pySBOL2
v1.0
Introduction
Installation
Getting Started with SBOL
Biological Parts Repositories
Computer-aided Design for Synthetic Biology
SBOL Extensions
API Reference
pySBOL2
Docs
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Index
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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__bool__() (sbol2.Document method)
(sbol2.Sequence method)
(sbol2.document.Document method)
(sbol2.sequence.Sequence method)
__contains__() (sbol2.property.Property method)
(sbol2.uridict.URIDict method)
__delitem__() (sbol2.uridict.URIDict method)
__getattribute__() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
__getitem__() (sbol2.OwnedObject method)
(sbol2.SearchQuery method)
(sbol2.property.OwnedObject method)
(sbol2.searchquery.SearchQuery method)
(sbol2.uridict.URIDict method)
__iter__() (sbol2.Document method)
(sbol2.document.Document method)
__len__() (sbol2.Document method)
(sbol2.OwnedObject method)
(sbol2.Sequence method)
(sbol2.document.Document method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
(sbol2.sequence.Sequence method)
__next__() (sbol2.Document method)
(sbol2.document.Document method)
__setattr__() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
__setitem__() (sbol2.OwnedObject method)
(sbol2.SearchQuery method)
(sbol2.property.OwnedObject method)
(sbol2.searchquery.SearchQuery method)
(sbol2.uridict.URIDict method)
__str__() (sbol2.Document method)
(sbol2.SBOLObject method)
(sbol2.document.Document method)
(sbol2.object.SBOLObject method)
(sbol2.property.Property method)
__uri__() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
__version__ (in module sbol2)
_added_to_document() (sbol2.ComponentDefinition method)
(sbol2.SBOLObject method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.object.SBOLObject method)
_compare_owned_objects() (in module sbol2.object)
_compare_properties() (in module sbol2.object)
_endedAtTime (sbol2.Activity attribute)
(sbol2.provo.Activity attribute)
_ensure_uri_ref() (sbol2.property.ReferencedObject method)
(sbol2.ReferencedObject method)
_entity (sbol2.provo.Usage attribute)
(sbol2.Usage attribute)
_is_transparent_attribute() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
_isHidden() (sbol2.property.Property method)
_make_search_item() (sbol2.partshop.PartShop method)
_make_validation_request() (in module sbol2.document)
_make_version() (sbol2.VersionProperty static method)
(sbol2.versionproperty.VersionProperty static method)
_makeQName() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
_nest() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
_role_set_role_integration() (sbol2.Component static method)
(sbol2.component.Component static method)
_roles (sbol2.Association attribute)
(sbol2.ComponentDefinition attribute)
(sbol2.ModuleDefinition attribute)
(sbol2.Usage attribute)
(sbol2.componentdefinition.ComponentDefinition attribute)
(sbol2.moduledefinition.ModuleDefinition attribute)
(sbol2.provo.Association attribute)
(sbol2.provo.Usage attribute)
_search() (sbol2.partshop.PartShop method)
_search_count() (sbol2.partshop.PartShop method)
_serialize() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
_set_transparent_attribute() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
_startedAtTime (sbol2.Activity attribute)
(sbol2.provo.Activity attribute)
_to_uri() (sbol2.property.ReferencedObject method)
(sbol2.ReferencedObject method)
_types (sbol2.ComponentDefinition attribute)
(sbol2.componentdefinition.ComponentDefinition attribute)
_uri2url() (sbol2.partshop.PartShop method)
_validate_url() (sbol2.partshop.PartShop method)
A
Activity (class in sbol2)
(class in sbol2.provo)
add() (sbol2.Document method)
(sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.ReferencedObject method)
(sbol2.URIProperty method)
(sbol2.document.Document method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
add_list() (sbol2.Document method)
(sbol2.document.Document method)
addAttachment() (sbol2.Document method)
(sbol2.document.Document method)
addCitation() (sbol2.Document method)
(sbol2.document.Document method)
addCollection() (sbol2.Document method)
(sbol2.document.Document method)
addComponentDefinition() (sbol2.Document method)
(sbol2.document.Document method)
addDownstreamFlank() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
addExtensionObject() (sbol2.Document method)
(sbol2.document.Document method)
addImplementation() (sbol2.Document method)
(sbol2.document.Document method)
addKeyword() (sbol2.Document method)
(sbol2.document.Document method)
addModel() (sbol2.Document method)
(sbol2.document.Document method)
addModuleDefinition() (sbol2.Document method)
(sbol2.document.Document method)
addNamespace() (sbol2.Document method)
(sbol2.document.Document method)
addPropertyValue() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
addReference() (sbol2.property.ReferencedObject method)
(sbol2.ReferencedObject method)
addRole() (sbol2.Association method)
(sbol2.Component method)
(sbol2.ComponentDefinition method)
(sbol2.ModuleDefinition method)
(sbol2.Participation method)
(sbol2.SequenceAnnotation method)
(sbol2.Usage method)
(sbol2.component.Component method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
(sbol2.participation.Participation method)
(sbol2.provo.Association method)
(sbol2.provo.Usage method)
(sbol2.sequenceannotation.SequenceAnnotation method)
addSequence() (sbol2.Document method)
(sbol2.document.Document method)
addToDocument() (sbol2.TopLevel method)
(sbol2.toplevel.TopLevel method)
addType() (sbol2.ComponentDefinition method)
(sbol2.Measurement method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.measurement.Measurement method)
addUpstreamFlank() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
adjoins() (sbol2.location.Range method)
(sbol2.Range method)
Agent (class in sbol2)
(class in sbol2.provo)
agent (sbol2.Activity attribute)
(sbol2.Association attribute)
(sbol2.provo.Activity attribute)
(sbol2.provo.Association attribute)
AliasedProperty (class in sbol2.dbtl)
Analysis (class in sbol2.dbtl)
append() (sbol2.Document method)
(sbol2.document.Document method)
apply() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
applyToComponentHierarchy() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
applyToModuleHierarchy() (sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
assemble() (sbol2.ComponentDefinition method)
(sbol2.ModuleDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
assemblePrimaryStructure() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
associated (sbol2.Activity attribute)
(sbol2.provo.Activity attribute)
Association (class in sbol2)
(class in sbol2.provo)
attachFile() (sbol2.partshop.PartShop method)
Attachment (class in sbol2)
(class in sbol2.attachment)
B
BIOPAX_COMPLEX (in module sbol2)
(in module sbol2.constants)
BIOPAX_DNA (in module sbol2)
(in module sbol2.constants)
BIOPAX_PROTEIN (in module sbol2)
(in module sbol2.constants)
BIOPAX_RNA (in module sbol2)
(in module sbol2.constants)
BIOPAX_SMALL_MOLECULE (in module sbol2)
(in module sbol2.constants)
Build (class in sbol2.dbtl)
build() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
build_graph() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
C
cacheObjects() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
cacheObjectsDocument() (sbol2.Document method)
(sbol2.document.Document method)
cast() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
catch_exceptions (in module sbol2.config)
CHECK_BEST_PRACTICES (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
CHECK_COMPLETENESS (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
CHECK_URI_COMPLIANCE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
clear() (sbol2.Document method)
(sbol2.OwnedObject method)
(sbol2.document.Document method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
Collection (class in sbol2)
(class in sbol2.collection)
CombinatorialDerivation (class in sbol2)
(class in sbol2.combinatorialderivation)
compare() (sbol2.Document method)
(sbol2.SBOLObject method)
(sbol2.document.Document method)
(sbol2.object.SBOLObject method)
compile() (sbol2.ComponentDefinition method)
(sbol2.Sequence method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.sequence.Sequence method)
Component (class in sbol2)
(class in sbol2.component)
ComponentDefinition (class in sbol2)
(class in sbol2.componentdefinition)
ComponentInstance (class in sbol2.component)
components (sbol2.ComponentDefinition attribute)
(sbol2.componentdefinition.ComponentDefinition attribute)
Config (class in sbol2)
(class in sbol2.config)
ConfigOptions (class in sbol2)
(class in sbol2.config)
connect() (sbol2.component.FunctionalComponent method)
(sbol2.FunctionalComponent method)
(sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
contains() (sbol2.location.Range method)
(sbol2.Range method)
(sbol2.SequenceAnnotation method)
(sbol2.sequenceannotation.SequenceAnnotation method)
convert() (sbol2.Document method)
(sbol2.document.Document method)
convert_from_user() (sbol2.DateTimeProperty method)
(sbol2.FloatProperty method)
(sbol2.IntProperty method)
(sbol2.LiteralProperty method)
(sbol2.URIProperty method)
(sbol2.VersionProperty method)
(sbol2.property.DateTimeProperty method)
(sbol2.property.FloatProperty method)
(sbol2.property.IntProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.URIProperty method)
(sbol2.versionproperty.VersionProperty method)
convert_ntriples_encoding_to_ascii() (sbol2.Document method)
(sbol2.document.Document method)
convert_to_user() (sbol2.DateTimeProperty method)
(sbol2.FloatProperty method)
(sbol2.IntProperty method)
(sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.TextProperty method)
(sbol2.URIProperty method)
(sbol2.VersionProperty method)
(sbol2.property.DateTimeProperty method)
(sbol2.property.FloatProperty method)
(sbol2.property.IntProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.TextProperty method)
(sbol2.property.URIProperty method)
(sbol2.versionproperty.VersionProperty method)
copy() (sbol2.Document method)
(sbol2.Identified method)
(sbol2.document.Document method)
(sbol2.identified.Identified method)
count() (sbol2.partshop.PartShop method)
create() (sbol2.Document method)
(sbol2.OwnedObject method)
(sbol2.document.Document method)
(sbol2.property.OwnedObject method)
createCut() (sbol2.location.OwnedLocation method)
createGenericLocation() (sbol2.location.OwnedLocation method)
createRange() (sbol2.location.OwnedLocation method)
Cut (class in sbol2)
(class in sbol2.location)
D
DateTimeProperty (class in sbol2)
(class in sbol2.property)
DEFAULT_NS (in module sbol2)
(in module sbol2.constants)
define() (sbol2.Participation method)
(sbol2.participation.Participation method)
deleteDownstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
deleteUpstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
Design (class in sbol2)
(class in sbol2.dbtl)
DIFF_FILE_NAME (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
disassemble() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
doc_serialize_rdf2xml() (sbol2.Document method)
(sbol2.document.Document method)
Document (class in sbol2)
(class in sbol2.document)
dress_document() (sbol2.Document method)
(sbol2.document.Document method)
DUPLICATE_URI_ERROR (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
E
EDAM_BIOPAX (in module sbol2)
(in module sbol2.constants)
EDAM_CELLML (in module sbol2)
(in module sbol2.constants)
EDAM_SBML (in module sbol2)
(in module sbol2.constants)
END_OF_LIST (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
EnzymeCatalysisInteraction (class in sbol2.dbtl)
error_code() (sbol2.SBOLError method)
(sbol2.sbolerror.SBOLError method)
Experiment (class in sbol2)
(class in sbol2.experiment)
ExperimentalData (class in sbol2)
(class in sbol2.experiment)
exportToFormat() (sbol2.Document method)
(sbol2.document.Document method)
extension_namespaces (in module sbol2.config)
extract() (sbol2.SequenceAnnotation method)
(sbol2.sequenceannotation.SequenceAnnotation method)
F
FAIL_ON_FIRST_ERROR (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
file_format (in module sbol2.config)
FileFormats (class in sbol2.config)
find() (sbol2.Document method)
(sbol2.OwnedObject method)
(sbol2.SBOLObject method)
(sbol2.document.Document method)
(sbol2.object.SBOLObject method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
find_persistent_identity() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
find_property() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
find_property_value() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
find_reference() (sbol2.Document method)
(sbol2.SBOLObject method)
(sbol2.document.Document method)
(sbol2.object.SBOLObject method)
find_resource() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
FloatProperty (class in sbol2)
(class in sbol2.property)
follows() (sbol2.location.Range method)
(sbol2.Range method)
(sbol2.SequenceAnnotation method)
(sbol2.sequenceannotation.SequenceAnnotation method)
FunctionalComponent (class in sbol2)
(class in sbol2.component)
functionalComponents (sbol2.ModuleDefinition attribute)
(sbol2.moduledefinition.ModuleDefinition attribute)
G
GeneProductionInteraction (class in sbol2.dbtl)
generate() (sbol2.Identified method)
(sbol2.identified.Identified method)
generate_analysis() (sbol2.dbtl.Analysis method)
generateDesign() (sbol2.dbtl.Design method)
(sbol2.Design method)
generateTopLevel() (sbol2.TopLevel method)
(sbol2.toplevel.TopLevel method)
GenericLocation (class in sbol2)
(class in sbol2.location)
get() (sbol2.Document method)
(sbol2.OwnedObject method)
(sbol2.ReferencedObject method)
(sbol2.document.Document method)
(sbol2.property.OwnedObject method)
(sbol2.property.ReferencedObject method)
get_int() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
get_uri() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
getAll() (sbol2.Document method)
(sbol2.document.Document method)
getAnnotation() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getClassName() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getCollection() (sbol2.Document method)
(sbol2.document.Document method)
getComponentDefinition() (sbol2.Document method)
(sbol2.document.Document method)
getCut() (sbol2.location.OwnedLocation method)
getDownstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getExtensionObject() (sbol2.Document method)
(sbol2.document.Document method)
getFileFormat() (in module sbol2.config)
(sbol2.Config static method)
(sbol2.config.Config static method)
getFirstComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getHomespace() (in module sbol2)
(in module sbol2.config)
(sbol2.Config static method)
(sbol2.config.Config static method)
getImplementation() (sbol2.Document method)
(sbol2.document.Document method)
getInSequentialOrder() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getKey() (sbol2.partshop.PartShop method)
getLastComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getLowerBound() (sbol2.property.Property method)
getModel() (sbol2.Document method)
(sbol2.document.Document method)
getModuleDefinition() (sbol2.Document method)
(sbol2.document.Document method)
getOption() (sbol2.Config static method)
(sbol2.config.Config static method)
getOwner() (sbol2.property.Property method)
getPrimaryStructure() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getPrimaryStructureComponents() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getProperties() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getPropertyValue() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getPropertyValueList() (sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.URIProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.URIProperty method)
getPropertyValues() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getRange() (sbol2.location.OwnedLocation method)
getRawValue() (sbol2.property.Property method)
getSequence() (sbol2.Document method)
(sbol2.document.Document method)
getSinglePropertyValue() (sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.URIProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.URIProperty method)
getSpoofedURL() (sbol2.partshop.PartShop method)
getTopLevel() (sbol2.Document method)
(sbol2.document.Document method)
getTypeURI() (sbol2.ComponentDefinition method)
(sbol2.Document method)
(sbol2.ModuleDefinition method)
(sbol2.SBOLObject method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.document.Document method)
(sbol2.moduledefinition.ModuleDefinition method)
(sbol2.object.SBOLObject method)
(sbol2.property.Property method)
getUpperBound() (sbol2.property.Property method)
getUpstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getURL() (sbol2.partshop.PartShop method)
getUser() (sbol2.partshop.PartShop method)
guess_args() (sbol2.property.Property static method)
H
hasDownstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
hasHomespace() (in module sbol2)
(in module sbol2.config)
(sbol2.Config static method)
(sbol2.config.Config static method)
hasUpstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
home (in module sbol2.config)
HOMESPACE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
I
Identified (class in sbol2)
(class in sbol2.identified)
igem_assembly_scars (in module sbol2.document)
IGEM_STANDARD_ASSEMBLY() (in module sbol2)
(in module sbol2.document)
IGEM_URI (in module sbol2)
(in module sbol2.constants)
Implementation (class in sbol2)
(class in sbol2.implementation)
increment_major() (sbol2.VersionProperty static method)
(sbol2.versionproperty.VersionProperty static method)
infer_resource_namespaces() (sbol2.Document method)
(sbol2.document.Document method)
initialize() (sbol2.TopLevel method)
(sbol2.toplevel.TopLevel method)
INSERT_TYPE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
insertDownstream() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
insertDownstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
insertUpstream() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
insertUpstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
integrateAtBaseCoordinate() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
Interaction (class in sbol2)
(class in sbol2.interaction)
interactions (sbol2.ModuleDefinition attribute)
(sbol2.moduledefinition.ModuleDefinition attribute)
IntProperty (class in sbol2)
(class in sbol2.property)
is_alphanumeric_or_underscore() (in module sbol2)
(in module sbol2.validation)
is_not_alphanumeric_or_underscore() (in module sbol2)
(in module sbol2.validation)
is_ownership_relation() (in module sbol2.SBOL2Serialize)
is_top_level() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
(sbol2.TopLevel method)
(sbol2.toplevel.TopLevel method)
isComplete() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
isMasked() (sbol2.component.FunctionalComponent method)
(sbol2.FunctionalComponent method)
isRegular() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
J
JSON (sbol2.config.FileFormats attribute)
L
LANGUAGE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
length() (sbol2.location.Range method)
(sbol2.Range method)
(sbol2.Sequence method)
(sbol2.SequenceAnnotation method)
(sbol2.sequence.Sequence method)
(sbol2.sequenceannotation.SequenceAnnotation method)
libsbol_rule_1() (in module sbol2.validation)
libsbol_rule_10() (in module sbol2.validation)
libsbol_rule_11() (in module sbol2.validation)
libsbol_rule_12() (in module sbol2.validation)
libsbol_rule_13() (in module sbol2.validation)
libsbol_rule_14() (in module sbol2.validation)
libsbol_rule_15() (in module sbol2.validation)
libsbol_rule_16() (in module sbol2.validation)
libsbol_rule_17() (in module sbol2.validation)
libsbol_rule_18() (in module sbol2.validation)
libsbol_rule_2() (in module sbol2.validation)
libsbol_rule_22() (in module sbol2.validation)
libsbol_rule_24() (in module sbol2.validation)
libsbol_rule_3() (in module sbol2.validation)
libsbol_rule_4() (in module sbol2.validation)
libsbol_rule_5() (in module sbol2.validation)
libsbol_rule_6() (in module sbol2.validation)
libsbol_rule_8() (in module sbol2.validation)
libsbol_rule_9() (in module sbol2.validation)
LIMIT_URI (in module sbol2.searchquery)
linearize() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
LiteralProperty (class in sbol2)
(class in sbol2.property)
Location (class in sbol2)
(class in sbol2.location)
logger (sbol2.object.SBOLObject attribute)
(sbol2.SBOLObject attribute)
(sbol2.partshop.PartShop attribute)
(sbol2.property.Property attribute)
login() (sbol2.partshop.PartShop method)
lower_bound (sbol2.property.Property attribute)
M
MAIN_FILE_NAME (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
MapsTo (class in sbol2.mapsto)
mask() (sbol2.component.FunctionalComponent method)
(sbol2.FunctionalComponent method)
Measurement (class in sbol2)
(class in sbol2.measurement)
Model (class in sbol2.model)
models (sbol2.ModuleDefinition attribute)
(sbol2.moduledefinition.ModuleDefinition attribute)
Module (class in sbol2)
(class in sbol2.module)
ModuleDefinition (class in sbol2)
(class in sbol2.moduledefinition)
modules (sbol2.ModuleDefinition attribute)
(sbol2.moduledefinition.ModuleDefinition attribute)
N
NODENAME_ABOUT (in module sbol2)
(in module sbol2.constants)
NODENAME_RESOURCE (in module sbol2)
(in module sbol2.constants)
NOT_FOUND_ERROR (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
ns_prefix_dict() (in module sbol2.SBOL2Serialize)
NTRIPLES (sbol2.config.FileFormats attribute)
O
OBJECT_TYPE_URI (in module sbol2.searchquery)
OFFSET_URI (in module sbol2.searchquery)
OM_HAS_NUMERICAL_VALUE (in module sbol2)
(in module sbol2.constants)
OM_HAS_UNIT (in module sbol2)
(in module sbol2.constants)
OM_MEASURE (in module sbol2)
(in module sbol2.constants)
OM_NS (in module sbol2)
(in module sbol2.constants)
OM_URI (in module sbol2)
(in module sbol2.constants)
options (in module sbol2.config)
overlaps() (sbol2.location.Range method)
(sbol2.Range method)
(sbol2.SequenceAnnotation method)
(sbol2.sequenceannotation.SequenceAnnotation method)
override() (sbol2.component.FunctionalComponent method)
(sbol2.FunctionalComponent method)
(sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
OwnedLocation (class in sbol2.location)
OwnedObject (class in sbol2)
(class in sbol2.property)
OWNERSHIP_PREDICATES (in module sbol2.SBOL2Serialize)
P
parse_all() (sbol2.Document method)
(sbol2.document.Document method)
parse_annotation_objects() (sbol2.Document method)
(sbol2.document.Document method)
parse_objects_inner() (sbol2.Document method)
(sbol2.document.Document method)
parse_properties_inner() (sbol2.Document method)
(sbol2.document.Document method)
parseClassName() (in module sbol2.config)
parseNamespace() (in module sbol2.config)
(in module sbol2.identified)
parsePropertyName() (in module sbol2.config)
parseURLDomain() (in module sbol2.config)
participate() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
Participation (class in sbol2)
(class in sbol2.participation)
PartShop (class in sbol2.partshop)
Plan (class in sbol2)
(class in sbol2.provo)
plan (sbol2.Activity attribute)
(sbol2.Association attribute)
(sbol2.provo.Activity attribute)
(sbol2.provo.Association attribute)
precedes() (sbol2.location.Range method)
(sbol2.Range method)
(sbol2.SequenceAnnotation method)
(sbol2.sequenceannotation.SequenceAnnotation method)
prefixify() (in module sbol2.SBOL2Serialize)
Property (class in sbol2.property)
PROV_URI (in module sbol2)
(in module sbol2.constants)
PROVIDE_DETAILED_STACK_TRACE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
PROVO (in module sbol2)
(in module sbol2.constants)
PROVO_ACTIVITY (in module sbol2)
(in module sbol2.constants)
PROVO_AGENT (in module sbol2)
(in module sbol2.constants)
PROVO_AGENT_PROPERTY (in module sbol2)
(in module sbol2.constants)
PROVO_ASSOCIATION (in module sbol2)
(in module sbol2.constants)
PROVO_ENDED_AT_TIME (in module sbol2)
(in module sbol2.constants)
PROVO_ENTITY (in module sbol2)
(in module sbol2.constants)
PROVO_HAD_PLAN (in module sbol2)
(in module sbol2.constants)
PROVO_HAD_ROLE (in module sbol2)
(in module sbol2.constants)
PROVO_PLAN (in module sbol2)
(in module sbol2.constants)
PROVO_QUALIFIED_ASSOCIATION (in module sbol2)
(in module sbol2.constants)
PROVO_QUALIFIED_USAGE (in module sbol2)
(in module sbol2.constants)
PROVO_STARTED_AT_TIME (in module sbol2)
(in module sbol2.constants)
PROVO_USAGE (in module sbol2)
(in module sbol2.constants)
PROVO_WAS_GENERATED_BY (in module sbol2)
(in module sbol2.constants)
PROVO_WAS_INFORMED_BY (in module sbol2)
(in module sbol2.constants)
pull() (sbol2.partshop.PartShop method)
PURL_URI (in module sbol2)
(in module sbol2.constants)
PYSBOL2_NS (in module sbol2)
(in module sbol2.constants)
Q
query_dict() (sbol2.SearchQuery method)
(sbol2.searchquery.SearchQuery method)
query_repository() (sbol2.Document method)
(sbol2.document.Document method)
R
Range (class in sbol2)
(class in sbol2.location)
RDF_URI (in module sbol2)
(in module sbol2.constants)
rdfNS (in module sbol2.SBOL2Serialize)
RDFXML (sbol2.config.FileFormats attribute)
read() (sbol2.Document method)
(sbol2.document.Document method)
readString() (sbol2.Document method)
(sbol2.document.Document method)
ReferencedObject (class in sbol2)
(class in sbol2.property)
referenceNamespace() (sbol2.Document method)
(sbol2.document.Document method)
register_extension_class() (sbol2.Config method)
(sbol2.config.Config method)
register_ownership_relation() (in module sbol2.SBOL2Serialize)
remove() (sbol2.OwnedObject method)
(sbol2.partshop.PartShop method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
removeCitation() (sbol2.Document method)
(sbol2.document.Document method)
removeKeyword() (sbol2.Document method)
(sbol2.document.Document method)
removeOwnedObject_int() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
removeOwnedObject_str() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
removeRole() (sbol2.Association method)
(sbol2.Component method)
(sbol2.ComponentDefinition method)
(sbol2.ModuleDefinition method)
(sbol2.Participation method)
(sbol2.SequenceAnnotation method)
(sbol2.Usage method)
(sbol2.component.Component method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
(sbol2.participation.Participation method)
(sbol2.provo.Association method)
(sbol2.provo.Usage method)
(sbol2.sequenceannotation.SequenceAnnotation method)
removeType() (sbol2.ComponentDefinition method)
(sbol2.Measurement method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.measurement.Measurement method)
replace_namespace() (in module sbol2.identified)
reportAmbiguity() (sbol2.dbtl.Analysis method)
reportCoverage() (sbol2.dbtl.Analysis method)
reportIdentity() (sbol2.dbtl.Analysis method)
request_comparison() (sbol2.Document method)
(sbol2.document.Document method)
RETURN_FILE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
S
SampleRoster (class in sbol2.dbtl)
SBO (in module sbol2)
(in module sbol2.constants)
SBO_BINDING_SITE (in module sbol2)
(in module sbol2.constants)
SBO_BIOCHEMICAL_REACTION (in module sbol2)
(in module sbol2.constants)
SBO_COFACTOR (in module sbol2)
(in module sbol2.constants)
SBO_CONTINUOUS (in module sbol2)
(in module sbol2.constants)
SBO_CONTROL (in module sbol2)
(in module sbol2.constants)
SBO_CONVERSION (in module sbol2)
(in module sbol2.constants)
SBO_DEGRADATION (in module sbol2)
(in module sbol2.constants)
SBO_DISCRETE (in module sbol2)
(in module sbol2.constants)
SBO_ENZYME (in module sbol2)
(in module sbol2.constants)
SBO_GENE (in module sbol2)
(in module sbol2.constants)
SBO_GENETIC_PRODUCTION (in module sbol2)
(in module sbol2.constants)
SBO_INHIBITED (in module sbol2)
(in module sbol2.constants)
SBO_INHIBITION (in module sbol2)
(in module sbol2.constants)
SBO_INHIBITOR (in module sbol2)
(in module sbol2.constants)
SBO_INTERACTION (in module sbol2)
(in module sbol2.constants)
SBO_LIGAND (in module sbol2)
(in module sbol2.constants)
SBO_NONCOVALENT_BINDING (in module sbol2)
(in module sbol2.constants)
SBO_NONCOVALENT_COMPLEX (in module sbol2)
(in module sbol2.constants)
SBO_PRODUCT (in module sbol2)
(in module sbol2.constants)
SBO_PROMOTER (in module sbol2)
(in module sbol2.constants)
SBO_REACTANT (in module sbol2)
(in module sbol2.constants)
SBO_SIDEPRODUCT (in module sbol2)
(in module sbol2.constants)
SBO_STIMULATED (in module sbol2)
(in module sbol2.constants)
SBO_STIMULATION (in module sbol2)
(in module sbol2.constants)
SBO_STIMULATOR (in module sbol2)
(in module sbol2.constants)
SBO_SUBSTRATE (in module sbol2)
(in module sbol2.constants)
sbol2 (module)
sbol2.attachment (module)
sbol2.collection (module)
sbol2.combinatorialderivation (module)
sbol2.component (module)
sbol2.componentdefinition (module)
sbol2.config (module)
sbol2.constants (module)
sbol2.dbtl (module)
sbol2.document (module)
sbol2.experiment (module)
sbol2.identified (module)
sbol2.implementation (module)
sbol2.interaction (module)
sbol2.location (module)
sbol2.mapsto (module)
sbol2.measurement (module)
sbol2.model (module)
sbol2.module (module)
sbol2.moduledefinition (module)
sbol2.object (module)
sbol2.participation (module)
sbol2.partshop (module)
sbol2.property (module)
sbol2.provo (module)
sbol2.SBOL2Serialize (module)
sbol2.sbolerror (module)
sbol2.searchquery (module)
sbol2.sequence (module)
sbol2.sequenceannotation (module)
sbol2.sequenceconstraint (module)
sbol2.toplevel (module)
sbol2.uridict (module)
sbol2.validation (module)
sbol2.versionproperty (module)
SBOL_ACCESS (in module sbol2)
(in module sbol2.constants)
SBOL_ACCESS_PRIVATE (in module sbol2)
(in module sbol2.constants)
SBOL_ACCESS_PUBLIC (in module sbol2)
(in module sbol2.constants)
SBOL_AT (in module sbol2)
(in module sbol2.constants)
SBOL_ATTACHMENT (in module sbol2)
(in module sbol2.constants)
SBOL_ATTACHMENTS (in module sbol2)
(in module sbol2.constants)
SBOL_BUILD (in module sbol2)
(in module sbol2.constants)
SBOL_COLLECTION (in module sbol2)
(in module sbol2.constants)
SBOL_COMBINATORIAL_DERIVATION (in module sbol2)
(in module sbol2.constants)
SBOL_COMPLIANT_URIS (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
SBOL_COMPONENT (in module sbol2)
(in module sbol2.constants)
SBOL_COMPONENT_DEFINITION (in module sbol2)
(in module sbol2.constants)
SBOL_COMPONENT_PROPERTY (in module sbol2)
(in module sbol2.constants)
SBOL_COMPONENTS (in module sbol2)
(in module sbol2.constants)
SBOL_CUT (in module sbol2)
(in module sbol2.constants)
SBOL_DATA_MODEL_REGISTER (in module sbol2.document)
(sbol2.Config attribute)
(sbol2.config.Config attribute)
SBOL_DEFINITION (in module sbol2)
(in module sbol2.constants)
SBOL_DESCRIPTION (in module sbol2)
(in module sbol2.constants)
SBOL_DESIGN (in module sbol2)
(in module sbol2.constants)
SBOL_DIRECTION (in module sbol2)
(in module sbol2.constants)
SBOL_DIRECTION_IN (in module sbol2)
(in module sbol2.constants)
SBOL_DIRECTION_IN_OUT (in module sbol2)
(in module sbol2.constants)
SBOL_DIRECTION_NONE (in module sbol2)
(in module sbol2.constants)
SBOL_DIRECTION_OUT (in module sbol2)
(in module sbol2.constants)
SBOL_DISPLAY_ID (in module sbol2)
(in module sbol2.constants)
SBOL_DOCUMENT (in module sbol2)
(in module sbol2.constants)
SBOL_DOCUMENTED (in module sbol2)
(in module sbol2.constants)
SBOL_ELEMENTS (in module sbol2)
(in module sbol2.constants)
SBOL_ENCODING (in module sbol2)
(in module sbol2.constants)
SBOL_ENCODING_IUPAC (in module sbol2)
(in module sbol2.constants)
SBOL_ENCODING_IUPAC_PROTEIN (in module sbol2)
(in module sbol2.constants)
SBOL_ENCODING_SMILES (in module sbol2)
(in module sbol2.constants)
SBOL_END (in module sbol2)
(in module sbol2.constants)
SBOL_ERROR_BAD_HTTP_REQUEST (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_COMPLIANCE (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_END_OF_LIST (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_FILE_NOT_FOUND (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_HTTP_UNAUTHORIZED (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_INVALID_ARGUMENT (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_MISSING_DOCUMENT (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_MISSING_NAMESPACE (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_NONCOMPLIANT_VERSION (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_NOT_FOUND (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_ORPHAN_OBJECT (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_PARSE (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_SERIALIZATION (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_TYPE_MISMATCH (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_ERROR_URI_NOT_UNIQUE (sbol2.sbolerror.SBOLErrorCode attribute)
(sbol2.SBOLErrorCode attribute)
SBOL_EXPERIMENT (in module sbol2)
(in module sbol2.constants)
SBOL_EXPERIMENTAL_DATA (in module sbol2)
(in module sbol2.constants)
SBOL_FRAMEWORK (in module sbol2)
(in module sbol2.constants)
SBOL_FUNCTIONAL_COMPONENT (in module sbol2)
(in module sbol2.constants)
SBOL_FUNCTIONAL_COMPONENTS (in module sbol2)
(in module sbol2.constants)
SBOL_GENERIC_LOCATION (in module sbol2)
(in module sbol2.constants)
SBOL_GENERIC_TOP_LEVEL (in module sbol2)
(in module sbol2.constants)
SBOL_IDENTIFIED (in module sbol2)
(in module sbol2.constants)
SBOL_IDENTITY (in module sbol2)
(in module sbol2.constants)
SBOL_IMPLEMENTATION (in module sbol2)
(in module sbol2.constants)
SBOL_INTERACTION (in module sbol2)
(in module sbol2.constants)
SBOL_INTERACTIONS (in module sbol2)
(in module sbol2.constants)
SBOL_LANGUAGE (in module sbol2)
(in module sbol2.constants)
SBOL_LEARN (in module sbol2)
(in module sbol2.constants)
SBOL_LOCAL (in module sbol2)
(in module sbol2.constants)
SBOL_LOCATION (in module sbol2)
(in module sbol2.constants)
SBOL_LOCATIONS (in module sbol2)
(in module sbol2.constants)
SBOL_MAPS_TO (in module sbol2)
(in module sbol2.constants)
SBOL_MAPS_TOS (in module sbol2)
(in module sbol2.constants)
SBOL_MEASUREMENTS (in module sbol2)
(in module sbol2.constants)
SBOL_MEMBERS (in module sbol2)
(in module sbol2.constants)
SBOL_MODEL (in module sbol2)
(in module sbol2.constants)
SBOL_MODELS (in module sbol2)
(in module sbol2.constants)
SBOL_MODULE (in module sbol2)
(in module sbol2.constants)
SBOL_MODULE_DEFINITION (in module sbol2)
(in module sbol2.constants)
SBOL_MODULES (in module sbol2)
(in module sbol2.constants)
SBOL_NAME (in module sbol2)
(in module sbol2.constants)
SBOL_OBJECT (in module sbol2)
(in module sbol2.constants)
SBOL_OPERATOR (in module sbol2)
(in module sbol2.constants)
SBOL_ORIENTATION (in module sbol2)
(in module sbol2.constants)
SBOL_ORIENTATION_INLINE (in module sbol2)
(in module sbol2.constants)
SBOL_ORIENTATION_REVERSE_COMPLEMENT (in module sbol2)
(in module sbol2.constants)
SBOL_PARTICIPANT (in module sbol2)
(in module sbol2.constants)
SBOL_PARTICIPATION (in module sbol2)
(in module sbol2.constants)
SBOL_PARTICIPATIONS (in module sbol2)
(in module sbol2.constants)
SBOL_PERSISTENT_IDENTITY (in module sbol2)
(in module sbol2.constants)
SBOL_RANGE (in module sbol2)
(in module sbol2.constants)
SBOL_REFINEMENT (in module sbol2)
(in module sbol2.constants)
SBOL_REFINEMENT_MERGE (in module sbol2)
(in module sbol2.constants)
SBOL_REFINEMENT_USE_LOCAL (in module sbol2)
(in module sbol2.constants)
SBOL_REFINEMENT_USE_REMOTE (in module sbol2)
(in module sbol2.constants)
SBOL_REFINEMENT_VERIFY_IDENTICAL (in module sbol2)
(in module sbol2.constants)
SBOL_REMOTE (in module sbol2)
(in module sbol2.constants)
SBOL_RESTRICTION (in module sbol2)
(in module sbol2.constants)
SBOL_RESTRICTION_OPPOSITE_ORIENTATION_AS (in module sbol2)
(in module sbol2.constants)
SBOL_RESTRICTION_PRECEDES (in module sbol2)
(in module sbol2.constants)
SBOL_RESTRICTION_SAME_ORIENTATION_AS (in module sbol2)
(in module sbol2.constants)
SBOL_ROLE_INTEGRATION (in module sbol2)
(in module sbol2.constants)
SBOL_ROLE_INTEGRATION_MERGE (in module sbol2)
(in module sbol2.constants)
SBOL_ROLE_INTEGRATION_OVERRIDE (in module sbol2)
(in module sbol2.constants)
SBOL_ROLES (in module sbol2)
(in module sbol2.constants)
sbol_rule_10202() (in module sbol2.validation)
sbol_rule_10204() (in module sbol2.validation)
SBOL_SEQUENCE (in module sbol2)
(in module sbol2.constants)
SBOL_SEQUENCE_ANNOTATION (in module sbol2)
(in module sbol2.constants)
SBOL_SEQUENCE_ANNOTATIONS (in module sbol2)
(in module sbol2.constants)
SBOL_SEQUENCE_CONSTRAINT (in module sbol2)
(in module sbol2.constants)
SBOL_SEQUENCE_CONSTRAINTS (in module sbol2)
(in module sbol2.constants)
SBOL_SEQUENCE_PROPERTY (in module sbol2)
(in module sbol2.constants)
SBOL_SOURCE (in module sbol2)
(in module sbol2.constants)
SBOL_SOURCE_LOCATIONS (in module sbol2)
(in module sbol2.constants)
SBOL_START (in module sbol2)
(in module sbol2.constants)
SBOL_STRATEGY (in module sbol2)
(in module sbol2.constants)
SBOL_SUBJECT (in module sbol2)
(in module sbol2.constants)
SBOL_TEMPLATE (in module sbol2)
(in module sbol2.constants)
SBOL_TEST (in module sbol2)
(in module sbol2.constants)
SBOL_TOP_LEVEL (in module sbol2)
(in module sbol2.constants)
SBOL_TYPED_URIS (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
SBOL_TYPES (in module sbol2)
(in module sbol2.constants)
SBOL_UNIT (in module sbol2)
(in module sbol2.constants)
SBOL_URI (in module sbol2)
(in module sbol2.constants)
SBOL_VALUE (in module sbol2)
(in module sbol2.constants)
SBOL_VARIABLE (in module sbol2)
(in module sbol2.constants)
SBOL_VARIABLE_COMPONENT (in module sbol2)
(in module sbol2.constants)
SBOL_VARIABLE_COMPONENTS (in module sbol2)
(in module sbol2.constants)
SBOL_VARIANT_COLLECTIONS (in module sbol2)
(in module sbol2.constants)
SBOL_VARIANT_DERIVATIONS (in module sbol2)
(in module sbol2.constants)
SBOL_VARIANTS (in module sbol2)
(in module sbol2.constants)
SBOL_VERSION (in module sbol2)
(in module sbol2.constants)
SBOL_WAS_DERIVED_FROM (in module sbol2)
(in module sbol2.constants)
SBOLCompliantTypes (in module sbol2.config)
SBOLError
,
[1]
SBOLErrorCode (class in sbol2)
(class in sbol2.sbolerror)
sbolNS (in module sbol2.SBOL2Serialize)
SBOLObject (class in sbol2)
(class in sbol2.object)
sbolRule10101() (in module sbol2.validation)
sbolRule10102() (in module sbol2.validation)
search() (sbol2.partshop.PartShop method)
search_advanced() (sbol2.partshop.PartShop method)
search_count() (sbol2.partshop.PartShop method)
search_count_advanced() (sbol2.partshop.PartShop method)
search_exact() (sbol2.partshop.PartShop method)
search_general() (sbol2.partshop.PartShop method)
search_metadata() (sbol2.Document method)
(sbol2.document.Document method)
SEARCH_QUERY_URI (in module sbol2.searchquery)
searchCount() (sbol2.partshop.PartShop method)
SearchQuery (class in sbol2)
(class in sbol2.searchquery)
Sequence (class in sbol2)
(class in sbol2.sequence)
sequence (sbol2.ComponentDefinition attribute)
(sbol2.componentdefinition.ComponentDefinition attribute)
SequenceAnnotation (class in sbol2)
(class in sbol2.sequenceannotation)
sequenceAnnotations (sbol2.ComponentDefinition attribute)
(sbol2.componentdefinition.ComponentDefinition attribute)
SequenceConstraint (class in sbol2.sequenceconstraint)
sequenceConstraints (sbol2.ComponentDefinition attribute)
(sbol2.componentdefinition.ComponentDefinition attribute)
sequences (sbol2.ComponentDefinition attribute)
(sbol2.componentdefinition.ComponentDefinition attribute)
SERIALIZATION_FORMAT (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
serialize_sboll2() (in module sbol2.SBOL2Serialize)
set() (sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.ReferencedObject method)
(sbol2.URIProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
setAnnotation() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
setFileFormat() (in module sbol2.config)
(sbol2.Config static method)
(sbol2.config.Config static method)
setHomespace() (in module sbol2)
(in module sbol2.config)
(sbol2.Config static method)
(sbol2.config.Config static method)
setInput() (sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
setInputFunctional() (sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
setOption() (sbol2.Config static method)
(sbol2.config.Config static method)
setOutput() (sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
setOutputFunctional() (sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
setPropertyValue() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
setPropertyValueList() (sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.ReferencedObject method)
(sbol2.URIProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
setSinglePropertyValue() (sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.ReferencedObject method)
(sbol2.URIProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
size() (sbol2.Document method)
(sbol2.document.Document method)
SmallMoleculeActivationInteraction (class in sbol2.dbtl)
SmallMoleculeInhibitionInteraction (class in sbol2.dbtl)
SO (in module sbol2)
(in module sbol2.constants)
SO_CDS (in module sbol2)
(in module sbol2.constants)
SO_CIRCULAR (in module sbol2)
(in module sbol2.constants)
SO_GENE (in module sbol2)
(in module sbol2.constants)
SO_LINEAR (in module sbol2)
(in module sbol2.constants)
SO_MISC (in module sbol2)
(in module sbol2.constants)
SO_PLASMID (in module sbol2)
(in module sbol2.constants)
SO_PROMOTER (in module sbol2)
(in module sbol2.constants)
SO_RBS (in module sbol2)
(in module sbol2.constants)
SO_SGRNA (in module sbol2)
(in module sbol2.constants)
SO_TERMINATOR (in module sbol2)
(in module sbol2.constants)
sort_version() (in module sbol2.property)
sparqlQuery() (sbol2.partshop.PartShop method)
spoof() (sbol2.partshop.PartShop method)
string_equal() (in module sbol2.config)
submit() (sbol2.partshop.PartShop method)
SUBSET_URI (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
summary() (sbol2.Document method)
(sbol2.document.Document method)
synthesize() (sbol2.Sequence method)
(sbol2.sequence.Sequence method)
SYSBIO_ANALYSIS (in module sbol2)
(in module sbol2.constants)
SYSBIO_BUILD (in module sbol2)
(in module sbol2.constants)
SYSBIO_DESIGN (in module sbol2)
(in module sbol2.constants)
SYSBIO_SAMPLE_ROSTER (in module sbol2)
(in module sbol2.constants)
SYSBIO_TEST (in module sbol2)
(in module sbol2.constants)
sysbio_type (sbol2.dbtl.Build attribute)
(sbol2.dbtl.SampleRoster attribute)
SYSBIO_URI (in module sbol2)
(in module sbol2.constants)
T
Test (class in sbol2.dbtl)
TEST_EQUALITY (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
TextProperty (class in sbol2)
(class in sbol2.property)
this (sbol2.object.SBOLObject attribute)
(sbol2.SBOLObject attribute)
TopLevel (class in sbol2)
(class in sbol2.toplevel)
TranscriptionalActivationInteraction (class in sbol2.dbtl)
TranscriptionRepressionInteraction (class in sbol2.dbtl)
type (sbol2.object.SBOLObject attribute)
(sbol2.SBOLObject attribute)
U
UNDEFINED (in module sbol2)
(in module sbol2.constants)
update_graph() (sbol2.Document method)
(sbol2.document.Document method)
update_uri() (sbol2.Identified method)
(sbol2.SBOLObject method)
(sbol2.TopLevel method)
(sbol2.identified.Identified method)
(sbol2.object.SBOLObject method)
(sbol2.toplevel.TopLevel method)
updateSequence() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
upper_bound (sbol2.property.Property attribute)
URI_PREFIX (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
URIDict (class in sbol2.uridict)
URIProperty (class in sbol2)
(class in sbol2.property)
Usage (class in sbol2)
(class in sbol2.provo)
usages (sbol2.Activity attribute)
(sbol2.provo.Activity attribute)
V
valid_lower_bound() (sbol2.property.Property static method)
valid_options (in module sbol2.config)
valid_upper_bound() (sbol2.property.Property static method)
VALIDATE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
validate() (in module sbol2.document)
(sbol2.Document method)
(sbol2.document.Document method)
(sbol2.property.Property method)
VALIDATOR_URL (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
value (sbol2.LiteralProperty attribute)
(sbol2.OwnedObject attribute)
(sbol2.ReferencedObject attribute)
(sbol2.URIProperty attribute)
(sbol2.property.LiteralProperty attribute)
(sbol2.property.OwnedObject attribute)
(sbol2.property.Property attribute)
(sbol2.property.ReferencedObject attribute)
(sbol2.property.URIProperty attribute)
VariableComponent (class in sbol2.combinatorialderivation)
VERBOSE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
verifyTarget() (sbol2.dbtl.Analysis method)
VERSION (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
version (sbol2.Identified attribute)
(sbol2.identified.Identified attribute)
VERSION_STRING (in module sbol2)
(in module sbol2.constants)
VersionProperty (class in sbol2)
(class in sbol2.versionproperty)
W
wasInformedBy (sbol2.Activity attribute)
(sbol2.provo.Activity attribute)
what() (sbol2.SBOLError method)
(sbol2.sbolerror.SBOLError method)
write() (sbol2.Document method)
(sbol2.document.Document method)
(sbol2.property.Property method)
writeString() (sbol2.Document method)
(sbol2.document.Document method)
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