enzymatic_movers¶

Bindings for protocols::enzymatic_movers namespace

class pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

WiP

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) -> None
__init__(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, enzyme_family: str) -> None
__init__(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover, arg0: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.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, object_to_copy: 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.

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_std_allocator_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

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

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

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¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

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

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const class std::basic_string<char> &) –> void

set_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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) -> None
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(class std::basic_ostream<char> &) const –> void

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

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover¶

Bases: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover

WiP

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover) -> None
__init__(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover, arg0: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

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

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.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, object_to_copy: 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¶

Return the name of the 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.

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¶: 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_std_allocator_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

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

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

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_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::enzymatic_movers::GlycosyltransferaseMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

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

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const class std::basic_string<char> &) –> void

set_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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover) -> None
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(class std::basic_ostream<char> &) const –> void

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

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator¶

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

MoverCreator allowing the MoverFactory to create a GlycosyltransferaseMover

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.protocols.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¶

Static method that returns the keyname for performance reasons.

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

provide_xml_schema(self: pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::enzymatic_movers::GlycosyltransferaseMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void