dna¶

Bindings for protocols::dna namespace

class pyrosetta.rosetta.protocols.dna.DnaDesignDef¶

Bases: pybind11_builtins.pybind11_object

command-line dna_defs are of the format “C.501.ADE” they are parsed here into this little class for convenience

__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.dna.DnaDesignDef, : str) -> None
__init__(self: pyrosetta.rosetta.protocols.dna.DnaDesignDef, arg0: pyrosetta.rosetta.protocols.dna.DnaDesignDef) -> 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.dna.DnaDesignDef) → 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).

assign(self: pyrosetta.rosetta.protocols.dna.DnaDesignDef, : pyrosetta.rosetta.protocols.dna.DnaDesignDef) → pyrosetta.rosetta.protocols.dna.DnaDesignDef¶: C++: protocols::dna::DnaDesignDef::operator=(const class protocols::dna::DnaDesignDef &) –> class protocols::dna::DnaDesignDef &

class pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign¶

Bases: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover

wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework

__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.dna.DnaInterfaceMultiStateDesign) -> None
__init__(self: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign, arg0: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign) -> 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.simple_moves.PackRotamersMover) → 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.dna.DnaInterfaceMultiStateDesign, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::dna::DnaInterfaceMultiStateDesign::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign, : pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign) → pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign¶: C++: protocols::dna::DnaInterfaceMultiStateDesign::operator=(const class protocols::dna::DnaInterfaceMultiStateDesign &) –> class protocols::dna::DnaInterfaceMultiStateDesign &

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.dna.DnaInterfaceMultiStateDesign) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

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

complex_type_generator_for_pack_rotamers_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator¶: C++: protocols::simple_moves::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

copy_dna_chains(self: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign, : pyrosetta.rosetta.protocols.dna.DnaChains) → None¶: C++: protocols::dna::DnaInterfaceMultiStateDesign::copy_dna_chains(class std::shared_ptr<class protocols::dna::DnaChains>) –> void

copy_targeted_dna(self: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → None¶: C++: protocols::dna::DnaInterfaceMultiStateDesign::copy_targeted_dna(const class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &) –> void

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::dna::DnaInterfaceMultiStateDesign::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

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

fpd

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

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

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

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

get_name(self: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign) → str¶: C++: protocols::dna::DnaInterfaceMultiStateDesign::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

ig(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase¶: C++: protocols::simple_moves::PackRotamersMover::ig() const –> class std::shared_ptr<const class core::pack::interaction_graph::AnnealableGraphBase>

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::dna::DnaInterfaceMultiStateDesign::mover_name() –> std::string

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

nloop(*args, **kwargs)¶

Overloaded function.

nloop(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, nloop_in: int) -> None

C++: protocols::simple_moves::PackRotamersMover::nloop(unsigned long) –> void

nloop(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> int

C++: protocols::simple_moves::PackRotamersMover::nloop() const –> unsigned long

output_results(self: pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::dna::DnaInterfaceMultiStateDesign::output_results(class core::pose::Pose &) –> void

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

register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

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

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

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

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

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

rotamer_sets(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets¶: C++: protocols::simple_moves::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(*args, **kwargs)¶

Overloaded function.

score_function(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <sf>

example(s):

packmover.score_function(scorefxn)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

score_function(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the ScoreFunction

example(s):

packmover.score_function()

See Also:

PackRotamersMover PackRotamersMover.task

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

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

setter for poses contained for rms

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

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

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

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

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::PackRotamersMover::show(class std::basic_ostream<char> &) const –> void

task(*args, **kwargs)¶

Overloaded function.

task(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Sets the PackerTask to <t>

example(s):

packmover.task(task_pack)

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::simple_moves::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

task(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

Returns the PackerTask

example(s):

packmover.task()

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::simple_moves::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

Sets the TaskFactory to <tf>

example(s):

packmover.task_factory(task_design)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

Returns the TaskFactory

example(s):

packmover.task_factory()

See Also:

PackRotamersMover PackRotamersMover.task

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

task_is_valid(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool

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.dna.PositionType¶

Bases: pybind11_builtins.pybind11_object

basic struct for remembering position/type information before/during/after design

__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.dna.PositionType) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.dna.PositionType, arg0: int) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.dna.PositionType, arg0: int, arg1: pyrosetta.rosetta.core.chemical.ResidueType) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.dna.PositionType, pos: int, rt: pyrosetta.rosetta.core.chemical.ResidueType, design: bool) -> 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).

pyrosetta.rosetta.protocols.dna.add_constraints_from_file(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::dna::add_constraints_from_file(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.dna.argrot_dna_dis2(*args, **kwargs)¶

Overloaded function.

argrot_dna_dis2(pose: pyrosetta.rosetta.core.pose.Pose, presid: int, pres: pyrosetta.rosetta.core.conformation.Residue, dres: pyrosetta.rosetta.core.conformation.Residue, threshold: float) -> float
argrot_dna_dis2(pose: pyrosetta.rosetta.core.pose.Pose, presid: int, pres: pyrosetta.rosetta.core.conformation.Residue, dres: pyrosetta.rosetta.core.conformation.Residue, threshold: float, base_only: bool) -> float

arginine rotamer sweep at a protein residue to see if it should be considered a (potentially) ‘dna-contacting’ residue

ashworth

C++: protocols::dna::argrot_dna_dis2(const class core::pose::Pose &, unsigned long, const class core::conformation::Residue &, const class core::conformation::Residue &, double, bool) –> double

pyrosetta.rosetta.protocols.dna.checkpoint_cleanup() → None¶: C++: protocols::dna::checkpoint_cleanup() –> void

pyrosetta.rosetta.protocols.dna.close_to_dna(*args, **kwargs)¶

Overloaded function.

close_to_dna(pres: pyrosetta.rosetta.core.conformation.Residue, dres: pyrosetta.rosetta.core.conformation.Residue, cut2: float) -> bool
close_to_dna(pres: pyrosetta.rosetta.core.conformation.Residue, dres: pyrosetta.rosetta.core.conformation.Residue, cut2: float, base_only: bool) -> bool

checks c-beta (except glycine) to base atom-atom distances, not including ribose or phosphate backbone.

ashworth

C++: protocols::dna::close_to_dna(const class core::conformation::Residue &, const class core::conformation::Residue &, double, bool) –> bool

pyrosetta.rosetta.protocols.dna.contact_distance2(*args, **kwargs)¶

Overloaded function.

contact_distance2(a_begin: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, a_end: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_begin: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_end: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >) -> float
contact_distance2(a_begin: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, a_end: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_begin: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_end: __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, threshold: float) -> float

distance check for contact between two sets of atoms

ashworth

C++: protocols::dna::contact_distance2(class __gnu_cxx::__normal_iterator<const class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >, class __gnu_cxx::__normal_iterator<const class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >, class __gnu_cxx::__normal_iterator<const class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >, class __gnu_cxx::__normal_iterator<const class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >, double) –> double

pyrosetta.rosetta.protocols.dna.dna_base_partner(na: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.AA¶: C++: protocols::dna::dna_base_partner(const enum core::chemical::AA &) –> enum core::chemical::AA

pyrosetta.rosetta.protocols.dna.dna_comp_name_str(dna: str) → str¶

also consider using the dna_base_partner function below

ashworth

C++: protocols::dna::dna_comp_name_str(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.protocols.dna.dna_full_name3(name3: str) → str¶

intended to convert any DNA “threeletter code” into the full three-letter code. Note that this does not (necessarily) return the same thing as residue_type::name3 (which returns ” N” format as of Dec 2008)

C++: protocols::dna::dna_full_name3(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.protocols.dna.find_basepairs(*args, **kwargs)¶

Overloaded function.

find_basepairs(pose: pyrosetta.rosetta.core.pose.Pose, dna_chains: pyrosetta.rosetta.protocols.dna.DnaChains) -> None
find_basepairs(pose: pyrosetta.rosetta.core.pose.Pose, dna_chains: pyrosetta.rosetta.protocols.dna.DnaChains, include_unpaired: bool) -> None

DnaChains version, adapted from pbradley’s code. More paranoid geometry checks, in order to allow highly distorted basepairs without making mistakes

ashworth

C++: protocols::dna::find_basepairs(const class core::pose::Pose &, class protocols::dna::DnaChains &, bool) –> void

pyrosetta.rosetta.protocols.dna.load_checkpoint(pose: pyrosetta.rosetta.core.pose.Pose, iter: int) → None¶: C++: protocols::dna::load_checkpoint(class core::pose::Pose &, unsigned long &) –> void

pyrosetta.rosetta.protocols.dna.load_dna_design_defs_from_file(defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t, filename: str, pdb_prefix: str) → None¶: C++: protocols::dna::load_dna_design_defs_from_file(class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.dna.load_dna_design_defs_from_options(*args, **kwargs)¶

Overloaded function.

load_dna_design_defs_from_options(defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) -> None
load_dna_design_defs_from_options(defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t, pdb_prefix: str) -> None

C++: protocols::dna::load_dna_design_defs_from_options(class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &, class std::basic_string<char>) –> void

pyrosetta.rosetta.protocols.dna.load_dna_design_defs_from_strings(defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t, str_defs: pyrosetta.rosetta.utility.vector1_std_string) → None¶

loads command-line dna design definitions (shorthand alternative to using resfile)

option value is string vector: i.e. -dna_defs C.-6 C.-5 or -dna_defs C.-6.GUA C.-5.CYT

ashworth

C++: protocols::dna::load_dna_design_defs_from_strings(class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

pyrosetta.rosetta.protocols.dna.make_base_pair_aware_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree¶: C++: protocols::dna::make_base_pair_aware_fold_tree(const class core::pose::Pose &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.dna.make_subdirs(: str) → None¶: C++: protocols::dna::make_subdirs(const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.dna.not_already_connected(pose: pyrosetta.rosetta.core.pose.Pose, num_jumps: int, this_chain: str, other_chain: str, jump_pairs: ObjexxFCL::FArray2D<unsigned long>) → bool¶: C++: protocols::dna::not_already_connected(const class core::pose::Pose &, const unsigned long, const char, const char, class ObjexxFCL::FArray2D<unsigned long> &) –> bool

pyrosetta.rosetta.protocols.dna.restrict_to_single_sequence(rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, single_sequence: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → None¶

for packing a single sequence out of a RotamerSets that (potentially) represents sequence variability

ashworth

C++: protocols::dna::restrict_to_single_sequence(class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, class utility::vector0<int, class std::allocator<int> > &) –> void

pyrosetta.rosetta.protocols.dna.set_base_segment_chainbreak_constraints(pose: pyrosetta.rosetta.core.pose.Pose, this_base: int, end_base: int) → None¶: C++: protocols::dna::set_base_segment_chainbreak_constraints(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.dna.substitute_residue(pose: pyrosetta.rosetta.core.pose.Pose, index: int, new_type: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: protocols::dna::substitute_residue(class core::pose::Pose &, unsigned long, const class core::chemical::ResidueType &) –> void

pyrosetta.rosetta.protocols.dna.write_checkpoint(pose: pyrosetta.rosetta.core.pose.Pose, iter: int) → None¶: C++: protocols::dna::write_checkpoint(class core::pose::Pose &, unsigned long) –> void

pyrosetta.rosetta.protocols.dna.z_axis_dist(pres: pyrosetta.rosetta.core.conformation.Residue, dres: pyrosetta.rosetta.core.conformation.Residue) → float¶

A sanity check for the arginine rotamer screen. Can prevent the design of positions that are best left alone because they are too far away along the helical axis (‘laterally’).

ashworth

C++: protocols::dna::z_axis_dist(const class core::conformation::Residue &, const class core::conformation::Residue &) –> double