loophash

Bindings for protocols::loophash namespace

class pyrosetta.rosetta.protocols.loophash.FastGapMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much.

__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.

1. __init__(self: pyrosetta.rosetta.protocols.loophash.FastGapMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.loophash.FastGapMover, arg0: pyrosetta.rosetta.protocols.loophash.FastGapMover) -> 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.loophash.FastGapMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loophash::FastGapMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loophash.FastGapMover, : pyrosetta.rosetta.protocols.loophash.FastGapMover) → pyrosetta.rosetta.protocols.loophash.FastGapMover

C++: protocols::loophash::FastGapMover::operator=(const class protocols::loophash::FastGapMover &) –> class protocols::loophash::FastGapMover &

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.loophash.FastGapMover) → pyrosetta.rosetta.protocols.moves.Mover

clone has to be overridden only if clone invocation is expected.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.loophash.FastGapMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loophash::FastGapMover::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.loophash.FastGapMover) → str

C++: protocols::loophash::FastGapMover::get_name() const –> std::string

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

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

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

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

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

max_rms(self: pyrosetta.rosetta.protocols.loophash.FastGapMover, setting: float) → pyrosetta.rosetta.protocols.loophash.FastGapMover

C++: protocols::loophash::FastGapMover::max_rms(const double) –> class protocols::loophash::FastGapMover &

min_rms(self: pyrosetta.rosetta.protocols.loophash.FastGapMover, setting: float) → pyrosetta.rosetta.protocols.loophash.FastGapMover

C++: protocols::loophash::FastGapMover::min_rms(const double) –> class protocols::loophash::FastGapMover &

name() → str

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

non_ideal(self: pyrosetta.rosetta.protocols.loophash.FastGapMover, setting: bool) → pyrosetta.rosetta.protocols.loophash.FastGapMover

C++: protocols::loophash::FastGapMover::non_ideal(const bool) –> class protocols::loophash::FastGapMover &

register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

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

////////////////////////////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.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.

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

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

2. 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.loophash.LeapIndex

Bases: pybind11_builtins.pybind11_object

The LeapIndex stores information about a particular Leap. It hold the oroiginal high precision rigid body transform

and an Index to a Backbone Database (BackboneDB) that has the actual phi psi angles. THe storage of the precise RT takes a

lot of space and may be deprecated at some point, since once it is hashed, it is rarely needed and can be recomputed if it is. Note that the length of the loop is not stored either, this is again done for saving memory, as huge lists of Leaps are typically created all with the same length. THe length is stored and handled by the owner of LeapIndex list. The LeapIndex does not store the actual backbone coordinates of the Leap. It merely contains an index (the BackboneIndex) which refers to a serial store of backbone triples (phi,psi, omega) which are stored somewhere else in a BackboneDB. THis is improtant to save memory storage since multiple Leaps cna share the same backbone triple and redundant storage would be hugely wasteful.

__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.loophash.LeapIndex) → 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).

class pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceLoader

%LoopHashLibraryLoader constructs a LoopHashLibrary instance from data provided by the %ResourceManager.

The %LoopHashLibraryLoader is given a LoopHashLibraryOptions containing a %vector of loop lengths from the ResourceManager. This information is then used to produce a LoopHashLibraryOP to return to the protocol.

__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.loophash.LoopHashLibraryLoader) → 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.loophash.LoopHashLibraryLoader, : pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader) → pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader

C++: protocols::loophash::LoopHashLibraryLoader::operator=(const class protocols::loophash::LoopHashLibraryLoader &) –> class protocols::loophash::LoopHashLibraryLoader &

default_options(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader) → pyrosetta.rosetta.basic.resource_manager.ResourceOptions

Return a ResourceOptionsOP with the default set of options.

C++: protocols::loophash::LoopHashLibraryLoader::default_options() const –> class std::shared_ptr<class basic::resource_manager::ResourceOptions>

class pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator

%LoopHashLibraryLoaderCreator allows the ResourceLoaderFactory to create a LoopHashLibraryLoader instance.

The LoopHashLibraryLoader class can be constructed from the string “LoopHashLibrary”, which enables a user to specify that this type of %resource is required for a particular %job in their XML input file.

__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.loophash.LoopHashLibraryLoaderCreator) → 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.loophash.LoopHashLibraryLoaderCreator, : pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator) → pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator

C++: protocols::loophash::LoopHashLibraryLoaderCreator::operator=(const class protocols::loophash::LoopHashLibraryLoaderCreator &) –> class protocols::loophash::LoopHashLibraryLoaderCreator &

create_resource_loader(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator) → pyrosetta.rosetta.basic.resource_manager.ResourceLoader

Return a up-casted owning pointer (ResourceLoaderOP) to the resource loader.

C++: protocols::loophash::LoopHashLibraryLoaderCreator::create_resource_loader() const –> class std::shared_ptr<class basic::resource_manager::ResourceLoader>

loader_type(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator) → str

Return the string identifier for the associated ResourceLoader (LoopHashLibrary).

C++: protocols::loophash::LoopHashLibraryLoaderCreator::loader_type() const –> std::string

class pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceOptions

%LoopHashLibraryOptions encapsulates the options associated with LoopHashLibrary %resources.

These options are read in from a resource definition file and each LoopHashLibrary resource has a corresponding %LoopHashLibraryOptions instance.

__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.

1. __init__(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions) -> None
2. __init__(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions, arg0: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions) -> 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.basic.resource_manager.ResourceOptions) → 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.loophash.LoopHashLibraryOptions, : pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions) → pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions

C++: protocols::loophash::LoopHashLibraryOptions::operator=(const class protocols::loophash::LoopHashLibraryOptions &) –> class protocols::loophash::LoopHashLibraryOptions &

loop_sizes(*args, **kwargs)

Overloaded function.

1. loop_sizes(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Return a %vector of loop sizes that will be used to construct a LoopHashLibrary.

C++: protocols::loophash::LoopHashLibraryOptions::loop_sizes() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

2. loop_sizes(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions, loop_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Set the loop sizes that will be used to construct a LoopHashLibrary to a %vector of loop lengths.

C++: protocols::loophash::LoopHashLibraryOptions::loop_sizes(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.basic.resource_manager.ResourceOptions) -> str

A name given to a particular ResourceOptions instance.

This function allows for better error message delivery.

C++: basic::resource_manager::ResourceOptions::name() const –> std::string

2. name(self: pyrosetta.rosetta.basic.resource_manager.ResourceOptions, setting: str) -> None

Set the name for this %ResoureOptions instance.

C++: basic::resource_manager::ResourceOptions::name(const class std::basic_string<char> &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions, tag: pyrosetta.rosetta.utility.tag.Tag) → None

Read the configuration of the LoopHashLibrary %resource from the tag generated from the resource definition

file.

C++: protocols::loophash::LoopHashLibraryOptions::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

show(self: pyrosetta.rosetta.basic.resource_manager.ResourceOptions, out: pyrosetta.rosetta.std.ostream) → None

Describe this instance to a given output stream

C++: basic::resource_manager::ResourceOptions::show(class std::basic_ostream<char> &) const –> void

type(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions) → str

Return the name of this class (LoopHashLibraryOptions).

C++: protocols::loophash::LoopHashLibraryOptions::type() const –> std::string

class pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator

%LoopHashLibraryOptionsCreator allows the ResourceLoaderFactory to create a LoopHashLibraryOptions instance.

The LoopHashLibraryOptions class can be constructed from the string “LoopHashLibraryOptions”, which enables a user to configure a LoopHashLibrary %resource in his/her resource definitions file.

__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.loophash.LoopHashLibraryOptionsCreator) → 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.loophash.LoopHashLibraryOptionsCreator, : pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator) → pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator

C++: protocols::loophash::LoopHashLibraryOptionsCreator::operator=(const class protocols::loophash::LoopHashLibraryOptionsCreator &) –> class protocols::loophash::LoopHashLibraryOptionsCreator &

create_options(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator) → pyrosetta.rosetta.basic.resource_manager.ResourceOptions

Return a up-casted owning pointer (ResourceOptionsOP) to the resource options.

C++: protocols::loophash::LoopHashLibraryOptionsCreator::create_options() const –> class std::shared_ptr<class basic::resource_manager::ResourceOptions>

options_type(self: pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator) → str

Return the string identifier for the associated ResourceOptions (LoopHashLibraryOptions).

C++: protocols::loophash::LoopHashLibraryOptionsCreator::options_type() const –> std::string

class pyrosetta.rosetta.protocols.loophash.LoopHashMap

Bases: pybind11_builtins.pybind11_object

the loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates.

__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.

1. __init__(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, loop_size: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, arg0: pyrosetta.rosetta.protocols.loophash.LoopHashMap) -> 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).

add_leap(*args, **kwargs)

Overloaded function.

1. add_leap(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, leap_index: pyrosetta.rosetta.protocols.loophash.LeapIndex, transform: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) -> None

Add a leap/loop to the HashMap

C++: protocols::loophash::LoopHashMap::add_leap(const struct protocols::loophash::LeapIndex &, class utility::fixedsizearray1<double, 6> &) –> void

2. add_leap(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, leap_index: pyrosetta.rosetta.protocols.loophash.LeapIndex, key: int) -> None

Add a leap/loop to the HashMap with a key, skipping hashing

C++: protocols::loophash::LoopHashMap::add_leap(const struct protocols::loophash::LeapIndex &, unsigned long) –> void

add_legacyleap(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, legacyleap_index: pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex) → None

Add an legacy leap/loop to the HashMap

C++: protocols::loophash::LoopHashMap::add_legacyleap(const struct protocols::loophash::LegacyLeapIndex &) –> void

assign(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, other: pyrosetta.rosetta.protocols.loophash.LoopHashMap) → pyrosetta.rosetta.protocols.loophash.LoopHashMap

C++: protocols::loophash::LoopHashMap::operator=(const class protocols::loophash::LoopHashMap &) –> class protocols::loophash::LoopHashMap &

get_loop_size(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap) → int

Query the loopsize of this LoopHashMap

C++: protocols::loophash::LoopHashMap::get_loop_size() const –> unsigned long

get_peptide(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, index: int) → pyrosetta.rosetta.protocols.loophash.LeapIndex

Obtain an index to a given peptide saved

C++: protocols::loophash::LoopHashMap::get_peptide(unsigned long) –> const struct protocols::loophash::LeapIndex &

lookup(*args, **kwargs)

Overloaded function.

1. lookup(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, transform: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t, result: pyrosetta.rosetta.std.vector_unsigned_long) -> None

Append to a bucket of vectors in the appropriate bin, lookup by transform

C++: protocols::loophash::LoopHashMap::lookup(class utility::fixedsizearray1<double, 6>, class std::vector<unsigned long, class std::allocator<unsigned long> > &) –> void

2. lookup(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, index: int, result: pyrosetta.rosetta.std.vector_unsigned_long) -> None

Append to a bucket of vectors in the appropriate bin, lookup by bin index

Using core::Size instead of boost::uinst64_t

C++: protocols::loophash::LoopHashMap::lookup(unsigned long, class std::vector<unsigned long, class std::allocator<unsigned long> > &) –> void

lookup_withkey(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, key: int, result: pyrosetta.rosetta.std.vector_unsigned_long) → None

Return a vector of loops with equal keys given a key

C++: protocols::loophash::LoopHashMap::lookup_withkey(unsigned long, class std::vector<unsigned long, class std::allocator<unsigned long> > &) –> void

mem_foot_print(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap) → None

Return the memory usage of this class

C++: protocols::loophash::LoopHashMap::mem_foot_print() –> void

n_loops(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap) → int

C++: protocols::loophash::LoopHashMap::n_loops() const –> unsigned long

radial_count(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, radius: int, center: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → int

count hits in the appropriate bin, radial lookup by transform

C++: protocols::loophash::LoopHashMap::radial_count(unsigned long, class utility::fixedsizearray1<double, 6>) const –> unsigned long

radial_lookup(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, radius: int, transform: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t, result: pyrosetta.rosetta.std.vector_unsigned_long) → None

Append to a bucket of vectors in the appropriate bin, radial lookup by transform

C++: protocols::loophash::LoopHashMap::radial_lookup(unsigned long, class utility::fixedsizearray1<double, 6>, class std::vector<unsigned long, class std::allocator<unsigned long> > &) –> void

radial_lookup_withkey(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, key: int, radius: int, result: pyrosetta.rosetta.std.vector_unsigned_long) → None

Return a vector of loops with equal keys given a key

C++: protocols::loophash::LoopHashMap::radial_lookup_withkey(unsigned long, unsigned long, class std::vector<unsigned long, class std::allocator<unsigned long> > &) –> void

read_db(*args, **kwargs)

Overloaded function.

1. read_db(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, filename: str, loopdb_range: Tuple[int, int], homolog_index: pyrosetta.rosetta.std.map_unsigned_long_bool) -> None

Basic IO functionality - allows reading and writing text states to/from disk

C++: protocols::loophash::LoopHashMap::read_db(class std::basic_string<char>, struct std::pair<unsigned long, unsigned long>, class std::map<unsigned long, bool, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, bool> > > &) –> void

2. read_db(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, filename: str) -> None

C++: protocols::loophash::LoopHashMap::read_db(class std::basic_string<char>) –> void

read_legacydb(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, filename: str) → None

Reads legacy binary dbs

C++: protocols::loophash::LoopHashMap::read_legacydb(class std::basic_string<char>) –> void

return_key(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, bb_index: int) → int

Returns a hashmap key given a member of a bucket

Don’t think boost implements this, have to manually look it up

C++: protocols::loophash::LoopHashMap::return_key(unsigned long) –> unsigned long

sort(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap) → None

Sorts the loopdb_ by leap_index.index

C++: protocols::loophash::LoopHashMap::sort() –> void

write_db(self: pyrosetta.rosetta.protocols.loophash.LoopHashMap, filename: str) → None

Basic IO functionality - allows reading and writing text states to/from disk

C++: protocols::loophash::LoopHashMap::write_db(class std::basic_string<char>) –> void

pyrosetta.rosetta.protocols.loophash.RealAngleToShort(angle: float) → int

C++: protocols::loophash::RealAngleToShort(double) –> short

pyrosetta.rosetta.protocols.loophash.ShortToRealAngle(angle: int) → float

C++: protocols::loophash::ShortToRealAngle(short) –> double

pyrosetta.rosetta.protocols.loophash.get_rmsd(bs1: pyrosetta.rosetta.protocols.loophash.BackboneSegment, bs2: pyrosetta.rosetta.protocols.loophash.BackboneSegment) → float

C++: protocols::loophash::get_rmsd(const class protocols::loophash::BackboneSegment &, const class protocols::loophash::BackboneSegment &) –> double

pyrosetta.rosetta.protocols.loophash.get_rt_over_leap(orig_pose: pyrosetta.rosetta.core.pose.Pose, ir: int, jr: int, rt_6: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → bool

This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues.

Returns true is successful or false if something went haywire and one should just ignore this loop (this can happen at the ends)

C++: protocols::loophash::get_rt_over_leap(const class core::pose::Pose &, unsigned long, unsigned long, class utility::fixedsizearray1<double, 6> &) –> bool

pyrosetta.rosetta.protocols.loophash.get_rt_over_leap_fast(pose: pyrosetta.rosetta.core.pose.Pose, ir: int, jr: int, rt_6: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → bool

This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues

Returns true is successful or false if something went haywire and one should just ignore this loop (this can happen at the ends)

THe difference between this and the get_rt_over_leap function is that this version doesnt make a copy of the pose which makes it faster.

However this means that the pose passed cannot be a const pose, even though the function restores the fold tree afterwards..

C++: protocols::loophash::get_rt_over_leap_fast(class core::pose::Pose &, unsigned long, unsigned long, class utility::fixedsizearray1<double, 6> &) –> bool

pyrosetta.rosetta.protocols.loophash.get_rt_over_leap_without_foldtree_bs(pose: pyrosetta.rosetta.core.pose.Pose, ir: int, jr: int, rt_6: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → bool

This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues.

C++: protocols::loophash::get_rt_over_leap_without_foldtree_bs(const class core::pose::Pose &, unsigned long, unsigned long, class utility::fixedsizearray1<double, 6> &) –> bool

pyrosetta.rosetta.protocols.loophash.loophash_main() → int

C++: protocols::loophash::loophash_main() –> int