enzymatic_movers

Bindings for protocols::enzymatic_movers namespace

class pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover

Bases: EnzymaticMover

This Mover simulates the activity of a virtual DNA methyltransferase enzyme on a Pose by methylating a nucleic-acid residue at a biologically relevant sequon position.

apply(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the corresponding move to <input_pose>.

C++: protocols::enzymatic_movers::EnzymaticMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover, : pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover) → pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover

C++: protocols::enzymatic_movers::DNAMethyltransferaseMover::operator=(const class protocols::enzymatic_movers::DNAMethyltransferaseMover &) –> class protocols::enzymatic_movers::DNAMethyltransferaseMover &

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.enzymatic_movers.DNAMethyltransferaseMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::enzymatic_movers::DNAMethyltransferaseMover::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>

ensure_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Definitely modify this site, if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::ensure_site(unsigned long) –> void

exclude_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Do not perform a reaction at this site, even if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::exclude_site(unsigned long) –> void

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

C++: protocols::enzymatic_movers::DNAMethyltransferaseMover::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_co_substrate(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the requested cosubstrate of this enzymatic reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::get_co_substrate(const unsigned long) const –> const std::string &

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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → float

Get the efficiency of this enzyme.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::get_efficiency() const –> double

get_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_ensured_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Return the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme() const –> std::string

get_enzyme_family(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the family name of this simulated enzyme.

This EnzymaticMover is a member of this enyzme family.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme_family() const –> std::string

get_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_excluded_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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_n_co_substrates(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_co_substrates() const –> unsigned long

get_n_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_reactive_sites() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover) → str

Return the name of the Mover.

C++: protocols::enzymatic_movers::DNAMethyltransferaseMover::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_reactive_site_atom_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the atom name of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_atom_name(const unsigned long) const –> const std::string &

get_reactive_site_sequence_position(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → int

Return the sequence position of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_sequence_position(const unsigned long) const –> unsigned long

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_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the species name of this simulated enzyme.

This EnzymaticMover is limited to reactions known to occur in the returned species.

C++: protocols::enzymatic_movers::EnzymaticMover::get_species() const –> std::string

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_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 mover_name() → str

C++: protocols::enzymatic_movers::DNAMethyltransferaseMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

perform_all_reactions(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Allow this EnzymaticMover to be promiscuous, performing a random transfer from among its possible

co-substrates.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_all_reactions() –> void

perform_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Set this EnzymaticMover to perform only its major reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_major_reaction_only() –> void

performs_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → bool

Does this enzyme only perform its major reaction?

C++: protocols::enzymatic_movers::EnzymaticMover::performs_major_reaction_only() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::enzymatic_movers::DNAMethyltransferaseMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Register options with the option system.

C++: protocols::enzymatic_movers::DNAMethyltransferaseMover::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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, setting: float) → None

Directly set the efficiency of this enzyme, ignoring whatever is in the database.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::set_efficiency(double) –> void

set_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, ensured_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_ensured_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, enzyme_name: str) → None

Set the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_enzyme(const std::string &) –> void

set_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, excluded_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_excluded_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

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

setter for poses contained for rms

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

set_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_pose_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(const class core::pose::Pose &) –> void

set_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, species_name: str) → None

Set the species name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_species(const 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.enzymatic_movers.EnzymaticMover) -> None

2. show(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of EnzymaticMover for debugging purposes.

C++: protocols::enzymatic_movers::EnzymaticMover::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

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

Get the set ‘type’ string

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

static xml_schema_complex_type_generator() → utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::enzymatic_movers::EnzymaticMover::xml_schema_complex_type_generator() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

class pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator

Bases: MoverCreator

MoverCreator allowing the MoverFactory to create a DNAMethyltransferaseMover.

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator, : pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator) → pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator

C++: protocols::enzymatic_movers::DNAMethyltransferaseMoverCreator::operator=(const class protocols::enzymatic_movers::DNAMethyltransferaseMoverCreator &) –> class protocols::enzymatic_movers::DNAMethyltransferaseMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

Return an up-casted owning pointer (MoverOP) to the mover.

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

keyname(self: pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator) → str

Return the key name for the associated Mover (DNAMethyltransferaseMover).

C++: protocols::enzymatic_movers::DNAMethyltransferaseMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover

Bases: Mover

This is a base class for any Mover that modifies the sequence of a Pose in a way that simulates the action of an enzyme. Any Mover inheriting from this base class must provide an enzyme family corresponding to a directory of enzyme data and must implement the perform_reaction() method, which modifies, adds, or removes (a) Residue(s). The core machinery of this base class uses the enzymatic data to search for potential reaction sites.

apply(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the corresponding move to <input_pose>.

C++: protocols::enzymatic_movers::EnzymaticMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, : pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover

C++: protocols::enzymatic_movers::EnzymaticMover::operator=(const class protocols::enzymatic_movers::EnzymaticMover &) –> class protocols::enzymatic_movers::EnzymaticMover &

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.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::enzymatic_movers::EnzymaticMover::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>

ensure_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Definitely modify this site, if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::ensure_site(unsigned long) –> void

exclude_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Do not perform a reaction at this site, even if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::exclude_site(unsigned long) –> void

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

C++: protocols::enzymatic_movers::EnzymaticMover::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_co_substrate(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the requested cosubstrate of this enzymatic reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::get_co_substrate(const unsigned long) const –> const std::string &

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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → float

Get the efficiency of this enzyme.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::get_efficiency() const –> double

get_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_ensured_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Return the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme() const –> std::string

get_enzyme_family(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the family name of this simulated enzyme.

This EnzymaticMover is a member of this enyzme family.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme_family() const –> std::string

get_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_excluded_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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_n_co_substrates(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_co_substrates() const –> unsigned long

get_n_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_reactive_sites() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Return the name of the Mover.

C++: protocols::enzymatic_movers::EnzymaticMover::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_reactive_site_atom_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the atom name of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_atom_name(const unsigned long) const –> const std::string &

get_reactive_site_sequence_position(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → int

Return the sequence position of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_sequence_position(const unsigned long) const –> unsigned long

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_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the species name of this simulated enzyme.

This EnzymaticMover is limited to reactions known to occur in the returned species.

C++: protocols::enzymatic_movers::EnzymaticMover::get_species() const –> std::string

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_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.enzymatic_movers.EnzymaticMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

perform_all_reactions(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Allow this EnzymaticMover to be promiscuous, performing a random transfer from among its possible

co-substrates.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_all_reactions() –> void

perform_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Set this EnzymaticMover to perform only its major reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_major_reaction_only() –> void

performs_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → bool

Does this enzyme only perform its major reaction?

C++: protocols::enzymatic_movers::EnzymaticMover::performs_major_reaction_only() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

static register_options() → None

Register options with the option system.

C++: protocols::enzymatic_movers::EnzymaticMover::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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, setting: float) → None

Directly set the efficiency of this enzyme, ignoring whatever is in the database.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::set_efficiency(double) –> void

set_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, ensured_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_ensured_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, enzyme_name: str) → None

Set the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_enzyme(const std::string &) –> void

set_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, excluded_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_excluded_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

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

setter for poses contained for rms

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

set_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_pose_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(const class core::pose::Pose &) –> void

set_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, species_name: str) → None

Set the species name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_species(const 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.enzymatic_movers.EnzymaticMover) -> None

2. show(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of EnzymaticMover for debugging purposes.

C++: protocols::enzymatic_movers::EnzymaticMover::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

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

Get the set ‘type’ string

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

static xml_schema_complex_type_generator() → utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::enzymatic_movers::EnzymaticMover::xml_schema_complex_type_generator() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

class pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover

Bases: EnzymaticMover

This Mover simulates the activity of a virtual glycosyltransferase enzyme on a Pose by glycosylating a residue at a biologically relevant sequon position.

apply(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the corresponding move to <input_pose>.

C++: protocols::enzymatic_movers::EnzymaticMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover, : pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover) → pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover

C++: protocols::enzymatic_movers::GlycosyltransferaseMover::operator=(const class protocols::enzymatic_movers::GlycosyltransferaseMover &) –> class protocols::enzymatic_movers::GlycosyltransferaseMover &

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.enzymatic_movers.GlycosyltransferaseMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::enzymatic_movers::GlycosyltransferaseMover::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>

ensure_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Definitely modify this site, if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::ensure_site(unsigned long) –> void

exclude_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Do not perform a reaction at this site, even if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::exclude_site(unsigned long) –> void

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

C++: protocols::enzymatic_movers::GlycosyltransferaseMover::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_co_substrate(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the requested cosubstrate of this enzymatic reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::get_co_substrate(const unsigned long) const –> const std::string &

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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → float

Get the efficiency of this enzyme.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::get_efficiency() const –> double

get_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_ensured_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Return the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme() const –> std::string

get_enzyme_family(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the family name of this simulated enzyme.

This EnzymaticMover is a member of this enyzme family.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme_family() const –> std::string

get_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_excluded_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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_n_co_substrates(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_co_substrates() const –> unsigned long

get_n_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_reactive_sites() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover) → str

Return the name of the Mover.

C++: protocols::enzymatic_movers::GlycosyltransferaseMover::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_reactive_site_atom_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the atom name of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_atom_name(const unsigned long) const –> const std::string &

get_reactive_site_sequence_position(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → int

Return the sequence position of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_sequence_position(const unsigned long) const –> unsigned long

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_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the species name of this simulated enzyme.

This EnzymaticMover is limited to reactions known to occur in the returned species.

C++: protocols::enzymatic_movers::EnzymaticMover::get_species() const –> std::string

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_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 mover_name() → str

C++: protocols::enzymatic_movers::GlycosyltransferaseMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

perform_all_reactions(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Allow this EnzymaticMover to be promiscuous, performing a random transfer from among its possible

co-substrates.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_all_reactions() –> void

perform_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Set this EnzymaticMover to perform only its major reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_major_reaction_only() –> void

performs_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → bool

Does this enzyme only perform its major reaction?

C++: protocols::enzymatic_movers::EnzymaticMover::performs_major_reaction_only() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::enzymatic_movers::GlycosyltransferaseMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Register options with the option system.

C++: protocols::enzymatic_movers::GlycosyltransferaseMover::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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, setting: float) → None

Directly set the efficiency of this enzyme, ignoring whatever is in the database.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::set_efficiency(double) –> void

set_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, ensured_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_ensured_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, enzyme_name: str) → None

Set the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_enzyme(const std::string &) –> void

set_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, excluded_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_excluded_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

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

setter for poses contained for rms

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

set_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_pose_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(const class core::pose::Pose &) –> void

set_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, species_name: str) → None

Set the species name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_species(const 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.enzymatic_movers.EnzymaticMover) -> None

2. show(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of EnzymaticMover for debugging purposes.

C++: protocols::enzymatic_movers::EnzymaticMover::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

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

Get the set ‘type’ string

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

static xml_schema_complex_type_generator() → utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::enzymatic_movers::EnzymaticMover::xml_schema_complex_type_generator() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

class pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator

Bases: MoverCreator

MoverCreator allowing the MoverFactory to create a GlycosyltransferaseMover

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator, : pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator) → pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator

C++: protocols::enzymatic_movers::GlycosyltransferaseMoverCreator::operator=(const class protocols::enzymatic_movers::GlycosyltransferaseMoverCreator &) –> class protocols::enzymatic_movers::GlycosyltransferaseMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

Return an up-casted owning pointer (MoverOP) to the mover.

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

keyname(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator) → str

Return the key name for the associated Mover (GlycosyltransferaseMover).

C++: protocols::enzymatic_movers::GlycosyltransferaseMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover

Bases: EnzymaticMover

This Mover simulates the activity of a virtual kinase enzyme on a Pose by phosphorylating a residue at a biologically relevant sequon position.

apply(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the corresponding move to <input_pose>.

C++: protocols::enzymatic_movers::EnzymaticMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover, : pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover) → pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover

C++: protocols::enzymatic_movers::KinaseMover::operator=(const class protocols::enzymatic_movers::KinaseMover &) –> class protocols::enzymatic_movers::KinaseMover &

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.enzymatic_movers.KinaseMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::enzymatic_movers::KinaseMover::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>

ensure_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Definitely modify this site, if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::ensure_site(unsigned long) –> void

exclude_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Do not perform a reaction at this site, even if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::exclude_site(unsigned long) –> void

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

C++: protocols::enzymatic_movers::KinaseMover::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_co_substrate(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the requested cosubstrate of this enzymatic reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::get_co_substrate(const unsigned long) const –> const std::string &

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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → float

Get the efficiency of this enzyme.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::get_efficiency() const –> double

get_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_ensured_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Return the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme() const –> std::string

get_enzyme_family(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the family name of this simulated enzyme.

This EnzymaticMover is a member of this enyzme family.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme_family() const –> std::string

get_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_excluded_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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_n_co_substrates(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_co_substrates() const –> unsigned long

get_n_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_reactive_sites() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover) → str

Return the name of the Mover.

C++: protocols::enzymatic_movers::KinaseMover::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_reactive_site_atom_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the atom name of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_atom_name(const unsigned long) const –> const std::string &

get_reactive_site_sequence_position(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → int

Return the sequence position of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_sequence_position(const unsigned long) const –> unsigned long

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_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the species name of this simulated enzyme.

This EnzymaticMover is limited to reactions known to occur in the returned species.

C++: protocols::enzymatic_movers::EnzymaticMover::get_species() const –> std::string

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_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 mover_name() → str

C++: protocols::enzymatic_movers::KinaseMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

perform_all_reactions(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Allow this EnzymaticMover to be promiscuous, performing a random transfer from among its possible

co-substrates.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_all_reactions() –> void

perform_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Set this EnzymaticMover to perform only its major reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_major_reaction_only() –> void

performs_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → bool

Does this enzyme only perform its major reaction?

C++: protocols::enzymatic_movers::EnzymaticMover::performs_major_reaction_only() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::enzymatic_movers::KinaseMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Register options with the option system.

C++: protocols::enzymatic_movers::KinaseMover::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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, setting: float) → None

Directly set the efficiency of this enzyme, ignoring whatever is in the database.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::set_efficiency(double) –> void

set_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, ensured_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_ensured_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, enzyme_name: str) → None

Set the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_enzyme(const std::string &) –> void

set_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, excluded_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_excluded_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

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

setter for poses contained for rms

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

set_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_pose_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(const class core::pose::Pose &) –> void

set_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, species_name: str) → None

Set the species name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_species(const 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.enzymatic_movers.EnzymaticMover) -> None

2. show(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of EnzymaticMover for debugging purposes.

C++: protocols::enzymatic_movers::EnzymaticMover::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

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

Get the set ‘type’ string

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

static xml_schema_complex_type_generator() → utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::enzymatic_movers::EnzymaticMover::xml_schema_complex_type_generator() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

class pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator

Bases: MoverCreator

MoverCreator allowing the MoverFactory to create a KinaseMover

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator, : pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator) → pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator

C++: protocols::enzymatic_movers::KinaseMoverCreator::operator=(const class protocols::enzymatic_movers::KinaseMoverCreator &) –> class protocols::enzymatic_movers::KinaseMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

Return an up-casted owning pointer (MoverOP) to the mover.

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

keyname(self: pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator) → str

Return the key name for the associated Mover (KinaseMover).

C++: protocols::enzymatic_movers::KinaseMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover

Bases: EnzymaticMover

This Mover simulates the activity of a virtual N-terminal acetyltransferase enzyme on a Pose by acetylating the N-terminus of a peptide at a biologically relevant sequon position.

apply(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the corresponding move to <input_pose>.

C++: protocols::enzymatic_movers::EnzymaticMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover, : pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover) → pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::operator=(const class protocols::enzymatic_movers::NTerminalAcetyltransferaseMover &) –> class protocols::enzymatic_movers::NTerminalAcetyltransferaseMover &

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.enzymatic_movers.NTerminalAcetyltransferaseMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::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>

ensure_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Definitely modify this site, if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::ensure_site(unsigned long) –> void

exclude_site(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, seqpos: int) → None

Do not perform a reaction at this site, even if it is within a consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::exclude_site(unsigned long) –> void

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

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::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_co_substrate(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the requested cosubstrate of this enzymatic reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::get_co_substrate(const unsigned long) const –> const std::string &

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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → float

Get the efficiency of this enzyme.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::get_efficiency() const –> double

get_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_ensured_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Return the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme() const –> std::string

get_enzyme_family(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the family name of this simulated enzyme.

This EnzymaticMover is a member of this enyzme family.

C++: protocols::enzymatic_movers::EnzymaticMover::get_enzyme_family() const –> std::string

get_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::get_excluded_sites() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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_n_co_substrates(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_co_substrates() const –> unsigned long

get_n_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → int

Return the current number of reactive sites.

C++: protocols::enzymatic_movers::EnzymaticMover::get_n_reactive_sites() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover) → str

Return the name of the Mover.

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::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_reactive_site_atom_name(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → str

Return the atom name of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_atom_name(const unsigned long) const –> const std::string &

get_reactive_site_sequence_position(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, index: int) → int

Return the sequence position of the requested reactive site.

C++: protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_sequence_position(const unsigned long) const –> unsigned long

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_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → str

Get the species name of this simulated enzyme.

This EnzymaticMover is limited to reactions known to occur in the returned species.

C++: protocols::enzymatic_movers::EnzymaticMover::get_species() const –> std::string

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_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 mover_name() → str

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

perform_all_reactions(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Allow this EnzymaticMover to be promiscuous, performing a random transfer from among its possible

co-substrates.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_all_reactions() –> void

perform_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → None

Set this EnzymaticMover to perform only its major reaction.

C++: protocols::enzymatic_movers::EnzymaticMover::perform_major_reaction_only() –> void

performs_major_reaction_only(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) → bool

Does this enzyme only perform its major reaction?

C++: protocols::enzymatic_movers::EnzymaticMover::performs_major_reaction_only() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Register options with the option system.

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::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_efficiency(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, setting: float) → None

Directly set the efficiency of this enzyme, ignoring whatever is in the database.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of

the time.

C++: protocols::enzymatic_movers::EnzymaticMover::set_efficiency(double) –> void

set_ensured_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, ensured_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are guaranteed to be modified, if they are within a consensus

sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_ensured_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_enzyme(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, enzyme_name: str) → None

Set the specific name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_enzyme(const std::string &) –> void

set_excluded_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, excluded_sites: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Pass a list of sequence positions that are forbidden from being modified, even if they are within a

consensus sequence match for this enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_excluded_sites(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

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

setter for poses contained for rms

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

set_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_pose_reactive_sites(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(const class core::pose::Pose &) –> void

set_species(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, species_name: str) → None

Set the species name of this simulated enzyme.

C++: protocols::enzymatic_movers::EnzymaticMover::set_species(const 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.enzymatic_movers.EnzymaticMover) -> None

2. show(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of EnzymaticMover for debugging purposes.

C++: protocols::enzymatic_movers::EnzymaticMover::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

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

Get the set ‘type’ string

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

static xml_schema_complex_type_generator() → utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::enzymatic_movers::EnzymaticMover::xml_schema_complex_type_generator() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

class pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator

Bases: MoverCreator

MoverCreator allowing the MoverFactory to create an NTerminalAcetyltransferaseMover.

assign(self: pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator, : pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator) → pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMoverCreator::operator=(const class protocols::enzymatic_movers::NTerminalAcetyltransferaseMoverCreator &) –> class protocols::enzymatic_movers::NTerminalAcetyltransferaseMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

Return an up-casted owning pointer (MoverOP) to the mover.

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

keyname(self: pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator) → str

Return the key name for the associated Mover (NTerminalAcetyltransferaseMover).

C++: protocols::enzymatic_movers::NTerminalAcetyltransferaseMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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