snugdock¶

Bindings for protocols::antibody::snugdock namespace

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

Bases: pyrosetta.rosetta.protocols.docking.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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock, arg0: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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_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

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> > &

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

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

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

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

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_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¶

////////////////////////////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_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::toolbox::task_operations::InterfaceTaskOperation) → None¶: C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::toolbox::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(class std::basic_string<char>) –> 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.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶: C++: protocols::docking::DockingHighRes::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¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> 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