remodel

Bindings for protocols::forge::remodel namespace

class pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed

Bases: pyrosetta.rosetta.utility.excn.Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str)None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed, : pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed)pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed

C++: protocols::forge::remodel::EXCN_RemoveCstsFailed::operator=(const class protocols::forge::remodel::EXCN_RemoveCstsFailed &) –> class protocols::forge::remodel::EXCN_RemoveCstsFailed &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception)None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception)None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception)str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception)int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str)None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception)str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream)None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception)str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception)str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator

Bases: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator

generic remodel constraint generator for use with arbitrary ConstraintGenerators

add_remodel_constraints_to_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

generates constraints and adds them to the pose

C++: protocols::forge::remodel::RemodelConstraintGenerator::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator, : pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator)pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator

C++: protocols::forge::remodel::GenericRemodelConstraintGenerator::operator=(const class protocols::forge::remodel::GenericRemodelConstraintGenerator &) –> class protocols::forge::remodel::GenericRemodelConstraintGenerator &

static attributes_for_remodel_constraint_generator(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::attributes_for_remodel_constraint_generator(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> 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.forge.remodel.GenericRemodelConstraintGenerator)pyrosetta.rosetta.protocols.moves.Mover

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

constraints(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::constraints() const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &

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>

generate_remodel_constraints(self: pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::GenericRemodelConstraintGenerator::generate_remodel_constraints(const class core::pose::Pose &) –> void

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator)str

C++: protocols::forge::remodel::GenericRemodelConstraintGenerator::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

id(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)str

C++: protocols::forge::remodel::RemodelConstraintGenerator::id() 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.forge.remodel.RemodelConstraintGenerator, : pyrosetta.rosetta.core.pose.Pose)None

Pose-specific setup routines go here

C++: protocols::forge::remodel::RemodelConstraintGenerator::init(const class core::pose::Pose &) –> void

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

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

static lookup_stored_constraints(id: str)pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::lookup_stored_constraints(const std::string &) –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

static name()str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap)None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options()None

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

remove_remodel_constraints_from_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose(class core::pose::Pose &) const –> void

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

seqmap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.core.id.SequenceMapping

C++: protocols::forge::remodel::RemodelConstraintGenerator::seqmap() const –> class std::shared_ptr<const class core::id::SequenceMapping>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob)None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

set_id(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, id: str)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_id(const std::string &) –> void

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

setter for poses contained for rms

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

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

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

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

set_seqmap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, seqmap: pyrosetta.rosetta.core.id.SequenceMapping)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_seqmap(class std::shared_ptr<const class core::id::SequenceMapping>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

set_vlb(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, vlb: pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_vlb(class std::weak_ptr<class protocols::forge::components::VarLengthBuild>) –> 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(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose)None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

vlb(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::vlb() const –> class std::weak_ptr<class protocols::forge::components::VarLengthBuild>

class pyrosetta.rosetta.protocols.forge.remodel.LineObject

Bases: pybind11_builtins.pybind11_object

property aminoAcidList
assign(self: pyrosetta.rosetta.protocols.forge.remodel.LineObject, : pyrosetta.rosetta.protocols.forge.remodel.LineObject)pyrosetta.rosetta.protocols.forge.remodel.LineObject

C++: protocols::forge::remodel::LineObject::operator=(const struct protocols::forge::remodel::LineObject &) –> struct protocols::forge::remodel::LineObject &

property constraint_definition
property design_type
property has_constraints
property has_ncaa
property index
property isDesignable
property ncaaList
property original_index
property resname
property sstype
class pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::forge::remodel::RemodelAccumulator::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None

C++: protocols::forge::remodel::RemodelAccumulator::apply(class core::pose::Pose &, double &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator, : pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator

C++: protocols::forge::remodel::RemodelAccumulator::operator=(const class protocols::forge::remodel::RemodelAccumulator &) –> class protocols::forge::remodel::RemodelAccumulator &

clear(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)None

C++: protocols::forge::remodel::RemodelAccumulator::clear() –> 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.forge.remodel.RemodelAccumulator)pyrosetta.rosetta.protocols.moves.Mover

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

cluster_loop(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)None

C++: protocols::forge::remodel::RemodelAccumulator::cluster_loop() –> void

cluster_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)None

C++: protocols::forge::remodel::RemodelAccumulator::cluster_pose() –> void

cluster_switch(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)bool

C++: protocols::forge::remodel::RemodelAccumulator::cluster_switch() –> bool

clustered_best_poses(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t

C++: protocols::forge::remodel::RemodelAccumulator::clustered_best_poses() –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

clustered_top_poses(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator, count: int)pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t

C++: protocols::forge::remodel::RemodelAccumulator::clustered_top_poses(unsigned long) –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

contents_in_pose_store(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t

C++: protocols::forge::remodel::RemodelAccumulator::contents_in_pose_store() –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

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.forge.remodel.RemodelAccumulator)pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)str

C++: protocols::forge::remodel::RemodelAccumulator::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 > > &

keep_top_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator, num_to_keep: int)None

C++: protocols::forge::remodel::RemodelAccumulator::keep_top_pose(unsigned long) –> void

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

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

static name()str

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

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

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

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

pop(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)pyrosetta.rosetta.core.pose.Pose

C++: protocols::forge::remodel::RemodelAccumulator::pop() –> class core::pose::Pose

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

recover_checkpoint(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)int

C++: protocols::forge::remodel::RemodelAccumulator::recover_checkpoint() –> unsigned long

static 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

run_cluster(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)None

C++: protocols::forge::remodel::RemodelAccumulator::run_cluster() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob)None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

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

setter for poses contained for rms

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

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

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

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

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

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(std::ostream &) const –> void

shrink_cluster(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator, num_top: int)None

C++: protocols::forge::remodel::RemodelAccumulator::shrink_cluster(unsigned long) –> void

size(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator)int

C++: protocols::forge::remodel::RemodelAccumulator::size() –> unsigned long

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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

write_checkpoint(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator, progress_point: int)None

C++: protocols::forge::remodel::RemodelAccumulator::write_checkpoint(unsigned long) –> void

class pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator

Bases: pyrosetta.rosetta.protocols.moves.Mover

pure virtual base class

add_remodel_constraints_to_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

generates constraints and adds them to the pose

C++: protocols::forge::remodel::RemodelConstraintGenerator::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, : pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator

C++: protocols::forge::remodel::RemodelConstraintGenerator::operator=(const class protocols::forge::remodel::RemodelConstraintGenerator &) –> class protocols::forge::remodel::RemodelConstraintGenerator &

static attributes_for_remodel_constraint_generator(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::attributes_for_remodel_constraint_generator(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> 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.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>

constraints(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::constraints() const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &

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>

generate_remodel_constraints(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::generate_remodel_constraints(const class core::pose::Pose &) –> void

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.Mover)str

Each derived class must specify its name. The class name.

C++: protocols::moves::Mover::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

id(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)str

C++: protocols::forge::remodel::RemodelConstraintGenerator::id() 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.forge.remodel.RemodelConstraintGenerator, : pyrosetta.rosetta.core.pose.Pose)None

Pose-specific setup routines go here

C++: protocols::forge::remodel::RemodelConstraintGenerator::init(const class core::pose::Pose &) –> void

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

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

static lookup_stored_constraints(id: str)pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::lookup_stored_constraints(const std::string &) –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

static name()str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap)None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options()None

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

remove_remodel_constraints_from_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose(class core::pose::Pose &) const –> void

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

seqmap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.core.id.SequenceMapping

C++: protocols::forge::remodel::RemodelConstraintGenerator::seqmap() const –> class std::shared_ptr<const class core::id::SequenceMapping>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob)None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

set_id(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, id: str)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_id(const std::string &) –> void

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

setter for poses contained for rms

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

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

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

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

set_seqmap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, seqmap: pyrosetta.rosetta.core.id.SequenceMapping)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_seqmap(class std::shared_ptr<const class core::id::SequenceMapping>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

set_vlb(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, vlb: pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_vlb(class std::weak_ptr<class protocols::forge::components::VarLengthBuild>) –> 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(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose)None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

vlb(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::vlb() const –> class std::weak_ptr<class protocols::forge::components::VarLengthBuild>

class pyrosetta.rosetta.protocols.forge.remodel.RemodelData

Bases: pybind11_builtins.pybind11_object

property LD_types
property abego
assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelData, : pyrosetta.rosetta.protocols.forge.remodel.RemodelData)pyrosetta.rosetta.protocols.forge.remodel.RemodelData

C++: protocols::forge::remodel::RemodelData::operator=(const class protocols::forge::remodel::RemodelData &) –> class protocols::forge::remodel::RemodelData &

property auto_design
property blueprint
collectInsertionPose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelData)None

C++: protocols::forge::remodel::RemodelData::collectInsertionPose() –> void

property design_mode
property design_neighbor
property disulfLandingRange
property disulfMobileRange
property dssp_updated_ss
getLoopsToBuildFromBlueprint(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelData, text_blueprint: str)None

C++: protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(std::string) –> void

getLoopsToBuildFromFile(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelData, filename: str)None

C++: protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(std::string) –> void

property has_design_info_
property insertPose
property insertionSS
property insertionSize
property loops_to_build
property natro_movemap_
property parsed_string_for_resfile
property pdb_start
property pdb_stop
property sequence
splitString(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelData, str: str, delim: str, results: pyrosetta.rosetta.std.vector_std_string)None

C++: protocols::forge::remodel::RemodelData::splitString(std::string, std::string, class std::vector<std::string, class std::allocator<std::string > > &) –> void

property ss
property total_chain_break_score
translateDSSP_ABEGO(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelData, ss: str, abego: str)None

C++: protocols::forge::remodel::RemodelData::translateDSSP_ABEGO(std::string &, std::string &) –> void

updateWithDsspAssignment(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelData, dsspSS: pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t)None

C++: protocols::forge::remodel::RemodelData::updateWithDsspAssignment(class ObjexxFCL::FArray1D<char> &) –> void

class pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, : pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover)pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover

C++: protocols::forge::remodel::RemodelDesignMover::operator=(const class protocols::forge::remodel::RemodelDesignMover &) –> class protocols::forge::remodel::RemodelDesignMover &

check_state(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover)bool

C++: protocols::forge::remodel::RemodelDesignMover::check_state() –> bool

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.forge.remodel.RemodelDesignMover)pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::forge::remodel::RemodelDesignMover::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>

find_disulfides_in_the_neighborhood(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, disulf_partners: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, match_rt_limit: float, rosetta_scripts_min_loop: int, rosetta_scripts_include_current_ds: bool, rosetta_scripts_keep_current_ds: bool, relax_bb_for_disulf: bool, use_match_rt: bool, use_disulf_fa_score: bool, disulf_fa_max: float)bool

C++: protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(class core::pose::Pose &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const double &, const unsigned long &, const bool &, const bool &, const bool &, const bool &, const bool &, const double) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover)pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover)str

C++: protocols::forge::remodel::RemodelDesignMover::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

make_disulfide(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, disulf_partners: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, mm: pyrosetta.rosetta.core.kinematics.MoveMap)None

C++: protocols::forge::remodel::RemodelDesignMover::make_disulfide(class core::pose::Pose &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

make_disulfide_fast(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, disulf_partners: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t)None

C++: protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast(class core::pose::Pose &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

mode1_1_packertask(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::mode1_1_packertask(class core::pose::Pose &) –> void

mode1_packertask(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::mode1_packertask(class core::pose::Pose &) –> void

mode2_packertask(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::mode2_packertask(class core::pose::Pose &) –> void

mode3_packertask(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::mode3_packertask(class core::pose::Pose &) –> void

mode4_packertask(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::mode4_packertask(class core::pose::Pose &) –> void

mode5_packertask(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::mode5_packertask(class core::pose::Pose &) –> void

mode6_packertask(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelDesignMover::mode6_packertask(class core::pose::Pose &) –> void

static name()str

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

reduce_task(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, core: bool, boundary: bool, surface: bool)None

C++: protocols::forge::remodel::RemodelDesignMover::reduce_task(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask> &, bool, bool, bool) –> void

static 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.forge.remodel.RemodelDesignMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction)None

C++: protocols::forge::remodel::RemodelDesignMover::scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob)None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

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

setter for poses contained for rms

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

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

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

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

set_state(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover, state_tag: str)None

C++: protocols::forge::remodel::RemodelDesignMover::set_state(std::string) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

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(std::ostream &) const –> void

task(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover)pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::forge::remodel::RemodelDesignMover::task() –> class std::shared_ptr<class core::pack::task::PackerTask> &

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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule

Bases: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO

add_constraints_to_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction, accept_blocks_missing_header: bool)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, bool) –> void

add_constraints_to_pose_for_block_without_clearing_and_header_processing(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction, cst_block: int)None

BE CAREFUL when using this function, it generates constraints

without clearing the internal data structures and reading in

the information in the pdb REMARKs

if you’re unsure use the above one

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose_for_block_without_clearing_and_header_processing(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, unsigned long) const –> void

add_pregenerated_constraints_to_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction)None

convenience function that will add constraints to the pose if they have

been previously generated. BE CAREFUL when using this function, it relies on the

pose having the same residue types at the same constrained positions as in the pose

that was originally used to generate the constraints. If in doubt, it’s safer to

regenerate the constraints before adding (i.e. use the above add_constraints_to_pose

function.)

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>) const –> void

allowed_res_name3_at_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int)pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::allowed_res_name3_at_position(const class core::pose::Pose &, const unsigned long) const –> class utility::vector1<std::string, class std::allocator<std::string > >

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelEnzdesCstModule::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule, : pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule)pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule

C++: protocols::forge::remodel::RemodelEnzdesCstModule::operator=(const class protocols::forge::remodel::RemodelEnzdesCstModule &) –> class protocols::forge::remodel::RemodelEnzdesCstModule &

blueprint_cst_definition(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(class core::pose::Pose &) –> void

clear_active_pose_constraints_for_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, cst_block: int)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::clear_active_pose_constraints_for_block(class core::pose::Pose &, unsigned long) const –> void

contains_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int)bool

are constraints specified for this position?

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::contains_position(const class core::pose::Pose &, const unsigned long) const –> bool

enable_constraint_scoreterms(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction)None

C++: protocols::forge::remodel::RemodelEnzdesCstModule::enable_constraint_scoreterms(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

enz_cst_params(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block: int)protocols::toolbox::match_enzdes_util::EnzConstraintParameters

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params(unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters>

enz_cst_params_missing_in_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose)pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_missing_in_pose(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters>, class std::allocator<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters> > >

enz_cst_params_size(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)int

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_size() –> unsigned long

get_self_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_ptr() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_weak_ptr() –> class std::weak_ptr<class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

initialize_with_mcfi_list(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, mcfi_list_vec: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_MatchConstraintFileInfoList_t)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::initialize_with_mcfi_list(class utility::vector1<class std::shared_ptr<class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList>, class std::allocator<class std::shared_ptr<class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList> > >) –> void

is_backbone_only_cst(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int)bool
are the constraints specified at this position

mediated through backbone interactions only?

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::is_backbone_only_cst(const class core::pose::Pose &, const unsigned long) const –> bool

mcfi_list(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block: int)protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_list(unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList>

mcfi_lists_size(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)int

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_size() const –> unsigned long

num_mcfi_lists(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)int

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::num_mcfi_lists() const –> unsigned long

ordered_constrained_positions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose)pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::ordered_constrained_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

process_pdb_header(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, accept_missing_blocks: bool)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(class core::pose::Pose &, bool) –> void

read_enzyme_cstfile(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, fname: str)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::read_enzyme_cstfile(std::string) –> void

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, smap: pyrosetta.rosetta.core.id.SequenceMapping)None

changing the constrained residues if the sequence length changes

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remap_resid(const class core::id::SequenceMapping &) –> void

remove_constraints_from_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, keep_covalent: bool, fail_on_constraints_missing: bool)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose(class core::pose::Pose &, const bool, const bool) const –> void

remove_constraints_from_pose_for_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, cst_block: int, fail_on_constraints_missing: bool)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose_for_block(class core::pose::Pose &, unsigned long, const bool) const –> void

remove_position_from_template_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, pos: int)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res(class core::pose::Pose &, unsigned long) const –> void

remove_position_from_template_res_for_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, pos: int, cst_block: int)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res_for_block(class core::pose::Pose &, unsigned long, unsigned long) const –> void

set_external_position_for_resA_in_parameter_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block: int, respos: int)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resA_in_parameter_block(unsigned long, unsigned long) –> void

set_external_position_for_resB_in_parameter_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block: int, respos: int)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resB_in_parameter_block(unsigned long, unsigned long) –> void

set_position_for_missing_res_in_parameter_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, cst_block: int, respos: int)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_position_for_missing_res_in_parameter_block(class core::pose::Pose &, unsigned long, unsigned long) const –> void

show_cst_definitions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::show_cst_definitions() const –> void

target_downstream_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::target_downstream_res() const –> const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &

update_pdb_remarks_for_backbone_params(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::update_pdb_remarks_for_backbone_params(class core::pose::Pose &) const –> void

use_all_blocks(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule)None

C++: protocols::forge::remodel::RemodelEnzdesCstModule::use_all_blocks() –> void

use_backbone_only_blocks(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule)None

C++: protocols::forge::remodel::RemodelEnzdesCstModule::use_backbone_only_blocks() –> void

class pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame

Bases: pyrosetta.rosetta.protocols.moves.Mover

align_segment(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelGlobalFrame::align_segment(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelGlobalFrame::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, : pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame)pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame

C++: protocols::forge::remodel::RemodelGlobalFrame::operator=(const class protocols::forge::remodel::RemodelGlobalFrame &) –> class protocols::forge::remodel::RemodelGlobalFrame &

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.forge.remodel.RemodelGlobalFrame)pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::forge::remodel::RemodelGlobalFrame::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.forge.remodel.RemodelGlobalFrame)pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_helical_params(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(class core::pose::Pose &) –> void

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.forge.remodel.RemodelGlobalFrame)str

C++: protocols::forge::remodel::RemodelGlobalFrame::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

identity_matrix(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t)None

C++: protocols::forge::remodel::RemodelGlobalFrame::identity_matrix(class numeric::xyzMatrix<double> &) –> void

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

static name()str

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

omega(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame)float

C++: protocols::forge::remodel::RemodelGlobalFrame::omega() –> double

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

radius(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame)float

C++: protocols::forge::remodel::RemodelGlobalFrame::radius() –> double

static 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

restore_original_cst(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelGlobalFrame::restore_original_cst(class core::pose::Pose &) –> void

rise(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame)float

C++: protocols::forge::remodel::RemodelGlobalFrame::rise() –> double

scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction)None

C++: protocols::forge::remodel::RemodelGlobalFrame::scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob)None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

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

setter for poses contained for rms

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

set_native_cst_set(*args, **kwargs)

Overloaded function.

  1. set_native_cst_set(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None

C++: protocols::forge::remodel::RemodelGlobalFrame::set_native_cst_set(const class core::scoring::constraints::ConstraintSet &) –> void

  1. set_native_cst_set(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::forge::remodel::RemodelGlobalFrame::set_native_cst_set(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_segment_size(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, segment_size: int)None

C++: protocols::forge::remodel::RemodelGlobalFrame::set_segment_size(unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

setup_CM_helical_constraint(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(class core::pose::Pose &) –> void

setup_helical_constraint(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint(class core::pose::Pose &) –> 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(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose)None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelLigandHandler::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler, : pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler)pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler

C++: protocols::forge::remodel::RemodelLigandHandler::operator=(const class protocols::forge::remodel::RemodelLigandHandler &) –> class protocols::forge::remodel::RemodelLigandHandler &

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.forge.remodel.RemodelLigandHandler)pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::forge::remodel::RemodelLigandHandler::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.forge.remodel.RemodelLigandHandler)pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler)str

C++: protocols::forge::remodel::RemodelLigandHandler::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

minimize(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelLigandHandler::minimize(class core::pose::Pose &) –> void

static name()str

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options()None

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

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

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

setter for poses contained for rms

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

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

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

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

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

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(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose)None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++.

add_fragments(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, fragset: pyrosetta.rosetta.core.fragment.FragSet)None

add a fragment set

C++: protocols::forge::remodel::RemodelLoopMover::add_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

add_loop(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, loop: pyrosetta.rosetta.protocols.loops.Loop)None

add a loop to model

C++: protocols::forge::remodel::RemodelLoopMover::add_loop(const class protocols::loops::Loop) –> void

allowed_closure_attempts(*args, **kwargs)

Overloaded function.

  1. allowed_closure_attempts(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> int

the allowed number of overall closure attempts before apply() exits

(default 3)

C++: protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts() const –> unsigned long

  1. allowed_closure_attempts(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, attempts: int) -> None

the allowed number of overall closure attempts before apply() exits

C++: protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts(const unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, pose: pyrosetta.rosetta.core.pose.Pose)None

apply defined moves to given Pose

Sets protocols::moves::MS_SUCCESS upon successful closure of

all loops, otherwise sets protocols::moves::FAIL_RETRY.

C++: protocols::forge::remodel::RemodelLoopMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

boost_closure_cycles(*args, **kwargs)

Overloaded function.

  1. boost_closure_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> int

the maximum number of possible lockdown closure cycles to perform

(default 30)

C++: protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles() const –> unsigned long

  1. boost_closure_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, cycles: int) -> None

the maximum number of possible lockdown closure cycles to perform

C++: protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles(const unsigned long) –> void

clear_fragments(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover)None

clear all fragment sets

C++: protocols::forge::remodel::RemodelLoopMover::clear_fragments() –> 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.forge.remodel.RemodelLoopMover)pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::forge::remodel::RemodelLoopMover::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>

false_movemap(*args, **kwargs)

Overloaded function.

  1. false_movemap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

get the false movemap

All movemaps are generated with respect to this movemap.

Any explicit False settings within this movemap will be retained in all descendant movemaps.

C++: protocols::forge::remodel::RemodelLoopMover::false_movemap() const –> const class core::kinematics::MoveMap &

  1. false_movemap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

set the false movemap to use

All movemaps are generated with respect to this movemap.

Any explicit False settings within this movemap will be retained in all descendant movemaps.

C++: protocols::forge::remodel::RemodelLoopMover::false_movemap(const class core::kinematics::MoveMap &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover)pyrosetta.rosetta.protocols.moves.Mover

create this type of object

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

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover)str

C++: protocols::forge::remodel::RemodelLoopMover::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

independent_cycles(*args, **kwargs)

Overloaded function.

  1. independent_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> int

the number of independent closure cycles to perform (default 8)

C++: protocols::forge::remodel::RemodelLoopMover::independent_cycles() const –> unsigned long

  1. independent_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, cycles: int) -> None

the number of independent closure cycles to perform

C++: protocols::forge::remodel::RemodelLoopMover::independent_cycles(const unsigned long) –> void

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

loophash_cycles(*args, **kwargs)

Overloaded function.

  1. loophash_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> int

the number of loophash closure cycles to perform (default 8)

C++: protocols::forge::remodel::RemodelLoopMover::loophash_cycles() const –> unsigned long

  1. loophash_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, cycles: int) -> None

the number of loophash closure cycles to perform

C++: protocols::forge::remodel::RemodelLoopMover::loophash_cycles(const unsigned long) –> void

loops(*args, **kwargs)

Overloaded function.

  1. loops(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> pyrosetta.rosetta.protocols.loops.Loops

the loops to model

C++: protocols::forge::remodel::RemodelLoopMover::loops() const –> const class std::shared_ptr<class protocols::loops::Loops>

  1. loops(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

set the loops to model

C++: protocols::forge::remodel::RemodelLoopMover::loops(const class std::shared_ptr<class protocols::loops::Loops>) –> void

max_linear_chainbreak(*args, **kwargs)

Overloaded function.

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> float

if linear chainbreak is <= this value, loop is considered closed

(default 0.07)

C++: protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak() const –> double

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, val: float) -> None

if linear chainbreak is <= this value, loop is considered closed

C++: protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak(const double) –> void

static name()str

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

randomize_loops(*args, **kwargs)

Overloaded function.

  1. randomize_loops(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> bool

randomize loops prior to running main protocol? (default true)

C++: protocols::forge::remodel::RemodelLoopMover::randomize_loops() const –> bool

  1. randomize_loops(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, flag: bool) -> None

randomize loops prior to running main protocol?

C++: protocols::forge::remodel::RemodelLoopMover::randomize_loops(const bool) –> void

randomize_stage(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, pose: pyrosetta.rosetta.core.pose.Pose)None

randomize loops

C++: protocols::forge::remodel::RemodelLoopMover::randomize_stage(class core::pose::Pose &) –> void

static register_options()None

C++: protocols::forge::remodel::RemodelLoopMover::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

remodelData(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, remodel_data: pyrosetta.rosetta.protocols.forge.remodel.RemodelData)None

adds the remodel data to thei remodelLoopMover object

C++: protocols::forge::remodel::RemodelLoopMover::remodelData(const class protocols::forge::remodel::RemodelData) –> void

repeat_generation_with_additional_residue(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, pose: pyrosetta.rosetta.core.pose.Pose, repeat_pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(class core::pose::Pose &, class core::pose::Pose &) –> void

repeat_propagation(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, pose: pyrosetta.rosetta.core.pose.Pose, repeat_pose: pyrosetta.rosetta.core.pose.Pose, repeat_number: int)None

C++: protocols::forge::remodel::RemodelLoopMover::repeat_propagation(class core::pose::Pose &, class core::pose::Pose &, unsigned long) –> void

repeat_sync(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, repeat_pose: pyrosetta.rosetta.core.pose.Pose, repeat_number: int)None

C++: protocols::forge::remodel::RemodelLoopMover::repeat_sync(class core::pose::Pose &, unsigned long) –> void

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(*args, **kwargs)

Overloaded function.

  1. scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

the ScoreFunction to use during modeling;

C++: protocols::forge::remodel::RemodelLoopMover::scorefunction() const –> const class core::scoring::ScoreFunction &

  1. scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

the ScoreFunction to use during modeling

C++: protocols::forge::remodel::RemodelLoopMover::scorefunction(const class core::scoring::ScoreFunction &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob)None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

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

setter for poses contained for rms

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

set_keep_input_foldtree(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, setting: bool)None

C++: protocols::forge::remodel::RemodelLoopMover::set_keep_input_foldtree(const bool) –> 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_param_from_options(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover)None

C++: protocols::forge::remodel::RemodelLoopMover::set_param_from_options() –> void

set_repeat_tail_length(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, length: int)None

C++: protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length(const unsigned long) –> void

set_seal_foldtree(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, setting: bool)None

C++: protocols::forge::remodel::RemodelLoopMover::set_seal_foldtree(const bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

set_user_provided_movers(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, movers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_moves_Mover_t)None

C++: protocols::forge::remodel::RemodelLoopMover::set_user_provided_movers(const class utility::vector1<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &) –> 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(std::ostream &) const –> void

simultaneous_cycles(*args, **kwargs)

Overloaded function.

  1. simultaneous_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> int

the number of simultaneous closure cycles to perform (default 2)

C++: protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles() const –> unsigned long

  1. simultaneous_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, cycles: int) -> None

the number of simultaneous closure cycles to perform

C++: protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles(const unsigned long) –> void

temperature(*args, **kwargs)

Overloaded function.

  1. temperature(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover) -> float

temperature for mc ( default 2.0 )

C++: protocols::forge::remodel::RemodelLoopMover::temperature() const –> double

  1. temperature(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, temp: float) -> None

temperature for mc

C++: protocols::forge::remodel::RemodelLoopMover::temperature(const 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

total_standard_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover)int
the total number of “standard” (equal to simul + independent)

to perform

C++: protocols::forge::remodel::RemodelLoopMover::total_standard_cycles() const –> unsigned long

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

user_provided_movers_apply_cycle(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover, cycle: int)None

C++: protocols::forge::remodel::RemodelLoopMover::user_provided_movers_apply_cycle(const unsigned long) –> void

class pyrosetta.rosetta.protocols.forge.remodel.RemodelMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, pose: pyrosetta.rosetta.core.pose.Pose)None

apply defined moves to given Pose

C++: protocols::forge::remodel::RemodelMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

centroid_loop_mover_str(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, loop_mover_str: str)None

the loop mover string to use during centroid build

set to either a string the create_loop_mover() LoopMoverFactory

recognizes or the “RemodelLoopMover”

C++: protocols::forge::remodel::RemodelMover::centroid_loop_mover_str(const std::string &) –> void

centroid_scorefunction(*args, **kwargs)

Overloaded function.

  1. centroid_scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

the centroid level score function, default “remodel_cen”

C++: protocols::forge::remodel::RemodelMover::centroid_scorefunction() const –> const class core::scoring::ScoreFunction &

  1. centroid_scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the centroid level score function

C++: protocols::forge::remodel::RemodelMover::centroid_scorefunction(const class core::scoring::ScoreFunction &) –> void

  1. centroid_scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the centroid level score function

C++: protocols::forge::remodel::RemodelMover::centroid_scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> 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.forge.remodel.RemodelMover)pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::forge::remodel::RemodelMover::clone() –> class std::shared_ptr<class protocols::moves::Mover>

confirm_sequence(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, pose: pyrosetta.rosetta.core.pose.Pose)bool

C++: protocols::forge::remodel::RemodelMover::confirm_sequence(class core::pose::Pose &) –> bool

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>

dr_cycles(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, cycles: int)None

set the number of design-refine cycles to perform

set this to 0 to skip design-refine

C++: protocols::forge::remodel::RemodelMover::dr_cycles(const unsigned long) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover)pyrosetta.rosetta.protocols.moves.Mover

create this type of object

C++: protocols::forge::remodel::RemodelMover::fresh_instance() –> class std::shared_ptr<class protocols::moves::Mover>

fullatom_scorefunction(*args, **kwargs)

Overloaded function.

  1. fullatom_scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

the full-atom level score function

C++: protocols::forge::remodel::RemodelMover::fullatom_scorefunction() const –> const class core::scoring::ScoreFunction &

  1. fullatom_scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the full-atom level score function

C++: protocols::forge::remodel::RemodelMover::fullatom_scorefunction(const class core::scoring::ScoreFunction &) –> void

  1. fullatom_scorefunction(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the full-atom level score function

C++: protocols::forge::remodel::RemodelMover::fullatom_scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover)str

C++: protocols::forge::remodel::RemodelMover::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

static loops_buns_polar_calc_name()str
the name for the loops’ buried unsatisfied polars

calculator

C++: protocols::forge::remodel::RemodelMover::loops_buns_polar_calc_name() –> std::string

max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, threshold: float)None

the maximum allowed linear chainbreak

C++: protocols::forge::remodel::RemodelMover::max_linear_chainbreak(const double) –> void

static mover_name()str

C++: protocols::forge::remodel::RemodelMover::mover_name() –> std::string

static name()str

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

static neighborhood_buns_polar_calc_name()str
the name for the loops’ neighborhood buried unsatisfied polars

calculator

C++: protocols::forge::remodel::RemodelMover::neighborhood_buns_polar_calc_name() –> std::string

static neighborhood_calc_name()str

the name for the loops’ neighborhood calculator

C++: protocols::forge::remodel::RemodelMover::neighborhood_calc_name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap)None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None

Provide the citation.

C++: protocols::forge::remodel::RemodelMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::forge::remodel::RemodelMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

redesign_loop_neighborhood(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMover, flag: bool)None
redesign the neighborhood around the loop? if false, then just

repacks during the design phase

C++: protocols::forge::remodel::RemodelMover::redesign_loop_neighborhood(const bool) –> void

static 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

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

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

setter for poses contained for rms

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

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

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

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

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

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(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose)None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator, : pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator)pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator

C++: protocols::forge::remodel::RemodelMoverCreator::operator=(const class protocols::forge::remodel::RemodelMoverCreator &) –> class protocols::forge::remodel::RemodelMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator)pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::forge::remodel::RemodelMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator)str

C++: protocols::forge::remodel::RemodelMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition)None

C++: protocols::forge::remodel::RemodelMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks, pose: pyrosetta.rosetta.core.pose.Pose, ptask: pyrosetta.rosetta.core.pack.task.PackerTask)None

C++: protocols::forge::remodel::RemodelRotamerLinks::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks, : pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks)pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks

C++: protocols::forge::remodel::RemodelRotamerLinks::operator=(const class protocols::forge::remodel::RemodelRotamerLinks &) –> class protocols::forge::remodel::RemodelRotamerLinks &

clone(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks)pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::forge::remodel::RemodelRotamerLinks::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname()str

C++: protocols::forge::remodel::RemodelRotamerLinks::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap)None

C++: protocols::forge::remodel::RemodelRotamerLinks::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::forge::remodel::RemodelRotamerLinks::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator, : pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator)pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator

C++: protocols::forge::remodel::RemodelRotamerLinksCreator::operator=(const class protocols::forge::remodel::RemodelRotamerLinksCreator &) –> class protocols::forge::remodel::RemodelRotamerLinksCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator)pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::forge::remodel::RemodelRotamerLinksCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator)str

C++: protocols::forge::remodel::RemodelRotamerLinksCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition)None

C++: protocols::forge::remodel::RemodelRotamerLinksCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet

Bases: pybind11_builtins.pybind11_object

property LD_types
property aa
property abego
assign(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet, rval: pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet)pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet

C++: protocols::forge::remodel::RemodelWorkingSet::operator=(const class protocols::forge::remodel::RemodelWorkingSet &) –> class protocols::forge::remodel::RemodelWorkingSet &

property begin
property buildDisulfide
property copy_begin
property copy_end
property design_matrix
property disulfide_cutpoint
property disulfide_jump_points
property disulfide_ss
property end
property hasInsertion
property insertionEndIndex
property insertionStartIndex
property loops
property manager
manualPackerTaskGen(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet, built_pose: pyrosetta.rosetta.core.pose.Pose, data: pyrosetta.rosetta.protocols.forge.remodel.RemodelData)None

C++: protocols::forge::remodel::RemodelWorkingSet::manualPackerTaskGen(const class core::pose::Pose &, const class protocols::forge::remodel::RemodelData &) –> void

property rvjump_pose
property safe_root_
property sequence
property src_begin
property src_end
property ss
property task
property translate_index
workingSetGen(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet, input_pose: pyrosetta.rosetta.core.pose.Pose, data: pyrosetta.rosetta.protocols.forge.remodel.RemodelData)None

C++: protocols::forge::remodel::RemodelWorkingSet::workingSetGen(const class core::pose::Pose &, const class protocols::forge::remodel::RemodelData &) –> void

class pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator, : pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator)pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator

C++: protocols::forge::remodel::ResidueVicinityCstGeneratorCreator::operator=(const class protocols::forge::remodel::ResidueVicinityCstGeneratorCreator &) –> class protocols::forge::remodel::ResidueVicinityCstGeneratorCreator &

create_mover(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator)pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::forge::remodel::ResidueVicinityCstGeneratorCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator)str

C++: protocols::forge::remodel::ResidueVicinityCstGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition)None

C++: protocols::forge::remodel::ResidueVicinityCstGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo

Bases: pybind11_builtins.pybind11_object

small helper class for the ResidueVicinityRCG

assign(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, : pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo

C++: protocols::forge::remodel::ResidueVicinityInfo::operator=(const class protocols::forge::remodel::ResidueVicinityInfo &) –> class protocols::forge::remodel::ResidueVicinityInfo &

desired_remodelres_in_vicinity(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)int

C++: protocols::forge::remodel::ResidueVicinityInfo::desired_remodelres_in_vicinity() const –> unsigned long

dis(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::forge::remodel::ResidueVicinityInfo::dis() const –> class std::shared_ptr<class core::scoring::func::Func>

loop_ang(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::forge::remodel::ResidueVicinityInfo::loop_ang() const –> class std::shared_ptr<class core::scoring::func::Func>

loop_dih(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::forge::remodel::ResidueVicinityInfo::loop_dih() const –> class std::shared_ptr<class core::scoring::func::Func>

loopres_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::forge::remodel::ResidueVicinityInfo::loopres_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

loopres_base2_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::forge::remodel::ResidueVicinityInfo::loopres_base2_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

loopres_base_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::forge::remodel::ResidueVicinityInfo::loopres_base_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

lt_dih(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::forge::remodel::ResidueVicinityInfo::lt_dih() const –> class std::shared_ptr<class core::scoring::func::Func>

old_seqpos(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)int

C++: protocols::forge::remodel::ResidueVicinityInfo::old_seqpos() const –> unsigned long

residue_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::forge::remodel::ResidueVicinityInfo::residue_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

residue_base2_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::forge::remodel::ResidueVicinityInfo::residue_base2_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

residue_base_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::forge::remodel::ResidueVicinityInfo::residue_base_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

set_dis(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, dis: pyrosetta.rosetta.core.scoring.func.Func)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_dis(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_loop_ang(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, loop_ang: pyrosetta.rosetta.core.scoring.func.Func)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_loop_ang(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_loop_dih(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, loop_dih: pyrosetta.rosetta.core.scoring.func.Func)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_loop_dih(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_loopres_base2_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, loopres_base2_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_loopres_base2_atoms(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_loopres_base_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, loopres_base_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_loopres_base_atoms(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_lt_dih(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, lt_dih: pyrosetta.rosetta.core.scoring.func.Func)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_lt_dih(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_residue_base2_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, residue_base2_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_residue_base2_atoms(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_residue_base_atoms(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, residue_base_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_residue_base_atoms(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_targ_ang(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, targ_ang: pyrosetta.rosetta.core.scoring.func.Func)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_targ_ang(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_targ_dih(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo, targ_dih: pyrosetta.rosetta.core.scoring.func.Func)None

C++: protocols::forge::remodel::ResidueVicinityInfo::set_targ_dih(class std::shared_ptr<class core::scoring::func::Func>) –> void

targ_ang(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::forge::remodel::ResidueVicinityInfo::targ_ang() const –> class std::shared_ptr<class core::scoring::func::Func>

targ_dih(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::forge::remodel::ResidueVicinityInfo::targ_dih() const –> class std::shared_ptr<class core::scoring::func::Func>

class pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG

Bases: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator

a RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions

in the remodeled loop to the desired positions, such that during remodeling, the remodeled

region will be driven towards the vicinity of these residues

add_remodel_constraints_to_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose(class core::pose::Pose &) –> void

add_rv_info(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG, rv_info: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo)None

C++: protocols::forge::remodel::ResidueVicinityRCG::add_rv_info(class std::shared_ptr<class protocols::forge::remodel::ResidueVicinityInfo>) –> void

apply(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

generates constraints and adds them to the pose

C++: protocols::forge::remodel::RemodelConstraintGenerator::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG, : pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG)pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG

C++: protocols::forge::remodel::ResidueVicinityRCG::operator=(const class protocols::forge::remodel::ResidueVicinityRCG &) –> class protocols::forge::remodel::ResidueVicinityRCG &

static attributes_for_remodel_constraint_generator(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::attributes_for_remodel_constraint_generator(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> 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

clear_rv_infos(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG)None

C++: protocols::forge::remodel::ResidueVicinityRCG::clear_rv_infos() –> void

clone(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG)pyrosetta.rosetta.protocols.moves.Mover

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

constraints(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::constraints() const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &

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.forge.remodel.ResidueVicinityRCG)pyrosetta.rosetta.protocols.moves.Mover

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

generate_remodel_constraints(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::ResidueVicinityRCG::generate_remodel_constraints(const class core::pose::Pose &) –> void

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover)protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover)str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover)pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG)str

C++: protocols::forge::remodel::ResidueVicinityRCG::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

id(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)str

C++: protocols::forge::remodel::RemodelConstraintGenerator::id() 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.forge.remodel.RemodelConstraintGenerator, : pyrosetta.rosetta.core.pose.Pose)None

Pose-specific setup routines go here

C++: protocols::forge::remodel::RemodelConstraintGenerator::init(const class core::pose::Pose &) –> void

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

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

static lookup_stored_constraints(id: str)pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::lookup_stored_constraints(const std::string &) –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

lstart(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG, lstart: int)None

C++: protocols::forge::remodel::ResidueVicinityRCG::lstart(const unsigned long) –> void

lstop(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG, lstop: int)None

C++: protocols::forge::remodel::ResidueVicinityRCG::lstop(const unsigned long) –> void

static mover_name()str

C++: protocols::forge::remodel::ResidueVicinityRCG::mover_name() –> std::string

static name()str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap)None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList)None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::forge::remodel::ResidueVicinityRCG::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static 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

remove_remodel_constraints_from_pose(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose(class core::pose::Pose &) const –> void

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

seqmap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.core.id.SequenceMapping

C++: protocols::forge::remodel::RemodelConstraintGenerator::seqmap() const –> class std::shared_ptr<const class core::id::SequenceMapping>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob)None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str)None

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

set_id(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, id: str)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_id(const std::string &) –> void

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

setter for poses contained for rms

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

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

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

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

set_rv_infos(self: pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG, rv_infos: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_forge_remodel_ResidueVicinityInfo_t)None

C++: protocols::forge::remodel::ResidueVicinityRCG::set_rv_infos(const class utility::vector1<class std::shared_ptr<class protocols::forge::remodel::ResidueVicinityInfo>, class std::allocator<class std::shared_ptr<class protocols::forge::remodel::ResidueVicinityInfo> > > &) –> void

set_seqmap(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, seqmap: pyrosetta.rosetta.core.id.SequenceMapping)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_seqmap(class std::shared_ptr<const class core::id::SequenceMapping>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str)None

Set the ‘type’ string

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

set_vlb(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator, vlb: pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t)None

C++: protocols::forge::remodel::RemodelConstraintGenerator::set_vlb(class std::weak_ptr<class protocols::forge::components::VarLengthBuild>) –> 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(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose)None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

vlb(self: pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator)pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t

C++: protocols::forge::remodel::RemodelConstraintGenerator::vlb() const –> class std::weak_ptr<class protocols::forge::components::VarLengthBuild>

class pyrosetta.rosetta.protocols.forge.remodel.Segment

Bases: pybind11_builtins.pybind11_object

property residues
pyrosetta.rosetta.protocols.forge.remodel.compute_center_of_mass(pose: pyrosetta.rosetta.core.pose.Pose, range_start: int, range_stop: int)pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::forge::remodel::compute_center_of_mass(const class core::pose::Pose &, unsigned long, unsigned long) –> class numeric::xyzVector<double>