simple_movers¶

Bindings for protocols::grafting::simple_movers namespace

class pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

Delete a region of a pose. Mover Wrapper to grafting utility function.

apply(self: pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover, : pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover) → pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::operator=(const class protocols::grafting::simple_movers::DeleteRegionMover &) –> class protocols::grafting::simple_movers::DeleteRegionMover &

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.grafting.simple_movers.DeleteRegionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::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.grafting.simple_movers.DeleteRegionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::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.

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.grafting.simple_movers.DeleteRegionMover) → str¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::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_std_allocator_std_string_t¶

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover_name() → str¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::grafting::simple_movers::DeleteRegionMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

region(self: pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover, res_start: str, res_end: str) → None¶

Set the region of the pose where deletion will occur

C++: protocols::grafting::simple_movers::DeleteRegionMover::region(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

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¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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_residue_selector(self: pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Sets the residue selector

C++: protocols::grafting::simple_movers::DeleteRegionMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

Insert a whole pose into another. Loops, linkers, whaterver. No modeling here. Wrapper to utility function insert_pose_into_pose.

Residues between start + end should be deleted before using this mover if needed.

apply(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover, : pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover) → pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::operator=(const class protocols::grafting::simple_movers::InsertPoseIntoPoseMover &) –> class protocols::grafting::simple_movers::InsertPoseIntoPoseMover &

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.grafting.simple_movers.InsertPoseIntoPoseMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::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>

end(*args, **kwargs)¶

Overloaded function.

end(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover, res_end: str) -> None

C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::end(const class std::basic_string<char> &) –> void

end(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover) -> str

C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::end() const –> const std::string &

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.

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.grafting.simple_movers.InsertPoseIntoPoseMover) → str¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::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_std_allocator_std_string_t¶

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover_name() → str¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

src_pose(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover, src_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::src_pose(const class core::pose::Pose &) –> void

start(*args, **kwargs)¶

Overloaded function.

start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover, res_start: str) -> None

C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::start(const class std::basic_string<char> &) –> void

start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover) -> str

C++: protocols::grafting::simple_movers::InsertPoseIntoPoseMover::start() const –> const std::string &

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

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

Keep a contiguous region of a pose, delete the rest. Re-detect disulfides

apply(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::KeepRegionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, : pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover) → pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover¶: C++: protocols::grafting::simple_movers::KeepRegionMover::operator=(const class protocols::grafting::simple_movers::KeepRegionMover &) –> class protocols::grafting::simple_movers::KeepRegionMover &

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.grafting.simple_movers.KeepRegionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::grafting::simple_movers::KeepRegionMover::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>

end(*args, **kwargs)¶

Overloaded function.

end(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, res_end: str) -> None

Set the last residue that we will keep

C++: protocols::grafting::simple_movers::KeepRegionMover::end(const class std::basic_string<char> &) –> void

end(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, res_end: int) -> None

C++: protocols::grafting::simple_movers::KeepRegionMover::end(unsigned long) –> void

end(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover) -> str

C++: protocols::grafting::simple_movers::KeepRegionMover::end() const –> const std::string &

fresh_instance(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::grafting::simple_movers::KeepRegionMover::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.

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.grafting.simple_movers.KeepRegionMover) → str¶: C++: protocols::grafting::simple_movers::KeepRegionMover::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_std_allocator_std_string_t¶

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover_name() → str¶: C++: protocols::grafting::simple_movers::KeepRegionMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::KeepRegionMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::grafting::simple_movers::KeepRegionMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

region(*args, **kwargs)¶

Overloaded function.

region(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, res_start: str, res_end: str) -> None

Set the region of the pose where we keep the residues

C++: protocols::grafting::simple_movers::KeepRegionMover::region(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

region(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover) -> Tuple[str, str]

C++: protocols::grafting::simple_movers::KeepRegionMover::region() const –> struct std::pair<std::string, std::string >

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¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

start(*args, **kwargs)¶

Overloaded function.

start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, res_start: str) -> None

Set the first residue that we will keep

C++: protocols::grafting::simple_movers::KeepRegionMover::start(const class std::basic_string<char> &) –> void

start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover, res_start: int) -> None

C++: protocols::grafting::simple_movers::KeepRegionMover::start(unsigned long) –> void

start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover) -> str

C++: protocols::grafting::simple_movers::KeepRegionMover::start() const –> const std::string &

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

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

Replace a region of residues with another from a pose piece. Wrapper to grafting utility function

Specify the start residue of the source pose, the residue where replacement will begin,: In addition to the number of residues (span) .

apply(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover, : pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover) → pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::operator=(const class protocols::grafting::simple_movers::ReplaceRegionMover &) –> class protocols::grafting::simple_movers::ReplaceRegionMover &

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.grafting.simple_movers.ReplaceRegionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::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.grafting.simple_movers.ReplaceRegionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::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.

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.grafting.simple_movers.ReplaceRegionMover) → str¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::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_std_allocator_std_string_t¶

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover_name() → str¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

src_pose(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover, from_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::grafting::simple_movers::ReplaceRegionMover::src_pose(const class core::pose::Pose &) –> void

src_pose_start(*args, **kwargs)¶

Overloaded function.

src_pose_start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover) -> str

C++: protocols::grafting::simple_movers::ReplaceRegionMover::src_pose_start() const –> const std::string &

src_pose_start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover, start: str) -> None

C++: protocols::grafting::simple_movers::ReplaceRegionMover::src_pose_start(const class std::basic_string<char> &) –> void

target_pose_start(*args, **kwargs)¶

Overloaded function.

target_pose_start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover) -> str

C++: protocols::grafting::simple_movers::ReplaceRegionMover::target_pose_start() const –> const std::string &

target_pose_start(self: pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover, start: str) -> None

C++: protocols::grafting::simple_movers::ReplaceRegionMover::target_pose_start(const class std::basic_string<char> &) –> 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) -> str

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

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void