A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus ¶
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) str ¶
C++: protocols::symmetric_docking::SymDockProtocol::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
- hurry(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, hurry: bool) None ¶
Skip population of the score map
C++: protocols::symmetric_docking::SymDockProtocol::hurry(const bool) –> void
- 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::symmetric_docking::SymDockProtocol::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
RosettaScripts Methods //////
C++: protocols::symmetric_docking::SymDockProtocol::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- recover_sidechains(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Recover sidechains from the native pose
C++: protocols::symmetric_docking::SymDockProtocol::recover_sidechains(class core::pose::Pose &, const class core::pose::Pose &) –> void
- register_options(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) None ¶
Register Options from the Commandline
C++: protocols::symmetric_docking::SymDockProtocol::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- score_only(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Only score the pose using docking config
C++: protocols::symmetric_docking::SymDockProtocol::score_only(class core::pose::Pose &) –> 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_default(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) None ¶
Setup options based on constructors
C++: protocols::symmetric_docking::SymDockProtocol::set_default() –> void
- set_dock_ppk(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, dock_ppk_in: bool) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::set_dock_ppk(bool) –> void
- set_dock_rtmin(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, dock_rtmin_in: bool) None ¶
Setters for Protocol Options
C++: protocols::symmetric_docking::SymDockProtocol::set_dock_rtmin(bool) –> void
- set_fullatom(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, fullatom_in: bool) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::set_fullatom(const bool) –> void
- set_highres_scorefxn(*args, **kwargs)¶
Overloaded function.
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, docking_score_high_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
C++: protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, docking_score_high_in: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_score_pack_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
C++: protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_local_refine(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, local_refine_in: bool) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::set_local_refine(const bool) –> void
- set_lowres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, docking_score_low_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::set_lowres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_max_repeats(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, max_repeats_in: int) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::set_max_repeats(const unsigned long) –> 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_sc_min(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, sc_min_in: bool) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::set_sc_min(bool) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- set_view(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, view_in: bool) None ¶
C++: protocols::symmetric_docking::SymDockProtocol::set_view(bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(*args, **kwargs)¶
Overloaded function.
task_factory(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
Set Task Factory for Packing
C++: protocols::symmetric_docking::SymDockProtocol::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
task_factory(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) -> pyrosetta.rosetta.core.pack.task.TaskFactory
C++: protocols::symmetric_docking::SymDockProtocol::task_factory() –> class std::shared_ptr<class core::pack::task::TaskFactory> &
- 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.symmetric_docking.SymDockProtocolCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator ¶
C++: protocols::symmetric_docking::SymDockProtocolCreator::operator=(const class protocols::symmetric_docking::SymDockProtocolCreator &) –> class protocols::symmetric_docking::SymDockProtocolCreator &
- create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::symmetric_docking::SymDockProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator) str ¶
C++: protocols::symmetric_docking::SymDockProtocolCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymDockProtocolCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- pyrosetta.rosetta.protocols.symmetric_docking.SymDock_main() None ¶
Define Main funciton for symmetric docking protocol
C++: protocols::symmetric_docking::SymDock_main() –> void
- class pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes ¶
C++: protocols::symmetric_docking::SymDockingHiRes::operator=(const class protocols::symmetric_docking::SymDockingHiRes &) –> class protocols::symmetric_docking::SymDockingHiRes &
- 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.symmetric_docking.SymDockingHiRes) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::symmetric_docking::SymDockingHiRes::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>
- design(*args, **kwargs)¶
Overloaded function.
design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, des: bool) -> None
C++: protocols::symmetric_docking::SymDockingHiRes::design(const bool) –> void
design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) -> bool
C++: protocols::symmetric_docking::SymDockingHiRes::design() const –> bool
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
- A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus ¶
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_mc(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
C++: protocols::symmetric_docking::SymDockingHiRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>
- get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) str ¶
C++: protocols::symmetric_docking::SymDockingHiRes::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_default(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_default(class core::pose::Pose &) –> void
- set_dock_mcm_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_dock_mcm_protocol(class core::pose::Pose &) –> void
- set_dock_min_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_dock_min_protocol() –> void
- set_dock_ppk_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol(class core::pose::Pose &) –> 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_min_type(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, min_type_in: str) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_min_type(std::string) –> void
- set_move_map(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_move_map(class std::shared_ptr<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_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_protocol(class core::pose::Pose &) –> void
- set_repack(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, repack_switch: bool) None ¶
C++: protocols::symmetric_docking::SymDockingHiRes::set_repack(bool) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- 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
- task_factory(*args, **kwargs)¶
Overloaded function.
task_factory(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, task: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
C++: protocols::symmetric_docking::SymDockingHiRes::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
task_factory(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) -> pyrosetta.rosetta.core.pack.task.TaskFactory
C++: protocols::symmetric_docking::SymDockingHiRes::task_factory() –> class std::shared_ptr<class core::pack::task::TaskFactory> &
- 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.symmetric_docking.SymDockingLowRes¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingLowRes::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes ¶
C++: protocols::symmetric_docking::SymDockingLowRes::operator=(const class protocols::symmetric_docking::SymDockingLowRes &) –> class protocols::symmetric_docking::SymDockingLowRes &
- 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.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::symmetric_docking::SymDockingLowRes::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_mc(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
C++: protocols::symmetric_docking::SymDockingLowRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>
- get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) str ¶
C++: protocols::symmetric_docking::SymDockingLowRes::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_pymol_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.moves.PyMOLMover ¶
C++: protocols::symmetric_docking::SymDockingLowRes::get_pymol_mover() –> class std::shared_ptr<class protocols::moves::PyMOLMover>
- 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
- rigid_body_trial(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingLowRes::rigid_body_trial(class core::pose::Pose &) –> 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_default(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingLowRes::set_default(class core::pose::Pose &) –> void
- set_default_mc(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingLowRes::set_default_mc(class core::pose::Pose &) –> void
- set_default_move_map(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingLowRes::set_default_move_map(class core::pose::Pose &) –> void
- set_default_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymDockingLowRes::set_default_protocol(class core::pose::Pose &) –> 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.symmetric_docking.SymFoldandDockMoveRbJumpMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::operator=(const class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover &) –> class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover &
- 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.symmetric_docking.SymFoldandDockMoveRbJumpMover) str ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::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::symmetric_docking::SymFoldandDockMoveRbJumpMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::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.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator::operator=(const class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator &) –> class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator) str ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::operator=(const class protocols::symmetric_docking::SymFoldandDockRbTrialMover &) –> class protocols::symmetric_docking::SymFoldandDockRbTrialMover &
- 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.symmetric_docking.SymFoldandDockRbTrialMover) str ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- init(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover) None ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::init() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static mover_name() str ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::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.symmetric_docking.SymFoldandDockRbTrialMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator::operator=(const class protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator &) –> class protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator) str ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::operator=(const class protocols::symmetric_docking::SymFoldandDockSlideTrialMover &) –> class protocols::symmetric_docking::SymFoldandDockSlideTrialMover &
- 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.symmetric_docking.SymFoldandDockSlideTrialMover) str ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::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::symmetric_docking::SymFoldandDockSlideTrialMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::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.symmetric_docking.SymFoldandDockSlideTrialMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator::operator=(const class protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator &) –> class protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator) str ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover¶
Bases:
SymSidechainMinMover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover) pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover ¶
C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::operator=(const class protocols::symmetric_docking::SymInterfaceSidechainMinMover &) –> class protocols::symmetric_docking::SymInterfaceSidechainMinMover &
- 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.symmetric_docking.SymInterfaceSidechainMinMover) str ¶
C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::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_default_options(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover) None ¶
C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::set_default_options() –> 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_interface_dist(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover, interface_dist_in: float) None ¶
C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::set_interface_dist(double) –> void
- set_minmover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, minmover_in: pyrosetta.rosetta.protocols.minimization_packing.MinMover) None ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::set_minmover(class std::shared_ptr<class protocols::minimization_packing::MinMover>) –> 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 &
- update_movemap(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::update_movemap(class core::pose::Pose &) –> void
- class pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking¶
Bases:
TaskOperation
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::symmetric_docking::SymRestrictTaskForDocking::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking, : pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking) pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking ¶
C++: protocols::symmetric_docking::SymRestrictTaskForDocking::operator=(const class protocols::symmetric_docking::SymRestrictTaskForDocking &) –> class protocols::symmetric_docking::SymRestrictTaskForDocking &
- clone(self: pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking) pyrosetta.rosetta.core.pack.task.operation.TaskOperation ¶
C++: protocols::symmetric_docking::SymRestrictTaskForDocking::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>
- parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Used to parse an xml-like tag to load parameters and properties.
C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.
C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- class pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover) pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::operator=(const class protocols::symmetric_docking::SymSidechainMinMover &) –> class protocols::symmetric_docking::SymSidechainMinMover &
- 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.symmetric_docking.SymSidechainMinMover) str ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::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_default_options(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover) None ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::set_default_options() –> 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_minmover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, minmover_in: pyrosetta.rosetta.protocols.minimization_packing.MinMover) None ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::set_minmover(class std::shared_ptr<class protocols::minimization_packing::MinMover>) –> 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 &
- update_movemap(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::symmetric_docking::SymSidechainMinMover::update_movemap(class core::pose::Pose &) –> void