relax

Bindings for protocols::relax namespace

class pyrosetta.rosetta.protocols.relax.CentroidRelax

Bases: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase

Relax a pose using Frank Dimaio’s smooth centroid statistics. Currently under optimization.

Minimize a centroid representation of a pose. Ramp VDW/Rama or both.

May tweak structure by up to ~2.5 A without constraints. Use custom constraints or coordinate constraints through relax options for best results. Using starting coordinate constraints, structure is tweaked by ~.3/.4 A Use increased VDW radii option for bb to improve bb-geometry when not using constraints

__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.relax.CentroidRelax) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, mm: pyrosetta.rosetta.core.kinematics.MoveMap, cen_scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  4. __init__(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, arg0: pyrosetta.rosetta.protocols.relax.CentroidRelax) -> 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.relax.CentroidRelax, pose: pyrosetta.rosetta.core.pose.Pose) → None

Applies the protocol, See notes

Setting ramp_rama and ramp_vdw to false switches to the BASIC protocol which is rounds of the centroid minmover

C++: protocols::relax::CentroidRelax::apply(class core::pose::Pose &) –> void

apply_disulfides(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::relax::RelaxProtocolBase::apply_disulfides(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, : pyrosetta.rosetta.protocols.relax.CentroidRelax) → pyrosetta.rosetta.protocols.relax.CentroidRelax

C++: protocols::relax::CentroidRelax::operator=(const class protocols::relax::CentroidRelax &) –> class protocols::relax::CentroidRelax &

cartesian(*args, **kwargs)

Overloaded function.

  1. cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::cartesian() const –> bool

  1. cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, newval: bool) -> None

Use cartesian (minimization step)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Requires scorefunction setup for non-ideal minimization.

C++: protocols::relax::RelaxProtocolBase::cartesian(bool) –> void

clear_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.relax.CentroidRelax) → pyrosetta.rosetta.protocols.moves.Mover

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

constrain_coords(*args, **kwargs)

Overloaded function.

  1. constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_coords() const –> bool

  1. constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_coords(bool) –> void

constrain_relax_segments(*args, **kwargs)

Overloaded function.

  1. constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments() const –> bool

  1. constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_segments: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments(bool) –> void

constrain_relax_to_native_coords(*args, **kwargs)

Overloaded function.

  1. constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords() const –> bool

  1. constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_native_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords(bool) –> void

constrain_relax_to_start_coords(*args, **kwargs)

Overloaded function.

  1. constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords() const –> bool

  1. constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_start_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords(bool) –> void

coord_constrain_sidechains(*args, **kwargs)

Overloaded function.

  1. coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains() const –> bool

  1. coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, coord_constrain_sidechains: bool) -> None

C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains(bool) –> void

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

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

do_final_repack(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, repack_sc: bool) → None

If a fullatom pose is passed, should we repack sidechains according to movemap?

C++: protocols::relax::CentroidRelax::do_final_repack(bool) –> void

dry_run(*args, **kwargs)

Overloaded function.

  1. dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::dry_run() const –> bool

  1. dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, setting: bool) -> None

C++: protocols::relax::RelaxProtocolBase::dry_run(bool) –> void

explicit_ramp_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → bool

C++: protocols::relax::RelaxProtocolBase::explicit_ramp_constraints() const –> bool

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

C++: protocols::relax::RelaxProtocolBase::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_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::relax::RelaxProtocolBase::get_movemap() –> class std::shared_ptr<class core::kinematics::MoveMap>

get_name(self: pyrosetta.rosetta.protocols.relax.CentroidRelax) → str

C++: protocols::relax::CentroidRelax::get_name() const –> std::string

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

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

get_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::relax::RelaxProtocolBase::get_scorefxn() const –> const class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_task_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::relax::RelaxProtocolBase::get_task_factory() const –> const class std::shared_ptr<class core::pack::task::TaskFactory> &

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

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

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

max_iter(*args, **kwargs)

Overloaded function.

  1. max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> int

C++: protocols::relax::RelaxProtocolBase::max_iter() const –> unsigned long

  1. max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, max_iter: int) -> None

C++: protocols::relax::RelaxProtocolBase::max_iter(unsigned long) –> void

min_type(*args, **kwargs)

Overloaded function.

  1. min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> str

C++: protocols::relax::RelaxProtocolBase::min_type() const –> std::string

  1. min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, min_type: str) -> None

C++: protocols::relax::RelaxProtocolBase::min_type(class std::basic_string<char>) –> void

minimize_bond_angles(*args, **kwargs)

Overloaded function.

  1. minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles() const –> bool

  1. minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_angles: bool) -> None

C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles(bool) –> void

minimize_bond_lengths(*args, **kwargs)

Overloaded function.

  1. minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths() const –> bool

  1. minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_lengths: bool) -> None

C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths(bool) –> void

name() → str

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

ramp_down_constraints(*args, **kwargs)

Overloaded function.

  1. ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints() const –> bool

  1. ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, ramp_down_constraints: bool) -> None

C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints(bool) –> void

register_options() → None

C++: protocols::relax::RelaxProtocolBase::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

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

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

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

set_cartesian(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, cart: bool) → None

Sets to use the cartesian minimizer.

C++: protocols::relax::CentroidRelax::set_cartesian(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_coordinate_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → None

C++: protocols::relax::RelaxProtocolBase::set_default_coordinate_settings() –> void

set_default_minimization_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → None

C++: protocols::relax::RelaxProtocolBase::set_default_minimization_settings() –> void

set_default_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → None

C++: protocols::relax::RelaxProtocolBase::set_default_movemap() –> void

set_defaults(self: pyrosetta.rosetta.protocols.relax.CentroidRelax) → None

C++: protocols::relax::CentroidRelax::set_defaults() –> void

set_fa_score_function(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, fa_score: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Sets fullatom scorefunction - only used for scoring the full atom pose before and after protocol.

C++: protocols::relax::CentroidRelax::set_fa_score_function(class std::shared_ptr<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_min_type(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, min: str) → None

Sets the minimizer type.

C++: protocols::relax::CentroidRelax::set_min_type(class std::basic_string<char>) –> void

set_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::relax::RelaxProtocolBase::set_movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

set_movemap_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, mm_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::relax::RelaxProtocolBase::set_movemap_factory(class std::shared_ptr<class core::select::movemap::MoveMapFactory>) –> void

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

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

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

set_ramp_rama(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, use: bool) → None

Ramp Rama according to centroid relax parameters

C++: protocols::relax::CentroidRelax::set_ramp_rama(bool) –> void

set_ramp_vdw(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, use: bool) → None

Ramp VDW according to centroid relax parameters

C++: protocols::relax::CentroidRelax::set_ramp_vdw(bool) –> void

set_rounds(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, rounds: int) → None

C++: protocols::relax::CentroidRelax::set_rounds(unsigned long) –> void

set_score_function(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, cen_score: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Sets main scorefunction used for centroid minimization.

C++: protocols::relax::CentroidRelax::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::relax::RelaxProtocolBase::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

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

set_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_increased_vdw_radii(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, use: bool) → None

use larger VDW radii for atoms - bb for now - default True (Courtesy of Frank Dimaio)

C++: protocols::relax::CentroidRelax::set_use_increased_vdw_radii(bool) –> void

set_use_rama2b(self: pyrosetta.rosetta.protocols.relax.CentroidRelax, use: bool) → None

Sets to use Rama2b instead of Rama - default True

C++: protocols::relax::CentroidRelax::set_use_rama2b(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.relax.ClassicRelax

Bases: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase

A functor class which implements the classic Rosetta++ pose_relax protocol

__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.relax.ClassicRelax, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, arg0: pyrosetta.rosetta.protocols.relax.ClassicRelax) -> None
  4. __init__(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) -> 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.relax.ClassicRelax, pose: pyrosetta.rosetta.core.pose.Pose) → None
Central Apply function

C++: protocols::relax::ClassicRelax::apply(class core::pose::Pose &) –> void

apply_disulfides(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::relax::RelaxProtocolBase::apply_disulfides(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, : pyrosetta.rosetta.protocols.relax.ClassicRelax) → pyrosetta.rosetta.protocols.relax.ClassicRelax

C++: protocols::relax::ClassicRelax::operator=(const class protocols::relax::ClassicRelax &) –> class protocols::relax::ClassicRelax &

cartesian(*args, **kwargs)

Overloaded function.

  1. cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::cartesian() const –> bool

  1. cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, newval: bool) -> None

Use cartesian (minimization step)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Requires scorefunction setup for non-ideal minimization.

C++: protocols::relax::RelaxProtocolBase::cartesian(bool) –> void

clear_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.relax.ClassicRelax) → pyrosetta.rosetta.protocols.moves.Mover

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

constrain_coords(*args, **kwargs)

Overloaded function.

  1. constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_coords() const –> bool

  1. constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_coords(bool) –> void

constrain_relax_segments(*args, **kwargs)

Overloaded function.

  1. constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments() const –> bool

  1. constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_segments: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments(bool) –> void

constrain_relax_to_native_coords(*args, **kwargs)

Overloaded function.

  1. constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords() const –> bool

  1. constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_native_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords(bool) –> void

constrain_relax_to_start_coords(*args, **kwargs)

Overloaded function.

  1. constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords() const –> bool

  1. constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_start_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords(bool) –> void

coord_constrain_sidechains(*args, **kwargs)

Overloaded function.

  1. coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains() const –> bool

  1. coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, coord_constrain_sidechains: bool) -> None

C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains(bool) –> void

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

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

dry_run(*args, **kwargs)

Overloaded function.

  1. dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::dry_run() const –> bool

  1. dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, setting: bool) -> None

C++: protocols::relax::RelaxProtocolBase::dry_run(bool) –> void

explicit_ramp_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → bool

C++: protocols::relax::RelaxProtocolBase::explicit_ramp_constraints() const –> bool

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

C++: protocols::relax::RelaxProtocolBase::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_checkpoints(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::relax::ClassicRelax::get_checkpoints() –> class protocols::checkpoint::CheckPointer &

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.relax.ClassicRelax, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.MonteCarlo
Accessors

C++: protocols::relax::ClassicRelax::get_mc(class core::pose::Pose &) –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::relax::RelaxProtocolBase::get_movemap() –> class std::shared_ptr<class core::kinematics::MoveMap>

get_name(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) → str

C++: protocols::relax::ClassicRelax::get_name() const –> std::string

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

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

get_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::relax::RelaxProtocolBase::get_scorefxn() const –> const class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_task_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::relax::RelaxProtocolBase::get_task_factory() const –> const class std::shared_ptr<class core::pack::task::TaskFactory> &

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

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

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

max_iter(*args, **kwargs)

Overloaded function.

  1. max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> int

C++: protocols::relax::RelaxProtocolBase::max_iter() const –> unsigned long

  1. max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, max_iter: int) -> None

C++: protocols::relax::RelaxProtocolBase::max_iter(unsigned long) –> void

min_type(*args, **kwargs)

Overloaded function.

  1. min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> str

C++: protocols::relax::RelaxProtocolBase::min_type() const –> std::string

  1. min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, min_type: str) -> None

C++: protocols::relax::RelaxProtocolBase::min_type(class std::basic_string<char>) –> void

minimize_bond_angles(*args, **kwargs)

Overloaded function.

  1. minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles() const –> bool

  1. minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_angles: bool) -> None

C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles(bool) –> void

minimize_bond_lengths(*args, **kwargs)

Overloaded function.

  1. minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths() const –> bool

  1. minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_lengths: bool) -> None

C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths(bool) –> void

name() → str

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

ramp_down_constraints(*args, **kwargs)

Overloaded function.

  1. ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints() const –> bool

  1. ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, ramp_down_constraints: bool) -> None

C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints(bool) –> void

register_options() → None

C++: protocols::relax::ClassicRelax::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

setPoseExtraScore(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::relax::ClassicRelax::setPoseExtraScore(class core::pose::Pose &) –> 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(*args, **kwargs)

Overloaded function.

  1. set_default(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::relax::ClassicRelax::set_default(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. set_default(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) -> None
  2. set_default(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, use_default_movemap: bool) -> None
Set default options from outside

C++: protocols::relax::ClassicRelax::set_default(const bool) –> void

set_default_coordinate_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → None

C++: protocols::relax::RelaxProtocolBase::set_default_coordinate_settings() –> void

set_default_minimization_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → None

C++: protocols::relax::RelaxProtocolBase::set_default_minimization_settings() –> void

set_default_minimizer(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) → None

C++: protocols::relax::ClassicRelax::set_default_minimizer() –> void

set_default_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → None

C++: protocols::relax::RelaxProtocolBase::set_default_movemap() –> void

set_default_moveset_phase1(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) → None

C++: protocols::relax::ClassicRelax::set_default_moveset_phase1() –> void

set_default_moveset_phase2(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) → None

C++: protocols::relax::ClassicRelax::set_default_moveset_phase2() –> void

set_default_moveset_phase3(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) → None

C++: protocols::relax::ClassicRelax::set_default_moveset_phase3() –> void

set_defaults(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) → None

C++: protocols::relax::RelaxProtocolBase::set_defaults() –> void

set_full_repack(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, new_pack_full_repack: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → None

C++: protocols::relax::ClassicRelax::set_full_repack(class std::shared_ptr<class protocols::simple_moves::PackRotamersMover>) –> 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_lj_ramp_cycles(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, param: int) → None
Set options from outside

C++: protocols::relax::ClassicRelax::set_lj_ramp_cycles(int) –> void

set_lj_ramp_inner_cycles(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, param: int) → None

C++: protocols::relax::ClassicRelax::set_lj_ramp_inner_cycles(int) –> void

set_mc(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, new_mc_: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None

C++: protocols::relax::ClassicRelax::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::relax::RelaxProtocolBase::set_movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

set_movemap_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, mm_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::relax::RelaxProtocolBase::set_movemap_factory(class std::shared_ptr<class core::select::movemap::MoveMapFactory>) –> void

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

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

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

set_rottrial(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, new_pack_rottrial: protocols::simple_moves::RotamerTrialsMover) → None

C++: protocols::relax::ClassicRelax::set_rottrial(class std::shared_ptr<class protocols::simple_moves::RotamerTrialsMover>) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::relax::RelaxProtocolBase::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_stage2_cycles(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, cycles2: int) → None

C++: protocols::relax::ClassicRelax::set_stage2_cycles(int) –> void

set_stage2_repack_period(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, repack2: int) → None

C++: protocols::relax::ClassicRelax::set_stage2_repack_period(int) –> void

set_stage3_cycles(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, cycles3: int) → None

C++: protocols::relax::ClassicRelax::set_stage3_cycles(int) –> void

set_start_rep_weight(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, param: float) → None

C++: protocols::relax::ClassicRelax::set_start_rep_weight(double) –> void

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

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

set_tolerance(self: pyrosetta.rosetta.protocols.relax.ClassicRelax, new_tolerance: float) → None

C++: protocols::relax::ClassicRelax::set_tolerance(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

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_coarse_vdw(self: pyrosetta.rosetta.protocols.relax.ClassicRelax) → None

C++: protocols::relax::ClassicRelax::use_coarse_vdw() –> void

pyrosetta.rosetta.protocols.relax.Relax_main(: bool) → int

C++: protocols::relax::Relax_main(bool) –> int

pyrosetta.rosetta.protocols.relax.add_coordinate_constraints_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, constraint_target_pose: pyrosetta.rosetta.core.pose.Pose, exclude_regions: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::relax::add_coordinate_constraints_to_pose(class core::pose::Pose &, const class core::pose::Pose &, class protocols::loops::Loops &) –> void

pyrosetta.rosetta.protocols.relax.add_virtual_residue_to_cterm(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::relax::add_virtual_residue_to_cterm(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.relax.coordinate_constrain_selection(pose: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, coord_sdev: float) → None

C++: protocols::relax::coordinate_constrain_selection(class core::pose::Pose &, class core::sequence::SequenceAlignment, double) –> void

pyrosetta.rosetta.protocols.relax.cyclize_pose(pose: pyrosetta.rosetta.core.pose.Pose) → None

Add terminal peptide bond and cyclic constraints to pose.

Gaurav Bhardwaj, Baker laboratory

Vikram K. Mulligan, Baker laboratory (vmullig.edu) – moved from protocols/forge/methods/util.hh/cc

C++: protocols::relax::cyclize_pose(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.relax.delete_virtual_residues(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::relax::delete_virtual_residues(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.relax.derive_sc_sc_restraints(pose: pyrosetta.rosetta.core.pose.Pose, upper_dist_cutoff: float) → None

C++: protocols::relax::derive_sc_sc_restraints(class core::pose::Pose &, const double) –> void

pyrosetta.rosetta.protocols.relax.fixH(pose: pyrosetta.rosetta.core.pose.Pose) → None

Rebuild all polymer bond-dependent atoms in the pose.

Rewritten from an earlier, uglier function that manually placed H atom in non-pro.

Vikram K. Mulligan, Baker laboratory (vmullig.edu).

C++: protocols::relax::fixH(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.relax.fix_worst_bad_ramas(*args, **kwargs)

Overloaded function.

  1. fix_worst_bad_ramas(original_pose: pyrosetta.rosetta.core.pose.Pose) -> None
  2. fix_worst_bad_ramas(original_pose: pyrosetta.rosetta.core.pose.Pose, how_many: int) -> None
  3. fix_worst_bad_ramas(original_pose: pyrosetta.rosetta.core.pose.Pose, how_many: int, skip_prob: float) -> None
  4. fix_worst_bad_ramas(original_pose: pyrosetta.rosetta.core.pose.Pose, how_many: int, skip_prob: float, limit_rms: float) -> None
  5. fix_worst_bad_ramas(original_pose: pyrosetta.rosetta.core.pose.Pose, how_many: int, skip_prob: float, limit_rms: float, limit_rama: float) -> None

C++: protocols::relax::fix_worst_bad_ramas(class core::pose::Pose &, unsigned long, double, double, double) –> void

pyrosetta.rosetta.protocols.relax.generate_bb_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose, coord_sdevs: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.core.scoring.constraints.ConstraintSet
Generate a set of coordinate constraints to backbone atoms using the
given standard deviations, with one sd per-reside. If no constraint should be applied to a given residue, give a -1 for the value of the sdev.

C++: protocols::relax::generate_bb_coordinate_constraints(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

pyrosetta.rosetta.protocols.relax.generate_relax_from_cmd(*args, **kwargs)

Overloaded function.

  1. generate_relax_from_cmd() -> pyrosetta.rosetta.protocols.relax.RelaxProtocolBase
  2. generate_relax_from_cmd(NULL_if_no_cmd: bool) -> pyrosetta.rosetta.protocols.relax.RelaxProtocolBase

C++: protocols::relax::generate_relax_from_cmd(bool) –> class std::shared_ptr<class protocols::relax::RelaxProtocolBase>

pyrosetta.rosetta.protocols.relax.get_per_residue_scores(pose: pyrosetta.rosetta.core.pose.Pose, scoretype: pyrosetta.rosetta.core.scoring.ScoreType) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::relax::get_per_residue_scores(class core::pose::Pose &, enum core::scoring::ScoreType) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.protocols.relax.make_dna_rigid(pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

Make DNA Rigid in movemap if found in pose

C++: protocols::relax::make_dna_rigid(class core::pose::Pose &, class core::kinematics::MoveMap &) –> void

pyrosetta.rosetta.protocols.relax.relax_pose(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, tag: str) → None

C++: protocols::relax::relax_pose(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.relax.setup_for_dna(scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set energy method options for DNA-DNA. Any other optimization for DNA relax should go here.

C++: protocols::relax::setup_for_dna(class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.protocols.relax.setup_membrane_topology(pose: pyrosetta.rosetta.core.pose.Pose, spanfile: str) → None

(pba) read in membrane topology

C++: protocols::relax::setup_membrane_topology(class core::pose::Pose &, class std::basic_string<char>) –> void