snugdock¶

Bindings for protocols::antibody::snugdock namespace

class pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock¶

Bases: DockingHighRes

MoveSet step of Snugdock as described in:

Sircar A, Gray JJ (2010) SnugDock: Paratope Structural Optimization duringAntibody-Antigen Docking Compensates

for Errors in Antibody Homology Models. PLoS Comput Biol 6(1): e1000644. doi:10.1371/journal.pcbi.1000644

This is the main high resolution step of the overall SnugDock protocol. See the Show method for a complete description of the algorithm.

add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) → None¶: C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void

apply(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::antibody::snugdock::SnugDock::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, rhs: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) → pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock¶: C++: protocols::antibody::snugdock::SnugDock::operator=(const class protocols::antibody::snugdock::SnugDock &) –> class protocols::antibody::snugdock::SnugDock &

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.antibody.snugdock.SnugDock) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::antibody::snugdock::SnugDock::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>

debug(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) → None¶: C++: protocols::antibody::snugdock::SnugDock::debug() –> void

fresh_instance(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::antibody::snugdock::SnugDock::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t¶: C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >

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.antibody.snugdock.SnugDock) → str¶: C++: protocols::antibody::snugdock::SnugDock::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → str¶: C++: protocols::docking::DockingHighRes::get_partners() const –> std::string

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

high_res_kink_constraint(*args, **kwargs)¶

Overloaded function.

high_res_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) -> bool

C++: protocols::antibody::snugdock::SnugDock::high_res_kink_constraint() const –> bool

high_res_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, setting: bool) -> None

C++: protocols::antibody::snugdock::SnugDock::high_res_kink_constraint(const bool) –> void

ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → bool¶: C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

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

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

movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → pyrosetta.rosetta.utility.vector1_int¶: C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &

static mover_name() → str¶: C++: protocols::antibody::snugdock::SnugDock::mover_name() –> std::string

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

number_of_high_resolution_cycles(*args, **kwargs)¶

Overloaded function.

number_of_high_resolution_cycles(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) -> int

C++: protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles() const –> unsigned long

number_of_high_resolution_cycles(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, number_of_high_resolution_cycles: int) -> None

C++: protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles(const unsigned long) –> void

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → str¶: C++: protocols::docking::DockingHighRes::partners() –> std::string

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::antibody::snugdock::SnugDock::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Associates relevant options with the SnugDock class

C++: protocols::antibody::snugdock::SnugDock::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.antibody.snugdock.SnugDock) → bool¶

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::antibody::snugdock::SnugDock::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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → bool¶: C++: protocols::docking::DockingHighRes::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → bool¶: C++: protocols::docking::DockingHighRes::sc_min() –> bool

scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_CDR_loops(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, cdr_loops: pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_protocols_loops_Loop) → None¶: C++: protocols::antibody::snugdock::SnugDock::set_CDR_loops(class std::map<enum protocols::antibody::CDRNameEnum, class protocols::loops::Loop, struct std::less<enum protocols::antibody::CDRNameEnum>, class std::allocator<struct std::pair<const enum protocols::antibody::CDRNameEnum, class protocols::loops::Loop> > >) –> void

set_ab_has_light_chain(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, ab_has_light_chain: bool) → None¶: C++: protocols::antibody::snugdock::SnugDock::set_ab_has_light_chain(bool) –> void

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) → None¶: C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> void

set_antibody_info(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, antibody_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo) → None¶: C++: protocols::antibody::snugdock::SnugDock::set_antibody_info(class std::shared_ptr<class protocols::antibody::AntibodyInfo>) –> 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_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) → None¶: C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) → None¶: C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → None¶: C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) → None¶: C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void

set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) → None¶: C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void

set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) → None¶: C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶: C++: protocols::antibody::snugdock::SnugDock::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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_vh_vl_jump(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, vh_vl_jump: bool) → None¶: C++: protocols::antibody::snugdock::SnugDock::set_vh_vl_jump(bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) -> None
show(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::antibody::snugdock::SnugDock::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) → pyrosetta.rosetta.core.pack.task.TaskFactory¶: C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator, : pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator) → pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator¶: C++: protocols::antibody::snugdock::SnugDockCreator::operator=(const class protocols::antibody::snugdock::SnugDockCreator &) –> class protocols::antibody::snugdock::SnugDockCreator &

create_mover(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::antibody::snugdock::SnugDockCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator) → str¶: C++: protocols::antibody::snugdock::SnugDockCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::antibody::snugdock::SnugDockCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::antibody::snugdock::SnugDockProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, rhs: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol) → pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol¶: C++: protocols::antibody::snugdock::SnugDockProtocol::operator=(const class protocols::antibody::snugdock::SnugDockProtocol &) –> class protocols::antibody::snugdock::SnugDockProtocol &

auto_generate_kink_constraint(*args, **kwargs)¶

Overloaded function.

auto_generate_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol) -> bool

C++: protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint() const –> bool

auto_generate_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, setting: bool) -> None

C++: protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint(const bool) –> 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.antibody.snugdock.SnugDockProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::antibody::snugdock::SnugDockProtocol::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

constrain_vlvh_qq(*args, **kwargs)¶

Overloaded function.

constrain_vlvh_qq(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol) -> bool

C++: protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq() const –> bool

constrain_vlvh_qq(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, setting: bool) -> None

C++: protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq(const 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>

fresh_instance(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::antibody::snugdock::SnugDockProtocol::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.antibody.snugdock.SnugDockProtocol) → str¶: C++: protocols::antibody::snugdock::SnugDockProtocol::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

high_res_kink_constraint(*args, **kwargs)¶

Overloaded function.

high_res_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol) -> bool

C++: protocols::antibody::snugdock::SnugDockProtocol::high_res_kink_constraint() const –> bool

high_res_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, setting: bool) -> None

C++: protocols::antibody::snugdock::SnugDockProtocol::high_res_kink_constraint(const bool) –> void

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

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

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

low_res_kink_constraint(*args, **kwargs)¶

Overloaded function.

low_res_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol) -> bool

C++: protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint() const –> bool

low_res_kink_constraint(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, setting: bool) -> None

C++: protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint(const bool) –> void

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

place_VRT_at_residue_COM(*args, **kwargs)¶

Overloaded function.

place_VRT_at_residue_COM(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.core.conformation.Residue

C++: protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM(const class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) –> class std::shared_ptr<class core::conformation::Residue>

place_VRT_at_residue_COM(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, start: int, stop: int) -> pyrosetta.rosetta.core.conformation.Residue

C++: protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM(const class core::pose::Pose &, unsigned long, unsigned long) –> class std::shared_ptr<class core::conformation::Residue>

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¶

Associates relevant options with the SnugDockProtocol class

C++: protocols::antibody::snugdock::SnugDockProtocol::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.antibody.snugdock.SnugDockProtocol) → bool¶

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::antibody::snugdock::SnugDockProtocol::reinitialize_for_new_input() const –> bool

repack_tf_from_residue_sets(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, ab_residues: pyrosetta.rosetta.std.set_unsigned_long_t, ag_residues: pyrosetta.rosetta.std.set_unsigned_long_t) → pyrosetta.rosetta.core.pack.task.TaskFactory¶: C++: protocols::antibody::snugdock::SnugDockProtocol::repack_tf_from_residue_sets(const class core::pose::Pose &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> class std::shared_ptr<class core::pack::task::TaskFactory>

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

setup_ab_ag_foldtree(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, antibody_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo) → None¶: C++: protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(class core::pose::Pose &, class std::shared_ptr<class protocols::antibody::AntibodyInfo>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol) -> None
show(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::antibody::snugdock::SnugDockProtocol::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 &