recon_design

Bindings for protocols::recon_design namespace

class pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence

Bases: pyrosetta.rosetta.protocols.moves.VectorPoseMover

Takes in multiple poses from the VectorPoseJobDistributor and finds the consensus sequence that optimizes energy of all input poses. Used in conjuction with MSDMover at the end of a protocol to make sure that you end up with one multistate solution. Only accessible through recon application.

apply(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, pose: pyrosetta.rosetta.core.pose.Pose) None
Movers derived from VectorPoseMover must define two apply methods:

apply and apply_mpi, depending on whether the protocol is run in MPI or not Running in MPI will distribute each pose to a separate node, so the mover will operate on one pose

C++: protocols::recon_design::FindConsensusSequence::apply(class core::pose::Pose &) –> void

apply_mpi(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::recon_design::FindConsensusSequence::apply_mpi(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, : pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence) pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence

C++: protocols::recon_design::FindConsensusSequence::operator=(const class protocols::recon_design::FindConsensusSequence &) –> class protocols::recon_design::FindConsensusSequence &

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.recon_design.FindConsensusSequence) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::recon_design::FindConsensusSequence::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>

designable_residues(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence) pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: protocols::recon_design::FindConsensusSequence::designable_residues() –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

fresh_instance(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::recon_design::FindConsensusSequence::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.recon_design.FindConsensusSequence) str

C++: protocols::recon_design::FindConsensusSequence::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 > > &

initialize_packer(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence) None
Set up the packer to be used when substituting different

candidate AAs and repacking before evaluating energy

C++: protocols::recon_design::FindConsensusSequence::initialize_packer() –> 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.recon_design.FindConsensusSequence, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

Read options from RosettaScripts

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

parse_resfiles(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence) None
Populates designable_residues_ with a list of designable residues corresponding

to the poses in poses_, corresponding element-wise (designables_residues[0] matches to poses_[0], etc)

C++: protocols::recon_design::FindConsensusSequence::parse_resfiles() –> void

pick_consensus_AA(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, res_link_index: int, candidate_AAs: pyrosetta.rosetta.utility.vector1_std_string) None
Based on all the input poses, find the optimal AA at position

res_link_index. candidate_AAs specifies all of the AAs present in any of poses_ at position res_link_index. Fitness is defined implicitly as the sum of energy of all poses.

C++: protocols::recon_design::FindConsensusSequence::pick_consensus_AA(unsigned long, class utility::vector1<std::string, class std::allocator<std::string > >) –> void

pick_consensus_AA_mpi(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, pose: pyrosetta.rosetta.core.pose.Pose, candidate_AAs: pyrosetta.rosetta.utility.vector1_std_string, pose_position: int) None

C++: protocols::recon_design::FindConsensusSequence::pick_consensus_AA_mpi(class core::pose::Pose &, class utility::vector1<std::string, class std::allocator<std::string > >, unsigned long) –> 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: utility::tag::XMLSchemaDefinition) None

Specify XML schema

C++: protocols::recon_design::FindConsensusSequence::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

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

resfile_at(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, index: int) str
Get the resfile corresponding to the pose at index. If

only one resfile is present then it will be returned regardless of the value of index

C++: protocols::recon_design::FindConsensusSequence::resfile_at(unsigned long) –> std::string

resfiles(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, resfiles: pyrosetta.rosetta.utility.vector1_std_string) None

C++: protocols::recon_design::FindConsensusSequence::resfiles(class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

score_function(*args, **kwargs)

Overloaded function.

  1. score_function(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Getters and setters

C++: protocols::recon_design::FindConsensusSequence::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

  1. score_function(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, : pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::recon_design::FindConsensusSequence::score_function(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_poses(self: pyrosetta.rosetta.protocols.moves.VectorPoseMover, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) None

Set the vector of poses for the mover to act upon

C++: protocols::moves::VectorPoseMover::set_poses(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<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

task_factory(*args, **kwargs)

Overloaded function.

  1. task_factory(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::recon_design::FindConsensusSequence::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

  1. task_factory(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, : pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::recon_design::FindConsensusSequence::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

test_AA(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence, pose_copy: pyrosetta.rosetta.core.pose.Pose, trial_AA: str, pose_position: int) float
Place a candidate AA (trial_AA) onto a pose (pose_copy)

at position pose_position and repack and measure the energy. Function returns the energy of that pose with the trial_AA

C++: protocols::recon_design::FindConsensusSequence::test_AA(class std::shared_ptr<class core::pose::Pose>, std::string, unsigned long) –> double

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, 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.recon_design.FindConsensusSequenceCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator, : pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator) pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator

C++: protocols::recon_design::FindConsensusSequenceCreator::operator=(const class protocols::recon_design::FindConsensusSequenceCreator &) –> class protocols::recon_design::FindConsensusSequenceCreator &

create_mover(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::recon_design::FindConsensusSequenceCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator) str

C++: protocols::recon_design::FindConsensusSequenceCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::recon_design::FindConsensusSequenceCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::recon_design::FindConsensusSequenceCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.recon_design.FitnessFilter

Bases: pyrosetta.rosetta.protocols.filters.VectorPoseFilter

Returns the sum of energy of input poses. Only accessible through recon application.

apply(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool
Movers derived from VectorPoseFilter must define two apply methods:

apply and apply_mpi, depending on whether the protocol is run in MPI or not Running in MPI will distribute each pose to a separate node, so the mover will operate on one pose

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

apply_mpi(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::recon_design::FitnessFilter::apply_mpi(const class core::pose::Pose &) const –> bool

calculate_fitness(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, : pyrosetta.rosetta.core.pose.Pose) float

Internal functions to get the fitness over all poses

C++: protocols::recon_design::FitnessFilter::calculate_fitness(const class core::pose::Pose &) const –> double

calculate_fitness_mpi(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::recon_design::FitnessFilter::calculate_fitness_mpi(const class core::pose::Pose &) const –> double

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

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

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

clone(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter) pyrosetta.rosetta.protocols.filters.Filter

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

fresh_instance(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter) pyrosetta.rosetta.protocols.filters.Filter

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

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

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

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

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

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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::recon_design::FitnessFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::recon_design::FitnessFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, : pyrosetta.rosetta.core.pose.Pose) float

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

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

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

set_poses(self: pyrosetta.rosetta.protocols.filters.VectorPoseFilter, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) None

Set the vector of poses for the mover to act upon

C++: protocols::filters::VectorPoseFilter::set_poses(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

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

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

sfxn(*args, **kwargs)

Overloaded function.

  1. sfxn(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::recon_design::FitnessFilter::sfxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

  1. sfxn(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, : pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::recon_design::FitnessFilter::sfxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

threshold(*args, **kwargs)

Overloaded function.

  1. threshold(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter) -> float

C++: protocols::recon_design::FitnessFilter::threshold() const –> double

  1. threshold(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilter, : float) -> None

C++: protocols::recon_design::FitnessFilter::threshold(double) –> void

class pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator, : pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator) pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator

C++: protocols::recon_design::FitnessFilterCreator::operator=(const class protocols::recon_design::FitnessFilterCreator &) –> class protocols::recon_design::FitnessFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::recon_design::FitnessFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator) str

C++: protocols::recon_design::FitnessFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::recon_design::FitnessFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.recon_design.MSDMover

Bases: pyrosetta.rosetta.protocols.moves.VectorPoseMover

Multistate design mover used for RECON multistate design Takes in multiple poses, applies residue linking constraints based on sequence of all input poses and runs a design submover that has been specified in the tag Only accessible through recon application.

apply(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, pose: pyrosetta.rosetta.core.pose.Pose) None
Movers derived from VectorPoseMover must define two apply methods:

apply and apply_mpi, depending on whether the protocol is run in MPI or not Running in MPI will distribute each pose to a separate node, so the mover will operate on one pose

C++: protocols::recon_design::MSDMover::apply(class core::pose::Pose &) –> void

apply_linked_constraints(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, pose: pyrosetta.rosetta.core.pose.Pose, other_pose_sequences: pyrosetta.rosetta.utility.vector1_std_string, my_designable_residues: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t
Based on the sequence of the other poses, apply a residue type constraint to

encourage poses to adopt same sequence. Returns a COP of the constraints that were applied so they can be removed later

C++: protocols::recon_design::MSDMover::apply_linked_constraints(class core::pose::Pose &, class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> 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> > >

apply_mpi(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::recon_design::MSDMover::apply_mpi(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, : pyrosetta.rosetta.protocols.recon_design.MSDMover) pyrosetta.rosetta.protocols.recon_design.MSDMover

C++: protocols::recon_design::MSDMover::operator=(const class protocols::recon_design::MSDMover &) –> class protocols::recon_design::MSDMover &

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.recon_design.MSDMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::recon_design::MSDMover::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>

design_mover(*args, **kwargs)

Overloaded function.

  1. design_mover(self: pyrosetta.rosetta.protocols.recon_design.MSDMover) -> pyrosetta.rosetta.protocols.moves.Mover

Getters and setters

C++: protocols::recon_design::MSDMover::design_mover() –> class std::shared_ptr<class protocols::moves::Mover>

  1. design_mover(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, design_mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::recon_design::MSDMover::design_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

designable_residues(self: pyrosetta.rosetta.protocols.recon_design.MSDMover) pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: protocols::recon_design::MSDMover::designable_residues() –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

fresh_instance(self: pyrosetta.rosetta.protocols.recon_design.MSDMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::recon_design::MSDMover::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.recon_design.MSDMover) str

C++: protocols::recon_design::MSDMover::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 name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

Read options from RosettaScripts

C++: protocols::recon_design::MSDMover::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: utility::tag::XMLSchemaDefinition) None

Specify XML schema

C++: protocols::recon_design::MSDMover::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

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

resfiles(*args, **kwargs)

Overloaded function.

  1. resfiles(self: pyrosetta.rosetta.protocols.recon_design.MSDMover) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::recon_design::MSDMover::resfiles() –> class utility::vector1<std::string, class std::allocator<std::string > >

  1. resfiles(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, resfiles: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::recon_design::MSDMover::resfiles(class utility::vector1<std::string, class std::allocator<std::string > >) –> 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_poses(self: pyrosetta.rosetta.protocols.moves.VectorPoseMover, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) None

Set the vector of poses for the mover to act upon

C++: protocols::moves::VectorPoseMover::set_poses(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

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

Set the ‘type’ string

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

setup_mover(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, pose: pyrosetta.rosetta.core.pose.Pose) None
Initialize mover by checking that input poses were passed correctly,

a design mover was specified, and finding the pose given to apply() in the poses_ vector

C++: protocols::recon_design::MSDMover::setup_mover(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 &

weight(*args, **kwargs)

Overloaded function.

  1. weight(self: pyrosetta.rosetta.protocols.recon_design.MSDMover, weight: float) -> None

C++: protocols::recon_design::MSDMover::weight(double) –> void

  1. weight(self: pyrosetta.rosetta.protocols.recon_design.MSDMover) -> float

C++: protocols::recon_design::MSDMover::weight() –> double

class pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator, : pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator) pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator

C++: protocols::recon_design::MSDMoverCreator::operator=(const class protocols::recon_design::MSDMoverCreator &) –> class protocols::recon_design::MSDMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::recon_design::MSDMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator) str

C++: protocols::recon_design::MSDMoverCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::recon_design::MSDMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::recon_design::MSDMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.recon_design.find_pose_in_vector(pose: pyrosetta.rosetta.core.pose.Pose, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) int

Given a list of poses, find the index of a particular pose

C++: protocols::recon_design::find_pose_in_vector(const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> unsigned long

pyrosetta.rosetta.protocols.recon_design.get_candidate_AAs(other_pose_sequences: pyrosetta.rosetta.utility.vector1_std_string, position_no: int) pyrosetta.rosetta.utility.vector1_std_string
Based on a list of sequences from poses, get all the AAs present at

the position given by position_no

C++: protocols::recon_design::get_candidate_AAs(class utility::vector1<std::string, class std::allocator<std::string > >, unsigned long) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.protocols.recon_design.get_designable_residues(pose: pyrosetta.rosetta.core.pose.Pose, resfile: str) pyrosetta.rosetta.utility.vector1_unsigned_long

Based on a pose and a resfile, get the indices of all designable residues

C++: protocols::recon_design::get_designable_residues(class core::pose::Pose &, std::string) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.recon_design.get_designable_sequence(pose: pyrosetta.rosetta.core.pose.Pose, designable_residues: pyrosetta.rosetta.utility.vector1_unsigned_long) str
Based on a pose and the indices of all designable residues, get a

string of all designable AAs concatenated

C++: protocols::recon_design::get_designable_sequence(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> std::string