pySBOL2
stable
Introduction
Installation
Getting Started with SBOL
Biological Parts Repositories
Computer-aided Design for Synthetic Biology
SBOL Extensions
API Reference
pySBOL2
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
_
__bool__() (sbol2.document.Document method)
(sbol2.Sequence 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.property.OwnedObject method)
(sbol2.SearchQuery method)
(sbol2.searchquery.SearchQuery method)
(sbol2.uridict.URIDict method)
__iter__() (sbol2.document.Document method)
__len__() (sbol2.document.Document method)
(sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
(sbol2.Sequence method)
(sbol2.sequence.Sequence method)
__next__() (sbol2.document.Document method)
__setattr__() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
__setitem__() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
(sbol2.SearchQuery method)
(sbol2.searchquery.SearchQuery method)
(sbol2.uridict.URIDict method)
__str__() (sbol2.document.Document method)
(sbol2.object.SBOLObject method)
(sbol2.property.Property method)
(sbol2.SBOLObject method)
__uri__() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
__version__ (in module sbol2)
_added_to_document() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
_append_graph() (sbol2.document.Document 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 method)
(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.componentdefinition.ComponentDefinition attribute)
(sbol2.ModuleDefinition attribute)
(sbol2.moduledefinition.ModuleDefinition attribute)
(sbol2.provo.Association attribute)
(sbol2.provo.Usage attribute)
(sbol2.Usage attribute)
_search() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
_search_count() (sbol2.PartShop method)
(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 method)
(sbol2.partshop.PartShop method)
_validate_url() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
A
Activity (class in sbol2)
(class in sbol2.provo)
add() (sbol2.document.Document method)
(sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
(sbol2.ReferencedObject method)
(sbol2.URIProperty method)
add_list() (sbol2.document.Document method)
addAttachment() (sbol2.document.Document method)
addCitation() (sbol2.document.Document method)
addCollection() (sbol2.document.Document method)
addComponentDefinition() (sbol2.document.Document method)
addDownstreamFlank() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
addExtensionObject() (sbol2.document.Document method)
addImplementation() (sbol2.document.Document method)
addKeyword() (sbol2.document.Document method)
addModel() (sbol2.document.Document method)
addModuleDefinition() (sbol2.document.Document method)
addNamespace() (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.component.Component method)
(sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
(sbol2.Participation method)
(sbol2.participation.Participation method)
(sbol2.provo.Association method)
(sbol2.provo.Usage method)
(sbol2.SequenceAnnotation method)
(sbol2.sequenceannotation.SequenceAnnotation method)
(sbol2.Usage method)
addSequence() (sbol2.document.Document method)
addToDocument() (sbol2.TopLevel method)
(sbol2.toplevel.TopLevel method)
addType() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.Measurement 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.Document method)
appendString() (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.componentdefinition.ComponentDefinition method)
(sbol2.ModuleDefinition 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 method)
(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)
broken_validation_request() (sbol2.validator.ValidationResult method)
Build (class in sbol2.dbtl)
build() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.validator.ValidationOptions method)
build_graph() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
C
cacheObjects() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
cacheObjectsDocument() (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_best_practices (sbol2.validator.ValidationOptions attribute)
CHECK_COMPLETENESS (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
check_completeness (sbol2.validator.ValidationOptions attribute)
CHECK_URI_COMPLIANCE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
check_uri_compliance (sbol2.validator.ValidationOptions attribute)
clear() (sbol2.document.Document method)
(sbol2.OwnedObject 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)
command() (sbol2.validator.ValidationOptions method)
compare() (sbol2.document.Document method)
(sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
compile() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.Sequence 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.Document method)
convert_from_user() (sbol2.DateTimeProperty method)
(sbol2.FloatProperty method)
(sbol2.IntProperty method)
(sbol2.LiteralProperty method)
(sbol2.property.DateTimeProperty method)
(sbol2.property.FloatProperty method)
(sbol2.property.IntProperty method)
(sbol2.property.LiteralProperty method)
(sbol2.property.URIProperty method)
(sbol2.URIProperty method)
(sbol2.VersionProperty method)
(sbol2.versionproperty.VersionProperty method)
convert_ntriples_encoding_to_ascii() (sbol2.document.Document method)
convert_to_user() (sbol2.DateTimeProperty method)
(sbol2.FloatProperty method)
(sbol2.IntProperty method)
(sbol2.LiteralProperty method)
(sbol2.OwnedObject 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.TextProperty method)
(sbol2.URIProperty method)
(sbol2.VersionProperty method)
(sbol2.versionproperty.VersionProperty method)
copy() (sbol2.document.Document method)
(sbol2.Identified method)
(sbol2.identified.Identified method)
count() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
create() (sbol2.document.Document method)
(sbol2.OwnedObject 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)
decipher() (sbol2.validator.ValidationResult method)
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)
diff_file_name (sbol2.validator.ValidationOptions attribute)
digest_errors() (sbol2.validator.ValidationResult method)
disassemble() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
do_validation() (in module sbol2.validator)
doc_serialize_rdf2xml() (sbol2.document.Document method)
Document (class in sbol2.document)
downloadAttachment() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
dress_document() (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)
execute() (sbol2.validator.ValidationRun method)
Experiment (class in sbol2)
(class in sbol2.experiment)
ExperimentalData (class in sbol2)
(class in sbol2.experiment)
exportToFormat() (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)
fail_on_first_error (sbol2.validator.ValidationOptions attribute)
file_format (in module sbol2.config)
FileFormats (class in sbol2.config)
find() (sbol2.document.Document method)
(sbol2.object.SBOLObject method)
(sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
(sbol2.SBOLObject 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.Document method)
(sbol2.object.SBOLObject method)
(sbol2.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.Document method)
(sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
(sbol2.property.ReferencedObject method)
(sbol2.ReferencedObject method)
get_int() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
get_uri() (sbol2.OwnedObject method)
(sbol2.property.OwnedObject method)
getAll() (sbol2.document.Document method)
getAnnotation() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getClassName() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getCollection() (sbol2.document.Document method)
getComponentDefinition() (sbol2.document.Document method)
getCut() (sbol2.location.OwnedLocation method)
getDownstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getExtensionObject() (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.Document method)
getInSequentialOrder() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getKey() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
getLastComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getLowerBound() (sbol2.property.Property method)
getModel() (sbol2.document.Document method)
getModuleDefinition() (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.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.URIProperty method)
(sbol2.URIProperty method)
getPropertyValues() (sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
getRange() (sbol2.location.OwnedLocation method)
getRawValue() (sbol2.property.Property method)
getSequence() (sbol2.document.Document method)
getSinglePropertyValue() (sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.URIProperty method)
(sbol2.URIProperty method)
getSpoofedURL() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
getTopLevel() (sbol2.document.Document method)
getTypeURI() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.document.Document method)
(sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
(sbol2.object.SBOLObject method)
(sbol2.property.Property method)
(sbol2.SBOLObject method)
getUpperBound() (sbol2.property.Property method)
getUpstreamComponent() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
getURL() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
getUser() (sbol2.PartShop method)
(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.document)
IGEM_URI (in module sbol2)
(in module sbol2.constants)
Implementation (class in sbol2)
(class in sbol2.implementation)
importFromFormat() (sbol2.document.Document method)
increment_major() (sbol2.VersionProperty static method)
(sbol2.versionproperty.VersionProperty static method)
infer_resource_namespaces() (sbol2.document.Document method)
initialize() (sbol2.TopLevel method)
(sbol2.toplevel.TopLevel method)
INSERT_TYPE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
insert_type (sbol2.validator.ValidationOptions 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
JAVA_LOCATION (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
JSON (sbol2.config.FileFormats attribute)
json() (sbol2.validator.ValidationResult method)
L
LANGUAGE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
language (sbol2.validator.ValidationOptions attribute)
length() (sbol2.location.Range method)
(sbol2.Range method)
(sbol2.Sequence method)
(sbol2.sequence.Sequence method)
(sbol2.SequenceAnnotation 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 property)
(sbol2.PartShop property)
(sbol2.partshop.PartShop property)
(sbol2.property.Property property)
(sbol2.SBOLObject property)
login() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
lower_bound (sbol2.property.Property property)
M
MAIN_FILE_NAME (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
main_file_name (sbol2.validator.ValidationOptions 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
sbol2
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.SBOL2Serialize
sbol2.sbolerror
sbol2.searchquery
sbol2.sequence
sbol2.sequenceannotation
sbol2.sequenceconstraint
sbol2.toplevel
sbol2.uridict
sbol2.validation
sbol2.validator
sbol2.versionproperty
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.Document method)
parse_annotation_objects() (sbol2.document.Document method)
parse_objects_inner() (sbol2.document.Document method)
parse_properties_inner() (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)
(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)
provide_detailed_stack_trace (sbol2.validator.ValidationOptions 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 method)
(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.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.Document method)
readString() (sbol2.document.Document method)
ReferencedObject (class in sbol2)
(class in sbol2.property)
referenceNamespace() (sbol2.document.Document method)
register_extension_class() (sbol2.Config static method)
(sbol2.config.Config static method)
register_ownership_relation() (in module sbol2.SBOL2Serialize)
remove() (sbol2.OwnedObject method)
(sbol2.PartShop method)
(sbol2.partshop.PartShop method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
removeCitation() (sbol2.document.Document method)
removeKeyword() (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.component.Component method)
(sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.ModuleDefinition method)
(sbol2.moduledefinition.ModuleDefinition method)
(sbol2.Participation method)
(sbol2.participation.Participation method)
(sbol2.provo.Association method)
(sbol2.provo.Usage method)
(sbol2.SequenceAnnotation method)
(sbol2.sequenceannotation.SequenceAnnotation method)
(sbol2.Usage method)
removeType() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
(sbol2.Measurement 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.Document method)
RETURN_FILE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
return_file (sbol2.validator.ValidationOptions 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.validator
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 method)
(sbol2.partshop.PartShop method)
search_advanced() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
search_count() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
search_count_advanced() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
search_exact() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
search_general() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
search_metadata() (sbol2.document.Document method)
SEARCH_QUERY_URI (in module sbol2.searchquery)
searchCount() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
SearchQuery (class in sbol2)
(class in sbol2.searchquery)
Sequence (class in sbol2)
(class in sbol2.sequence)
sequence (sbol2.ComponentDefinition property)
(sbol2.componentdefinition.ComponentDefinition property)
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.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.Property method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
(sbol2.ReferencedObject method)
(sbol2.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.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
(sbol2.ReferencedObject method)
(sbol2.URIProperty method)
setSinglePropertyValue() (sbol2.LiteralProperty method)
(sbol2.OwnedObject method)
(sbol2.property.LiteralProperty method)
(sbol2.property.OwnedObject method)
(sbol2.property.ReferencedObject method)
(sbol2.property.URIProperty method)
(sbol2.ReferencedObject method)
(sbol2.URIProperty method)
size() (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 method)
(sbol2.partshop.PartShop method)
spoof() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
string_equal() (in module sbol2.config)
submit() (sbol2.PartShop method)
(sbol2.partshop.PartShop method)
SUBSET_URI (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
subset_uri (sbol2.validator.ValidationOptions attribute)
summary() (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 property)
(sbol2.dbtl.SampleRoster property)
SYSBIO_URI (in module sbol2)
(in module sbol2.constants)
T
Test (class in sbol2.dbtl)
TEST_EQUALITY (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
test_equality (sbol2.validator.ValidationOptions attribute)
TextProperty (class in sbol2)
(class in sbol2.property)
this (sbol2.object.SBOLObject property)
(sbol2.SBOLObject property)
TopLevel (class in sbol2)
(class in sbol2.toplevel)
TranscriptionalActivationInteraction (class in sbol2.dbtl)
TranscriptionRepressionInteraction (class in sbol2.dbtl)
type (sbol2.object.SBOLObject property)
(sbol2.SBOLObject property)
U
UNDEFINED (in module sbol2)
(in module sbol2.constants)
update_graph() (sbol2.document.Document method)
update_uri() (sbol2.Identified method)
(sbol2.identified.Identified method)
(sbol2.object.SBOLObject method)
(sbol2.SBOLObject method)
(sbol2.TopLevel method)
(sbol2.toplevel.TopLevel method)
updateSequence() (sbol2.ComponentDefinition method)
(sbol2.componentdefinition.ComponentDefinition method)
upper_bound (sbol2.property.Property property)
URI_PREFIX (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
uri_prefix (sbol2.validator.ValidationOptions 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.Document method)
(sbol2.property.Property method)
VALIDATE_ONLINE (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
ValidationOptions (class in sbol2.validator)
ValidationResult (class in sbol2.validator)
ValidationRun (class in sbol2.validator)
VALIDATOR_URL (sbol2.config.ConfigOptions attribute)
(sbol2.ConfigOptions attribute)
value (sbol2.LiteralProperty property)
(sbol2.OwnedObject property)
(sbol2.property.LiteralProperty property)
(sbol2.property.OwnedObject property)
(sbol2.property.Property property)
(sbol2.property.ReferencedObject property)
(sbol2.property.URIProperty property)
(sbol2.ReferencedObject property)
(sbol2.URIProperty property)
VariableComponent (class in sbol2)
(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)
(sbol2.validator.ValidationOptions 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.Document method)
(sbol2.property.Property method)
writeString() (sbol2.document.Document method)
Read the Docs
v: stable
Versions
latest
stable
v1.4.1
v1.4
v1.3
v1.2
v1.1
v1.0
Downloads
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.