docking

Bindings for protocols::docking namespace

class pyrosetta.rosetta.protocols.docking.ConformerSwitchMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

this mover does the conformer swap in RosettaDock’s ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, arg0: protocols::docking::DockingEnsemble) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, ensemble: protocols::docking::DockingEnsemble, random_conformer: bool) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, arg0: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) -> 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.docking.ConformerSwitchMover) → 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).

apply(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::ConformerSwitchMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, : pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) → pyrosetta.rosetta.protocols.docking.ConformerSwitchMover

C++: protocols::docking::ConformerSwitchMover::operator=(const class protocols::docking::ConformerSwitchMover &) –> class protocols::docking::ConformerSwitchMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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.docking.ConformerSwitchMover) → str

C++: protocols::docking::ConformerSwitchMover::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_temperature(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) → float

C++: protocols::docking::ConformerSwitchMover::get_temperature() const –> double

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::docking::ConformerSwitchMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::docking::ConformerSwitchMover::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_random_confomer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, rand: bool) → None

C++: protocols::docking::ConformerSwitchMover::set_random_confomer(bool) –> void

set_temperature(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, temp_in: float) → None

C++: protocols::docking::ConformerSwitchMover::set_temperature(double) –> 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.

  1. show(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::ConformerSwitchMover::show(class std::basic_ostream<char> &) const –> void

switch_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, pose: pyrosetta.rosetta.core.pose.Pose, conf_num: int) → None

C++: protocols::docking::ConformerSwitchMover::switch_conformer(class core::pose::Pose &, unsigned long) –> 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.

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

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

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

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

use_random_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) → bool

C++: protocols::docking::ConformerSwitchMover::use_random_conformer() const –> bool

class pyrosetta.rosetta.protocols.docking.DockSetupMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

allows docking using simulated or parallel tempering

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, arg0: pyrosetta.rosetta.protocols.docking.DockSetupMover) -> 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.docking.DockSetupMover) → 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).

apply(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockSetupMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, rhs: pyrosetta.rosetta.protocols.docking.DockSetupMover) → pyrosetta.rosetta.protocols.docking.DockSetupMover

assignment operator

C++: protocols::docking::DockSetupMover::operator=(const class protocols::docking::DockSetupMover &) –> class protocols::docking::DockSetupMover &

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.docking.DockSetupMover) → pyrosetta.rosetta.protocols.moves.Mover

clone

C++: protocols::docking::DockSetupMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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.docking.DockSetupMover) → str

C++: protocols::docking::DockSetupMover::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::docking::DockSetupMover::mover_name() –> std::string

name() → str

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

partners(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) → str

C++: protocols::docking::DockSetupMover::partners() const –> const std::string &

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::docking::DockSetupMover::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_defaults(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) → None

Assigns default values to primitive members

C++: protocols::docking::DockSetupMover::set_defaults() –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, setting: str) → None

C++: protocols::docking::DockSetupMover::set_partners(const class std::basic_string<char> &) –> 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.

  1. show(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::DockSetupMover::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.

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

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

  1. 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.docking.DockingEnsemble

Bases: pybind11_builtins.pybind11_object

this mover does the conformer swap in RosettaDock’s ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, start_res: int, end_res: int, jump_id: int, ensemble_file_path: str, partner: str, scorefxn_low: pyrosetta.rosetta.core.scoring.ScoreFunction, scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, arg0: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> 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__

Return str(self).

__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).

assign(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, : pyrosetta.rosetta.protocols.docking.DockingEnsemble) → pyrosetta.rosetta.protocols.docking.DockingEnsemble

C++: protocols::docking::DockingEnsemble::operator=(const class protocols::docking::DockingEnsemble &) –> class protocols::docking::DockingEnsemble &

calculate_highres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) → None

C++: protocols::docking::DockingEnsemble::calculate_highres_ref_energy(unsigned long) –> void

calculate_lowres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingEnsemble::calculate_lowres_ref_energy(class core::pose::Pose &) –> void

conf_size(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → int

C++: protocols::docking::DockingEnsemble::conf_size() –> unsigned long

end_res(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → int

C++: protocols::docking::DockingEnsemble::end_res() –> unsigned long

get_conformer(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::docking::DockingEnsemble::get_conformer(unsigned long) –> class core::pose::Pose &

get_conformer_cen(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::docking::DockingEnsemble::get_conformer_cen(unsigned long) –> class core::pose::Pose &

get_current_confnum(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → int

C++: protocols::docking::DockingEnsemble::get_current_confnum() –> unsigned long

highres_reference_energy(*args, **kwargs)

Overloaded function.

  1. highres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> float

C++: protocols::docking::DockingEnsemble::highres_reference_energy(unsigned long) –> double

  1. highres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> float

C++: protocols::docking::DockingEnsemble::highres_reference_energy() –> double

jump_id(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → int

C++: protocols::docking::DockingEnsemble::jump_id() –> unsigned long

lowres_reference_energy(*args, **kwargs)

Overloaded function.

  1. lowres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> float

C++: protocols::docking::DockingEnsemble::lowres_reference_energy(unsigned long) –> double

  1. lowres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> float

C++: protocols::docking::DockingEnsemble::lowres_reference_energy() –> double

partner(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → str

C++: protocols::docking::DockingEnsemble::partner() –> std::string

recover_conformer_sidechains(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingEnsemble::recover_conformer_sidechains(class core::pose::Pose &) –> void

scorefxn_low(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::docking::DockingEnsemble::scorefxn_low() –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_current_confnum(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) → None

C++: protocols::docking::DockingEnsemble::set_current_confnum(unsigned long) –> void

set_packer(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, packer: pyrosetta.rosetta.protocols.moves.SequenceMover) → None

C++: protocols::docking::DockingEnsemble::set_packer(class std::shared_ptr<class protocols::moves::SequenceMover>) –> void

size(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → int

C++: protocols::docking::DockingEnsemble::size() –> unsigned long

start_res(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → int

C++: protocols::docking::DockingEnsemble::start_res() –> unsigned long

update_pdblist_file(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) → None

C++: protocols::docking::DockingEnsemble::update_pdblist_file() –> void

class pyrosetta.rosetta.protocols.docking.DockingHighResFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_docking_DockingHighResFactory_t

DockingHighResFactory uses the MoverFactory to create instances of DockingHighRes

__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__

Initialize self. See help(type(self)) for accurate signature.

__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__

Return str(self).

__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).

create_docking_high_res_mover(self: pyrosetta.rosetta.protocols.docking.DockingHighResFactory, type_name: pyrosetta.rosetta.protocols.docking.DHR_Type) → pyrosetta.rosetta.protocols.docking.DockingHighRes

Create the specified DockingHighRes

C++: protocols::docking::DockingHighResFactory::create_docking_high_res_mover(const enum protocols::docking::DHR_Type &) –> class std::shared_ptr<class protocols::docking::DockingHighRes>

get_instance() → protocols::docking::DockingHighResFactory

C++: utility::SingletonBase<protocols::docking::DockingHighResFactory>::get_instance() –> class protocols::docking::DockingHighResFactory *

class pyrosetta.rosetta.protocols.docking.DockingHighResFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given

  1. interface_score must be negative

/// ++ had: 1-score filter 2-fa_rep filter 3-interfaceE filter 4-chainbreak filter TTD: add these other filters

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, arg0: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) -> 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__

Return str(self).

__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).

apply(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::docking::DockingHighResFilter::apply(const class core::pose::Pose &) const –> bool

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingHighResFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingHighResFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str

C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str

C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.filters.Filter) → str

C++: protocols::filters::Filter::name() const –> std::string

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_moveable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::docking::DockingHighResFilter::set_moveable_jumps(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_score_cutoff(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, new_cutoff: float) → None

C++: protocols::docking::DockingHighResFilter::set_score_cutoff(double) –> void

set_score_margin(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, new_score_margin: float) → None

C++: protocols::docking::DockingHighResFilter::set_score_margin(double) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, scorefunction: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::docking::DockingHighResFilter::set_scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None

C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.docking.DockingHighResLegacy

Bases: pyrosetta.rosetta.protocols.docking.DockingHighRes

this mover does the high resolution refinement stage of the RosettaDock 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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, rb_jump: int, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, rb_jump: int, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  4. __init__(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, movable_jumps: pyrosetta.rosetta.utility.vector1_int, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  5. __init__(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, arg0: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) -> 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__

Return str(self).

__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.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingHighResLegacy::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, : pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → pyrosetta.rosetta.protocols.docking.DockingHighResLegacy

C++: protocols::docking::DockingHighResLegacy::operator=(const class protocols::docking::DockingHighResLegacy &) –> class protocols::docking::DockingHighResLegacy &

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.docking.DockingHighResLegacy) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingHighResLegacy::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>

define_loops(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose, loop_set: pyrosetta.rosetta.protocols.loops.Loops, interface_dist: float) → None

C++: protocols::docking::DockingHighResLegacy::define_loops(const class core::pose::Pose &, class std::shared_ptr<class protocols::loops::Loops>, double &) –> void

design(*args, **kwargs)

Overloaded function.

  1. design(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, des: bool) -> None

C++: protocols::docking::DockingHighResLegacy::design(const bool) –> void

  1. design(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) -> bool

C++: protocols::docking::DockingHighResLegacy::design() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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_mc(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::docking::DockingHighResLegacy::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_name(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → str

C++: protocols::docking::DockingHighResLegacy::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_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → float

C++: protocols::docking::DockingHighResLegacy::get_rot_magnitude() –> double

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_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → float

C++: protocols::docking::DockingHighResLegacy::get_trans_magnitude() –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

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::docking::DockingHighResLegacy::mover_name() –> std::string

name() → str

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

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::docking::DockingHighResLegacy::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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → bool

C++: protocols::docking::DockingHighResLegacy::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → bool

C++: protocols::docking::DockingHighResLegacy::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_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_default(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingHighResLegacy::set_default(class core::pose::Pose &) –> void

set_dock_mcm_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(class core::pose::Pose &) –> void

set_dock_min_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) → None

C++: protocols::docking::DockingHighResLegacy::set_dock_min_protocol() –> void

set_dock_ppk_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(class core::pose::Pose &) –> 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_min_type(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, min_type_in: str) → None

C++: protocols::docking::DockingHighResLegacy::set_min_type(class std::basic_string<char>) –> 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_move_map(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::docking::DockingHighResLegacy::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

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

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) → None

C++: protocols::docking::DockingHighRes::set_partners(class std::basic_string<char>) –> void

set_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingHighResLegacy::set_protocol(class core::pose::Pose &) –> void

set_repack(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, repack_switch: bool) → None

C++: protocols::docking::DockingHighResLegacy::set_repack(bool) –> void

set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, rot_magnitude: float) → None

C++: protocols::docking::DockingHighResLegacy::set_rot_magnitude(double) –> void

set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, rt_min: bool) → None

C++: protocols::docking::DockingHighResLegacy::set_rt_min(bool) –> void

set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, sc_min: bool) → None

C++: protocols::docking::DockingHighResLegacy::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.DockingHighResLegacy, task: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::docking::DockingHighResLegacy::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

set_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, trans_magnitude: float) → None

C++: protocols::docking::DockingHighResLegacy::set_trans_magnitude(double) –> 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
  2. 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

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.

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

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

  1. 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.docking.DockingInitialPerturbation

Bases: pyrosetta.rosetta.protocols.moves.Mover

this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, arg0: int) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, rb_jump: int, slide: bool) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, arg0: pyrosetta.rosetta.utility.vector1_int) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, movable_jumps: pyrosetta.rosetta.utility.vector1_int, slide: bool) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, arg0: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) -> 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__

Return str(self).

__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).

apply(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingInitialPerturbation::apply(class core::pose::Pose &) –> void

apply_body(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int) → None

C++: protocols::docking::DockingInitialPerturbation::apply_body(class core::pose::Pose &, unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, : pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) → pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation

C++: protocols::docking::DockingInitialPerturbation::operator=(const class protocols::docking::DockingInitialPerturbation &) –> class protocols::docking::DockingInitialPerturbation &

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.docking.DockingInitialPerturbation) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingInitialPerturbation::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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.docking.DockingInitialPerturbation) → str

C++: protocols::docking::DockingInitialPerturbation::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 > > &

init(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) → None

Calls set_dault, register_from_options and init_from_options

C++: protocols::docking::DockingInitialPerturbation::init() –> void

init_from_options(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) → None

Assigns user specified values to primitive members using command line options

C++: protocols::docking::DockingInitialPerturbation::init_from_options() –> void

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::docking::DockingInitialPerturbation::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::docking::DockingInitialPerturbation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

register_options() → None

Associates relevant options with the DockingInitialPerturbation class

C++: protocols::docking::DockingInitialPerturbation::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_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, center: bool) → None

C++: protocols::docking::DockingInitialPerturbation::set_center(bool) –> 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_default(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) → None

Sets members to default values

C++: protocols::docking::DockingInitialPerturbation::set_default() –> void

set_dock_pert(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, dock_pert: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::docking::DockingInitialPerturbation::set_dock_pert(class utility::vector1<double, class std::allocator<double> >) –> 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_randomize1(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize1: bool) → None

set functions

C++: protocols::docking::DockingInitialPerturbation::set_randomize1(bool) –> void

set_randomize2(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize2: bool) → None

C++: protocols::docking::DockingInitialPerturbation::set_randomize2(bool) –> void

set_spin(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, spin: bool) → None

C++: protocols::docking::DockingInitialPerturbation::set_spin(bool) –> void

set_tilt(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::docking::DockingInitialPerturbation::set_tilt(class utility::vector1<double, class std::allocator<double> >) –> void

set_tilt1_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt_center: str) → None

C++: protocols::docking::DockingInitialPerturbation::set_tilt1_center(class std::basic_string<char>) –> void

set_tilt2_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt_center: str) → None

C++: protocols::docking::DockingInitialPerturbation::set_tilt2_center(class std::basic_string<char>) –> 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

set_uniform_trans(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, uniform_trans: float) → None

C++: protocols::docking::DockingInitialPerturbation::set_uniform_trans(double) –> void

set_use_ellipsoidal_randomization(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, use_ellipsoidal_randomization: bool) → None

C++: protocols::docking::DockingInitialPerturbation::set_use_ellipsoidal_randomization(bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
  2. 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.

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

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

  1. 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.docking.DockingLowResFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

Low-resolution (centroid-mode) filter for docking. Checks (1) at least some contact is being made between docking partners,

  1. clashes are limited so partners are not overlapping

and (3) constraints, if present, are met

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, arg0: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) -> 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__

Return str(self).

__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).

apply(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

add docking constraints

C++: protocols::docking::DockingLowResFilter::apply(const class core::pose::Pose &) const –> bool

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingLowResFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingLowResFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str

C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str

C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.filters.Filter) → str

C++: protocols::filters::Filter::name() const –> std::string

report(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingLowResFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_use_constraints(*args, **kwargs)

Overloaded function.

  1. set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, flag: bool) -> None
  2. set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, flag: bool, cutoff: float) -> None

C++: protocols::docking::DockingLowResFilter::set_use_constraints(bool, double) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None

C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.docking.DockingProtocol

Bases: pyrosetta.rosetta.protocols.moves.Mover

This is the standard RosettaDock protocol

RosettaDock protocol based on [refs…Gray2003, Wang2005, Chaudhury 2007 … ]

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: int) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: int, arg1: bool) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: int, arg1: bool, arg2: bool) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: int, arg1: bool, arg2: bool, arg3: bool) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: int, arg1: bool, arg2: bool, arg3: bool, arg4: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, rb_jump_in: int, low_res_protocol_only: bool, docking_local_refine: bool, autofoldtree: bool, docking_score_low: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_score_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: pyrosetta.rosetta.utility.vector1_int) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: pyrosetta.rosetta.utility.vector1_int, arg1: bool) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: pyrosetta.rosetta.utility.vector1_int, arg1: bool, arg2: bool) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: pyrosetta.rosetta.utility.vector1_int, arg1: bool, arg2: bool, arg3: bool) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: pyrosetta.rosetta.utility.vector1_int, arg1: bool, arg2: bool, arg3: bool, arg4: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, movable_jumps: pyrosetta.rosetta.utility.vector1_int, low_res_protocol_only: bool, docking_local_refine: bool, autofoldtree: bool, docking_score_low: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_score_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, arg0: pyrosetta.rosetta.protocols.docking.DockingProtocol) -> 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.docking.DockingProtocol) → 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_low_resolution_step(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, additional_low_resolution_mover: pyrosetta.rosetta.protocols.moves.Mover) → None

C++: protocols::docking::DockingProtocol::add_additional_low_resolution_step(class std::shared_ptr<class protocols::moves::Mover>) –> void

add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) → None

C++: protocols::docking::DockingProtocol::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void

add_jump(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, jump_number: int) → None

C++: protocols::docking::DockingProtocol::add_jump(const unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, rhs: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.docking.DockingProtocol

assignment operator

C++: protocols::docking::DockingProtocol::operator=(const class protocols::docking::DockingProtocol &) –> class protocols::docking::DockingProtocol &

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.docking.DockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingProtocol::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>

docking_highres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.docking.DockingHighRes

C++: protocols::docking::DockingProtocol::docking_highres_mover() const –> class std::shared_ptr<const class protocols::docking::DockingHighRes>

docking_lowres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.docking.DockingLowRes

C++: protocols::docking::DockingProtocol::docking_lowres_mover() const –> class std::shared_ptr<const class protocols::docking::DockingLowRes>

fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingProtocol::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.DockingProtocol) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingProtocol::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.docking.DockingProtocol) → str

C++: protocols::docking::DockingProtocol::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

movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.utility.vector1_int

returns ref to the jumps vector for docking

C++: protocols::docking::DockingProtocol::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &

mover_name() → str

C++: protocols::docking::DockingProtocol::mover_name() –> std::string

name() → str

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → str

returns the docking partners chain identifiers

C++: protocols::docking::DockingProtocol::partners() const –> std::string

perturber(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation

C++: protocols::docking::DockingProtocol::perturber() const –> class std::shared_ptr<const class protocols::docking::DockingInitialPerturbation>

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::docking::DockingProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

register_options() → None

Associates relevant options with the DockingProtocol class

C++: protocols::docking::DockingProtocol::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.docking.DockingProtocol) → bool

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

C++: protocols::docking::DockingProtocol::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) → None

C++: protocols::docking::DockingProtocol::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_autofoldtree(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, autofoldtree: bool) → None

C++: protocols::docking::DockingProtocol::set_autofoldtree(const bool) –> void

set_cst_weight(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, cst_weight: float) → None

C++: protocols::docking::DockingProtocol::set_cst_weight(const double) –> 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_default(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → None

Assigns default values to primitive members

C++: protocols::docking::DockingProtocol::set_default() –> void

set_design(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, design: bool) → None

C++: protocols::docking::DockingProtocol::set_design(const bool) –> void

set_dock_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, dock_min: bool) → None

C++: protocols::docking::DockingProtocol::set_dock_min(const bool) –> void

set_docking_highres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_highres_mover: pyrosetta.rosetta.protocols.docking.DockingHighRes) → None

C++: protocols::docking::DockingProtocol::set_docking_highres_mover(class std::shared_ptr<class protocols::docking::DockingHighRes>) –> void

set_docking_local_refine(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_local_refine: bool) → None

C++: protocols::docking::DockingProtocol::set_docking_local_refine(const bool) –> void

set_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ensemble1: str) → None

C++: protocols::docking::DockingProtocol::set_ensemble1(const class std::basic_string<char> &) –> void

set_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ensemble2: str) → None

C++: protocols::docking::DockingProtocol::set_ensemble2(const class std::basic_string<char> &) –> void

set_highres_scorefxn(*args, **kwargs)

Overloaded function.

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the score function that will be used in the high-resolution phase.
The same score function will be used for evaluating moves, packing and discriminating

C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing

C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_output: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating

C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_ignore_default_docking_task(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ignore_default_docking_task: bool) → None

C++: protocols::docking::DockingProtocol::set_ignore_default_docking_task(const bool) –> void

set_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, inner_cycles: int) → None

C++: protocols::docking::DockingProtocol::set_inner_cycles(unsigned long) –> 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.DockingProtocol, interface_definition: protocols::toolbox::task_operations::InterfaceTaskOperation) → None

C++: protocols::docking::DockingProtocol::set_interface_definition_task_operation(class std::shared_ptr<class protocols::toolbox::task_operations::InterfaceTaskOperation>) –> void

set_low_res_protocol_only(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, low_res_protocol_only: bool) → None

C++: protocols::docking::DockingProtocol::set_low_res_protocol_only(const bool) –> void

set_lowres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_low: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Sets the score function that will be used in the low-resolution phase

C++: protocols::docking::DockingProtocol::set_lowres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, jump_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::docking::DockingProtocol::set_movable_jumps(const 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_no_filters(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, no_filters: bool) → None

C++: protocols::docking::DockingProtocol::set_no_filters(bool) –> void

set_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, outer_cycles: int) → None

C++: protocols::docking::DockingProtocol::set_outer_cycles(unsigned long) –> void

set_partners(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, partners: str) → None

C++: protocols::docking::DockingProtocol::set_partners(const class std::basic_string<char> &) –> void

set_recover_sidechains_filename(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, file: str) → None

C++: protocols::docking::DockingProtocol::set_recover_sidechains_filename(const class std::basic_string<char> &) –> void

set_reporting(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, report: bool) → None

C++: protocols::docking::DockingProtocol::set_reporting(bool) –> void

set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, rt_min: bool) → None

C++: protocols::docking::DockingProtocol::set_rt_min(bool) –> void

set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, sc_min: bool) → None

C++: protocols::docking::DockingProtocol::set_sc_min(bool) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::docking::DockingProtocol::set_task_factory(class std::shared_ptr<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

set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, use_csts: bool) → None

C++: protocols::docking::DockingProtocol::set_use_constraints(const bool) –> void

set_use_legacy_protocol(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, use_legacy_protocol: bool) → None

C++: protocols::docking::DockingProtocol::set_use_legacy_protocol(const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::DockingProtocol::show(class std::basic_ostream<char> &) const –> void

sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → None

Instantiates non-primitive members based on the value of the primitive members

C++: protocols::docking::DockingProtocol::sync_objects_with_flags() –> void

task_factory(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::docking::DockingProtocol::task_factory() –> 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

to_all_atom(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingProtocol::to_all_atom() const –> class std::shared_ptr<const class protocols::moves::Mover>

to_centroid(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → protocols::simple_moves::SwitchResidueTypeSetMover

C++: protocols::docking::DockingProtocol::to_centroid() const –> class std::shared_ptr<const class protocols::simple_moves::SwitchResidueTypeSetMover>

type(*args, **kwargs)

Overloaded function.

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

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

  1. 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.docking.DockingSlideIntoContact

Bases: pyrosetta.rosetta.protocols.moves.Mover

Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently).

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, rb_jump: int) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, rb_jump: int, slide_axis: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None
  4. __init__(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, rb_jump: int, slide_axis: pyrosetta.rosetta.numeric.xyzVector_double_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, scoretype_for_contact: pyrosetta.rosetta.core.scoring.ScoreType) -> None
  5. __init__(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, rb_jump: int, slide_axis: pyrosetta.rosetta.numeric.xyzVector_double_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, scoretype_for_contact: pyrosetta.rosetta.core.scoring.ScoreType, threshold: float) -> None
  6. __init__(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, arg0: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) -> 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.docking.DockingSlideIntoContact) → 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).

apply(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::DockingSlideIntoContact::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, : pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) → pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact

C++: protocols::docking::DockingSlideIntoContact::operator=(const class protocols::docking::DockingSlideIntoContact &) –> class protocols::docking::DockingSlideIntoContact &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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_jump_num(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) → int

C++: protocols::docking::DockingSlideIntoContact::get_jump_num() const –> unsigned long

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.docking.DockingSlideIntoContact) → str

C++: protocols::docking::DockingSlideIntoContact::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

name() → str

C++: protocols::moves::Mover::name() –> 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

set_use_delta(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, setting: bool) → None

C++: protocols::docking::DockingSlideIntoContact::set_use_delta(bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::DockingSlideIntoContact::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.

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

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

  1. 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.docking.EllipsoidalRandomizationMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover approximates one docking partner as an ellipsoid and docks the other partner along a random normal to said ellipsoid; sliding the partners into contact is necessary to complete this docking move.

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, arg0: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : int, : bool) -> 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.docking.EllipsoidalRandomizationMover) → 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).

apply(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) → None

Applies EllipsoidalRandomizationMover mover.

C++: protocols::docking::EllipsoidalRandomizationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, object_to_copy: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover

Assignment operator

C++: protocols::docking::EllipsoidalRandomizationMover::operator=(const class protocols::docking::EllipsoidalRandomizationMover &) –> class protocols::docking::EllipsoidalRandomizationMover &

calculate_axes(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.numeric.xyzMatrix_double_t

Calculates ellipsoid axes from atomic coordinates.

C++: protocols::docking::EllipsoidalRandomizationMover::calculate_axes(class core::pose::Pose &) –> class numeric::xyzMatrix<double>

calculate_geometry(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) → Tuple[pyrosetta.rosetta.numeric.xyzMatrix_double_t, pyrosetta.rosetta.numeric.xyzVector_double_t]

Defines geometry required for docking move.

C++: protocols::docking::EllipsoidalRandomizationMover::calculate_geometry(class core::pose::Pose &) –> struct std::pair<class numeric::xyzMatrix<double>, class numeric::xyzVector<double> >

calculate_plane_axes(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

Calculates two vectors defining a plane at the docking interface.

C++: protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(class core::pose::Pose &) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::EllipsoidalRandomizationMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

copy_data(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, object_to_copy_to: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, object_to_copy_from: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → None

Copies data members from one object to another.

C++: protocols::docking::EllipsoidalRandomizationMover::copy_data(class protocols::docking::EllipsoidalRandomizationMover, class protocols::docking::EllipsoidalRandomizationMover) –> 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.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::EllipsoidalRandomizationMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_a_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → float

C++: protocols::docking::EllipsoidalRandomizationMover::get_a_axis() const –> double

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_b_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → float

C++: protocols::docking::EllipsoidalRandomizationMover::get_b_axis() const –> double

get_c_alpha_centroid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::docking::EllipsoidalRandomizationMover::get_c_alpha_centroid() const –> class numeric::xyzVector<double>

get_c_alpha_non_ellipsoid_centroid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::docking::EllipsoidalRandomizationMover::get_c_alpha_non_ellipsoid_centroid() const –> class numeric::xyzVector<double>

get_c_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → float

C++: protocols::docking::EllipsoidalRandomizationMover::get_c_axis() const –> double

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_interface_residues(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose, : float) → pyrosetta.rosetta.utility.vector1_bool

Identifies residues at interface of docking partners.

C++: protocols::docking::EllipsoidalRandomizationMover::get_interface_residues(class core::pose::Pose &, double) –> class utility::vector1<bool, class std::allocator<bool> >

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.docking.EllipsoidalRandomizationMover) → str

Returns mover name.

C++: protocols::docking::EllipsoidalRandomizationMover::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_normal_to_plane(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::docking::EllipsoidalRandomizationMover::get_normal_to_plane() const –> class numeric::xyzVector<double>

get_partner_residue_start_stop(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose, : bool) → pyrosetta.rosetta.utility.vector1_unsigned_long

Identifies first and last residues of a docking partner.

C++: protocols::docking::EllipsoidalRandomizationMover::get_partner_residue_start_stop(class core::pose::Pose &, bool) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_random_point_on_ellipsoid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::docking::EllipsoidalRandomizationMover::get_random_point_on_ellipsoid() const –> class numeric::xyzVector<double>

get_rotation_matrix(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzMatrix_double_t

Calculates a rotation matrix to superimpose source vector to target vector.

C++: protocols::docking::EllipsoidalRandomizationMover::get_rotation_matrix(class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> class numeric::xyzMatrix<double>

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_slide_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.numeric.xyzVector_double_t

Get the axis for sliding partners into contact.

C++: protocols::docking::EllipsoidalRandomizationMover::get_slide_axis() const –> class numeric::xyzVector<double>

get_spin_center(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → pyrosetta.rosetta.numeric.xyzVector_double_t

Get the point about which to spin the docking partner.

C++: protocols::docking::EllipsoidalRandomizationMover::get_spin_center() const –> class numeric::xyzVector<double>

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 > > &

init_from_options(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → None

Initializes data members from options.

C++: protocols::docking::EllipsoidalRandomizationMover::init_from_options() –> void

inward_normal_to_plane(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

Calculates normal vector from a plane at the docking interface.

C++: protocols::docking::EllipsoidalRandomizationMover::inward_normal_to_plane(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> class numeric::xyzVector<double>

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

name() → str

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

normal_to_ellipsoid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

Calculates normal vector to a point on ellipsoid.

C++: protocols::docking::EllipsoidalRandomizationMover::normal_to_ellipsoid(class numeric::xyzVector<double>) –> class numeric::xyzVector<double>

point_on_ellipsoid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzMatrix_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

Selects a random point on ellipsoid surface.

C++: protocols::docking::EllipsoidalRandomizationMover::point_on_ellipsoid(class numeric::xyzMatrix<double>) –> class numeric::xyzVector<double>

recalculate_z_coordinate(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculates 3rd coordinate of a point on ellipsoid surface given first 2 coordinates.

C++: protocols::docking::EllipsoidalRandomizationMover::recalculate_z_coordinate(class numeric::xyzVector<double>) –> double

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_default(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) → None

Sets up the default values for the object including the movemap and minimization type.

C++: protocols::docking::EllipsoidalRandomizationMover::set_default() –> void

set_foldtree(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) → None

Sets pose fold tree based on -partners flag.

C++: protocols::docking::EllipsoidalRandomizationMover::set_foldtree(class core::pose::Pose &) –> void

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

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

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

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_partners(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : str) → None

Set the partners_ string.

C++: protocols::docking::EllipsoidalRandomizationMover::set_partners(const class std::basic_string<char> &) –> 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.

  1. show(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, output: pyrosetta.rosetta.std.ostream) -> None

Generates string representation of EllipsoidalRandomizationMover.

C++: protocols::docking::EllipsoidalRandomizationMover::show(class std::basic_ostream<char> &) const –> void

single_beta_sample(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : float, : float) → float

Returns a sample from a beta distribution.

C++: protocols::docking::EllipsoidalRandomizationMover::single_beta_sample(double, double) –> double

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.

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

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

  1. 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.docking.FaDockingSlideIntoContact

Bases: pyrosetta.rosetta.protocols.moves.Mover

Slides docking partners together by monitoring fa_rep.

If partners are already touching, no change is made. Separation will be 1A or less after calling this function.

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, rb_jump: int) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, rb_jumps: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
  4. __init__(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, rb_jump: int, slide_axis: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None
  5. __init__(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, arg0: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) -> 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.docking.FaDockingSlideIntoContact) → 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).

apply(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::FaDockingSlideIntoContact::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, : pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) → pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact

C++: protocols::docking::FaDockingSlideIntoContact::operator=(const class protocols::docking::FaDockingSlideIntoContact &) –> class protocols::docking::FaDockingSlideIntoContact &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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_jump_num(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) → int

C++: protocols::docking::FaDockingSlideIntoContact::get_jump_num() const –> unsigned long

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.docking.FaDockingSlideIntoContact) → str

C++: protocols::docking::FaDockingSlideIntoContact::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_tolerance(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) → float

C++: protocols::docking::FaDockingSlideIntoContact::get_tolerance() const –> double

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

name() → str

C++: protocols::moves::Mover::name() –> 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.

  1. show(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::FaDockingSlideIntoContact::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.

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

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

  1. 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.docking.SlideIntoContact

Bases: pyrosetta.rosetta.protocols.moves.Mover

More general function for low-res or highres DockingSlideIntoContact

Both DockingSlideIntoContact and FaDockingSlideIntoContact have their
issues and are not as general as they could be; they should be a single class, not two; since they are called quite often, I am rewriting the class for now and will replace it’s use later on

Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently).

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, jump: int) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, arg0: pyrosetta.rosetta.protocols.docking.SlideIntoContact) -> 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__

Return str(self).

__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).

apply(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::SlideIntoContact::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, : pyrosetta.rosetta.protocols.docking.SlideIntoContact) → pyrosetta.rosetta.protocols.docking.SlideIntoContact

C++: protocols::docking::SlideIntoContact::operator=(const class protocols::docking::SlideIntoContact &) –> class protocols::docking::SlideIntoContact &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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_jump_num(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) → int

C++: protocols::docking::SlideIntoContact::get_jump_num() const –> unsigned long

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.docking.SlideIntoContact) → str

C++: protocols::docking::SlideIntoContact::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_sfxn_name(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) → str

C++: protocols::docking::SlideIntoContact::get_sfxn_name() const –> std::string

get_stepsize(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) → float

C++: protocols::docking::SlideIntoContact::get_stepsize() const –> double

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

move_apart_first(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, yesno: bool) → None

C++: protocols::docking::SlideIntoContact::move_apart_first(bool) –> void

name() → str

C++: protocols::moves::Mover::name() –> 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

scorefunction(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, sfxn_name: str, scoretype_for_sliding: str) → None

scorefunction and scoreterm used for evaluating closeness of partners

C++: protocols::docking::SlideIntoContact::scorefunction(class std::basic_string<char>, class std::basic_string<char>) –> 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_starting_rep(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, starting_rep: float) → None

C++: protocols::docking::SlideIntoContact::set_starting_rep(double) –> 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.

  1. show(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::SlideIntoContact::show(class std::basic_ostream<char> &) const –> void

slide_axis(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, slide_axis: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::docking::SlideIntoContact::slide_axis(const class numeric::xyzVector<double> &) –> void

stepsize(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, stepsize: float) → None

C++: protocols::docking::SlideIntoContact::stepsize(double) –> 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.

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

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

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

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

vary_stepsize(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, yesno: bool) → None

C++: protocols::docking::SlideIntoContact::vary_stepsize(bool) –> void

class pyrosetta.rosetta.protocols.docking.TemperedDocking

Bases: pyrosetta.rosetta.protocols.moves.Mover

allows docking using simulated or parallel tempering

__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.

  1. __init__(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, arg0: pyrosetta.rosetta.protocols.docking.TemperedDocking) -> 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.docking.TemperedDocking) → 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_jump(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, jump_number: int) → None

C++: protocols::docking::TemperedDocking::add_jump(const long) –> void

apply(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::TemperedDocking::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, rhs: pyrosetta.rosetta.protocols.docking.TemperedDocking) → pyrosetta.rosetta.protocols.docking.TemperedDocking

assignment operator

C++: protocols::docking::TemperedDocking::operator=(const class protocols::docking::TemperedDocking &) –> class protocols::docking::TemperedDocking &

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.docking.TemperedDocking) → pyrosetta.rosetta.protocols.moves.Mover

clone

C++: protocols::docking::TemperedDocking::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

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.docking.TemperedDocking) → str

returns the docking partners chain identifiers

C++: protocols::docking::TemperedDocking::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

movable_jumps(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) → pyrosetta.rosetta.utility.vector1_int

C++: protocols::docking::TemperedDocking::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &

name() → str

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

partners(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) → str

C++: protocols::docking::TemperedDocking::partners() const –> std::string

register_options() → None

Associates relevant options with the TemperedDocking class

C++: protocols::docking::TemperedDocking::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_autofoldtree(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, setting: bool) → None

@ return const ref to the jumps vector for docking

C++: protocols::docking::TemperedDocking::set_autofoldtree(bool) –> 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_defaults(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) → None

Assigns default values to primitive members

C++: protocols::docking::TemperedDocking::set_defaults() –> void

set_highres_scorefxn(*args, **kwargs)

Overloaded function.

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the score function that will be used in the high-resolution phase.
The same score function will be used for evaluating moves, packing and discriminating

C++: protocols::docking::TemperedDocking::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing

C++: protocols::docking::TemperedDocking::set_highres_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_output: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating

C++: protocols::docking::TemperedDocking::set_highres_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

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

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_lowres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_low: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Sets the score function that will be used in the low-resolution phase

C++: protocols::docking::TemperedDocking::set_lowres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, setting: pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::docking::TemperedDocking::set_movable_jumps(const 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.TemperedDocking, setting: str) → None

C++: protocols::docking::TemperedDocking::set_partners(const class std::basic_string<char> &) –> void

set_sc_min(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, sc_min: bool) → None

C++: protocols::docking::TemperedDocking::set_sc_min(bool) –> 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

set_use_constraints(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, setting: bool) → None

C++: protocols::docking::TemperedDocking::set_use_constraints(bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) -> None
  2. show(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::TemperedDocking::show(class std::basic_ostream<char> &) const –> void

sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) → None

Instantiates non-primitive members based on the value of the primitive members

C++: protocols::docking::TemperedDocking::sync_objects_with_flags() –> 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

to_centroid(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::TemperedDocking::to_centroid() const –> class std::shared_ptr<const class protocols::moves::Mover>

type(*args, **kwargs)

Overloaded function.

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

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

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

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

pyrosetta.rosetta.protocols.docking.calc_CA_Irmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → float

calcluates the CA-atom RMSD of all residues within 5A of the interface at superposition along those same atoms

C++: protocols::docking::calc_CA_Irmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_Fnat(*args, **kwargs)

Overloaded function.

  1. calc_Fnat(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float
Calculates the fraction of native contacts recovered between the input and native pose. A native-contact is defined
as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure

C++: protocols::docking::calc_Fnat(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double

  1. calc_Fnat(pose: pyrosetta.rosetta.core.pose.Pose, list_file: str, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float

Calculates the fraction of native contacts from the given native contacts pair list

C++: protocols::docking::calc_Fnat(const class core::pose::Pose &, const class std::basic_string<char> &, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_Fnonnat(*args, **kwargs)

Overloaded function.

  1. calc_Fnonnat(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float
Calculates the fraction of non-native contacts recovered between the input and native pose. A native-contact is defined
as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. Fnonnat = Nnon-native-contact/Nnative_contact

C++: protocols::docking::calc_Fnonnat(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double

  1. calc_Fnonnat(pose: pyrosetta.rosetta.core.pose.Pose, list_file: str, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float

Calculates the fraction of non-native contacts from the given native contacts pari list

C++: protocols::docking::calc_Fnonnat(const class core::pose::Pose &, const class std::basic_string<char> &, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_Irmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → float

Calculates the all-atom RMSD of all residues within 5A of the interface at superposition along those same atoms

C++: protocols::docking::calc_Irmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_Lrmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → float

Calculates C-alpha RMSD of the smaller partner after superposition of the larger partner

C++: protocols::docking::calc_Lrmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_P1rmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → float

Calculates C-alpha RMSD of the superimposed larger partner

The larger partner is the fixed partner; this is mostly for
membrane proteins, where we move the partners apart, then do relax on both partners

C++: protocols::docking::calc_P1rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_P2rmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → float

Calculates C-alpha RMSD of the superimposed smaller partner

This calculates the RMSD of the smaller partner after superimposing it
The computed RMSD is not from the docking, but from the flexible backbone relax

C++: protocols::docking::calc_P2rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_interaction_energy(pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → float

Calculates the difference in energy between the inputted complex, and the complex with the two partners at 500A from each other

C++: protocols::docking::calc_interaction_energy(const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double

pyrosetta.rosetta.protocols.docking.calc_intf_score(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, jump: int) → float
Compute interface score between the input complex and complex with
the two partners at 500A from each other

C++: protocols::docking::calc_intf_score(const class core::pose::Pose &, const class std::shared_ptr<class core::scoring::ScoreFunction>, const int) –> double

pyrosetta.rosetta.protocols.docking.calc_res_contact(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, dist_cutoff: float) → bool

C++: protocols::docking::calc_res_contact(class std::shared_ptr<class core::conformation::Residue>, class std::shared_ptr<class core::conformation::Residue>, double) –> bool

pyrosetta.rosetta.protocols.docking.move_apart(pose: pyrosetta.rosetta.core.pose.Pose, jump: int, axis: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::docking::move_apart(class core::pose::Pose &, int, const class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.docking.move_together(pose: pyrosetta.rosetta.core.pose.Pose, jump: int, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::docking::move_together(class core::pose::Pose &, int, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

pyrosetta.rosetta.protocols.docking.setup_foldtree(*args, **kwargs)

Overloaded function.

  1. setup_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, partner_chainID: str, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> None
Setup FoldTree for docking across an interface.
The partners are described by a string for the partner chains (using pdb_chain identification) separated by “_”. The foldtree is set up such that the jump points are at the center of masses of the two partners.

C++: protocols::docking::setup_foldtree(class core::pose::Pose &, const class std::basic_string<char> &, class utility::vector1<int, class std::allocator<int> > &) –> void

  1. setup_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, partner1: pyrosetta.rosetta.utility.vector1_bool, movable_jumps: pyrosetta.rosetta.utility.vector1_int, ft: pyrosetta.rosetta.core.kinematics.FoldTree) -> None
Setup foldtree for docking across an interface.
The partners are described by a vector of booleans of the same length as the number of residues in the pose. The FoldTree is set up such that the jump points are at the center of masses of the two partners.

C++: protocols::docking::setup_foldtree(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<int, class std::allocator<int> > &, class core::kinematics::FoldTree &) –> void