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- builtins.object
-
- FallbackConfiguration
- FallbackConfigurationCreator
- JobOptions
- ResourceConfiguration
- ResourceLoader
- ResourceLoaderCreator
- ResourceLocator
- ResourceLocatorCreator
- ResourceManager
-
- LazyResourceManager
- ResourceManagerCreator
- ResourceOptions
- ResourceOptionsCreator
- ResourceStream
- rosetta.utility.SingletonBase_basic_resource_manager_FallbackConfigurationFactory_t(builtins.object)
-
- FallbackConfigurationFactory
- rosetta.utility.SingletonBase_basic_resource_manager_ResourceLoaderFactory_t(builtins.object)
-
- ResourceLoaderFactory
- rosetta.utility.SingletonBase_basic_resource_manager_ResourceLocatorFactory_t(builtins.object)
-
- ResourceLocatorFactory
- rosetta.utility.SingletonBase_basic_resource_manager_ResourceManagerFactory_t(builtins.object)
-
- ResourceManagerFactory
- rosetta.utility.SingletonBase_basic_resource_manager_ResourceOptionsFactory_t(builtins.object)
-
- ResourceOptionsFactory
class FallbackConfiguration(builtins.object) |
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The %FallbackConfiguration class describes how a resource should
be created if the ResourceManager is not being used, i.e., if resources
have been specified through flags on the command line instead of through
a resource-definition file.
A protocol will still query the ResourceManager
for its desired resource in such a case (by its "resource_description")
and if no resource has been provided for that description, then the
ResourceManager will ask the FallbackConfigurationFactory for the
%FallbackConfiguration that has been registered for that resource
description (this registration logic is handled by the
FallbackConfigurationCreator) and ask it to provide the information
necessary to create the appropriate resource from the command line.
For example, a user can define the loop they are interested in modeling to
the loop-modeling protocol via the LoopsFileData resource. The loop modeling
protocol once was but is no longer responsible for opening a text file
and creating a LoopsFileData object from that text file; instead it asks the
ResourceManager directly for the resource. For the sake of backwards
compatibility, the ResourceManager must have some way of creating a
LoopsFileData object from the command line. If someone is using the loop modeling
application, but does not provide a resource definition, then the
LoopsFileFallbackConfiguration (derived from %FallbackConfiguration)
will be called upon by the ResourceManager for three things:
1) the name of the ResourceLoader to use to create the resource ("LoopsFile"),
2) the locator_id for the Resource (which it goes to the command line to find), and
3) a ResourceOptionsOP which is either null (meaning "use the default") or is in
some way initialized with options from the command line. With these three bits, the
ResourceManager will go the appropriate ResourceLoader and request the construction
of the Resource as usual, opening the file using the default ResourceLocator
(for the JD2ResourceManager, this is the FileSystemResourceLocator).
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.basic.resource_manager.FallbackConfiguration) -> NoneType
2. __init__(rosetta.basic.resource_manager.FallbackConfiguration, rosetta.basic.resource_manager.FallbackConfiguration) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.basic.resource_manager.FallbackConfiguration, : rosetta.basic.resource_manager.FallbackConfiguration) -> rosetta.basic.resource_manager.FallbackConfiguration
- could_not_create_resource_error_message(...) from builtins.PyCapsule
- could_not_create_resource_error_message(self : rosetta.basic.resource_manager.FallbackConfiguration, desc : str) -> str
If the %FallbackConfiguration has not been provided the appropriate set
of command line flags needed to construct the Resource given the
resource description, then return an error message informing the user
what options must be provided on the command line.
- fallback_specified(...) from builtins.PyCapsule
- fallback_specified(self : rosetta.basic.resource_manager.FallbackConfiguration, desc : str) -> bool
Return true if a fallback been provided for the given resource description.
It is possible that the fallback configuration would be unable to deliver
a requested resource, e.g. if the appropriate command line option has not been provided.
- get_locator_id(...) from builtins.PyCapsule
- get_locator_id(self : rosetta.basic.resource_manager.FallbackConfiguration, desc : str) -> str
Return the locator id that the resource locator should use to
find the data used to construct the desired resource - e.g. the file name.
- get_resource_loader(...) from builtins.PyCapsule
- get_resource_loader(self : rosetta.basic.resource_manager.FallbackConfiguration, desc : str) -> str
Return the name of the resource loader that should be used to instantiate the
desired resource
- get_resource_options(...) from builtins.PyCapsule
- get_resource_options(self : rosetta.basic.resource_manager.FallbackConfiguration, desc : str) -> rosetta.basic.resource_manager.ResourceOptions
Return a pointer to the ResourceOptions object that the
ResourceLoader will use to instantiate the given resource. Return 0
if the default ResourceOptions specified by the appropriate ResourceLoader
should be used.
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class FallbackConfigurationFactory(rosetta.utility.SingletonBase_basic_resource_manager_FallbackConfigurationFactory_t) |
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The %FallbackConfigurationFactory is a singleton factory with which
FallbackConfigurationCreator objects should be registered. The "fallback" system
serves as a mechanism for preserving command-line functionality even
while switching more protocols from requesting resources from the
ResourceManager rather than reading directly from the command line.
When a resource with a particular resource-description string is requested
from the ResourceManager, and the ResourceManager does not have any instructions
on how to load a resource matching that description, then the ResourceManager
will then ask the FallbackConfigurationFactory for help. The
FallbackConfigurationFactory can first answer "does this resource description
match any resource descriptions for which you have a registered
FallbackConfigurationCreator?" and if the answer is "yes", then the
ResourceManager can request that FallbackConfigurationCreator and ask,
first, if it is able to construct a resource (FallbackConfigurations
often read from the command line, and it's possible that the required
flags have not been put on the command line), and if so, then request data
from the FallbackConfiguration needed to contruct that resource.
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- Method resolution order:
- FallbackConfigurationFactory
- rosetta.utility.SingletonBase_basic_resource_manager_FallbackConfigurationFactory_t
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- create_fallback_configuration(...) from builtins.PyCapsule
- create_fallback_configuration(self : rosetta.basic.resource_manager.FallbackConfigurationFactory, resource_description : str) -> rosetta.basic.resource_manager.FallbackConfiguration
- factory_register(...) from builtins.PyCapsule
- factory_register(self : rosetta.basic.resource_manager.FallbackConfigurationFactory, creator : rosetta.basic.resource_manager.FallbackConfigurationCreator) -> NoneType
- has_fallback_for_resource(...) from builtins.PyCapsule
- has_fallback_for_resource(self : rosetta.basic.resource_manager.FallbackConfigurationFactory, desc : str) -> bool
- set_throw_on_double_registration(...) from builtins.PyCapsule
- set_throw_on_double_registration(rosetta.basic.resource_manager.FallbackConfigurationFactory) -> NoneType
Only useful for unit testing. Since factory registration happens (sometimes) at
load time, there may be no one to catch a thrown exception in the event of a name collision
two FallbackConfigurationCreators that register for the same
Methods inherited from rosetta.utility.SingletonBase_basic_resource_manager_FallbackConfigurationFactory_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> basic::resource_manager::FallbackConfigurationFactory
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class JobOptions(builtins.object) |
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The %JobOptions class holds job-specific options (i.e. command line flags). It can be used
by the ResourceManager to hold options for a particular job, so that the ResourceManager can
retrieve those options as needed. It is basically a bag for 12 OptionKey/OptionKeyValue
maps, one for every kind of OptionKey.
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.basic.resource_manager.JobOptions, rhs : rosetta.basic.resource_manager.JobOptions) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.basic.resource_manager.JobOptions) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.basic.resource_manager.JobOptions) -> str
- add_option(...) from builtins.PyCapsule
- add_option(*args, **kwargs)
Overloaded function.
1. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanOptionKey, val : bool) -> NoneType
Set the value for the indicated boolean option
2. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanVectorOptionKey, val : rosetta.utility.vector1_bool) -> NoneType
Set the value for the indicated boolean-vector option
3. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileOptionKey, val : rosetta.utility.file.FileName) -> NoneType
Set the value for the indicated file option
4. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileVectorOptionKey, val : rosetta.utility.vector1_utility_file_FileName) -> NoneType
Set the value for the indicated file-vector option
5. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerOptionKey, val : int) -> NoneType
Set the value for the indicated integer option
6. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerVectorOptionKey, val : rosetta.utility.vector1_int) -> NoneType
Set the value for the indicated integer-vector option
7. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathOptionKey, val : rosetta.utility.file.PathName) -> NoneType
Set the value for the indicated path option
8. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathVectorOptionKey, val : rosetta.utility.vector1_utility_file_PathName) -> NoneType
Set the value for the indicated path-vector option
9. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealOptionKey, val : float) -> NoneType
Set the value for the indicated real option
10. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealVectorOptionKey, val : rosetta.utility.vector1_double) -> NoneType
Set the value for the indicated real-vector option
11. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringOptionKey, val : str) -> NoneType
Set the value for the indicated string option
12. add_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringVectorOptionKey, val : rosetta.utility.vector1_std_string) -> NoneType
Set the value for the indicated string-vector option
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.basic.resource_manager.JobOptions, : rosetta.basic.resource_manager.JobOptions) -> rosetta.basic.resource_manager.JobOptions
- get_option(...) from builtins.PyCapsule
- get_option(*args, **kwargs)
Overloaded function.
1. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanOptionKey) -> bool
Return the value of the indicated boolean option
2. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanVectorOptionKey) -> rosetta.utility.vector1_bool
Return the value of the indicated boolean-vector option
3. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileOptionKey) -> rosetta.utility.file.FileName
Return the value of the indicated file option
4. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileVectorOptionKey) -> rosetta.utility.vector1_utility_file_FileName
Return the value of the indicated file-vector option
5. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerOptionKey) -> int
Return the value of the indicated integer option
6. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerVectorOptionKey) -> rosetta.utility.vector1_int
Return the value of the indicated integer-vector option
7. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathOptionKey) -> rosetta.utility.file.PathName
Return the value of the indicated path option
8. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathVectorOptionKey) -> rosetta.utility.vector1_utility_file_PathName
Return the value of the indicated path-vector option
9. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealOptionKey) -> float
Return the value of the indicated real option
10. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealVectorOptionKey) -> rosetta.utility.vector1_double
Return the value of the indicated real-vector option
11. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringOptionKey) -> str
Return the value of the indicated string option
12. get_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringVectorOptionKey) -> rosetta.utility.vector1_std_string
Return the value of the indicated string-vector option
- has_option(...) from builtins.PyCapsule
- has_option(*args, **kwargs)
Overloaded function.
1. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanOptionKey) -> bool
Return true if a value for the indicated boolean option has been set
2. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanVectorOptionKey) -> bool
Return true if a value for the indicated boolean-vector option has been set
3. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileOptionKey) -> bool
Return true if a value for the indicated file option has been set
4. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileVectorOptionKey) -> bool
Return true if a value for the indicated file-vector option has been set
5. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerOptionKey) -> bool
Return true if a value for the indicated integer option has been set
6. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerVectorOptionKey) -> bool
Return true if a value for the indicated integer-vector option has been set
7. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathOptionKey) -> bool
Return true if a value for the indicated path option has been set
8. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathVectorOptionKey) -> bool
Return true if a value for the indicated path-vector option has been set
9. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealOptionKey) -> bool
Return true if a value for the indicated real option has been set
10. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealVectorOptionKey) -> bool
Return true if a value for the indicated real-vector option has been set
11. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringOptionKey) -> bool
Return true if a value for the indicated string option has been set
12. has_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringVectorOptionKey) -> bool
Return true if a value for the indicated string-vector option has been set
- insertion_order(...) from builtins.PyCapsule
- insertion_order(rosetta.basic.resource_manager.JobOptions) -> rosetta.std.list_std_pair_utility_options_OptionTypes_std_string_std_allocator_std_pair_utility_options_OptionTypes_std_string_t
- remove_option(...) from builtins.PyCapsule
- remove_option(*args, **kwargs)
Overloaded function.
1. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanOptionKey) -> NoneType
Unset the value for the indicated boolean option
2. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.BooleanVectorOptionKey) -> NoneType
Unset the value for the indicated boolean-vector option
3. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileOptionKey) -> NoneType
Unset the value for the indicated file option
4. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.FileVectorOptionKey) -> NoneType
Unset the value for the indicated file-vector option
5. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerOptionKey) -> NoneType
Unset the value for the indicated integer option
6. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.IntegerVectorOptionKey) -> NoneType
Unset the value for the indicated integer-vector option
7. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathOptionKey) -> NoneType
Unset the value for the indicated path option
8. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.PathVectorOptionKey) -> NoneType
Unset the value for the indicated path-vector option
9. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealOptionKey) -> NoneType
Unset the value for the indicated real option
10. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.RealVectorOptionKey) -> NoneType
Unset the value for the indicated real-vector option
11. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringOptionKey) -> NoneType
Unset the value for the indicated string option
12. remove_option(self : rosetta.basic.resource_manager.JobOptions, key : rosetta.utility.options.StringVectorOptionKey) -> NoneType
Unset the value for the indicated string-vector option
- track_insertion_order(...) from builtins.PyCapsule
- track_insertion_order(self : rosetta.basic.resource_manager.JobOptions, setting : bool) -> NoneType
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class LazyResourceManager(ResourceManager) |
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This is a mule class, meant to be derived from. It's job
is to hold ResourceOptions and ResourceLocator objects by name (tag)
as well as the ResourceConfigurations which serve as complete
descriptions for how to construct a Resource. It should be thought
of as a mule by classes that derive from it: it won't do anything
on its own, but it can be directed to do things. The point of the
class is to ake it easier to create ResourceManagers besides the
JD2ResourceManager, which, at the time of this documentation,
is the only class that derives from the LazyResourceManager.
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- Method resolution order:
- LazyResourceManager
- ResourceManager
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.basic.resource_manager.LazyResourceManager) -> str
- add_job_options(...) from builtins.PyCapsule
- add_job_options(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str, job_options : rosetta.basic.resource_manager.JobOptions) -> NoneType
- add_resource_configuration(...) from builtins.PyCapsule
- add_resource_configuration(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str, resource_configuration : rosetta.basic.resource_manager.ResourceConfiguration) -> NoneType
- add_resource_locator(...) from builtins.PyCapsule
- add_resource_locator(self : rosetta.basic.resource_manager.LazyResourceManager, locator_tag : str, resource_locator : basic::resource_manager::ResourceLocator) -> NoneType
- add_resource_options(...) from builtins.PyCapsule
- add_resource_options(self : rosetta.basic.resource_manager.LazyResourceManager, resource_options_tag : str, resource_options : rosetta.basic.resource_manager.ResourceOptions) -> NoneType
- add_resource_tag_by_job_tag(...) from builtins.PyCapsule
- add_resource_tag_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str, resource_tag : str) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.basic.resource_manager.LazyResourceManager, : rosetta.basic.resource_manager.LazyResourceManager) -> rosetta.basic.resource_manager.LazyResourceManager
- clear(...) from builtins.PyCapsule
- clear(rosetta.basic.resource_manager.LazyResourceManager) -> NoneType
wipe out all data; useful for unit testing, but hard to fathom how it would be useful
otherwise.
- create_resources(...) from builtins.PyCapsule
- create_resources(self : rosetta.basic.resource_manager.LazyResourceManager, : str) -> NoneType
Create all the resources for a particular job; this should be implemented by the derived
class. The implementation in this class calls utility::exit
- find_resource_configuration(...) from builtins.PyCapsule
- find_resource_configuration(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> rosetta.basic.resource_manager.ResourceConfiguration
- find_resource_locator(...) from builtins.PyCapsule
- find_resource_locator(self : rosetta.basic.resource_manager.LazyResourceManager, locator_tag : str) -> basic::resource_manager::ResourceLocator
- find_resource_options(...) from builtins.PyCapsule
- find_resource_options(self : rosetta.basic.resource_manager.LazyResourceManager, resource_options_tag : str) -> rosetta.basic.resource_manager.ResourceOptions
- find_resource_tag_by_job_tag(...) from builtins.PyCapsule
- find_resource_tag_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str) -> str
- free_resource_by_job_tag(...) from builtins.PyCapsule
- free_resource_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str) -> NoneType
- free_resource_by_tag(...) from builtins.PyCapsule
- free_resource_by_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> NoneType
- get_count_of_jobs_associated_with_resource_tag(...) from builtins.PyCapsule
- get_count_of_jobs_associated_with_resource_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> int
- get_job_options(...) from builtins.PyCapsule
- get_job_options(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> rosetta.basic.resource_manager.JobOptions
- get_resource_tags_for_job_tag(...) from builtins.PyCapsule
- get_resource_tags_for_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> rosetta.std.list_std_string_std_allocator_std_string_t
- has_job_options(...) from builtins.PyCapsule
- has_job_options(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> bool
- has_resource(...) from builtins.PyCapsule
- has_resource(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> bool
Does a resource with a given name exist?
- has_resource_configuration(...) from builtins.PyCapsule
- has_resource_configuration(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> bool
has a ResourceConfiguration been provided to the LazyResourceManager for a Resource with a particular ResourceTag?
- has_resource_locator(...) from builtins.PyCapsule
- has_resource_locator(self : rosetta.basic.resource_manager.LazyResourceManager, locator_tag : str) -> bool
has a ResourceLocator object been provided to the LazyResourceManager which has a particular LocatorTag?
- has_resource_options(...) from builtins.PyCapsule
- has_resource_options(self : rosetta.basic.resource_manager.LazyResourceManager, resource_options_tag : str) -> bool
has a ResourceOptions object been provided to the LazyResourceManager which has a particular ResourceOptionsTag?
- has_resource_tag_by_job_tag(...) from builtins.PyCapsule
- has_resource_tag_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str) -> bool
- mark_job_tag_as_complete(...) from builtins.PyCapsule
- mark_job_tag_as_complete(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> NoneType
remove the Job tag from incomplete_job_sets_ for each resource
Methods inherited from ResourceManager:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> rosetta.basic.resource_manager.ResourceManager
Deprecated access to a global (not-quite singleton) ResourceManager instance that
should be removed
- get_option(...) from builtins.PyCapsule
- get_option(*args, **kwargs)
Overloaded function.
1. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanOptionKey) -> bool
Retrieve the boolean value represented by the given option key
2. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanVectorOptionKey) -> rosetta.utility.vector1_bool
Retrieve the vector of boolean values represented by the given option key
3. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileOptionKey) -> rosetta.utility.file.FileName
Retrieve the FileName value represented by the given option key
4. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileVectorOptionKey) -> rosetta.utility.vector1_utility_file_FileName
Retrieve the vector of FileName values represented by the given option key
5. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerOptionKey) -> int
Retrieve the integer value represented by the given option key
6. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerVectorOptionKey) -> rosetta.utility.vector1_int
Retrieve the vector of integer values represented by the given option key
7. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathOptionKey) -> rosetta.utility.file.PathName
Retrieve the PathName value represented by the given option key
8. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathVectorOptionKey) -> rosetta.utility.vector1_utility_file_PathName
Retrieve the vector of PathName values represented by the given option key
9. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealOptionKey) -> float
Retrieve the Real value represented by the given option key
10. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealVectorOptionKey) -> rosetta.utility.vector1_double
Retrieve the vector of Real values represented by the given option key
11. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringOptionKey) -> str
Retrieve the string value represented by the given option key
12. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringVectorOptionKey) -> rosetta.utility.vector1_std_string
Retrieve the vector of string values represented by the given option key
- has_option(...) from builtins.PyCapsule
- has_option(*args, **kwargs)
Overloaded function.
1. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
2. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
3. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
4. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
5. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
6. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
7. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
8. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
9. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
10. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
11. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
12. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
- has_resource_with_description(...) from builtins.PyCapsule
- has_resource_with_description(self : rosetta.basic.resource_manager.ResourceManager, resource_description : str) -> bool
A protocol may ask whether a resource with a given resource description
has been provided. It is possible that some resources are available sometimes
when running a protocol, but not always (e.g. when running abinitio, sometimes
you don't know what the native structure is).
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class ResourceLoaderFactory(rosetta.utility.SingletonBase_basic_resource_manager_ResourceLoaderFactory_t) |
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Instantiates ResourceLoaders. Creators may be registered with
the Factory at any point, though it is recommended they be registered
at load time. If two Creators are registered and they both give the
same name for the ResourceLoader they say they will instantiate, then
the Factory will exit with an error message.
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- Method resolution order:
- ResourceLoaderFactory
- rosetta.utility.SingletonBase_basic_resource_manager_ResourceLoaderFactory_t
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- available_resource_loaders(...) from builtins.PyCapsule
- available_resource_loaders(rosetta.basic.resource_manager.ResourceLoaderFactory) -> rosetta.std.list_std_string_std_allocator_std_string_t
Return a list of all the resource loaders available
- create_resource_loader(...) from builtins.PyCapsule
- create_resource_loader(self : rosetta.basic.resource_manager.ResourceLoaderFactory, loader_type : str) -> rosetta.basic.resource_manager.ResourceLoader
Instantiates a resource loader ofa given type; throws
an exception if no loader with this type has been previously
registered.
- factory_register(...) from builtins.PyCapsule
- factory_register(self : rosetta.basic.resource_manager.ResourceLoaderFactory, creator : rosetta.basic.resource_manager.ResourceLoaderCreator) -> NoneType
Register a ResourceLoaderCreator with the factory. The factory
asks the Creator for the name of the ResourceLoader that it will create;
if another Creator has already registered with the factory that proports
to instantiate another ResourceLoader with the same name, then it will
exit with an error message, or, if set_throw_on_double_registration()
has previously been called, throw an exception.
- has_resource_loader(...) from builtins.PyCapsule
- has_resource_loader(self : rosetta.basic.resource_manager.ResourceLoaderFactory, loader_type : str) -> bool
Returns true if a resource loader of the given type has been
registered with the factory
- set_throw_on_double_registration(...) from builtins.PyCapsule
- set_throw_on_double_registration(rosetta.basic.resource_manager.ResourceLoaderFactory) -> NoneType
Only useful for unit testing. Since factory registration happens (sometimes) at
load time, there may be no one to catch a thrown exception in the event of a name collision
two FallbackConfigurationCreators that register for the same
Methods inherited from rosetta.utility.SingletonBase_basic_resource_manager_ResourceLoaderFactory_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> basic::resource_manager::ResourceLoaderFactory
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class ResourceLocator(builtins.object) |
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%ResourceLocator classes are responsible for retrieving data
from a data store that will be used to construct a Resource. This
data store could be a file system or a database or any other
place where data is stored.
The ResourceManager asks the ResourceLocator to produce a
ResourceStream object when given a "locator_id." A "locator_id"
is what's needed to identify a data source from a data store:
for example, for the FileSystemResourceLocator, the locator id
is a file name; for the DatabaseResourceLocator, it would be
a database query.
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Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.basic.resource_manager.ResourceLocator, : rosetta.basic.resource_manager.ResourceLocator) -> rosetta.basic.resource_manager.ResourceLocator
- locate_resource_stream(...) from builtins.PyCapsule
- locate_resource_stream(self : rosetta.basic.resource_manager.ResourceLocator, locator_id : str) -> rosetta.basic.resource_manager.ResourceStream
Create and return a ResourceStream object from the given locator_id
so that its stream can be passed to the ResourceLoader
- locator_tag(...) from builtins.PyCapsule
- locator_tag(*args, **kwargs)
Overloaded function.
1. locator_tag(self : rosetta.basic.resource_manager.ResourceLocator, locator_tag : str) -> NoneType
Set the name for this %ResourceLocator
2. locator_tag(rosetta.basic.resource_manager.ResourceLocator) -> str
Return the name for this %ResourceLocator
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.basic.resource_manager.ResourceLocator, tag : utility::tag::Tag) -> NoneType
Initialize the parameters for this %ResourceLocator from the contents of
an XML file.
- type(...) from builtins.PyCapsule
- type(rosetta.basic.resource_manager.ResourceLocator) -> str
Return the class name for this %ResourceLocator instance.
This function allows for better error message delivery.
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class ResourceLocatorFactory(rosetta.utility.SingletonBase_basic_resource_manager_ResourceLocatorFactory_t) |
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The %ResourceLocatorFactory instantiates ResourceLocator objects given their corresponding
locator-type strings. It uses the load-time factory registration scheme, meaning that it is a
singleton and takes an instance of a Creator object (a ResourceLocatorCreator) in its
"factory_register" method. Templated instances of the ResourceLocatorRegistrator classes should
be placed in the library init.cc files (e.g. core/init/init.cc or
protocols/init/init.ResourceLocatorRegistrators.ihh)
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- Method resolution order:
- ResourceLocatorFactory
- rosetta.utility.SingletonBase_basic_resource_manager_ResourceLocatorFactory_t
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- create_resource_locator(...) from builtins.PyCapsule
- create_resource_locator(self : rosetta.basic.resource_manager.ResourceLocatorFactory, locator_type : str, locator_tag : str, tags : utility::tag::Tag) -> rosetta.basic.resource_manager.ResourceLocator
Create a ResourceLocator given its locator_type, giving the newly created instance the name locator_tag
- factory_register(...) from builtins.PyCapsule
- factory_register(self : rosetta.basic.resource_manager.ResourceLocatorFactory, creator : rosetta.basic.resource_manager.ResourceLocatorCreator) -> NoneType
This function is called on the singleton instance to give a ResourceLocatorCreator to the
factory, usually through the constructor of a ResourceLocatorRegistrator class.
- set_throw_on_double_registration(...) from builtins.PyCapsule
- set_throw_on_double_registration(rosetta.basic.resource_manager.ResourceLocatorFactory) -> NoneType
Only useful for unit testing. Since factory registration happens (sometimes) at
load time, there may be no one to catch a thrown exception in the event of a name collision
between two ResourceLocatorCreators that register for the same name.
Methods inherited from rosetta.utility.SingletonBase_basic_resource_manager_ResourceLocatorFactory_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> basic::resource_manager::ResourceLocatorFactory
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class ResourceManager(builtins.object) |
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The ResourceManager is a singleton class responsible for holding, distributing,
and eventually deallocating resources which may be shared between multiple jobs. A
protocol may communicate directly with the ResourceManager, requesting resources, but
remaining unaware of where those resources came from, or whether the same resource is
being used in multiple contexts.
A protocol should request a resource using a "resource description" (a string), which
is a generic way of referring to a piece of data. For example, a protocol might request
the native Pose, by asking for a resource with the description "native". The
ResourceManager's job is to return the resource matching that description; when
the "native" is requested, it is requested in some context (e.g. in a protocol running
under JD2) and the ResourceManager serves as a backbone in which to deliever
context-specific data to the protocol, while keeping the protocol ignorant and
independent of the surrounding context. That way protocols can run in JD2 just as
effectively as the could run in some other job-management environment, without
having to assume responsibility for instantiating resources themselves.
NOTE: Because the logic for deciding which of the derived ResourceManager classes
should be instantiated depends on the options system, the ResourceManager should
not be requested until after core::init::init() has been called (i.e. it should not
be requested at load time.)
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Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.basic.resource_manager.ResourceManager) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.basic.resource_manager.ResourceManager, : rosetta.basic.resource_manager.ResourceManager) -> rosetta.basic.resource_manager.ResourceManager
- clear(...) from builtins.PyCapsule
- clear(rosetta.basic.resource_manager.ResourceManager) -> NoneType
wipe out all data; useful for unit testing, but hard to
fathom how it would be useful otherwise.
- get_instance(...) from builtins.PyCapsule
- get_instance() -> rosetta.basic.resource_manager.ResourceManager
Deprecated access to a global (not-quite singleton) ResourceManager instance that
should be removed
- get_option(...) from builtins.PyCapsule
- get_option(*args, **kwargs)
Overloaded function.
1. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanOptionKey) -> bool
Retrieve the boolean value represented by the given option key
2. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanVectorOptionKey) -> rosetta.utility.vector1_bool
Retrieve the vector of boolean values represented by the given option key
3. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileOptionKey) -> rosetta.utility.file.FileName
Retrieve the FileName value represented by the given option key
4. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileVectorOptionKey) -> rosetta.utility.vector1_utility_file_FileName
Retrieve the vector of FileName values represented by the given option key
5. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerOptionKey) -> int
Retrieve the integer value represented by the given option key
6. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerVectorOptionKey) -> rosetta.utility.vector1_int
Retrieve the vector of integer values represented by the given option key
7. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathOptionKey) -> rosetta.utility.file.PathName
Retrieve the PathName value represented by the given option key
8. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathVectorOptionKey) -> rosetta.utility.vector1_utility_file_PathName
Retrieve the vector of PathName values represented by the given option key
9. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealOptionKey) -> float
Retrieve the Real value represented by the given option key
10. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealVectorOptionKey) -> rosetta.utility.vector1_double
Retrieve the vector of Real values represented by the given option key
11. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringOptionKey) -> str
Retrieve the string value represented by the given option key
12. get_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringVectorOptionKey) -> rosetta.utility.vector1_std_string
Retrieve the vector of string values represented by the given option key
- has_option(...) from builtins.PyCapsule
- has_option(*args, **kwargs)
Overloaded function.
1. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
2. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.BooleanVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
3. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
4. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.FileVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
5. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
6. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.IntegerVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
7. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
8. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.PathVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
9. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
10. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.RealVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
11. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
12. has_option(self : rosetta.basic.resource_manager.ResourceManager, key : rosetta.utility.options.StringVectorOptionKey) -> bool
Return whether or not a value has been provided for the given option key either
on the command line or through for the current job.
- has_resource(...) from builtins.PyCapsule
- has_resource(self : rosetta.basic.resource_manager.ResourceManager, resource_tag : str) -> bool
Does a resource with a given name exist?
- has_resource_with_description(...) from builtins.PyCapsule
- has_resource_with_description(self : rosetta.basic.resource_manager.ResourceManager, resource_description : str) -> bool
A protocol may ask whether a resource with a given resource description
has been provided. It is possible that some resources are available sometimes
when running a protocol, but not always (e.g. when running abinitio, sometimes
you don't know what the native structure is).
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class ResourceOptions(builtins.object) |
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The %ResourceOptions class is responsible for describing all
the data requried for instanting a particular resource, except for the
data stream (i.e. the file) that contains the data for the resource.
For example, when reading in a PDB file, there are 30 different options
for how that PDB file should be turned into a Pose. That data is now
held in an ImportPoseOptions object. The purpose of the %ResourceOptions
class is to allow different jobs to load resources in different ways, or
for one job to load two different resources of the same type in different
ways. For example, a protocol may need both a centroid pose and a
fullatom pose to be loaded in from disk; however, if the logic for
loading a pose in from disk is controlled by the options system alone,
this becomes impossible.
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.basic.resource_manager.ResourceOptions) -> NoneType
2. __init__(self : rosetta.basic.resource_manager.ResourceOptions, name : str) -> NoneType
3. __init__(rosetta.basic.resource_manager.ResourceOptions, rosetta.basic.resource_manager.ResourceOptions) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.basic.resource_manager.ResourceOptions) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.basic.resource_manager.ResourceOptions, : rosetta.basic.resource_manager.ResourceOptions) -> rosetta.basic.resource_manager.ResourceOptions
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.basic.resource_manager.ResourceOptions) -> str
A name given to a particular ResourceOptions instance.
This function allows for better error message delivery.
2. name(self : rosetta.basic.resource_manager.ResourceOptions, setting : str) -> NoneType
Set the name for this %ResoureOptions instance.
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.basic.resource_manager.ResourceOptions, tag : utility::tag::Tag) -> NoneType
Initialize from the recursive "tag" structure.
- type(...) from builtins.PyCapsule
- type(rosetta.basic.resource_manager.ResourceOptions) -> str
The class name (its type) for a particular ResourceOptions instance.
This function allows for better error message delivery.
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