sbol2
¶
Submodules¶
sbol2.SBOL2Serialize
sbol2.attachment
sbol2.collection
sbol2.combinatorialderivation
sbol2.component
sbol2.componentdefinition
sbol2.config
sbol2.constants
sbol2.dbtl
sbol2.document
sbol2.experiment
sbol2.identified
sbol2.implementation
sbol2.interaction
sbol2.location
sbol2.mapsto
sbol2.measurement
sbol2.model
sbol2.module
sbol2.moduledefinition
sbol2.object
sbol2.participation
sbol2.partshop
sbol2.property
sbol2.provo
sbol2.sbolerror
sbol2.searchquery
sbol2.sequence
sbol2.sequenceannotation
sbol2.sequenceconstraint
sbol2.toplevel
sbol2.uridict
sbol2.validation
sbol2.versionproperty
Package Contents¶
Classes¶
Attachment (uri=URIRef(‘example’), *, type_uri=SBOL_ATTACHMENT, version=VERSION_STRING, source=’‘) |
All SBOL classes derived from TopLevel appear as top level nodes |
Collection (uri=URIRef(‘example’), version=VERSION_STRING, *, type_uri=SBOL_COLLECTION) |
All SBOL classes derived from TopLevel appear as top level nodes |
CombinatorialDerivation (type_uri=SBOL_COMBINATORIAL_DERIVATION, uri=URIRef(‘example’), strategy=’http://sbols.org/v2#enumerate’, version=VERSION_STRING) |
|
Component (uri=URIRef(‘example’), definition=’‘, access=SBOL_ACCESS_PUBLIC, version=VERSION_STRING) |
|
FunctionalComponent (uri=URIRef(‘example’), definition=’‘, access=SBOL_ACCESS_PUBLIC, direction=SBOL_DIRECTION_NONE, version=VERSION_STRING) |
|
ComponentDefinition (uri=URIRef(‘example’), component_type=URIRef(BIOPAX_DNA), version=VERSION_STRING, type_uri=SBOL_COMPONENT_DEFINITION) |
The ComponentDefinition class represents the structural entities |
Config () |
A class which contains global configuration variables |
ConfigOptions () |
Generic enumeration. |
Design (uri=’example’, version=VERSION_STRING, structure=None, function=None) |
This class represents a biological Design. |
Document (filename=None) |
The Document is a container for all SBOL data objects. |
Experiment (uri=URIRef(‘example’), version=VERSION_STRING) |
|
ExperimentalData (uri=URIRef(‘example’), version=VERSION_STRING) |
|
Identified (type_uri=SBOL_IDENTIFIED, uri=URIRef(‘example’), version=VERSION_STRING) |
|
Implementation (uri=URIRef(‘example’), version=VERSION_STRING, *, type_uri=SBOL_IMPLEMENTATION) |
|
Interaction (uri=’example’, interaction_type=SBO_INTERACTION, *, type_uri=SBOL_INTERACTION, version=VERSION_STRING) |
|
Location (uri=URIRef(‘example’), orientation=SBOL_ORIENTATION_INLINE, *, type_uri=SBOL_LOCATION, version=VERSION_STRING) |
The Location class specifies the strand orientation of a Component. |
Range (uri=URIRef(‘example’), start=1, end=2, *, type_uri=SBOL_RANGE, version=VERSION_STRING) |
A Range object specifies a region via discrete, |
Cut (uri=URIRef(‘example’), at=0, *, type_uri=SBOL_CUT, version=VERSION_STRING) |
The Cut class specifies a location between |
GenericLocation (uri=URIRef(‘example’), *, type_uri=SBOL_GENERIC_LOCATION, version=VERSION_STRING) |
the GenericLocation class is included as a starting point |
Measurement (uri=URIRef(‘example’), value=0.0, unit=’‘, version=VERSION_STRING) |
The purpose of the Measure class is to link a numerical value |
Module (uri=’example’, *, definition=’‘, version=VERSION_STRING, type_uri=SBOL_MODULE) |
An SBOLObject converts a Python data structure into an RDF triple store |
ModuleDefinition (uri=rdflib.URIRef(‘example’), version=VERSION_STRING, type_uri=SBOL_MODULE_DEFINITION) |
ModuleDefinition is a principle top-level class for |
SBOLObject (type_uri=rdflib.URIRef(UNDEFINED), uri=rdflib.URIRef(‘example’)) |
An SBOLObject converts a Python data structure into an RDF triple store |
Participation (type_uri=SBOL_PARTICIPATION, uri=URIRef(‘example’), participant=’‘, version=VERSION_STRING) |
|
SearchQuery (search_target: str = SBOL_COMPONENT_DEFINITION, offset: int = 0, limit: int = 25) |
Search terms to support PartShop advanced search. |
DateTimeProperty (property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None) |
Member properties of all SBOL objects are defined |
FloatProperty (property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None) |
Member properties of all SBOL objects are defined |
IntProperty (property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None) |
Member properties of all SBOL objects are defined |
LiteralProperty (property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None) |
Member properties of all SBOL objects are defined |
OwnedObject (property_owner, sbol_uri, builder, lower_bound, upper_bound, validation_rules=None, first_object=None) |
Member properties of all SBOL objects are defined |
ReferencedObject (property_owner, type_uri, reference_type_uri, lower_bound, upper_bound, validation_rules, initial_value=None) |
Member properties of all SBOL objects are defined |
TextProperty (property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None) |
Member properties of all SBOL objects are defined |
URIProperty (property_owner, type_uri, lower_bound, upper_bound, validation_rules, initial_value=None) |
Member properties of all SBOL objects are defined |
Activity (uri=URIRef(‘example’), action_type=’‘, version=VERSION_STRING, type_uri=PROVO_ACTIVITY) |
A generated Entity is linked through a wasGeneratedBy |
Agent (uri=URIRef(‘example’), version=VERSION_STRING, type_uri=PROVO_AGENT) |
Examples of agents are person, organisation or software. |
Association (uri=URIRef(‘example’), agent=None, role=None, version=VERSION_STRING, type_uri=PROVO_ASSOCIATION) |
|
Plan (uri=URIRef(‘example’), version=VERSION_STRING, type_uri=PROVO_PLAN) |
|
Usage (uri=URIRef(‘example’), entity=None, role=None, version=VERSION_STRING, type_uri=PROVO_USAGE) |
|
SBOLErrorCode () |
Generic enumeration. |
Sequence (uri=URIRef(‘example’), elements=’‘, encoding=SBOL_ENCODING_IUPAC, version=VERSION_STRING, type_uri=SBOL_SEQUENCE) |
The primary structure (eg, nucleotide or amino acid sequence) |
SequenceAnnotation (uri=’example’, version=VERSION_STRING) |
|
TopLevel (type_uri=SBOL_TOP_LEVEL, uri=URIRef(‘example’), version=VERSION_STRING) |
All SBOL classes derived from TopLevel appear as top level nodes |
VersionProperty (property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None) |
Member properties of all SBOL objects are defined |
Functions¶
getHomespace () |
|
hasHomespace () |
|
setHomespace (ns) |
|
IGEM_STANDARD_ASSEMBLY (parts_list) |
|
is_alphanumeric_or_underscore (c) |
|
is_not_alphanumeric_or_underscore (c) |
-
sbol2.
__version__
= 1.0¶
-
class
sbol2.
Attachment
(uri=URIRef('example'), *, type_uri=SBOL_ATTACHMENT, version=VERSION_STRING, source='')¶ Bases:
sbol2.toplevel.TopLevel
All SBOL classes derived from TopLevel appear as top level nodes in the RDF/XML document tree and SBOL files.
-
class
sbol2.
Collection
(uri=URIRef('example'), version=VERSION_STRING, *, type_uri=SBOL_COLLECTION)¶ Bases:
sbol2.toplevel.TopLevel
All SBOL classes derived from TopLevel appear as top level nodes in the RDF/XML document tree and SBOL files.
-
class
sbol2.
CombinatorialDerivation
(type_uri=SBOL_COMBINATORIAL_DERIVATION, uri=URIRef('example'), strategy='http://sbols.org/v2#enumerate', version=VERSION_STRING)¶ Bases:
sbol2.toplevel.TopLevel
-
class
sbol2.
Component
(uri=URIRef('example'), definition='', access=SBOL_ACCESS_PUBLIC, version=VERSION_STRING)¶ Bases:
sbol2.component.ComponentInstance
-
addRole
(self, new_role)¶
-
removeRole
(self, index=0)¶
-
static
_role_set_role_integration
(sbol_obj, arg)¶ SBOL 2.3.0 says that if a Component has roles then it MUST specify a roleIntegration.
-
-
class
sbol2.
FunctionalComponent
(uri=URIRef('example'), definition='', access=SBOL_ACCESS_PUBLIC, direction=SBOL_DIRECTION_NONE, version=VERSION_STRING)¶ Bases:
sbol2.component.ComponentInstance
-
connect
(self, interface_component)¶
-
mask
(self, masked_component)¶
-
override
(selfself, masked_component)¶
-
isMasked
(self)¶
-
-
class
sbol2.
ComponentDefinition
(uri=URIRef('example'), component_type=URIRef(BIOPAX_DNA), version=VERSION_STRING, type_uri=SBOL_COMPONENT_DEFINITION)¶ Bases:
sbol2.toplevel.TopLevel
The ComponentDefinition class represents the structural entities of a biological design.
The primary usage of this class is to represent structural entities with designed sequences, such as DNA, RNA, and proteins, but it can also be used to represent any other entity that is part of a design, such as small molecules, proteins, and complexes.
-
_types
¶
-
_roles
¶
-
components
¶
-
sequences
¶
-
sequenceAnnotations
¶
-
sequenceConstraints
¶
-
sequence
¶
-
_added_to_document
(self, doc)¶ Classes can override this method to do extra work when being added to a document.
-
addType
(self, new_type)¶
-
removeType
(self, index=0)¶
-
addRole
(self, new_role)¶
-
removeRole
(self, index=0)¶
-
assemble
(self, component_list, assembly_method=None, doc=None)¶ Assembles ComponentDefinitions into an abstraction hierarchy.
The resulting data structure is a partial design, still lacking a primary structure or explicit sequence. To form a primary structure out of the ComponentDefinitions, call linearize after calling assemble. To fully realize the target sequence, use Sequence::assemble(). :param component_list: Either a list of URIs for the constituent ComponentDefinitions or a list of subcomponents. A list of displayIds is also acceptable if using SBOL-compliant URIs. :param assembly_method: An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence. :param doc: The Document to which the assembled ComponentDefinitions will be added. If not set, then you must add this ComponentDefinition to a Document before calling this method. :return: None
-
assemblePrimaryStructure
(self, primary_structure, assembly_method=None, doc=None)¶ Assembles ComponentDefinition into a linear primary structure.
The resulting data structure is a partial design, still lacking an explicit sequence. To fully realize the target sequence, use Sequence::assemble(). :param primary_structure: Either a list of URIs for the constituent ComponentDefinitions or a list of subcomponents. A list of displayIds is also acceptable if using SBOL-compliant URIs. :param assembly_standard: An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence. :param doc: The Document to which the assembled ComponentDefinitions will be added. If not set, then you must add this ComponentDefinition to a Document before calling this method. :return: None
-
compile
(self, assembly_method=None)¶ Compiles an abstraction hierarchy of ComponentDefinitions into a nucleotide sequence.
If no Sequence object is associated with this ComponentDefinition, one will be automatically instantiated :return: A string representing the nucleotide sequence for this ComponentDefinition.
-
updateSequence
(self, composite_sequence='')¶ Assemble a parent ComponentDefinition’s Sequence from its subcomponent Sequences.
Parameters: composite_sequence – A recursive parameter, use default value. Returns: The assembled parent sequence.
-
getInSequentialOrder
(self)¶ Get the primary sequence of a design in terms of its sequentially ordered Components.
Returns: A list of Components.
-
hasUpstreamComponent
(self, component)¶ Checks if the specified Component has a Component upstream in linear arrangement on the DNA strand.
Checks that the appropriate SequenceConstraint exists. :param current_component: A Component in this ComponentDefinition. :return: True if found, False if not
-
getUpstreamComponent
(self, component)¶ Get the upstream component.
Parameters: component – A Component in this ComponentDefinition. Returns: The upstream component.
-
hasDownstreamComponent
(self, component)¶ Checks if the specified Component has a Component downstream in linear arrangement on the DNA strand.
Checks that the appropriate SequenceConstraint exists. :param current_component: A Component in this ComponentDefinition. :return: True if found, False if not.
-
getDownstreamComponent
(self, component)¶ Get the downstream component.
Parameters: current_component – A Component in this ComponentDefinition. Returns: The downstream component.
-
deleteDownstreamComponent
(self, upstream_component)¶
-
deleteUpstreamComponent
(self, downstream_component)¶
-
insertUpstreamComponent
(self, downstream, insert)¶
-
insertDownstreamComponent
(self, upstream, insert)¶
-
getFirstComponent
(self)¶ Gets the first Component in a linear sequence.
Returns: The first component in sequential order.
-
getLastComponent
(self)¶ Gets the last Component in a linear sequence.
Returns: The last component in sequential order.
-
applyToComponentHierarchy
(self, callback=None, user_data=None)¶ Perform an operation on every Component in a structurally-linked hierarchy of Components by applying a callback function. If no callback is specified, the default behavior is to return a list of each Component in the hierarchy.
Parameters: - callback – The callback function to apply.
- user_data – Arbitrary user data which can be passed
in and out of the callback as an argument. :return: A list of all Components in the hierarchy.
-
getPrimaryStructureComponents
(self)¶ Get the primary sequence of a design in terms of its sequentially ordered Components.
Returns: A list of Components.
-
getPrimaryStructure
(self)¶ Get the primary sequence of a design in terms of its sequentially ordered ComponentDefinitions.
Returns: A list of ComponentDefinitions.
-
insertDownstream
(self, target, component_to_insert)¶ Insert a Component downstream of another in a primary sequence, shifting any adjacent Components downstream as well.
Parameters: target – The target Component will be upstream of the insert Component after this operation. :param component_to_insert: The insert Component is inserted downstream of the target Component. :return: None
-
insertUpstream
(self, target, component_to_insert)¶ Insert a Component upstream of another in a primary sequence, shifting any adjacent Components upstream as well.
Parameters: target – The target Component will be downstream of the insert Component after this operation. :param component_to_insert: The insert Component is inserted upstream of the target Component. :return:
-
addUpstreamFlank
(self, target, elements)¶ A useful method when building up SBOL representations of natural DNA sequences.
For example, it is often necessary to specify components that are assumed to have no meaningful role in the design, but are nevertheless important to fill in regions of sequence. This method autoconstructs a ComponentDefinition and Sequence object to create an arbitrary flanking sequence around design Components. The new ComponentDefinition will have Sequence Ontology type of flanking_region or SO:0000239. :param target: The new flanking sequence will be placed upstream of the target. :param elements: The primary sequence elements will be assigned to the autoconstructed Sequence object. The encoding is inferred. :return: None
-
addDownstreamFlank
(self, target, elements)¶ A useful method when building up SBOL representations of natural DNA sequences.
For example, it is often necessary to specify components that are assumed to have no meaningful role in the design, but are nevertheless important to fill in regions of sequence. This method autoconstructs a ComponentDefinition and Sequence object to create an arbitrary flanking sequence around design Components. The new ComponentDefinition will have Sequence Ontology type of flanking_sequence. :param target: The new flanking sequence will be placed downstream of the target. :param elements: The primary sequence elements will be assigned to the autoconstructed Sequence object. The encoding is inferred. :return: None
-
isRegular
(self, msg=None)¶ Use this diagnose an irregular design.
Recursively checks if this ComponentDefinition defines a SequenceAnnotation and Range for every Sequence. Regularity is more stringent than completeness. A design must be complete to be regular. :param msg: An optional message for diagnosing the irregularity, if any is found. :return: True if the abstraction hierarchy is regular, False otherwise.
-
isComplete
(self, msg=None)¶ Use this diagnose an incomplete design.
Recursively checks if this ComponentDefinition defines a SequenceAnnotation and Range for every Sequence. Completeness does not guarantee regularity. :param msg: An optional message for diagnosing the irregularity, if any is found. :return: True if the abstraction hierarchy is complete, False otherwise.
-
disassemble
(self, range_start=1)¶ Instantiates a Component for every SequenceAnnotation
When converting from a flat GenBank file to a flat SBOL file, the result is a ComponentDefinition with SequenceAnnotations. This method will convert the flat SBOL file into hierarchical SBOL.Parameters: range_start – Returns: None
-
linearize
(self, components=None)¶ TODO document
Parameters: components – An optional list of component definitions or URIs. If None, an empty list of ComponentDefinitions is assumed. :return: None
-
build
(self)¶ TODO document
Returns: A ComponentDefinition.
-
participate
(self, species)¶ A convenience method that assigns a component to participate in a biochemical reaction.
Behind the scenes, it auto-constructs a FunctionalComponent for this ComponentDefinition and assigns it to a Participation.
Parameters: species – A Participation object (ie. participant species in a biochemical Interaction). :return: None
-
getTypeURI
(self)¶ Returns: The uniform resource identifier that describes the RDF-type of this SBOL Object.
-
integrateAtBaseCoordinate
(self, target_cd, insert_cd, base_coordinate)¶ Construct SBOL representing a genetic insert. Inserts insert_cd into self at base_coordinate.
This method constructs a new ComponentDefinition that is annotated with the original sequence and the inserted sequence such that the new DNA sequence can be generated. This method does not generate the new sequence itself.
The new sequence is not generated to avoid duplicating very long sequences in memory when they are not needed.
-
-
class
sbol2.
Config
¶ A class which contains global configuration variables for the libSBOL environment.
Configuration variables are accessed through the setOption and getOption methods.
-
SBOL_DATA_MODEL_REGISTER
¶
-
register_extension_class
(builder, type_uri)¶ Register an extension class and its namespace, so custom data can be embedded into and read from SBOL files.
Parameters: - builder – A no-argument constructor
- type_uri – An RDF type URI for the extension class
-
static
setHomespace
(ns)¶ Setting the Homespace has several advantages. It simplifies object creation and retrieval from Documents. In addition, it serves as a way for a user to claim ownership of new objects. Generally users will want to specify a Homespace that corresponds to their organization’s web domain. :param ns: The namespace to use as the Homespace :return: None
-
static
getHomespace
()¶ Returns: The Homespace (a string representing the default namespace).
-
static
hasHomespace
()¶ Returns: True if Homespace is set, False otherwise.
-
static
setFileFormat
(_file_format)¶ Parameters: _file_format – The file format to use. Returns: None
-
static
getFileFormat
()¶ Returns: The file format.
-
static
setOption
(option, val)¶ Configure options for libSBOL. Access online validation and conversion.
Option | Description | Values | # noqa:————————— | :———————————————————————– | :————– |homespace | Enable validation and conversion requests through the online validator | http://examples.org |sbol_compliant_uris | Enables autoconstruction of SBOL-compliant URIs from displayIds | True or False |sbol_typed_uris | Include the SBOL type in SBOL-compliant URIs | True or False |output_format | File format for serialization | True or False |validate | Enable validation and conversion requests through the online validator | True or False |validator_url | The http request endpoint for validation | A valid URL, set to<br>http://www.async.ece.utah.edu/sbol-validator/endpoint.php by default |language | File format for conversion | SBOL2, SBOL1, FASTA, GenBank |test_equality | Report differences between two files | True or False |check_uri_compliance | If set to false, URIs in the file will not be checked for compliance<br>with the SBOL specification | True or False |check_completeness | If set to false, not all referenced objects must be described within<br>the given main_file | True or False |check_best_practices | If set to true, the file is checked for the best practice rules set<br>in the SBOL specification | True or False |fail_on_first_error | If set to true, the validator will fail at the first error | True or False |provide_detailed_stack_trace | If set to true (and failOnFirstError is true) the validator will<br>provide a stack trace for the first validation error | True or False |uri_prefix | Required for conversion from FASTA and GenBank to SBOL1 or SBOL2,<br>used to generate URIs | True or False |version | Adds the version to all URIs and to the document | A valid Maven version string |return_file | Whether or not to return the file contents as a string | True or False |Parameters: - option – The option key
- val – The option value (str or bool expected)
Returns: None
-
static
getOption
(option)¶ Get current option value for online validation and conversion
Parameters: option – The option key Returns: The option value
-
-
class
sbol2.
ConfigOptions
¶ Bases:
enum.Enum
Generic enumeration.
Derive from this class to define new enumerations.
-
HOMESPACE
= homespace¶
-
SBOL_COMPLIANT_URIS
= sbol_compliant_uris¶
-
SBOL_TYPED_URIS
= sbol_typed_uris¶
-
SERIALIZATION_FORMAT
= serialization_format¶
-
VALIDATE
= validate¶
-
VALIDATOR_URL
= validator_url¶
-
LANGUAGE
= language¶
-
TEST_EQUALITY
= test_equality¶
-
CHECK_URI_COMPLIANCE
= check_uri_compliance¶
-
CHECK_COMPLETENESS
= check_completeness¶
-
CHECK_BEST_PRACTICES
= check_best_practices¶
-
FAIL_ON_FIRST_ERROR
= fail_on_first_error¶
-
PROVIDE_DETAILED_STACK_TRACE
= provide_detailed_stack_trace¶
-
URI_PREFIX
= uri_prefix¶
-
SUBSET_URI
= subset_uri¶
-
VERSION
= version¶
-
INSERT_TYPE
= insert_type¶
-
MAIN_FILE_NAME
= main_file_name¶
-
DIFF_FILE_NAME
= diff_file_name¶
-
RETURN_FILE
= return_file¶
-
VERBOSE
= verbose¶
-
-
sbol2.
getHomespace
()¶
-
sbol2.
hasHomespace
()¶
-
sbol2.
setHomespace
(ns)¶
-
sbol2.
DEFAULT_NS
= http://examples.org/¶
-
sbol2.
SBOL_URI
= http://sbols.org/v2¶
-
sbol2.
RDF_URI
= http://www.w3.org/1999/02/22-rdf-syntax-ns#¶
-
sbol2.
PURL_URI
= http://purl.org/dc/terms/¶
-
sbol2.
PROV_URI
= http://www.w3.org/ns/prov¶
-
sbol2.
PROVO
= http://www.w3.org/ns/prov¶
-
sbol2.
SYSBIO_URI
= http://sys-bio.org¶
-
sbol2.
OM_URI
= http://www.ontology-of-units-of-measure.org/resource/om-2/¶
-
sbol2.
PYSBOL2_NS
¶
-
sbol2.
NODENAME_ABOUT
= rdf:about¶
-
sbol2.
NODENAME_RESOURCE
= rdf:resource¶
-
sbol2.
VERSION_STRING
= 1¶
-
sbol2.
SBOL_DOCUMENT
¶
-
sbol2.
SBOL_IDENTIFIED
¶
-
sbol2.
SBOL_DOCUMENTED
¶
-
sbol2.
SBOL_TOP_LEVEL
¶
-
sbol2.
SBOL_GENERIC_TOP_LEVEL
¶
-
sbol2.
SBOL_SEQUENCE_ANNOTATION
¶
-
sbol2.
SBOL_COMPONENT
¶
-
sbol2.
SBOL_FUNCTIONAL_COMPONENT
¶
-
sbol2.
SBOL_COMPONENT_DEFINITION
¶
-
sbol2.
SBOL_SEQUENCE
¶
-
sbol2.
SBOL_MODULE_DEFINITION
¶
-
sbol2.
SBOL_MODULE
¶
-
sbol2.
SBOL_MODEL
¶
-
sbol2.
SBOL_MAPS_TO
¶
-
sbol2.
SBOL_INTERACTION
¶
-
sbol2.
SBOL_PARTICIPATION
¶
-
sbol2.
SBOL_SEQUENCE_CONSTRAINT
¶
-
sbol2.
SBOL_LOCATION
¶
-
sbol2.
SBOL_RANGE
¶
-
sbol2.
SBOL_CUT
¶
-
sbol2.
SBOL_COLLECTION
¶
-
sbol2.
SBOL_GENERIC_LOCATION
¶
-
sbol2.
SBOL_VARIABLE_COMPONENT
¶
-
sbol2.
SBOL_COMBINATORIAL_DERIVATION
¶
-
sbol2.
SBOL_ATTACHMENT
¶
-
sbol2.
SBOL_IMPLEMENTATION
¶
-
sbol2.
SBOL_EXPERIMENT
¶
-
sbol2.
SBOL_EXPERIMENTAL_DATA
¶
-
sbol2.
UNDEFINED
¶
-
sbol2.
SBOL_IDENTITY
¶
-
sbol2.
SBOL_PERSISTENT_IDENTITY
¶
-
sbol2.
SBOL_VERSION
¶
-
sbol2.
SBOL_DISPLAY_ID
¶
-
sbol2.
SBOL_NAME
¶
-
sbol2.
SBOL_DESCRIPTION
¶
-
sbol2.
SBOL_TYPES
¶
-
sbol2.
SBOL_START
¶
-
sbol2.
SBOL_END
¶
-
sbol2.
SBOL_SEQUENCE_ANNOTATIONS
¶
-
sbol2.
SBOL_COMPONENTS
¶
-
sbol2.
SBOL_COMPONENT_PROPERTY
¶
-
sbol2.
SBOL_ROLES
¶
-
sbol2.
SBOL_ELEMENTS
¶
-
sbol2.
SBOL_ENCODING
¶
-
sbol2.
SBOL_SEQUENCE_PROPERTY
¶
-
sbol2.
SBOL_WAS_DERIVED_FROM
¶
-
sbol2.
SBOL_DEFINITION
¶
-
sbol2.
SBOL_ACCESS
¶
-
sbol2.
SBOL_DIRECTION
¶
-
sbol2.
SBOL_MODELS
¶
-
sbol2.
SBOL_MODULES
¶
-
sbol2.
SBOL_FUNCTIONAL_COMPONENTS
¶
-
sbol2.
SBOL_INTERACTIONS
¶
-
sbol2.
SBOL_MAPS_TOS
¶
-
sbol2.
SBOL_PARTICIPATIONS
¶
-
sbol2.
SBOL_PARTICIPANT
¶
-
sbol2.
SBOL_LOCAL
¶
-
sbol2.
SBOL_REMOTE
¶
-
sbol2.
SBOL_REFINEMENT
¶
-
sbol2.
SBOL_SOURCE
¶
-
sbol2.
SBOL_LANGUAGE
¶
-
sbol2.
SBOL_FRAMEWORK
¶
-
sbol2.
SBOL_SEQUENCE_CONSTRAINTS
¶
-
sbol2.
SBOL_SUBJECT
¶
-
sbol2.
SBOL_OBJECT
¶
-
sbol2.
SBOL_RESTRICTION
¶
-
sbol2.
SBOL_ORIENTATION
¶
-
sbol2.
SBOL_LOCATIONS
¶
-
sbol2.
SBOL_SOURCE_LOCATIONS
¶
-
sbol2.
SBOL_ROLE_INTEGRATION
¶
-
sbol2.
SBOL_MEMBERS
¶
-
sbol2.
SBOL_AT
¶
-
sbol2.
SBOL_OPERATOR
¶
-
sbol2.
SBOL_VARIABLE_COMPONENTS
¶
-
sbol2.
SBOL_VARIABLE
¶
-
sbol2.
SBOL_VARIANTS
¶
-
sbol2.
SBOL_VARIANT_COLLECTIONS
¶
-
sbol2.
SBOL_VARIANT_DERIVATIONS
¶
-
sbol2.
SBOL_STRATEGY
¶
-
sbol2.
SBOL_TEMPLATE
¶
-
sbol2.
SBOL_ATTACHMENTS
¶
-
sbol2.
SBOL_MEASUREMENTS
¶
-
sbol2.
SBOL_UNIT
¶
-
sbol2.
SBOL_VALUE
¶
-
sbol2.
SBOL_ACCESS_PRIVATE
¶
-
sbol2.
SBOL_ACCESS_PUBLIC
¶
-
sbol2.
SBOL_DIRECTION_IN
¶
-
sbol2.
SBOL_DIRECTION_OUT
¶
-
sbol2.
SBOL_DIRECTION_IN_OUT
¶
-
sbol2.
SBOL_DIRECTION_NONE
¶
-
sbol2.
SBOL_RESTRICTION_PRECEDES
¶
-
sbol2.
SBOL_RESTRICTION_SAME_ORIENTATION_AS
¶
-
sbol2.
SBOL_RESTRICTION_OPPOSITE_ORIENTATION_AS
¶
-
sbol2.
SBOL_ENCODING_IUPAC
= http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html¶
-
sbol2.
SBOL_ENCODING_IUPAC_PROTEIN
= http://www.chem.qmul.ac.uk/iupac/AminoAcid/¶
-
sbol2.
SBOL_ENCODING_SMILES
= http://www.opensmiles.org/opensmiles.html¶
-
sbol2.
SBOL_ORIENTATION_INLINE
¶
-
sbol2.
SBOL_ORIENTATION_REVERSE_COMPLEMENT
¶
-
sbol2.
SBOL_REFINEMENT_USE_REMOTE
¶
-
sbol2.
SBOL_REFINEMENT_USE_LOCAL
¶
-
sbol2.
SBOL_REFINEMENT_VERIFY_IDENTICAL
¶
-
sbol2.
SBOL_REFINEMENT_MERGE
¶
-
sbol2.
SBOL_ROLE_INTEGRATION_MERGE
¶
-
sbol2.
SBOL_ROLE_INTEGRATION_OVERRIDE
¶
-
sbol2.
SBOL_DESIGN
¶
-
sbol2.
SBOL_BUILD
¶
-
sbol2.
SBOL_TEST
¶
-
sbol2.
SBOL_LEARN
¶
-
sbol2.
PROVO_ACTIVITY
¶
-
sbol2.
PROVO_USAGE
¶
-
sbol2.
PROVO_ASSOCIATION
¶
-
sbol2.
PROVO_AGENT
¶
-
sbol2.
PROVO_PLAN
¶
-
sbol2.
PROVO_WAS_GENERATED_BY
¶
-
sbol2.
PROVO_STARTED_AT_TIME
¶
-
sbol2.
PROVO_ENDED_AT_TIME
¶
-
sbol2.
PROVO_QUALIFIED_ASSOCIATION
¶
-
sbol2.
PROVO_QUALIFIED_USAGE
¶
-
sbol2.
PROVO_WAS_INFORMED_BY
¶
-
sbol2.
PROVO_HAD_PLAN
¶
-
sbol2.
PROVO_HAD_ROLE
¶
-
sbol2.
PROVO_AGENT_PROPERTY
¶
-
sbol2.
PROVO_ENTITY
¶
-
sbol2.
SBO
= http://identifiers.org/biomodels.sbo/SBO:¶
-
sbol2.
SBO_INTERACTION
¶
-
sbol2.
SBO_INHIBITION
¶
-
sbol2.
SBO_GENETIC_PRODUCTION
¶
-
sbol2.
SBO_NONCOVALENT_BINDING
¶
-
sbol2.
SBO_STIMULATION
¶
-
sbol2.
SBO_DEGRADATION
¶
-
sbol2.
SBO_CONTROL
¶
-
sbol2.
SBO_BIOCHEMICAL_REACTION
¶
-
sbol2.
SBO_STIMULATED
¶
-
sbol2.
SBO_CONVERSION
¶
-
sbol2.
SBO_PROMOTER
¶
-
sbol2.
SBO_GENE
¶
-
sbol2.
SBO_INHIBITOR
¶
-
sbol2.
SBO_INHIBITED
¶
-
sbol2.
SBO_STIMULATOR
¶
-
sbol2.
SBO_REACTANT
¶
-
sbol2.
SBO_PRODUCT
¶
-
sbol2.
SBO_LIGAND
¶
-
sbol2.
SBO_NONCOVALENT_COMPLEX
¶
-
sbol2.
SBO_BINDING_SITE
¶
-
sbol2.
SBO_SUBSTRATE
¶
-
sbol2.
SBO_COFACTOR
¶
-
sbol2.
SBO_SIDEPRODUCT
¶
-
sbol2.
SBO_ENZYME
¶
-
sbol2.
SO
= http://identifiers.org/so/SO:¶
-
sbol2.
SO_MISC
¶
-
sbol2.
SO_GENE
¶
-
sbol2.
SO_PROMOTER
¶
-
sbol2.
SO_CDS
¶
-
sbol2.
SO_RBS
¶
-
sbol2.
SO_TERMINATOR
¶
-
sbol2.
SO_SGRNA
¶
-
sbol2.
SO_LINEAR
¶
-
sbol2.
SO_CIRCULAR
¶
-
sbol2.
SO_PLASMID
¶
-
sbol2.
BIOPAX_DNA
= http://www.biopax.org/release/biopax-level3.owl#DnaRegion¶
-
sbol2.
BIOPAX_RNA
= http://www.biopax.org/release/biopax-level3.owl#RnaRegion¶
-
sbol2.
BIOPAX_PROTEIN
= http://www.biopax.org/release/biopax-level3.owl#Protein¶
-
sbol2.
BIOPAX_SMALL_MOLECULE
= http://www.biopax.org/release/biopax-level3.owl#SmallMolecule¶
-
sbol2.
BIOPAX_COMPLEX
= http://www.biopax.org/release/biopax-level3.owl#Complex¶
-
sbol2.
EDAM_SBML
= http://identifiers.org/edam/format_2585¶
-
sbol2.
EDAM_CELLML
= http://identifiers.org/edam/format_3240¶
-
sbol2.
EDAM_BIOPAX
= http://identifiers.org/edam/format_3156¶
-
sbol2.
SBO_CONTINUOUS
¶
-
sbol2.
SBO_DISCRETE
¶
-
sbol2.
SYSBIO_DESIGN
¶
-
sbol2.
SYSBIO_BUILD
¶
-
sbol2.
SYSBIO_TEST
¶
-
sbol2.
SYSBIO_ANALYSIS
¶
-
sbol2.
SYSBIO_SAMPLE_ROSTER
¶
-
sbol2.
IGEM_URI
= http://wiki.synbiohub.org/wiki/Terms/igem¶
-
sbol2.
OM_NS
¶
-
sbol2.
OM_MEASURE
:str¶
-
sbol2.
OM_HAS_UNIT
:str¶
-
sbol2.
OM_HAS_NUMERICAL_VALUE
:str¶
-
class
sbol2.
Design
(uri='example', version=VERSION_STRING, structure=None, function=None)¶ Bases:
TopLevel
This class represents a biological Design. A Design is a conceptual representation of a biological system that a synthetic biologist intends to build. A Design is the first object created in libSBOL’s formalized Design-Build-Test-Analysis workflow.
-
generateDesign
(self, uri, agent=None, plan=None, usages=None)¶
-
-
class
sbol2.
Document
(filename=None)¶ Bases:
sbol2.identified.Identified
The Document is a container for all SBOL data objects.
In a previous era, engineers might sit at a drafting board and draft a design by hand. The engineer’s drafting sheet in LibSBOL is called a Document. The Document serves as a container, initially empty, for SBOL data objects. All file I/O operations are performed on the Document to populate it with SBOL objects representing design elements.
-
compare
(self, other)¶ Compare two SBOLObjects. The behavior is currently undefined for objects with custom annotations or extension classes.
Parameters: other – The object being compared to this one. Returns: True if the objects are identical, False if they are different.
-
addCitation
(self, new_citation)¶
-
removeCitation
(self, index=0)¶
-
addKeyword
(self, new_keyword)¶
-
removeKeyword
(self, index=0)¶
-
add
(self, sbol_obj)¶ Register an object in the Document.
Parameters: sbol_obj – The SBOL object(s) you want to serialize. Either a single object or a list of objects. Returns: None
-
add_list
(self, sbol_objs)¶
-
addNamespace
(self, namespace, prefix)¶ Add a new namespace to the Document.
Parameters: - namespace – The namespace, eg. http://sbols.org/v2#
- prefix – The namespace prefix, eg. sbol
Returns:
-
addComponentDefinition
(self, sbol_obj)¶ Convenience method for adding a component definition.
Parameters: sbol_obj – component definition Returns: None
-
addModuleDefinition
(self, sbol_obj)¶ Convenience method for adding a module definition.
Parameters: sbol_obj – module definition Returns: None
-
addCollection
(self, sbol_obj)¶ Convenience method for adding a collection.
Parameters: sbol_obj – a Collection Returns: None
-
addSequence
(self, sbol_obj)¶ Convenience method for adding a sequence.
Parameters: sbol_obj – sequence Returns: None
-
addModel
(self, sbol_obj)¶ Convenience method for adding a model.
Parameters: sbol_obj – model Returns: None
-
addImplementation
(self, implementation)¶ Convenience method for adding an implementation.
-
addAttachment
(self, attachment)¶ Add an attachment to this document.
-
create
(self, uri)¶ Creates another SBOL object derived from TopLevel and adds it to the Document. NOTE: originally from ReferencedObject :param uri: In “open world” mode, this is a full URI and the same as the returned URI. If the default namespace for libSBOL has been configured, then this argument should simply be a local identifier. If SBOL-compliance is enabled, this argument should be the intended displayId of the new object. A full URI is automatically generated and returned. :return: The full URI of the created object
-
get
(self, uri)¶ Finds the SBOL object with the given URI.
Parameters: uri (str) – URI of the extension object Returns: The matching SBOLObject Return type: SBOLObject Raises: SBOLError if the given uri is not found
-
getAll
(self)¶ Retrieve a list of objects from the Document.
Returns: A list of objects from the Document.
-
getComponentDefinition
(self, uri)¶
-
getModuleDefinition
(self, uri)¶
-
getSequence
(self, uri)¶
-
getModel
(self, uri)¶
-
getImplementation
(self, uri)¶
-
getCollection
(self, uri: str)¶
-
write
(self, filename)¶ Serialize all objects in this Document to an RDF/XML file.
Parameters: filename – The full name of the file you want to write (including file extension). :return: A string with the validation results, or empty string if validation is disabled.
-
read
(self, filename)¶ Read an RDF/XML file and attach the SBOL objects to this Document.
Existing contents of the Document will be wiped. :param filename: The full name of the file you want to read (including file extension). :return: None
-
readString
(self, sbol_str)¶ Convert text in SBOL into data objects.
Parameters: sbol_str – A string formatted in SBOL. Returns: None
-
writeString
(self)¶ Convert data objects in this Document into textual SBOL.
Returns: A string representation of the objects in this Document.
-
append
(self, filename)¶ Read an RDF/XML file and attach the SBOL objects to this Document.
New objects will be added to the existing contents of the Document. :param filename: The full name of the file you want to read (including file extension). :return: None
-
parse_all
(self)¶
-
parse_objects_inner
(self, subject, obj)¶
-
parse_properties_inner
(self, subject, predicate, obj)¶
-
find_reference
(self, uri)¶ Find objects that reference the given URI. Returns a list of objects. The list will be empty if no references were found.
-
parse_annotation_objects
(self)¶ Parse leftover objects from reading and link them up where they belong. These are usually extension-type objects.
-
infer_resource_namespaces
(self)¶
-
dress_document
(self)¶
-
convert_ntriples_encoding_to_ascii
(self, s)¶
-
request_comparison
(self, diff_file)¶ Perform comparison on Documents using the online validation tool.
This is for cross-validation of SBOL documents with libSBOLj. Document comparison can also be performed using the built-in compare method. :param diff_file: :return: The comparison results
-
clear
(self, clear_graph=True)¶ Delete all properties and objects in the Document.
Returns: None
-
query_repository
(self, command)¶ Parameters: command – Returns: str
-
search_metadata
(self, role, type, name, collection)¶ Parameters: - role –
- type –
- name –
- collection –
Returns: str
-
doc_serialize_rdf2xml
(self, outfile)¶ Serialize RDF XML. :param outfile: output file :return: None
-
update_graph
(self)¶ Update the RDF triples representation of data. :return:
-
validate
(self)¶ Run validation on this Document via the online validation tool.
Returns: A string containing a message with the validation results Return type: str
-
size
(self)¶ Get the total number of objects in the Document, including SBOL core object and custom annotation objects.
Returns: The total number of objects in the Document.
-
__len__
(self)¶ Get the total number of objects in the Document, including SBOL core object and custom annotation objects.
(Returns the same thing as size())
Returns: The total number of objects in the Document.
-
__bool__
(self)¶
-
__str__
(self)¶ Produce a string representation of the Document.
Returns: A string representation of the Document.
-
__iter__
(self)¶
-
__next__
(self)¶
-
cacheObjectsDocument
(self)¶
-
referenceNamespace
(self, uri)¶ Replaces the namespace with a reference and removes the default namespace, shortening the URI. :param uri: :return: str
-
summary
(self)¶ Produce a string representation of the Document.
Returns: A string representation of the Document.
-
find
(self, uri)¶ Search recursively for an SBOLObject in this Document that matches the uri.
Parameters: uri – The identity of the object to search for. Returns: A pointer to the SBOLObject, or NULL if an object with this identity doesn’t exist.
-
getTypeURI
(self)¶ Returns: The uniform resource identifier that describes the RDF-type of this SBOL Object.
-
getTopLevel
(self, uri)¶
-
copy
(self, target_namespace=None, target_doc=None, version=None)¶
-
exportToFormat
(self, language: str, output_path: str)¶
-
convert
(self, language, output_path)¶
-
getExtensionObject
(self, uri: str)¶ Deprecated. Use Document.get instead.
Parameters: uri (str) – URI of the extension object Returns: The matching SBOLObject Return type: SBOLObject Raises: SBOLError if the given uri is not found
-
addExtensionObject
(self, obj: SBOLObject)¶ Deprecated. Use Document.add instead.
Parameters: obj (SBOLObject) – An SBOLObject to add to this document Returns: None
-
-
sbol2.
IGEM_STANDARD_ASSEMBLY
(parts_list)¶
-
class
sbol2.
Experiment
(uri=URIRef('example'), version=VERSION_STRING)¶ Bases:
sbol2.toplevel.TopLevel
-
class
sbol2.
ExperimentalData
(uri=URIRef('example'), version=VERSION_STRING)¶ Bases:
sbol2.toplevel.TopLevel
-
class
sbol2.
Identified
(type_uri=SBOL_IDENTIFIED, uri=URIRef('example'), version=VERSION_STRING)¶ Bases:
sbol2.object.SBOLObject
-
version
:Union[str, VersionProperty]¶
-
generate
(self)¶
-
update_uri
(self)¶ Recursively generates SBOL compliant ids for an object and all its owned objects, then checks to make sure that these ids are unique. :return: None
-
copy
(self, target_doc=None, target_namespace=None, version=None)¶
-
-
class
sbol2.
Implementation
(uri=URIRef('example'), version=VERSION_STRING, *, type_uri=SBOL_IMPLEMENTATION)¶ Bases:
sbol2.toplevel.TopLevel
-
class
sbol2.
Interaction
(uri='example', interaction_type=SBO_INTERACTION, *, type_uri=SBOL_INTERACTION, version=VERSION_STRING)¶ Bases:
sbol2.identified.Identified
-
class
sbol2.
Location
(uri=URIRef('example'), orientation=SBOL_ORIENTATION_INLINE, *, type_uri=SBOL_LOCATION, version=VERSION_STRING)¶ Bases:
sbol2.identified.Identified
The Location class specifies the strand orientation of a Component.
-
class
sbol2.
Range
(uri=URIRef('example'), start=1, end=2, *, type_uri=SBOL_RANGE, version=VERSION_STRING)¶ Bases:
sbol2.location.Location
A Range object specifies a region via discrete, inclusive start and end positions that correspond to indices for characters in the elements String of a Sequence. Note that the index of the first location is 1, as is typical practice in biology, rather than 0, as is typical practice in computer science.
-
precedes
(self, comparand)¶
-
follows
(self, comparand)¶
-
adjoins
(self, comparand)¶
-
contains
(self, comparand)¶
-
overlaps
(self, comparand)¶
-
length
(self)¶
-
-
class
sbol2.
Cut
(uri=URIRef('example'), at=0, *, type_uri=SBOL_CUT, version=VERSION_STRING)¶ Bases:
sbol2.location.Location
The Cut class specifies a location between two coordinates of a Sequence’s elements.
-
class
sbol2.
GenericLocation
(uri=URIRef('example'), *, type_uri=SBOL_GENERIC_LOCATION, version=VERSION_STRING)¶ Bases:
sbol2.location.Location
the GenericLocation class is included as a starting point for specifying regions on Sequence objects with encoding properties other than IUPAC and potentially nonlinear structure. This class can also be used to set the orientation of a SequenceAnnotation and any associated Component when their parent ComponentDefinition is a partial design that lacks a Sequence.
-
class
sbol2.
Measurement
(uri=URIRef('example'), value=0.0, unit='', version=VERSION_STRING)¶ Bases:
sbol2.identified.Identified
The purpose of the Measure class is to link a numerical value to a unit of measure.
-
addType
(self, new_type)¶
-
removeType
(self, index=0)¶
-
-
class
sbol2.
Module
(uri='example', *, definition='', version=VERSION_STRING, type_uri=SBOL_MODULE)¶ Bases:
sbol2.identified.Identified
An SBOLObject converts a Python data structure into an RDF triple store and contains methods for serializing and parsing RDF triples.
-
class
sbol2.
ModuleDefinition
(uri=rdflib.URIRef('example'), version=VERSION_STRING, type_uri=SBOL_MODULE_DEFINITION)¶ Bases:
sbol2.toplevel.TopLevel
ModuleDefinition is a principle top-level class for describing the function of a design.
-
_roles
¶
-
modules
¶
-
interactions
¶
-
functionalComponents
¶
-
models
¶
-
addRole
(self, new_role)¶
-
removeRole
(self, index=0)¶
-
setOutput
(self, output)¶ Defines an output for a sub-Module. Useful for top-down assembly of Modules and sub-Modules.
If a FunctionalComponent with the given definition does not exist yet, one will be autoconstructed. Otherwise the FunctionalComponent with the given definition will be inferred. Be warned that this inference may fail if there is more than one FunctionalComponent with the same definition.
Parameters: output – A ComponentDefinition that defines the output Returns: A FunctionalComponent that is derived from the argument ComponentDefinition and configured as this ModuleDefinition’s output (it’s direction property is set to SBOL_DIRECTION_OUT)
-
setOutputFunctional
(self, output)¶ Configures a FunctionalComponent as an output for a Module.
Useful for bottom-up assembly of Modules and sub-Modules.
Parameters: output – The FunctionalComponent that will be configured Returns: None
-
setInput
(self, input)¶ Defines an input for a sub-Module. Useful for top-down assembly of Modules and sub-Modules.
If a FunctionalComponent with the given definition does not exist yet, one will be autoconstructed. Otherwise the FunctionalComponent with the given definition will be inferred. Be warned that this inference may fail if there is more than one FunctionalComponent with the same definition.
Parameters: input – A ComponentDefinition that defines the input. Returns: A FunctionalComponent that is derived from the argument ComponentDefinition and configured as this ModuleDefinition’s input (it’s direction property is set to SBOL_DIRECTION_IN).
-
setInputFunctional
(self, input)¶ Configures a FunctionalComponent as an input for a Module.
Useful for bottom-up assembly of Modules and sub-Modules.
Parameters: input – The FunctionalComponent that will be configured. Returns: None
-
connect
(self, output, input)¶ Connects the output of a sub-Module with the input of another sub-Module. Auto-constructs MapsTo objects.
Parameters: output – A FunctionalComponent configured as a Module output (see setOutput). :param input: A FunctionalComponent configured as a Module input (see setInput). :return: None
-
override
(self, highlevel, lowlevel)¶ Overrides a low-level component in an abstract sub-Module with a high-level component in a parent ModuleDefinition, for example when overriding an abstract template Module with explicit components.
Parameters: - highlevel – A high-level FunctionalComponent
- lowlevel – A low-level FunctionalComponent in a nested sub-Module
Returns: None
-
applyToModuleHierarchy
(self, callback=None, user_data=None)¶ Perform an operation on every ModuleDefinition in a structurally-linked hierarchy of ModuleDefinitions by applying a callback function. If no callback is specified, the default behavior is to return a list of each ModuleDefinition in the hierarchy.
Parameters: - callback – A callback function
- user_data – Arbitrary user data which can be passed in and out
of the callback as an argument. :return: A list of all ModuleDefinitions in the hierarchy.
-
assemble
(self, list_of_modules)¶ Assemble a high-level ModuleDefinition from lower-level submodules.
Autoconstructs Module objects in the process.
Parameters: list_of_modules – A list of submodule ModuleDefinitions. Returns: None
-
getTypeURI
(self)¶ Returns: The uniform resource identifier that describes the RDF-type of this SBOL Object.
-
-
class
sbol2.
SBOLObject
(type_uri=rdflib.URIRef(UNDEFINED), uri=rdflib.URIRef('example'))¶ An SBOLObject converts a Python data structure into an RDF triple store and contains methods for serializing and parsing RDF triples.
-
logger
¶
-
type
¶
-
this
¶
-
_serialize
(self)¶
-
_nest
(self)¶
-
_makeQName
(self, uri)¶
-
__uri__
(self)¶ Returns a URIRef representing this object.
Returns: The identity of this object as an rdflib.URIRef Return type: rdflib.URIRef
-
getTypeURI
(self)¶ Returns: The uniform resource identifier that describes the RDF-type of this SBOL Object.
-
getClassName
(self, rdf_type)¶ Parses a local class name from the RDF-type of this SBOL Object.
-
cast
(self, cls)¶
-
find
(self, uri)¶ Search this object recursively to see if an object or any child object with URI already exists.
Parameters: uri – The URI to search for. Returns: The SBOLObject associated with this URI if it exists, None otherwise.
-
cacheObjects
(self, objectCache)¶ TODO document
Parameters: objectCache – a dictionary mapping strings to SBOLObjects Returns: None
-
find_property
(self, uri)¶ Search this object recursively to see if it contains a member property with the given RDF type.
Parameters: uri – The RDF type of the property to search for. Returns: The SBOLObject that contains a member property with the specified RDF type, None otherwise
-
find_property_value
(self, uri, value, matches=None)¶ Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.
Parameters: - uri – The RDF type of the property to search for.
- value – The property value to match.
- matches –
Returns: A vector containing all objects found that contain
a member property with the specified RDF type
-
find_reference
(self, uri)¶ Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.
Parameters: uri – A URI, either an ontology term or an object reference, to search for. :return: A vector containing all objects found that contain the URI in a property value.
-
compare
(self, other)¶ Compare two SBOLObjects. The behavior is currently undefined for objects with custom annotations or extension classes.
Parameters: other – The object being compared to this one. Returns: True if the objects are identical, False if they are different.
-
getPropertyValue
(self, property_uri: str)¶ Get the value of a custom annotation property by its URI.
Parameters: property_uri (str) – The URI for the property. Returns: The value of the property. Return type: str Raises: SBOLError(SBOL_ERROR_NOT_FOUND) if property does not exist
-
getPropertyValues
(self, property_uri: str)¶ Get all values of a custom annotation property by its URI.
Parameters: property_uri (str) – The URI for the property. Returns: A vector of property values. Return type: list of strings Raises: SBOLError(SBOL_ERROR_NOT_FOUND) if property does not exist
-
getProperties
(self)¶ Gets URIs for all properties contained by this object. This includes SBOL core properties as well as custom annotations. Use this to find custom extension data in an SBOL file.
Returns: A vector of URIs that identify the properties contained in this object.
-
setPropertyValue
(self, property_uri, val)¶ Set and overwrite the value for a user-defined annotation property.
Parameters: - property_uri –
- val – A string
Returns: None
-
addPropertyValue
(self, property_uri, val)¶ Append a value to a user-defined annotation property.
Parameters: - property_uri –
- val – Either a literal or URI value.
Returns: None
-
setAnnotation
(self, property_uri, val)¶ Set the value for a user-defined annotation property. Synonymous with setPropertyValue.
Parameters: - property_uri –
- val – If the value is a URI,
it should be surrounded by angle brackets, else it will be interpreted as a literal value. :return: None
-
getAnnotation
(self, property_uri)¶ Get the value of a custom annotation property by its URI. Synonymous with getPropertyValue.
Parameters: property_uri – The URI for the property. Returns: The value of the property or SBOL_ERROR_NOT_FOUND.
-
apply
(self, callback, user_data)¶ Recursively call this callback function on the user_data provided :param callback: the callback function :param user_data: the input to the callback :return: None
-
update_uri
(self)¶ Recursively generates SBOL compliant ids for an object and all its owned objects, then checks to make sure that these ids are unique. :return: None
-
build_graph
(self, graph)¶
-
__str__
(self)¶ Return str(self).
-
is_top_level
(self)¶
-
__getattribute__
(self, name)¶ Return getattr(self, name).
-
_is_transparent_attribute
(self, name)¶
-
_set_transparent_attribute
(self, name, value)¶
-
__setattr__
(self, name, value)¶ Implement setattr(self, name, value).
-
_added_to_document
(self, doc)¶ Classes can override this method to do extra work when being added to a document.
-
-
class
sbol2.
Participation
(type_uri=SBOL_PARTICIPATION, uri=URIRef('example'), participant='', version=VERSION_STRING)¶ Bases:
sbol2.identified.Identified
-
addRole
(self, new_role)¶
-
removeRole
(self, index=0)¶
-
define
(self, species, role='')¶
-
-
class
sbol2.
SearchQuery
(search_target: str = SBOL_COMPONENT_DEFINITION, offset: int = 0, limit: int = 25)¶ Bases:
sbol2.toplevel.TopLevel
Search terms to support PartShop advanced search.
-
__setitem__
(self, key, value)¶
-
__getitem__
(self, item)¶
-
query_dict
(self)¶ Convert this search query to a query dictionary suitable for urllib.parse.urlencode().
-
-
class
sbol2.
DateTimeProperty
(property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None)¶ Bases:
sbol2.property.LiteralProperty
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
convert_to_user
(self, value)¶
-
convert_from_user
(self, value)¶
-
-
class
sbol2.
FloatProperty
(property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None)¶ Bases:
sbol2.property.LiteralProperty
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
convert_to_user
(self, value: rdflib.Literal)¶
-
convert_from_user
(self, value: Any)¶ Raises: ValueError if value cannot be converted to float
-
-
class
sbol2.
IntProperty
(property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None)¶ Bases:
sbol2.property.LiteralProperty
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
convert_to_user
(self, value)¶
-
convert_from_user
(self, value)¶
-
-
class
sbol2.
LiteralProperty
(property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None)¶ Bases:
sbol2.property.Property
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
value
¶
-
getSinglePropertyValue
(self)¶
-
getPropertyValueList
(self)¶
-
set
(self, new_value)¶
-
setSinglePropertyValue
(self, new_value)¶
-
setPropertyValueList
(self, new_value)¶
-
add
(self, new_value)¶ Appends the new value to a list of values, for properties that allow it.
-
convert_to_user
(self, value)¶
-
convert_from_user
(self, value)¶
-
-
class
sbol2.
OwnedObject
(property_owner, sbol_uri, builder, lower_bound, upper_bound, validation_rules=None, first_object=None)¶ Bases:
sbol2.property.Property
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
value
¶
-
create
(self, uri, builder=None)¶ Creates an instance appropriate for this owned object collection.
uri - the name of the object
-
add
(self, sbol_obj)¶ Appends the new value to a list of values, for properties that allow it.
-
__getitem__
(self, id)¶
-
get_int
(self, id)¶
-
find
(self, query)¶ Check if a value in this property matches the query.
-
get_uri
(self, id)¶
-
find_persistent_identity
(self, search_uri)¶
-
find_resource
(self, uri, resource_namespaces, object_store, parent_obj, typedURI=False)¶
-
get
(self, uri='')¶
-
__setitem__
(self, rdf_type, sbol_obj)¶
-
convert_to_user
(self, value)¶
-
getSinglePropertyValue
(self)¶
-
getPropertyValueList
(self)¶
-
set
(self, new_value)¶
-
setSinglePropertyValue
(self, new_value)¶
-
setPropertyValueList
(self, new_value)¶
-
remove
(self, identifier)¶ id can be either an integer index or a string URI
-
removeOwnedObject_int
(self, index)¶
-
removeOwnedObject_str
(self, uri)¶
-
clear
(self)¶ Clear all property values.
-
__len__
(self)¶
-
-
class
sbol2.
ReferencedObject
(property_owner, type_uri, reference_type_uri, lower_bound, upper_bound, validation_rules, initial_value=None)¶ Bases:
sbol2.property.URIProperty
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
value
¶
-
get
(self, item)¶ Return reference object at this index. :param item (int) the index
-
set
(self, new_value)¶
-
_to_uri
(self, obj)¶ Converts strings, URIRefs, and sbol.Identified instances into rdflib.URIRefs.
-
setSinglePropertyValue
(self, new_value)¶
-
setPropertyValueList
(self, new_value)¶
-
add
(self, uri)¶ Appends the new value to a list of values, for properties that allow it.
-
addReference
(self, uri)¶
-
_ensure_uri_ref
(self, thing)¶ This method ensures that what gets returned is an rdflib.URIRef. If the set methods are working properly, this should be unnecessary. Hence the warning message if what it finds is not a URIRef. The goal is to remove this method eventually.
-
-
class
sbol2.
TextProperty
(property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None)¶ Bases:
sbol2.property.LiteralProperty
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
convert_to_user
(self, value)¶
-
-
class
sbol2.
URIProperty
(property_owner, type_uri, lower_bound, upper_bound, validation_rules, initial_value=None)¶ Bases:
sbol2.property.Property
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
value
¶
-
getSinglePropertyValue
(self)¶
-
getPropertyValueList
(self)¶
-
set
(self, new_value)¶
-
setSinglePropertyValue
(self, new_value)¶
-
setPropertyValueList
(self, value)¶
-
add
(self, new_value)¶ Appends the new value to a list of values, for properties that allow it.
-
convert_to_user
(self, value)¶
-
convert_from_user
(self, value)¶
-
-
class
sbol2.
Activity
(uri=URIRef('example'), action_type='', version=VERSION_STRING, type_uri=PROVO_ACTIVITY)¶ Bases:
sbol2.toplevel.TopLevel
A generated Entity is linked through a wasGeneratedBy relationship to an Activity, which is used to describe how different Agents
and other entities were used. An Activity is linked through aa qualifiedAssociation to Associations, to describe the role of agents, and is linked through qualifiedUsage to Usages to describe the role of other entities used as part of the activity. Moreover, each Activity includes optional startedAtTime and endedAtTime properties. When using Activity to capture how an entity was derived, it is expected that any additional information needed will be attached as annotations. This may include software settings or textual notes. Activities can also be linked together using the wasInformedBy relationship to provide dependency without explicitly specifying start and end times.
-
_startedAtTime
¶
-
_endedAtTime
¶
-
wasInformedBy
¶
-
associated
¶
-
usages
¶
-
agent
¶
-
plan
¶
-
-
class
sbol2.
Agent
(uri=URIRef('example'), version=VERSION_STRING, type_uri=PROVO_AGENT)¶ Bases:
sbol2.toplevel.TopLevel
Examples of agents are person, organisation or software. These agents should be annotated with additional information, such as software version needed to be able to run the same software again.
-
class
sbol2.
Association
(uri=URIRef('example'), agent=None, role=None, version=VERSION_STRING, type_uri=PROVO_ASSOCIATION)¶ Bases:
sbol2.identified.Identified
-
agent
¶
-
_roles
¶
-
plan
¶
-
addRole
(self, new_role)¶
-
removeRole
(self, index=0)¶
-
-
class
sbol2.
Plan
(uri=URIRef('example'), version=VERSION_STRING, type_uri=PROVO_PLAN)¶ Bases:
sbol2.toplevel.TopLevel
-
class
sbol2.
Usage
(uri=URIRef('example'), entity=None, role=None, version=VERSION_STRING, type_uri=PROVO_USAGE)¶ Bases:
sbol2.identified.Identified
-
_entity
¶
-
_roles
¶
-
addRole
(self, new_role)¶
-
removeRole
(self, index=0)¶
-
-
exception
sbol2.
SBOLError
(err: SBOLErrorCode, message: Any)¶ Bases:
Exception
Common base class for all non-exit exceptions.
-
what
(self)¶
-
error_code
(self)¶
-
-
class
sbol2.
SBOLErrorCode
¶ Bases:
enum.Enum
Generic enumeration.
Derive from this class to define new enumerations.
-
DUPLICATE_URI_ERROR
= 1¶
-
NOT_FOUND_ERROR
= 2¶
-
SBOL_ERROR_NOT_FOUND
= 3¶
-
END_OF_LIST
= 4¶
-
SBOL_ERROR_END_OF_LIST
= 5¶
-
SBOL_ERROR_SERIALIZATION
= 6¶
-
SBOL_ERROR_PARSE
= 7¶
-
SBOL_ERROR_MISSING_NAMESPACE
= 8¶
-
SBOL_ERROR_NONCOMPLIANT_VERSION
= 9¶
-
SBOL_ERROR_COMPLIANCE
= 10¶
-
SBOL_ERROR_MISSING_DOCUMENT
= 11¶
-
SBOL_ERROR_INVALID_ARGUMENT
= 12¶
-
SBOL_ERROR_FILE_NOT_FOUND
= 13¶
-
SBOL_ERROR_ORPHAN_OBJECT
= 14¶
-
SBOL_ERROR_TYPE_MISMATCH
= 15¶
-
SBOL_ERROR_BAD_HTTP_REQUEST
= 16¶
-
SBOL_ERROR_URI_NOT_UNIQUE
= 17¶
-
SBOL_ERROR_HTTP_UNAUTHORIZED
= 18¶
-
-
class
sbol2.
Sequence
(uri=URIRef('example'), elements='', encoding=SBOL_ENCODING_IUPAC, version=VERSION_STRING, type_uri=SBOL_SEQUENCE)¶ Bases:
sbol2.toplevel.TopLevel
The primary structure (eg, nucleotide or amino acid sequence) of a ComponentDefinition object.
-
__len__
(self)¶ Returns: The length of the primary sequence in the elements property.
-
__bool__
(self)¶
-
length
(self)¶ Returns: The length of the primary sequence in the elements property.
-
synthesize
(self, clone_id)¶ Parameters: clone_id – A URI for the build, or displayId if working in SBOLCompliant mode. :return:
-
compile
(self, composite_sequence='', assembly_method=None)¶
-
-
class
sbol2.
SequenceAnnotation
(uri='example', version=VERSION_STRING)¶ Bases:
sbol2.identified.Identified
-
addRole
(self, new_role)¶
-
removeRole
(self, index=0)¶
-
precedes
(self, comparand)¶ Tests if the comparand SequenceAnnotation precedes this one according to base coordinates
Parameters: comparand – Another SequenceAnnotation Returns: true or false
-
follows
(self, comparand)¶ Tests if the comparand SequenceAnnotation follows this one according to base coordinates
Parameters: comparand – Another SequenceAnnotation Returns: true or false
-
contains
(self, comparand)¶ Tests if the comparand SequenceAnnotation is contained within the same start and end base coordinates as this one. This is mutually exclusive with overlaps.
Parameters: comparand – Another SequenceAnnotation Returns: true or false
-
overlaps
(self, comparand)¶ Tests if the comparand SequenceAnnotation overlaps with this one in the primary sequence
Parameters: comparand – Another SequenceAnnotation Returns: true or false
-
extract
(self, start_reference=1)¶ Convert a SequenceAnnotation to a subcomponent
Parameters: start_reference – Returns: A ComponentDefinition representing the subcomponent
-
length
(self)¶ Returns: The length of a SequenceAnnotation in base coordinates.
-
-
class
sbol2.
TopLevel
(type_uri=SBOL_TOP_LEVEL, uri=URIRef('example'), version=VERSION_STRING)¶ Bases:
sbol2.identified.Identified
All SBOL classes derived from TopLevel appear as top level nodes in the RDF/XML document tree and SBOL files.
-
addToDocument
(self, document)¶
-
generateTopLevel
(self, uri, agent=None, plan=None, usages=None)¶ Parameters: uri – A URI for the new object, or a displayId if operating in SBOLCompliant mode Returns:
-
initialize
(self, uri)¶
-
update_uri
(self)¶ Recursively generates SBOL compliant ids for an object and all its owned objects, then checks to make sure that these ids are unique. :return: None
-
is_top_level
(self)¶
-
-
sbol2.
is_alphanumeric_or_underscore
(c)¶
-
sbol2.
is_not_alphanumeric_or_underscore
(c)¶
-
class
sbol2.
VersionProperty
(property_owner, type_uri, lower_bound, upper_bound, validation_rules=None, initial_value=None)¶ Bases:
sbol2.property.LiteralProperty
Member properties of all SBOL objects are defined using a Property object.
The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.
-
convert_to_user
(self, value)¶
-
convert_from_user
(self, value)¶
-
static
_make_version
(major: int, minor: int, micro: int)¶
-
static
increment_major
(version: str)¶
-