movers¶
Bindings for protocols::denovo_design::movers namespace
- class pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover¶
Bases:
Mover
Adds a segment to the structuredata
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::AddSegmentDataMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, : pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover) pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover ¶
C++: protocols::denovo_design::movers::AddSegmentDataMover::operator=(const class protocols::denovo_design::movers::AddSegmentDataMover &) –> class protocols::denovo_design::movers::AddSegmentDataMover &
- 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.denovo_design.movers.AddSegmentDataMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::AddSegmentDataMover::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.denovo_design.movers.AddSegmentDataMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::AddSegmentDataMover::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.denovo_design.movers.AddSegmentDataMover) str ¶
C++: protocols::denovo_design::movers::AddSegmentDataMover::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::denovo_design::movers::AddSegmentDataMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::AddSegmentDataMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::AddSegmentDataMover::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_abego(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, abego: str) None ¶
Sets the abego of the segment to be created
C++: protocols::denovo_design::movers::AddSegmentDataMover::set_abego(const std::string &) –> 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_secstruct(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, secstruct: str) None ¶
Sets the secondary structure of the segment to be created
C++: protocols::denovo_design::movers::AddSegmentDataMover::set_secstruct(const std::string &) –> void
- set_segment_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, name: str) None ¶
Sets the name of the segment which will be created
C++: protocols::denovo_design::movers::AddSegmentDataMover::set_segment_name(const std::string &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::denovo_design::movers::AddSegmentDataMover::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.denovo_design.movers.AddSegmentDataMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator ¶
C++: protocols::denovo_design::movers::AddSegmentDataMoverCreator::operator=(const class protocols::denovo_design::movers::AddSegmentDataMoverCreator &) –> class protocols::denovo_design::movers::AddSegmentDataMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::AddSegmentDataMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator) str ¶
C++: protocols::denovo_design::movers::AddSegmentDataMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover¶
Bases:
Mover
Aligns one residue onto another
- add_target_selector(*args, **kwargs)¶
Overloaded function.
add_target_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template)
Clones the residue selector
C++: protocols::denovo_design::movers::AlignResiduesMover::add_target_selector(const class core::select::residue_selector::ResidueSelector &) –> void
add_target_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template)
Directly stores the ResidueSelectorCOP
C++: protocols::denovo_design::movers::AlignResiduesMover::add_target_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- add_template_selector(*args, **kwargs)¶
Overloaded function.
add_template_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
Adds residue selector that selects the template (i.e. the reference residues that we are aligning to)
Clones the residue selector
C++: protocols::denovo_design::movers::AlignResiduesMover::add_template_selector(const class core::select::residue_selector::ResidueSelector &) –> void
add_template_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
Adds residue selector that selects the template (i.e. the reference residues that we are aligning to)
Directly stores the ResidueSelectorCOP
C++: protocols::denovo_design::movers::AlignResiduesMover::add_template_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::AlignResiduesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, : pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover ¶
C++: protocols::denovo_design::movers::AlignResiduesMover::operator=(const class protocols::denovo_design::movers::AlignResiduesMover &) –> class protocols::denovo_design::movers::AlignResiduesMover &
- 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
- clear_target_selectors(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) None ¶
clears the list of target residue selectors
C++: protocols::denovo_design::movers::AlignResiduesMover::clear_target_selectors() –> void
- clear_template_selectors(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) None ¶
clears the list of template residue selectors
C++: protocols::denovo_design::movers::AlignResiduesMover::clear_template_selectors() –> void
- clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::AlignResiduesMover::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.denovo_design.movers.AlignResiduesMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::AlignResiduesMover::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.denovo_design.movers.AlignResiduesMover) str ¶
C++: protocols::denovo_design::movers::AlignResiduesMover::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::denovo_design::movers::AlignResiduesMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::AlignResiduesMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::AlignResiduesMover::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_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, id: str) None ¶
Sets the ID of this mover
C++: protocols::denovo_design::movers::AlignResiduesMover::set_id(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.denovo_design.movers.AlignResiduesMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::denovo_design::movers::AlignResiduesMover::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.denovo_design.movers.AlignResiduesMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator ¶
C++: protocols::denovo_design::movers::AlignResiduesMoverCreator::operator=(const class protocols::denovo_design::movers::AlignResiduesMoverCreator &) –> class protocols::denovo_design::movers::AlignResiduesMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::AlignResiduesMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator) str ¶
C++: protocols::denovo_design::movers::AlignResiduesMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator) pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator ¶
C++: protocols::denovo_design::movers::BridgeChainsCreator::operator=(const class protocols::denovo_design::movers::BridgeChainsCreator &) –> class protocols::denovo_design::movers::BridgeChainsCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::BridgeChainsCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator) str ¶
C++: protocols::denovo_design::movers::BridgeChainsCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover¶
Bases:
Mover
Creates a bridge connection between two chains using remodel
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::apply(class core::pose::Pose &) –> void
- architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::architect() const –> const class protocols::denovo_design::connection::ConnectionArchitect &
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, : pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::operator=(const class protocols::denovo_design::movers::BridgeChainsMover &) –> class protocols::denovo_design::movers::BridgeChainsMover &
- 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.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::BridgeChainsMover::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>
- dry_run(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) bool ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::dry_run() const –> bool
- fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::BridgeChainsMover::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.denovo_design.movers.BridgeChainsMover) str ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::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::denovo_design::movers::BridgeChainsMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) int ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::overlap() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::BridgeChainsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::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
- scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::scorefxn() const –> const class core::scoring::ScoreFunction &
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_dry_run(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, dry_run: bool) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_dry_run(const bool) –> void
- set_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, my_id: str) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_id(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_iterations(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, iterations: int) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_iterations(const unsigned long) –> void
- set_motifs(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, motifs_str: str, cut_resis_str: str) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_motifs(const std::string &, const std::string &) –> 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_overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, overlap_val: int) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_overlap(const unsigned long) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_scorefxn(const class core::scoring::ScoreFunction &) –> void
- set_segment1_ids(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, segments: str) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_segment1_ids(const std::string &) –> void
- set_segment2_ids(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, segments: str) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::set_segment2_ids(const std::string &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- static setup_attlist_for_derived_classes(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None ¶
C++: protocols::denovo_design::movers::BridgeChainsMover::setup_attlist_for_derived_classes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::denovo_design::movers::BridgeChainsMover::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.denovo_design.movers.BridgeChainsMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator ¶
C++: protocols::denovo_design::movers::BridgeChainsMoverCreator::operator=(const class protocols::denovo_design::movers::BridgeChainsMoverCreator &) –> class protocols::denovo_design::movers::BridgeChainsMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::BridgeChainsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator) str ¶
C++: protocols::denovo_design::movers::BridgeChainsMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover¶
Bases:
FoldArchitectMover
- add_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None ¶
Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt
C++: protocols::denovo_design::movers::FoldArchitectMover::add_filter(const class protocols::filters::Filter &) –> void
- add_postfold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Adds a mover to the list of postfold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::add_postfold_mover(const class protocols::moves::Mover &) –> void
- add_prefold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Adds a mover to the list of prefold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::add_prefold_mover(const class protocols::moves::Mover &) –> void
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover, : pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover) pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover ¶
C++: protocols::denovo_design::movers::BuildDeNovoBackboneMover::operator=(const class protocols::denovo_design::movers::BuildDeNovoBackboneMover &) –> class protocols::denovo_design::movers::BuildDeNovoBackboneMover &
- clear_filters(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None ¶
Clears the list of filters used to indicate whether a given folding attempt is successful
C++: protocols::denovo_design::movers::FoldArchitectMover::clear_filters() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clear_postfold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None ¶
Clears the list of postfold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::clear_postfold_movers() –> void
- clear_prefold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None ¶
Clears the list of prefold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::clear_prefold_movers() –> void
- clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.BuildDeNovoBackboneMover) str ¶
C++: protocols::denovo_design::movers::BuildDeNovoBackboneMover::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
- id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) str ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::id() const –> 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::denovo_design::movers::BuildDeNovoBackboneMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::FoldArchitectMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::BuildDeNovoBackboneMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static provide_xml_schema_with_name(xsd: utility::tag::XMLSchemaDefinition, mover_name: str) None ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema_with_name(class utility::tag::XMLSchemaDefinition &, const std::string &) –> 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_architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, architect: pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect) None ¶
Sets the architect that will be used to build blueprints dynamically
C++: protocols::denovo_design::movers::FoldArchitectMover::set_architect(const class protocols::denovo_design::architects::DeNovoArchitect &) –> void
- set_build_overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, overlap_val: int) None ¶
Sets the number of residues of overlap to use between build phases
C++: protocols::denovo_design::movers::FoldArchitectMover::set_build_overlap(const unsigned long) –> void
- set_builder(*args, **kwargs)¶
Overloaded function.
set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None
Sets the pose builder that will be used to create the extended-chain pose
Clones the provided PoseBuilder
C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(const class protocols::denovo_design::components::PoseBuilder &) –> void
set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None
Sets the pose builder that will be used to create the extended-chain pose
Uses/stores the provided PoseBuilder pointer directly
C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(class std::shared_ptr<class protocols::denovo_design::components::PoseBuilder>) –> 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_debug(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, debug: bool) None ¶
The debug value of the poseBuilder will be set based on this
C++: protocols::denovo_design::movers::FoldArchitectMover::set_debug(const bool) –> void
- set_dump_pdbs(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, dump: bool) None ¶
If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted
C++: protocols::denovo_design::movers::FoldArchitectMover::set_dump_pdbs(const bool) –> void
- set_folder(*args, **kwargs)¶
Overloaded function.
set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None
Sets the pose folder that will be used to sample conformations.
Clones the PoseFolder
C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(const class protocols::denovo_design::components::PoseFolder &) –> void
set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None
Sets the pose folder that will be used to sample conformations
Uses the provided PoseFolder pointer directly
C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>) –> void
- set_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, id_value: str) None ¶
Sets the ID of this mover
C++: protocols::denovo_design::movers::FoldArchitectMover::set_id(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_iterations_per_phase(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, niter: int) None ¶
Sets the number of folding attempts for each build phase
C++: protocols::denovo_design::movers::FoldArchitectMover::set_iterations_per_phase(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_perturber(*args, **kwargs)¶
Overloaded function.
set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None
Sets the perturber that will be used to change the plans of the architects
Clones the provided Perturber
C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(const class protocols::denovo_design::components::StructureDataPerturber &) –> void
set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None
Sets the perturber that will be used to change the plans of the architects
Uses/stores the provided Perturber pointer directly
C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>) –> void
- set_score_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None ¶
Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false
C++: protocols::denovo_design::movers::FoldArchitectMover::set_score_filter(const class protocols::filters::Filter &) –> void
- set_start_segments(*args, **kwargs)¶
Overloaded function.
set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None
sets names of segments to be included in the starting build phase
Comma-separated string containing segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const std::string &) –> void
set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None
sets names of segments to be included in the starting build phase
Set of segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void
- set_stop_segments(*args, **kwargs)¶
Overloaded function.
set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None
sets names of segments to be included in the final build phase
Comma-separated string containing segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const std::string &) –> void
set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None
sets names of segments to be included in the final build phase
Set of segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_from_xml_file(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_file: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Reads/parses an XML file and uses it to set up the mover
C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_file(const std::string &, class basic::datacache::DataMap &) –> void
- setup_from_xml_string(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_string: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Reads/parses an XML string and uses it to set up the mover
C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_string(const std::string &, class basic::datacache::DataMap &) –> void
- setup_from_xml_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Reads/parses a Tag object and uses it to set up the mover
C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> 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.denovo_design.movers.BuildDeNovoBackboneMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator ¶
C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::operator=(const class protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator &) –> class protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator) str ¶
C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.denovo_design.movers.CutAndJump¶
Bases:
pybind11_object
- property cutpoint¶
- property jump¶
- class pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover¶
Bases:
Mover
declares covalent bond
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the mover
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, : pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover) pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::operator=(const class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover &) –> class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover &
- 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.denovo_design.movers.DeclareStructureDataCovalentBondMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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.denovo_design.movers.DeclareStructureDataCovalentBondMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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.denovo_design.movers.DeclareStructureDataCovalentBondMover) str ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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::denovo_design::movers::DeclareStructureDataCovalentBondMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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_atom1(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, atom: str) None ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::set_atom1(const std::string &) –> void
- set_atom2(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, atom: str) None ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::set_atom2(const std::string &) –> 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.denovo_design.movers.DeclareStructureDataCovalentBondMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, output: pyrosetta.rosetta.std.ostream) -> None
Show the contents of the Mover
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::operator=(const class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator &) –> class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator) str ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed¶
Bases:
Exception
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed, : pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed) pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed ¶
C++: protocols::denovo_design::movers::EXCN_FilterFailed::operator=(const class protocols::denovo_design::movers::EXCN_FilterFailed &) –> class protocols::denovo_design::movers::EXCN_FilterFailed &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- filter_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed) str ¶
C++: protocols::denovo_design::movers::EXCN_FilterFailed::filter_name() const –> const std::string &
- filter_num(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed) int ¶
C++: protocols::denovo_design::movers::EXCN_FilterFailed::filter_num() const –> unsigned long
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold¶
Bases:
Exception
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold, : pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold) pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold ¶
C++: protocols::denovo_design::movers::EXCN_NothingToFold::operator=(const class protocols::denovo_design::movers::EXCN_NothingToFold &) –> class protocols::denovo_design::movers::EXCN_NothingToFold &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::ExtendChainMover::apply(class core::pose::Pose &) –> void
- architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect ¶
C++: protocols::denovo_design::movers::ExtendChainMover::architect() const –> const class protocols::denovo_design::architects::DeNovoArchitect &
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, : pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover ¶
C++: protocols::denovo_design::movers::ExtendChainMover::operator=(const class protocols::denovo_design::movers::ExtendChainMover &) –> class protocols::denovo_design::movers::ExtendChainMover &
- 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.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::ExtendChainMover::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.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::ExtendChainMover::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.denovo_design.movers.ExtendChainMover) str ¶
C++: protocols::denovo_design::movers::ExtendChainMover::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::denovo_design::movers::ExtendChainMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Parses the ExtendChainTags
C++: protocols::denovo_design::movers::ExtendChainMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::ExtendChainMover::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_chain(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, chain: int) None ¶
C++: protocols::denovo_design::movers::ExtendChainMover::set_chain(const unsigned long) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_dry_run(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, dry_run: bool) None ¶
C++: protocols::denovo_design::movers::ExtendChainMover::set_dry_run(const bool) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_prepend(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, prepend: bool) None ¶
C++: protocols::denovo_design::movers::ExtendChainMover::set_prepend(const bool) –> void
- set_segment_names(*args, **kwargs)¶
Overloaded function.
set_segment_names(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, segment_names_str: str) -> None
C++: protocols::denovo_design::movers::ExtendChainMover::set_segment_names(const std::string &) –> void
set_segment_names(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, seg_names: pyrosetta.rosetta.std.vector_std_string) -> None
C++: protocols::denovo_design::movers::ExtendChainMover::set_segment_names(const class std::vector<std::string, class std::allocator<std::string > > &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.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.denovo_design.movers.ExtendChainMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator ¶
C++: protocols::denovo_design::movers::ExtendChainMoverCreator::operator=(const class protocols::denovo_design::movers::ExtendChainMoverCreator &) –> class protocols::denovo_design::movers::ExtendChainMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::ExtendChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator) str ¶
C++: protocols::denovo_design::movers::ExtendChainMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign¶
Bases:
FastRelax
- add_constraint_generator(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, generator: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) None ¶
Adds a constraint generator. Currently only used if ramp_down_constraints is set. If constraint generators are present, each time the constraint weights are changed, the constraint generators will be used to selectively remove constraint-generated constraints and add new ones
C++: protocols::denovo_design::movers::FastDesign::add_constraint_generator(class std::shared_ptr<const class protocols::constraint_generator::ConstraintGenerator>) –> void
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the FastDesign. Overloaded apply function from mover base class.
C++: protocols::denovo_design::movers::FastDesign::apply(class core::pose::Pose &) –> void
- apply_disulfides(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::relax::RelaxProtocolBase::apply_disulfides(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, : pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign ¶
C++: protocols::denovo_design::movers::FastDesign::operator=(const class protocols::denovo_design::movers::FastDesign &) –> class protocols::denovo_design::movers::FastDesign &
- batch_apply(*args, **kwargs)¶
Overloaded function.
batch_apply(self: pyrosetta.rosetta.protocols.relax.FastRelax, input_structs: pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t) -> None
batch_apply(self: pyrosetta.rosetta.protocols.relax.FastRelax, input_structs: pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, input_csts: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None
batch_apply(self: pyrosetta.rosetta.protocols.relax.FastRelax, input_structs: pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, input_csts: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, decay_rate: float) -> None
Batch Relax, a new even faster way to relax entire batches of structures.
C++: protocols::relax::FastRelax::batch_apply(class std::vector<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, double) –> void
- cartesian(*args, **kwargs)¶
Overloaded function.
cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::cartesian() const –> bool
cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, newval: bool) -> None
Use cartesian (minimization step)
Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Requires scorefunction setup for non-ideal minimization.
C++: protocols::relax::RelaxProtocolBase::cartesian(bool) –> void
- clear_constraint_generators(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) None ¶
Clears the list of constraint generators
C++: protocols::denovo_design::movers::FastDesign::clear_constraint_generators() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) pyrosetta.rosetta.protocols.moves.Mover ¶
return a copy of this class in an owning pointer
C++: protocols::denovo_design::movers::FastDesign::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- static complex_type_generator_for_fast_relax(: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator ¶
C++: protocols::relax::FastRelax::complex_type_generator_for_fast_relax(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>
- constrain_coords(*args, **kwargs)¶
Overloaded function.
constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::constrain_coords() const –> bool
constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_coords: bool) -> None
C++: protocols::relax::RelaxProtocolBase::constrain_coords(bool) –> void
- constrain_relax_segments(*args, **kwargs)¶
Overloaded function.
constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments() const –> bool
constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_segments: bool) -> None
C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments(bool) –> void
- constrain_relax_to_native_coords(*args, **kwargs)¶
Overloaded function.
constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords() const –> bool
constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_native_coords: bool) -> None
C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords(bool) –> void
- constrain_relax_to_start_coords(*args, **kwargs)¶
Overloaded function.
constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords() const –> bool
constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_start_coords: bool) -> None
C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords(bool) –> void
- coord_constrain_sidechains(*args, **kwargs)¶
Overloaded function.
coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains() const –> bool
coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, coord_constrain_sidechains: bool) -> None
C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains(bool) –> void
- 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>
- default_repeats(self: pyrosetta.rosetta.protocols.relax.FastRelax) int ¶
Return the number of repeats
C++: protocols::relax::FastRelax::default_repeats() const –> unsigned long
- dry_run(*args, **kwargs)¶
Overloaded function.
dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::dry_run() const –> bool
dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, setting: bool) -> None
C++: protocols::relax::RelaxProtocolBase::dry_run(bool) –> void
- dualspace(*args, **kwargs)¶
Overloaded function.
dualspace(self: pyrosetta.rosetta.protocols.relax.FastRelax, val: bool) -> None
Use the dualspace (Dihedral + Cartesian) relax protocol (Default false)
Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Recommended to set minimize_bond_angles to true as well. Requires scorefunction setup for non-ideal minimization.
C++: protocols::relax::FastRelax::dualspace(bool) –> void
dualspace(self: pyrosetta.rosetta.protocols.relax.FastRelax) -> bool
C++: protocols::relax::FastRelax::dualspace() –> bool
- fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) pyrosetta.rosetta.protocols.moves.Mover ¶
return a fresh instance of this class in an owning pointer
C++: protocols::denovo_design::movers::FastDesign::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_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) pyrosetta.rosetta.core.kinematics.MoveMap ¶
C++: protocols::relax::RelaxProtocolBase::get_movemap() –> class std::shared_ptr<class core::kinematics::MoveMap>
- get_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) str ¶
C++: protocols::denovo_design::movers::FastDesign::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_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::relax::RelaxProtocolBase::get_scorefxn() const –> const class std::shared_ptr<const class core::scoring::ScoreFunction>
- 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_task_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::relax::RelaxProtocolBase::get_task_factory() const –> const class std::shared_ptr<class core::pack::task::TaskFactory> &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- max_iter(*args, **kwargs)¶
Overloaded function.
max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> int
C++: protocols::relax::RelaxProtocolBase::max_iter() const –> unsigned long
max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, max_iter: int) -> None
C++: protocols::relax::RelaxProtocolBase::max_iter(unsigned long) –> void
- min_type(*args, **kwargs)¶
Overloaded function.
min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> str
C++: protocols::relax::RelaxProtocolBase::min_type() const –> std::string
min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, min_type: str) -> None
C++: protocols::relax::RelaxProtocolBase::min_type(std::string) –> void
- minimize_bond_angles(*args, **kwargs)¶
Overloaded function.
minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles() const –> bool
minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_angles: bool) -> None
C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles(bool) –> void
- minimize_bond_lengths(*args, **kwargs)¶
Overloaded function.
minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths() const –> bool
minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_lengths: bool) -> None
C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths(bool) –> void
- movemap_disables_packing_of_fixed_chi_positions(self: pyrosetta.rosetta.protocols.relax.FastRelax) bool ¶
- Get whether the MoveMap can automatically disable packing of positions
where sidechain minimization is prohibited. Default false.
C++: protocols::relax::FastRelax::movemap_disables_packing_of_fixed_chi_positions() const –> bool
- static mover_name() str ¶
C++: protocols::denovo_design::movers::FastDesign::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Parses the FastDesignTags
C++: protocols::denovo_design::movers::FastDesign::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::denovo_design::movers::FastDesign::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::FastDesign::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- ramp_down_constraints(*args, **kwargs)¶
Overloaded function.
ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool
C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints() const –> bool
ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, ramp_down_constraints: bool) -> None
C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints(bool) –> void
- static register_options() None ¶
C++: protocols::relax::RelaxProtocolBase::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_clear_designable_residues(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, clear_res: bool) None ¶
If set, residues that are designable will be mutated to alanine before design
C++: protocols::denovo_design::movers::FastDesign::set_clear_designable_residues(const bool) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_default_coordinate_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None ¶
C++: protocols::relax::RelaxProtocolBase::set_default_coordinate_settings() –> void
- set_default_minimization_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None ¶
C++: protocols::relax::RelaxProtocolBase::set_default_minimization_settings() –> void
- set_default_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None ¶
C++: protocols::relax::RelaxProtocolBase::set_default_movemap() –> void
- set_defaults(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None ¶
C++: protocols::relax::RelaxProtocolBase::set_defaults() –> void
- set_enable_design(self: pyrosetta.rosetta.protocols.relax.FastRelax, val: bool) None ¶
- sets the enable_design option.
Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.)
C++: protocols::relax::FastRelax::set_enable_design(const bool) –> void
- set_force_nonideal(self: pyrosetta.rosetta.protocols.relax.FastRelax, val: bool) None ¶
Force us to batchrelax with nonideal geometry (using additional memory)
C++: protocols::relax::FastRelax::set_force_nonideal(bool) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::relax::RelaxProtocolBase::set_movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void
- set_movemap_disables_packing_of_fixed_chi_positions(self: pyrosetta.rosetta.protocols.relax.FastRelax, setting: bool) None ¶
- Set whether the MoveMap can automatically disable packing of positions
where sidechain minimization is prohibited. Default false.
C++: protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions(const bool) –> void
- set_movemap_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, mm_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
C++: protocols::relax::RelaxProtocolBase::set_movemap_factory(class std::shared_ptr<class core::select::movemap::MoveMapFactory>) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::relax::RelaxProtocolBase::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_script_from_lines(self: pyrosetta.rosetta.protocols.relax.FastRelax, filelines: pyrosetta.rosetta.std.vector_std_string) None ¶
replace schedule by providing lines of commands explicitly
C++: protocols::relax::FastRelax::set_script_from_lines(const class std::vector<std::string, class std::allocator<std::string > > &) –> void
- set_script_to_batchrelax_default(*args, **kwargs)¶
Overloaded function.
set_script_to_batchrelax_default(self: pyrosetta.rosetta.protocols.relax.FastRelax) -> None
set_script_to_batchrelax_default(self: pyrosetta.rosetta.protocols.relax.FastRelax, standard_repeats: int) -> None
- Override the stored script with the default script for batchrelax
Ignores ‘-default_repeat’ value
C++: protocols::relax::FastRelax::set_script_to_batchrelax_default(unsigned long) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::relax::RelaxProtocolBase::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
- set_to_default(self: pyrosetta.rosetta.protocols.relax.FastRelax) None ¶
Initializes class using option system. This is called by the constructors
C++: protocols::relax::FastRelax::set_to_default() –> 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_up_default_task_factory(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) None ¶
Create the default task factory. Must be called before design can occur.
C++: protocols::denovo_design::movers::FastDesign::set_up_default_task_factory() –> 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.denovo_design.movers.FastDesignCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator) pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator ¶
C++: protocols::denovo_design::movers::FastDesignCreator::operator=(const class protocols::denovo_design::movers::FastDesignCreator &) –> class protocols::denovo_design::movers::FastDesignCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::FastDesignCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator) str ¶
C++: protocols::denovo_design::movers::FastDesignCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover¶
Bases:
Mover
Mover that builds and folds a structure via fragment insertion
- add_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None ¶
Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt
C++: protocols::denovo_design::movers::FoldArchitectMover::add_filter(const class protocols::filters::Filter &) –> void
- add_postfold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Adds a mover to the list of postfold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::add_postfold_mover(const class protocols::moves::Mover &) –> void
- add_prefold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Adds a mover to the list of prefold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::add_prefold_mover(const class protocols::moves::Mover &) –> void
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::operator=(const class protocols::denovo_design::movers::FoldArchitectMover &) –> class protocols::denovo_design::movers::FoldArchitectMover &
- clear_filters(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None ¶
Clears the list of filters used to indicate whether a given folding attempt is successful
C++: protocols::denovo_design::movers::FoldArchitectMover::clear_filters() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clear_postfold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None ¶
Clears the list of postfold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::clear_postfold_movers() –> void
- clear_prefold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None ¶
Clears the list of prefold movers
C++: protocols::denovo_design::movers::FoldArchitectMover::clear_prefold_movers() –> void
- clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.FoldArchitectMover) str ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::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
- id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) str ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::id() const –> 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::denovo_design::movers::FoldArchitectMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::FoldArchitectMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static provide_xml_schema_with_name(xsd: utility::tag::XMLSchemaDefinition, mover_name: str) None ¶
C++: protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema_with_name(class utility::tag::XMLSchemaDefinition &, const std::string &) –> 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_architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, architect: pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect) None ¶
Sets the architect that will be used to build blueprints dynamically
C++: protocols::denovo_design::movers::FoldArchitectMover::set_architect(const class protocols::denovo_design::architects::DeNovoArchitect &) –> void
- set_build_overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, overlap_val: int) None ¶
Sets the number of residues of overlap to use between build phases
C++: protocols::denovo_design::movers::FoldArchitectMover::set_build_overlap(const unsigned long) –> void
- set_builder(*args, **kwargs)¶
Overloaded function.
set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None
Sets the pose builder that will be used to create the extended-chain pose
Clones the provided PoseBuilder
C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(const class protocols::denovo_design::components::PoseBuilder &) –> void
set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None
Sets the pose builder that will be used to create the extended-chain pose
Uses/stores the provided PoseBuilder pointer directly
C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(class std::shared_ptr<class protocols::denovo_design::components::PoseBuilder>) –> 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_debug(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, debug: bool) None ¶
The debug value of the poseBuilder will be set based on this
C++: protocols::denovo_design::movers::FoldArchitectMover::set_debug(const bool) –> void
- set_dump_pdbs(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, dump: bool) None ¶
If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted
C++: protocols::denovo_design::movers::FoldArchitectMover::set_dump_pdbs(const bool) –> void
- set_folder(*args, **kwargs)¶
Overloaded function.
set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None
Sets the pose folder that will be used to sample conformations.
Clones the PoseFolder
C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(const class protocols::denovo_design::components::PoseFolder &) –> void
set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None
Sets the pose folder that will be used to sample conformations
Uses the provided PoseFolder pointer directly
C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>) –> void
- set_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, id_value: str) None ¶
Sets the ID of this mover
C++: protocols::denovo_design::movers::FoldArchitectMover::set_id(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_iterations_per_phase(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, niter: int) None ¶
Sets the number of folding attempts for each build phase
C++: protocols::denovo_design::movers::FoldArchitectMover::set_iterations_per_phase(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_perturber(*args, **kwargs)¶
Overloaded function.
set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None
Sets the perturber that will be used to change the plans of the architects
Clones the provided Perturber
C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(const class protocols::denovo_design::components::StructureDataPerturber &) –> void
set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None
Sets the perturber that will be used to change the plans of the architects
Uses/stores the provided Perturber pointer directly
C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>) –> void
- set_score_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None ¶
Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false
C++: protocols::denovo_design::movers::FoldArchitectMover::set_score_filter(const class protocols::filters::Filter &) –> void
- set_start_segments(*args, **kwargs)¶
Overloaded function.
set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None
sets names of segments to be included in the starting build phase
Comma-separated string containing segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const std::string &) –> void
set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None
sets names of segments to be included in the starting build phase
Set of segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void
- set_stop_segments(*args, **kwargs)¶
Overloaded function.
set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None
sets names of segments to be included in the final build phase
Comma-separated string containing segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const std::string &) –> void
set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None
sets names of segments to be included in the final build phase
Set of segment names
C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_from_xml_file(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_file: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Reads/parses an XML file and uses it to set up the mover
C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_file(const std::string &, class basic::datacache::DataMap &) –> void
- setup_from_xml_string(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_string: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Reads/parses an XML string and uses it to set up the mover
C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_string(const std::string &, class basic::datacache::DataMap &) –> void
- setup_from_xml_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Reads/parses a Tag object and uses it to set up the mover
C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> 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.denovo_design.movers.FoldArchitectMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator ¶
C++: protocols::denovo_design::movers::FoldArchitectMoverCreator::operator=(const class protocols::denovo_design::movers::FoldArchitectMoverCreator &) –> class protocols::denovo_design::movers::FoldArchitectMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::FoldArchitectMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator) str ¶
C++: protocols::denovo_design::movers::FoldArchitectMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover¶
Bases:
Mover
Creates and sets a new fold tree for the pose by traversing a FoldGraph
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover) pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::operator=(const class protocols::denovo_design::movers::FoldTreeFromFoldGraphMover &) –> class protocols::denovo_design::movers::FoldTreeFromFoldGraphMover &
- static class_name() str ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::class_name() –> std::string
- 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.denovo_design.movers.FoldTreeFromFoldGraphMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMover) str ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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_roots(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, roots: pyrosetta.rosetta.std.vector_std_string) None ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::set_roots(const class std::vector<std::string, class std::allocator<std::string > > &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator::operator=(const class protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator &) –> class protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator) str ¶
C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
Describe the schema for the Mover that this Creator is responsible for
C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover¶
Bases:
Mover
Converts a StructureData for a symmetric pose into an asymmetric representation
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, : pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover) pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::operator=(const class protocols::denovo_design::movers::MakeAsymmetricStructureDataMover &) –> class protocols::denovo_design::movers::MakeAsymmetricStructureDataMover &
- 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.denovo_design.movers.MakeAsymmetricStructureDataMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMover) str ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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::denovo_design::movers::MakeAsymmetricStructureDataMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::operator=(const class protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator &) –> class protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator) str ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand, : pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand) pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand ¶
C++: protocols::denovo_design::movers::RelaxScriptCommand::operator=(const struct protocols::denovo_design::movers::RelaxScriptCommand &) –> struct protocols::denovo_design::movers::RelaxScriptCommand &
- property command¶
- property nparams¶
- property param1¶
- property param2¶
- property param3¶
- property param4¶
- class pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover¶
Bases:
Mover
Rotates a segment in the pose
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::denovo_design::movers::RotateSegmentMover::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, random: float) -> None
C++: protocols::denovo_design::movers::RotateSegmentMover::apply(class core::pose::Pose &, const double) const –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, : pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover) pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover ¶
C++: protocols::denovo_design::movers::RotateSegmentMover::operator=(const class protocols::denovo_design::movers::RotateSegmentMover &) –> class protocols::denovo_design::movers::RotateSegmentMover &
- static class_name() str ¶
C++: protocols::denovo_design::movers::RotateSegmentMover::class_name() –> std::string
- 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.denovo_design.movers.RotateSegmentMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::RotateSegmentMover::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.denovo_design.movers.RotateSegmentMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::RotateSegmentMover::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.denovo_design.movers.RotateSegmentMover) str ¶
C++: protocols::denovo_design::movers::RotateSegmentMover::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.denovo_design.movers.RotateSegmentMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::RotateSegmentMover::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_rotation_range(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, start: float, stop: float) None ¶
C++: protocols::denovo_design::movers::RotateSegmentMover::set_rotation_range(const double, const double) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- 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.denovo_design.movers.RotateSegmentMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator ¶
C++: protocols::denovo_design::movers::RotateSegmentMoverCreator::operator=(const class protocols::denovo_design::movers::RotateSegmentMoverCreator &) –> class protocols::denovo_design::movers::RotateSegmentMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::RotateSegmentMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator) str ¶
C++: protocols::denovo_design::movers::RotateSegmentMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
Describe the schema for the Mover that this Creator is responsible for
C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange, : pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange) pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange ¶
C++: protocols::denovo_design::movers::RotationRange::operator=(const class protocols::denovo_design::movers::RotationRange &) –> class protocols::denovo_design::movers::RotationRange &
- property start¶
- property stop¶
- class pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover¶
Bases:
Mover
Creates a sealed foldtree, and removes all cutpoints from the pose
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::SealFoldTreeMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover, : pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover) pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover ¶
C++: protocols::denovo_design::movers::SealFoldTreeMover::operator=(const class protocols::denovo_design::movers::SealFoldTreeMover &) –> class protocols::denovo_design::movers::SealFoldTreeMover &
- static class_name() str ¶
C++: protocols::denovo_design::movers::SealFoldTreeMover::class_name() –> std::string
- 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.denovo_design.movers.SealFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover) str ¶
C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator ¶
C++: protocols::denovo_design::movers::SealFoldTreeMoverCreator::operator=(const class protocols::denovo_design::movers::SealFoldTreeMoverCreator &) –> class protocols::denovo_design::movers::SealFoldTreeMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::SealFoldTreeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator) str ¶
C++: protocols::denovo_design::movers::SealFoldTreeMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
Describe the schema for the Mover that this Creator is responsible for
C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover, : pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover) pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover ¶
C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::operator=(const class protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover &) –> class protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover &
- static class_name() str ¶
C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::class_name() –> const std::string
- 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.denovo_design.movers.SetPoseSecstructFromStructureDataMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::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.denovo_design.movers.SetPoseSecstructFromStructureDataMover) str ¶
C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::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.denovo_design.movers.SetResidueAliasMover¶
Bases:
Mover
Sets a residue alias in the StructureData
- apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::denovo_design::movers::SetResidueAliasMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, : pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover) pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover ¶
C++: protocols::denovo_design::movers::SetResidueAliasMover::operator=(const class protocols::denovo_design::movers::SetResidueAliasMover &) –> class protocols::denovo_design::movers::SetResidueAliasMover &
- 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.denovo_design.movers.SetResidueAliasMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::SetResidueAliasMover::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.denovo_design.movers.SetResidueAliasMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::denovo_design::movers::SetResidueAliasMover::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.denovo_design.movers.SetResidueAliasMover) str ¶
C++: protocols::denovo_design::movers::SetResidueAliasMover::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::denovo_design::movers::SetResidueAliasMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::denovo_design::movers::SetResidueAliasMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::movers::SetResidueAliasMover::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_alias_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, alias: str) None ¶
Sets the name of the alias
C++: protocols::denovo_design::movers::SetResidueAliasMover::set_alias_name(const std::string &) –> 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_resid(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, resid: int) None ¶
Sets the residue within the segment to which the alias refers
C++: protocols::denovo_design::movers::SetResidueAliasMover::set_resid(const unsigned long) –> void
- set_segment_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, segment: str) None ¶
Sets the name of the segment that contains the residue to which the alias refers
C++: protocols::denovo_design::movers::SetResidueAliasMover::set_segment_name(const std::string &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover) -> None
show(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::denovo_design::movers::SetResidueAliasMover::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.denovo_design.movers.SetResidueAliasMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator ¶
C++: protocols::denovo_design::movers::SetResidueAliasMoverCreator::operator=(const class protocols::denovo_design::movers::SetResidueAliasMoverCreator &) –> class protocols::denovo_design::movers::SetResidueAliasMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::movers::SetResidueAliasMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator) str ¶
C++: protocols::denovo_design::movers::SetResidueAliasMoverCreator::keyname() const –> std::string
- pyrosetta.rosetta.protocols.denovo_design.movers.add_overlap_to_loops(loops: pyrosetta.rosetta.protocols.loops.Loops, overlap: int, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.select.residue_selector.ResidueVector ¶
goes through loops and adds overlapping residues
C++: protocols::denovo_design::movers::add_overlap_to_loops(class protocols::loops::Loops &, const unsigned long, const class core::pose::Pose &) –> class core::select::residue_selector::ResidueVector
- pyrosetta.rosetta.protocols.denovo_design.movers.calc_dihedral(p1: pyrosetta.rosetta.numeric.xyzVector_double_t, p2: pyrosetta.rosetta.numeric.xyzVector_double_t, p3: pyrosetta.rosetta.numeric.xyzVector_double_t, p4: pyrosetta.rosetta.numeric.xyzVector_double_t) float ¶
C++: protocols::denovo_design::movers::calc_dihedral(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double