API

class Activity(*args)[source]

A generated Entity is linked through a wasGeneratedBy relationship to an Activity, which is used to describe how different Agents and other entities were used. An Activity is linked through a qualifiedAssociation to Associations, to describe the role of agents, and is linked through qualifiedUsage to Usages to describe the role of other entities used as part of the activity. Moreover, each Activity includes optional startedAtTime and endedAtTime properties. When using Activity to capture how an entity was derived, it is expected that any additional information needed will be attached as annotations. This may include software settings or textual notes. Activities can also be linked together using the wasInformedBy relationship to provide dependency without explicitly specifying start and end times.

  • startedAtTime : DateTimeProperty

  • endedAtTime : DateTimeProperty

    The endedAtTime property is OPTIONAL and contains a dateTime (see section Section 12.7) value, indicating when the activity ended.

  • wasInformedBy : ReferencedObject

    The wasInformedBy property is OPTIONAL and contains a URI of another activity.

  • associations : OwnedObject< Association >

    The qualifiedAssociation property is OPTIONAL and MAY contain a set of URIs that refers to Association.

  • usages : OwnedObject< Usage >

    The qualifiedUsage property is OPTIONAL and MAY contain a set of URIs that refers to Usage objects.

  • agent : OwnedObject< Agent >

    An Agent object may be specified here, and it will be synced with the Association::agent property.

  • plan : OwnedObject< Plan >

    A Plan object may be specified here, and it will be synced with the Association::plan property.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/provo.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

generateAnalysis(uris, test_usages, analysis_usages=None)[source]

Generate one or more Analysis objects.

  • uris :
    One or more identifiers for the new Analysis object(s). If the sbol_compliant_uris option configuration is enabled, then the user should specify simple identifiers for the objects. Otherwise the user must provide full URIs each consisting of a scheme, namespace, and identifier.
  • test_usages :
    A singleton Test object, list of Test objects, or None. Test usages represent raw experimental data used to generate an Analysis.
  • analysis_usages :
    A singleton Analysis object, list of Analysis objects, or None. Analysis usages represent other analyses that the user wants to integrate into a single data set or data sheet.

A singleton Analysis or list of Analyses depending on whether the user specifies a single URI or list of URIs.

generateBuild(uris, design_usages, build_usages=None)[source]

Generate one or more Build objects

  • uris :
    One or more identifiers for the new Build object(s). If the sbol_compliant_uris option configuration is enabled, then the user should specify simple identifiers for the objects. Otherwise the user must provide full URIs each consisting of a scheme, namespace, and identifier.
  • design_usages :
    A singleton Design object, list of Design objects, or None. Design usages represent the engineer’s intent or “blueprint” for the Build target.
  • build_usages :
    A singleton Build object, list of Build objects, or None. Build usages represent physical components, such as laboratory samples, that are assembled into the target Build.

A singleton Build or list of Builds depending on whether the user specifies a single URI or list of URIs.

generateDesign(uris, analysis_usages, design_usages=None)[source]

Generate one or more Design objects

  • uris :
    One or more identifiers for the new Design object(s). If the sbol_compliant_uris option configuration is enabled, then the user should specify simple identifiers for the objects. Otherwise the user must provide full URIs each consisting of a scheme, namespace, and identifier.
  • analysis_usages :
    A singleton Analysis object, list of Analysis objects, or None. Analysis usages represent a prediction or forward-specification of the new Design’s intended structure or function.
  • design_usages :
    A singleton Design object, list of Design objects, or None. Design usages may represent previous Designs that are being tranformed or composed into the new Design.

A singleton Design or list of Designs depending on whether the user specifies a single URI or list of URIs.

generateTest(uris, build_usages, test_usages=None)[source]

Generate one or more Test objects

  • uris :
    One or more identifiers for the new Test object(s). If the sbol_compliant_uris option configuration is enabled, then the user should specify simple identifiers for the objects. Otherwise the user must provide full URIs each consisting of a scheme, namespace, and identifier.
  • build_usages :
    A singleton Build object, list of Build objects, or None. Build usages represent samples or analytes used in an experimental measurement.
  • test_usages :
    A singleton Test object, list of Test objects, or None. Test usages represent other measurements or raw data that the user wants to integrate into a single data set.

A singleton Test or list of Tests depending on whether the user specifies a single URI or list of URIs.

class ActivityProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Agent(*args)[source]

Examples of agents are person, organisation or software. These agents should be annotated with additional information, such as software version, needed to be able to run the same software again.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/provo.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class AgentProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class AliasedOwnedFunctionalComponent(property_owner, sbol_uri, alias_uri, lower_bound, upper_bound, validation_rules)[source]
  • alias : rdf_type
  • python_iter : std::vector< std::string >::iterator
add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
create(uri)[source]

create(uri) -> SBOLClass &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

get(*args)[source]

get(uri=”“) -> SBOLClass &

set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class Analysis(*args)[source]
  • rawData : ReferencedObject

    A reference to a Test object which contains the raw data for an Analysis.

  • dataFiles : ReferencedObject

    References to file Attachments which contain experimental data sets.

  • dataSheet : ReferencedObject

    A reference to a datasheet file.

  • consensusSequence : OwnedObject< Sequence >

    A sequence object that represents a consensus sequence from DNA sequencing data.

  • fittedModel : OwnedObject< Model >

    A Model derived from fitting an experimental data set.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

reportAmbiguity()[source]
`reportAmbiguity() -> std::unordered_map< std::string, std::tuple< int, int,
float > >`
reportCoverage()[source]
`reportCoverage() -> std::unordered_map< std::string, std::tuple< int, int,
float > >`
reportError()[source]
`reportError() -> std::unordered_map< std::string, std::tuple< int, int, float >
>`
reportIdentity()[source]
`reportIdentity() -> std::unordered_map< std::string, std::tuple< int, int,
float > >`
verifyTarget(consensus_sequence)[source]

verifyTarget(consensus_sequence)

Compare a consensus Sequence to the target Sequence.

class AnalysisProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Association(*args)[source]

An Association is linked to an Agent through the agent relationship. The Association includes the hadRole property to qualify the role of the Agent in the Activity.

  • agent : ReferencedObject

    The agent property is REQUIRED and MUST contain a URI that refers to an Agent object.

  • roles : URIProperty

    The hadRole property is REQUIRED and MUST contain a URI that refers to a particular term describing the usage of the agent.

  • plan : ReferencedObject

    The hadPlan property is OPTIONAL and contains a URI that refers to a Plan.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/provo.h

class AssociationProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Attachment(*args)[source]

The Attachment class is a general container for data files, especially experimental data files. Attachment is a TopLevel object, and any other TopLevel object can refer to a list of attachments.

  • source : URIProperty

    The source is a link to the external file and is REQUIRED.

  • format : URIProperty

  • size : IntProperty

  • hash : TextProperty

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/attachment.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class AttachmentProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Build(*args)[source]

A Build is a realization of a Design. For practical purposes, a Build can represent a biological clone, a plasmid, or other laboratory sample. For a given Design, there may be multiple Builds realized in the lab. A Build represents the second step in libSBOL’s formalized Design-Build-Test-Analyze workflow.

  • design : ReferencedObject

    A reference to a Design object which represents the intended structure and function for this Build.

  • structure : OwnedObject< ComponentDefinition >

    The experimentally verified structure of the construct as verified by DNA sequencing or other analysis.

  • behavior : OwnedObject< ModuleDefinition >

    The observed behavior of the constructed system.

  • sysbio_type : URIProperty

  • _structure : ReferencedObject

  • _behavior : ReferencedObject

  • built : URIProperty

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/dbtl.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class BuildProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Collection(*args)[source]

The Collection class is a class that groups together a set of TopLevel objects that have something in common.

Some examples of Collection objects: . Results of a query to find all ComponentDefinition objects in a repository that function as promoters . A set of ModuleDefinition objects representing a library of genetic logic gates. . A ModuleDefinition for a complexdesign, and all of the ModuleDefinition, ComponentDefinition, Sequence, and Model objects used to provide its full specification.

  • members : URIProperty

    The members property of a Collection is OPTIONAL and MAY contain a set of URI references to zero or more TopLevel objects.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/collection.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class CollectionProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class CombinatorialDerivation(*args)[source]

A ComponentDeriviation specifies the composition of a combinatorial design or variant library for common use cases in synthetic biology, such as tuning the performance of a genetic circuit or biosynthetic pathway through combinatorial DNA assembly and screening.

  • strategy : URIProperty

    The strategy property is OPTIONAL and has a data type of URI.

    Table 1 provides a list of REQUIRED strategy URIs. If the strategy property is not empty, then it MUST contain a URI from Table 1. This property recommends how many ComponentDefinition objects a user SHOULD derive from the template ComponentDefinition. Strategy URI

    Description

    http://sbols.org/v2#enumerate

    A user SHOULD derive all ComponentDefinition objects with a unique substructure as specified by the Component objects contained by the template ComponentDefinition and the VariableComponent objects contained by the CombinatorialDerivation.

    http://sbols.org/v2#sample

    A user SHOULD derive a subset of all ComponentDefinition objects with a unique substructure as specified by the Component objects contained by the template ComponentDefinition and the VariableComponent objects contained by the CombinatorialDerivation. The manner in which this subset is chosen is for the user to decide.

  • masterTemplate : ReferencedObject

    The master property is REQUIRED and MUST contain a URI that refers to a ComponentDefinition. This ComponentDefinition is expected to serve as a template for the derivation of new ComponentDefinition objects. Consequently, its components property SHOULD contain one or more Component objects that describe its substructure (referred to hereafter as template Component objects), and its sequenceConstraints property MAY also contain one or more SequenceConstraint objects that constrain this substructure.

  • variableComponents : OwnedObject< VariableComponent >

    VariableComponent objects denote the choices available when deriving the library of variants specified by a CombinatorialDerivation.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/combinatorialderivation.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class CombinatorialDerivationProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Component(*args)[source]

The Component class is used to compose ComponentDefinition objects into a structural hierarchy. For example, the ComponentDefinition of a gene could contain four Component objects: a promoter, RBS, CDS, and terminator. In turn, the ComponentDefinition of the promoter Component could contain Component objects defined as various operator sites.

  • roles : URIProperty

    The expected purpose and function of a genetic part are described by the roles property of ComponentDefinition.

    However, the same building block might be used for a different purpose in an actual design. In other words, purpose and function are sometimes determined by context. The roles property comprises an OPTIONAL set of zero or more role URIs describing the purpose or potential function of this Components included sub-ComponentDefinition in the context of its parent ComponentDefinition. If provided, these role URIs MUST identify terms from appropriate ontologies. Roles are not restricted to describing biological function; they may annotate a Components function in any domain for which an ontology exists. It is RECOMMENDED that these role URIs identify terms that are compatible with the type properties of both this Components parent ComponentDefinition and its included sub-ComponentDefinition. For example, a role of a Component which belongs to a ComponentDefinition of type DNA and includes a sub-ComponentDefinition of type DNA might refer to terms from the Sequence Ontology. See documentation for ComponentDefinition for a table of recommended ontology terms for roles.

  • roleIntegration : URIProperty

    A roleIntegration specifies the relationship between a Component instances own set of roles and the set of roles on the included sub- ComponentDefinition.

    The roleIntegration property has a data type of URI. A Component instance with zero roles MAY OPTIONALLY specify a roleIntegration. A Component instance with one or more roles MUST specify a roleIntegration from the table below If zero Component roles are given and no Component roleIntegration is given, then http://sbols.org/v2#mergeRoles is assumed. It is RECOMMENDED to specify a set of Component roles only if the integrated result set of roles would differ from the set of roles belonging to this Components included sub-ComponentDefinition. roleIntegration URI

    Description

    http://sbols.org/v2#overrideRoles

    In the context of this Component, ignore any roles given for the included sub-ComponentDefinition.

    Instead use only the set of zero or more roles given for this Component.

    http://sbols.org/v2#mergeRoles

    Use the union of the two sets: both the set of zero or more roles given for this Component as well

    as the set of zero or more roles given for the included sub- ComponentDefinition.

  • definition : ReferencedObject

    The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance.

    As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance. The definition property MUST NOT refer to the same ComponentDefinition as the one that contains the ComponentInstance. Furthermore, ComponentInstance objects MUST NOT form a cyclical chain of references via their definition properties and the ComponentDefinition objects that contain them. For example, consider the ComponentInstance objects A and B and the ComponentDefinition objects X and Y . The reference chain X contains A, A isdefinedby Y, Y contains B, and B isdefinedby X iscyclical.

  • access : URIProperty

    The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo.

    The value of the access property MUST be one of the following URIs. Access URI

    Description

    http://sbols.org/v2#public

    The ComponentInstance MAY be referred to by remote MapsTo objects

    http://sbols.org/v2#private

    The ComponentInstance MAY be referred to by remote MapsTo objects

  • mapsTos : OwnedObject< MapsTo >

    The mapsTos property is OPTIONAL and MAY contain a set of MapsTo objects that refer to and link together ComponentInstance objects (both Component objects and FunctionalComponent objects) within a larger design.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/component.h

class ComponentDefinition(*args)[source]

The ComponentDefinition class represents the structural entities of a biological design.

The primary usage of this class is to represent structural entities with designed sequences, such as DNA, RNA, and proteins, but it can also be used to represent any other entity that is part of a design, such as small molecules, proteins, and complexes

  • types : URIProperty

    The types property is a REQUIRED set of URIs that specifies the category of biochemical or physical entity (for example DNA, protein, or small molecule) that a ComponentDefinition object abstracts for the purpose of engineering design.

    The types property of every ComponentDefinition MUST contain one or more URIs that MUST identify terms from appropriate ontologies, such as the BioPAX ontology or the ontology of Chemical Entities of Biological Interest. See the table below for examples. Type

    URI for BioPAX Term

    LibSBOL symbol

    DNA

    http://www.biopax.org/release/biopax-level3.owl#DnaRegion

    BIOPAX_DNA

    RNA

    http://www.biopax.org/release/biopax-level3.owl#RnaRegion

    BIOPAX_RNA

    Protein

    http://www.biopax.org/release/biopax-level3.owl#Protein

    BIOPAX_PROTEIN

    Small Molecule

    http://www.biopax.org/release/biopax-level3.owl#SmallMolecule

    BIOPAX_SMALL_MOLECULE

    Complex

    http://www.biopax.org/release/biopax-level3.owl#Complex

    BIOPAX_COMPLEX

  • roles : URIProperty

    The roles property is an OPTIONAL set of URIs that clarifies the potential function of the entity represented by a ComponentDefinition in a biochemical or physical context.

    The roles property of a ComponentDefinition MAY contain one or more URIs that MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO). See the table below for common examples Role

    URI for Sequence Ontology Term

    LibSBOL symbol

    Miscellaneous

    http://identifiers.org/so/SO:0000001

    SO_MISC

    Promoter

    http://identifiers.org/so/SO:0000167

    SO_PROMOTER

    RBS

    http://identifiers.org/so/SO:0000139

    SO_RBS

    CDS

    http://identifiers.org/so/SO:0000316

    SO_CDS

    Terminator

    http://identifiers.org/so/SO:0000141

    SO_TERMINATOR

    Gene

    http://identifiers.org/so/SO:0000704

    Operator

    http://identifiers.org/so/SO:0000057

    Engineered Gene

    http://identifiers.org/so/SO:0000280

    mRNA

    http://identifiers.org/so/SO:0000234

    Effector

    http://identifiers.org/chebi/CHEBI:35224

  • components : OwnedObject< Component >

    The components property is OPTIONAL and MAY specify a set of Component objects that are contained by the ComponentDefinition. The components properties of ComponentDefinition objects can be used to construct a hierarchy of Component and ComponentDefinition objects. If a ComponentDefinition in such a hierarchy refers to one or more Sequence objects, and there exist ComponentDefinition objects lower in the hierarchy that refer to Sequence objects with the same encoding, then the elements properties of these Sequence objects SHOULD be consistent with each other, such that well-defined mappings exist from the lower level elements to the higher level elements. This mapping is also subject to any restrictions on the positions of the Component objects in the hierarchy that are imposed by the SequenceAnnotation or SequenceConstraint objects contained by the ComponentDefinition objects in the hierarchy. The set of relations between Component and ComponentDefinition objects is strictly acyclic.

  • sequences : ReferencedObject

    The sequences property is OPTIONAL and MAY include a URI that refer to a Sequence object. The referenced object defines the primary structure of the ComponentDefinition.

  • sequence : OwnedObject< Sequence >

  • sequenceAnnotations : OwnedObject< SequenceAnnotation >

    The sequenceAnnotations property is OPTIONAL and MAY contain a set of SequenceAnnotation objects. Each SequenceAnnotation specifies and describes a potentially discontiguous region on the Sequence objects referred to by the ComponentDefinition.

  • sequenceConstraints : OwnedObject< SequenceConstraint >

    The sequenceConstraints property is OPTIONAL and MAY contain a set of SequenceConstraint objects. These objects describe any restrictions on the relative, sequence-based positions and/or orientations of the Component objects contained by the ComponentDefinition. For example, the ComponentDefinition of a gene might specify that the position of its promoter Component precedes that of its CDS Component. This is particularly useful when a ComponentDefinition lacks a Sequence and therefore cannot specify the precise, sequence-based positions of its Component objects using SequenceAnnotation objects.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/componentdefinition.h

addDownstreamFlank(target, elements)[source]

addDownstreamFlank(target, elements)

This may be a useful method when building up SBOL representations of natural DNA sequences.

For example it is often necessary to specify components that are assumed to have no meaningful role in the design, but are nevertheless important to fill in regions of sequence. This method autoconstructs a ComponentDefinition and Sequence object to create an arbitrary flanking sequence around design Components. The new ComponentDefinition will have Sequence Ontology type of flanking_sequence.

  • target :
    The new flanking sequence will be placed downstream of the target
  • elements :
    The primary sequence elements will be assigned to the autoconstructed Sequence object. The encoding is inferred
addUpstreamFlank(target, elements)[source]

addUpstreamFlank(target, elements)

This may be a useful method when building up SBOL representations of natural DNA sequences.

For example it is often necessary to specify components that are assumed to have no meaningful role in the design, but are nevertheless important to fill in regions of sequence. This method autoconstructs a ComponentDefinition and Sequence object to create an arbitrary flanking sequence around design Components. The new ComponentDefinition will have Sequence Ontology type of flanking_region or SO:0000239

  • target :
    The new flanking sequence will be placed upstream of the target
  • elements :
    The primary sequence elements will be assigned to the autoconstructed Sequence object. The encoding is inferred
assemble(*args)[source]

assemble(list_of_uris, assembly_standard=”“)

Assembles ComponentDefinitions into an abstraction hierarchy.

The resulting data structure is a partial design, still lacking a primary structure or explicit sequence. To form a primary structure out of the ComponentDefinitions, call linearize after calling assemble. To fully realize the target sequence, use Sequence::assemble().

  • list_of_uris :
    A list of URIs for the constituent ComponentDefinitions, or displayIds if using SBOL-compliant URIs
  • assembly_standard :
    An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence
assemblePrimaryStructure(*args)[source]

assemblePrimaryStructure(primary_structure, doc, assembly_standard=”“)

Assembles ComponentDefinition into a linear primary structure.

The resulting data structure is a partial design, still lacking an explicit sequence. To fully realize the target sequence, use Sequence::assemble().

  • list_of_components :
    A list of subcomponents that will compose this ComponentDefinition
  • doc :
    The Document to which the assembled ComponentDefinitions will be added
  • assembly_standard :
    An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence
build()[source]

build() -> ComponentDefinition &

compile()[source]

compile() -> std::string

Compiles an abstraction hierarchy of ComponentDefinitions into a nucleotide sequence. If no Sequence object is associated with this ComponentDefinition, one will be automatically instantiated.

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

disassemble(range_start=1)[source]

disassemble(range_start=1)

Instantiates a Component for every SequenceAnnotation. When converting from a flat GenBank file to a flat SBOL file, the result is a ComponentDefinition with SequenceAnnotations. This method will convert the flat SBOL file into hierarchical SBOL.

getDownstreamComponent(current_component)[source]

getDownstreamComponent(current_component) -> Component &

Get the downstream Component.

The downstream component

getFirstComponent()[source]

getFirstComponent() -> Component &

Gets the first Component in a linear sequence.

The first component in sequential order

getInSequentialOrder()[source]

getInSequentialOrder() -> std::vector< Component * >

Orders this ComponentDefinition’s member Components into a linear arrangement based on Sequence Constraints.

Primary sequence structure

getLastComponent()[source]

getLastComponent() -> Component &

Gets the last Component in a linear sequence.

The last component in sequential order

getPrimaryStructure()[source]

getPrimaryStructure() -> std::vector< ComponentDefinition * >

Get the primary sequence of a design in terms of its sequentially ordered Components.

getUpstreamComponent(current_component)[source]

getUpstreamComponent(current_component) -> Component &

Get the upstream Component.

The upstream component

hasDownstreamComponent(current_component)[source]

hasDownstreamComponent(current_component) -> int

Checks if the specified Component has a Component downstream in linear arrangement on the DNA strand.

Checks that the appropriate SequenceConstraint exists.

  • current_component :
    A Component in this ComponentDefinition

1 if found, 0 if not

hasUpstreamComponent(current_component)[source]

hasUpstreamComponent(current_component) -> int

Checks if the specified Component has a Component upstream in linear arrangement on the DNA strand.

Checks that the appropriate SequenceConstraint exists.

  • current_component :
    A Component in this ComponentDefinition

1 if found, 0 if not

insertDownstream(target, insert)[source]

insertDownstream(target, insert)

Insert a Component downstream of another in a primary sequence, shifting any adjacent Components dowstream as well.

  • target :
    The target Component will be upstream of the insert Component after this operation.
  • insert :
    The insert Component is inserted downstream of the target Component.
insertUpstream(target, insert)[source]

insertUpstream(target, insert)

Insert a Component upstream of another in a primary sequence, shifting any adjacent Components upstream as well.

  • target :
    The target Component will be downstream of the insert Component after this operation.
  • insert :
    The insert Component is inserted upstream of the target Component.
isComplete(*args)[source]

isComplete() -> bool

Recursively verifies that the parent Document contains a ComponentDefinition and Sequence for each and every ComponentDefinition in the abstraction hierarchy.

If a ComponentDefinition is not complete, some objects are missing from the Document or externally linked. Diagnose with isComplete(std::string &msg)

true if the abstraction hierarchy is complete, false otherwise.

isRegular(*args)[source]

isRegular() -> bool

Recursively checks if this ComponentDefinition defines a SequenceAnnotation and Range for every Sequence.

Regularity is more stringent than completeness. A design must be complete to be regular. If the Component is irregular, diagnose with isRegular(std::string &msg)

true if the abstraction hierarchy is regular, false otherwise.

linearize(*args)[source]

linearize(list_of_uris)

participate(species)[source]

participate(species)

A convenience method that assigns a component to participate in a biochemical reaction.

Behind the scenes, it auto-constructs a FunctionalComponent for this ComponentDefinition and assigns it to a Participation

  • species :
    A Participation object (ie, participant species in a biochemical Interaction).
updateSequence(*args)[source]

updateSequence(composite_sequence=”“) -> std::string

Assemble a parent ComponentDefinition’s Sequence from its subcomponent Sequences.

  • composite_sequence :
    A recursive parameter, use default value

The assembled parent sequence

class ComponentDefinitionProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class ComponentInstance(*args, **kwargs)[source]
  • definition : ReferencedObject

    The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance.

    As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance. The definition property MUST NOT refer to the same ComponentDefinition as the one that contains the ComponentInstance. Furthermore, ComponentInstance objects MUST NOT form a cyclical chain of references via their definition properties and the ComponentDefinition objects that contain them. For example, consider the ComponentInstance objects A and B and the ComponentDefinition objects X and Y . The reference chain X contains A, A isdefinedby Y, Y contains B, and B isdefinedby X iscyclical.

  • access : URIProperty

    The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo.

    The value of the access property MUST be one of the following URIs. Access URI

    Description

    http://sbols.org/v2#public

    The ComponentInstance MAY be referred to by remote MapsTo objects

    http://sbols.org/v2#private

    The ComponentInstance MAY be referred to by remote MapsTo objects

  • mapsTos : OwnedObject< MapsTo >

    The mapsTos property is OPTIONAL and MAY contain a set of MapsTo objects that refer to and link together ComponentInstance objects (both Component objects and FunctionalComponent objects) within a larger design.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

class ComponentProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Config[source]

A class which contains global configuration variables for the libSBOL environment. Intended to be used like a static class, configuration variables are accessed through the Config::setOptions and Config::getOptions methods.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/config.h

static getOption(option)[source]

getOption(option) -> std::string

Get current option value for online validation and conversion.

  • option :
    The option key
static setOption(*args)[source]

setOption(option, value)

Config_getOption(option)[source]

getOption(option) -> std::string

Get current option value for online validation and conversion.

  • option :
    The option key
Config_setOption(*args)[source]

setOption(option, value)

class Cut(*args)[source]

The Cut class specifies a location between two coordinates of a Sequence’s elements. class Cut : public Location.

  • at : IntProperty

    This property specifies the location between this nucleotide coordinate (or other sequence element) and the nucleotide coordinate immediately following it. When equal to zero, the specified region is immediately before the first nucleotide or character in the elements.

  • orientation : URIProperty

    The orientation indicates how a region of double-stranded DNA represented by the parent SequenceAnnotation and its associated Component are oriented.

    The orientation may be one of the following values. By default it is set to SBOL_ORIENTATION_INLINE. Orientation URI

    libSBOL Symbol

    http://sbols.org/v2#inline

    SBOL_ORIENTATION_INLINE

    http://sbols.org/v2#reverseComplement

    SBOL_ORIENTATION_REVERSE_COMPLEMENT

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/location.h

class DateTimeProperty(*args)[source]

Contains a DateTime string following XML Schema.

  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/properties.h

stampTime()[source]

stampTime() -> std::string

Set this property with the current time.

class Design(*args)[source]

This class represents a biological Design. A Design is a conceptual representation of a biological system that a synthetic biologist intends to build. A Design is the first object created in libSBOL’s formalized Design- Build-Test-Analysis workflow.

  • structure : OwnedObject< ComponentDefinition >

    The target biological structure for synthesis or other molecular assembly.

  • function : OwnedObject< ModuleDefinition >

    The intended function and predicted behavior of the Design object.

  • characterization : ReferencedObject

    A reference to an Analysis or multiple Analysis objects that contain characterization data, previously verified experimental knowledge, or explanatory models that inform a Design.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/dbtl.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class DesignProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Document(*args)[source]

Read and write SBOL using a Document class. The Document is a container for Components, Modules, and all other SBOLObjects.

  • designs : OwnedObject< Design >

  • builds : OwnedObject< Build >

  • tests : OwnedObject< Test >

  • analyses : OwnedObject< Analysis >

  • componentDefinitions : OwnedObject< ComponentDefinition >

  • moduleDefinitions : OwnedObject< ModuleDefinition >

  • models : OwnedObject< Model >

  • sequences : OwnedObject< Sequence >

  • collections : OwnedObject< Collection >

  • activities : OwnedObject< Activity >

  • plans : OwnedObject< Plan >

  • agents : OwnedObject< Agent >

  • attachments : OwnedObject< Attachment >

  • combinatorialderivations : OwnedObject< CombinatorialDerivation >

  • implementations : OwnedObject< Implementation >

  • sampleRosters : OwnedObject< SampleRoster >

  • citations : URIProperty

  • keywords : URIProperty

  • python_iter : iterator

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/document.h

addComponentDefinition(*args)[source]

addComponentDefinition(sbol_obj)

addModel(*args)[source]

addModel(sbol_obj)

addModuleDefinition(*args)[source]

addModuleDefinition(sbol_obj)

addNamespace(*args)[source]

addNamespace(ns, prefix)

Add a new namespace to this Document.

  • ns :
    The namespace, eg. http://sbols.org/v2#
  • prefix :
    The namespace prefix, eg. sbol
addSequence(*args)[source]

addSequence(sbol_obj)

append(filename)[source]

append(filename)

Read an RDF/XML file and attach the SBOL objects to this Document.

New objects will be added to the existing contents of the Document

  • filename :
    The full name of the file you want to read (including file extension)
copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

countTriples()[source]

countTriples() -> int

end()[source]

end() -> iterator

find(uri)[source]

find(uri) -> SBOLObject *

Search recursively for an SBOLObject in this Document that matches the uri.

  • uri :
    The identity of the object to search for

A pointer to the SBOLObject, or NULL if an object with this identity doesn’t exist

find_property(uri)[source]

find_property(uri) -> SBOLObject *

Search this object recursively to see if it contains a member property with the given RDF type.

  • uri :
    The RDF type of the property to search for.

A pointer to the object that contains a member property with the specified RDF type, NULL otherwise

find_reference(uri)[source]

find_reference(uri) -> std::vector< SBOLObject * >

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

  • uri :
    A URI, either an ontology term or an object reference, to search for

A vector containing all objects found that contain the URI in a property value

generate(world, sbol_serializer, sbol_buffer, sbol_buffer_len, ios, base_uri)[source]

generate() -> SBOLClass &

getActivity(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getAgent(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getAnalysis(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getAttachment(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getBuild(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getCollection(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getCombinatorialDerivation(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getComponentDefinition(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getDesign(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getImplementation(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getModel(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getModuleDefinition(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getNamespaces()[source]

getNamespaces() -> std::vector< std::string >

A vector of namespaces Get namespaces contained in this Document

getPlan(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getSampleRoster(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getSequence(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
getTest(uri)[source]

get(uri) -> SBOLClass &

Retrieve an object from the Document.

  • uri :
    The identity of the SBOL object you want to retrieve
  • SBOLClass :
    The type of SBOL object
query_repository(command)[source]

query_repository(command) -> std::string

read(filename)[source]

read(filename)

Read an RDF/XML file and attach the SBOL objects to this Document.

Existing contents of the Document will be wiped.

  • filename :
    The full name of the file you want to read (including file extension)
readString(*args)[source]

readString(sbol)

Convert text in SBOL into data objects.

  • sbol :
    A string formatted in SBOL
request_comparison(diff_file)[source]

request_comparison(diff_file) -> std::string

Perform comparison on Documents using the online validation tool.

This is for cross-validation of SBOL documents with libSBOLj. Document comparison can also be performed using the built-in compare method.

The comparison results

request_validation(sbol)[source]

request_validation(sbol) -> std::string

search_metadata(role, type, name, collection)[source]

search_metadata(role, type, name, collection) -> std::string

summary()[source]

summary() -> std::string

Get a summary of objects in the Document, including SBOL core object and custom annotation objects.

validate()[source]

validate() -> std::string

Run validation on this Document via the online validation tool.

A string containing a message with the validation results

author: KC

write(filename)[source]

write(filename) -> std::string

Serialize all objects in this Document to an RDF/XML file.

  • filename :
    The full name of the file you want to write (including file extension)

A string with the validation results, or empty string if validation is disabled

writeString()[source]

writeString() -> std::string

Convert data objects in this Document into textual SBOL.

class EnzymeCatalysisInteraction(*args)[source]
  • enzyme : AliasedProperty< FunctionalComponent >

  • substrates : AliasedProperty< FunctionalComponent >

  • products : AliasedProperty< FunctionalComponent >

  • cofactors : AliasedProperty< FunctionalComponent >

  • sideproducts : AliasedProperty< FunctionalComponent >

  • types : URIProperty

    The types property is a REQUIRED set of URIs that describes the behavior represented by an Interaction.

    The types property MUST contain one or more URIs that MUST identify terms from appropriate ontologies. It is RECOMMENDED that at least one of the URIs contained by the types property refer to a term from the occurring entity branch of the Systems Biology Ontology (SBO). (See http://www.ebi.ac.uk/sbo/main/) The following table provides a list of possible SBO terms for the types property and their corresponding URIs. Type

    URI for SBO Term

    LibSBOL symbol

    Biochemical Reaction

    http://identifiers.org/biomodels.sbo/SBO:0000176

    SBO_BIOCHEMICAL_REACTION

    Inhibition

    http://identifiers.org/biomodels.sbo/SBO:0000169

    SBO_INHIBITION

    Stimulation

    http://identifiers.org/biomodels.sbo/SBO:0000170

    SBO_STIMULATION

    Genetic Production

    http://identifiers.org/biomodels.sbo/SBO:0000589

    SBO_GENETIC_PRODUCTION

    Non-Covalent Binding

    http://identifiers.org/biomodels.sbo/SBO:0000177

    SBO_NONCOVALENT_BINDING

    Degradation

    http://identifiers.org/biomodels.sbo/SBO:0000179

    SBO_DEGRADATION

    Control

    http://identifiers.org/biomodels.sbo/SBO:0000168

    SBO_CONTROL

  • participations : OwnedObject< Participation >

    The participations property is an OPTIONAL and MAY contain a set of Participation objects, each of which identifies the roles that its referenced FunctionalComponent plays in the Interaction. Even though an Interaction generally contains at least one Participation, the case of zero Participation objects is allowed because it is plausible that a designer might want to specify that an Interaction will exist, even if its participants have not yet been determined.

  • functionalComponents : OwnedObject< FunctionalComponent >

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

class FloatProperty(*args)[source]

FloatProperty objects are used to contain floats.

They can be used as member objects inside custom SBOL Extension classes.

  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/properties.h

get()[source]

get() -> double

Get the float value.

An integer

getAll()[source]

getAll() -> std::vector< double >

class FunctionalComponent(*args)[source]

The FunctionalComponent class is used to specify the functional usage of a ComponentDefinition inside a ModuleDefinition. The ModuleDefinition describes how the that describes how the FunctionalComponent interacts with others and summarizes their aggregate function.

  • direction : URIProperty

    Each FunctionalComponent MUST specify via the direction property whether it serves as an input, output, both, or neither for its parent ModuleDefinition object.

    The value for this property MUST be one of the URIs given in the table below. Direction URI

    Description

    LibSBOL Symbol

    http://sbols.org/v2#in

    Indicates that the FunctionalComponent is an input.

    SBOL_DIRECTION_IN

    http://sbols.org/v2#out

    Indicates that the FunctionalComponent is an output.

    SBOL_DIRECTION_OUT

    http://sbols.org/v2#inout

    Indicates that the FunctionalComponent is both an input and output

    SBOL_DIRECTION_IN_OUT

    http://sbols.org/v2#none

    Indicates that the FunctionalComponent is neither an input or output.

    SBOL_DIRECTION_NONE

  • definition : ReferencedObject

    The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance.

    As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance. The definition property MUST NOT refer to the same ComponentDefinition as the one that contains the ComponentInstance. Furthermore, ComponentInstance objects MUST NOT form a cyclical chain of references via their definition properties and the ComponentDefinition objects that contain them. For example, consider the ComponentInstance objects A and B and the ComponentDefinition objects X and Y . The reference chain X contains A, A isdefinedby Y, Y contains B, and B isdefinedby X iscyclical.

  • access : URIProperty

    The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo.

    The value of the access property MUST be one of the following URIs. Access URI

    Description

    http://sbols.org/v2#public

    The ComponentInstance MAY be referred to by remote MapsTo objects

    http://sbols.org/v2#private

    The ComponentInstance MAY be referred to by remote MapsTo objects

  • mapsTos : OwnedObject< MapsTo >

    The mapsTos property is OPTIONAL and MAY contain a set of MapsTo objects that refer to and link together ComponentInstance objects (both Component objects and FunctionalComponent objects) within a larger design.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/component.h

connect(interface_component)[source]

connect(interface_component)

This method connects module inputs and outputs.

This convenience method auto-constructs a MapsTo object. See Biosystem Design for an example

  • interface_component :
    An input or output component from another ModuleDefinition that corresponds with this component.
isMasked()[source]

isMasked() -> int

Used to tell if a FunctionalComponent is linked to an equivalent FunctionalComponent in another ModuleDefinition.

1 if the FunctionalComponent has been over-rided by another FunctionalComponent, 0 if it hasn’t.

mask(masked_component)[source]

mask(masked_component)

This method is used to state that FunctionalComponents in separate ModuleDefinitions are functionally equivalent.

Using this method will override the FunctionalComponent in the argument with the FunctionalComponent calling the method. This is useful for overriding a generic, template component with an explicitly defined component. This convenience method auto-constructs a MapsTo object. See Biosystem Design for an example

  • masked_component :
    The FunctionalComponent that is being masked (over-ridden)
override(masked_component)[source]

override(masked_component)

This method is used to state that FunctionalComponents in separate ModuleDefinitions are functionally equivalent.

Using this method will override the FunctionalComponent in the argument with the FunctionalComponent calling the method. This is useful for overriding a generic, template component with an explicitly defined component. This convenience method auto-constructs a MapsTo object. See Biosystem Design for an example

  • masked_component :
    The FunctionalComponent that is being masked (over-ridden)
class FunctionalComponentProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class GeneProductionInteraction(uri, gene, product)[source]
  • gene : AliasedProperty< FunctionalComponent >

  • product : AliasedProperty< FunctionalComponent >

  • types : URIProperty

    The types property is a REQUIRED set of URIs that describes the behavior represented by an Interaction.

    The types property MUST contain one or more URIs that MUST identify terms from appropriate ontologies. It is RECOMMENDED that at least one of the URIs contained by the types property refer to a term from the occurring entity branch of the Systems Biology Ontology (SBO). (See http://www.ebi.ac.uk/sbo/main/) The following table provides a list of possible SBO terms for the types property and their corresponding URIs. Type

    URI for SBO Term

    LibSBOL symbol

    Biochemical Reaction

    http://identifiers.org/biomodels.sbo/SBO:0000176

    SBO_BIOCHEMICAL_REACTION

    Inhibition

    http://identifiers.org/biomodels.sbo/SBO:0000169

    SBO_INHIBITION

    Stimulation

    http://identifiers.org/biomodels.sbo/SBO:0000170

    SBO_STIMULATION

    Genetic Production

    http://identifiers.org/biomodels.sbo/SBO:0000589

    SBO_GENETIC_PRODUCTION

    Non-Covalent Binding

    http://identifiers.org/biomodels.sbo/SBO:0000177

    SBO_NONCOVALENT_BINDING

    Degradation

    http://identifiers.org/biomodels.sbo/SBO:0000179

    SBO_DEGRADATION

    Control

    http://identifiers.org/biomodels.sbo/SBO:0000168

    SBO_CONTROL

  • participations : OwnedObject< Participation >

    The participations property is an OPTIONAL and MAY contain a set of Participation objects, each of which identifies the roles that its referenced FunctionalComponent plays in the Interaction. Even though an Interaction generally contains at least one Participation, the case of zero Participation objects is allowed because it is plausible that a designer might want to specify that an Interaction will exist, even if its participants have not yet been determined.

  • functionalComponents : OwnedObject< FunctionalComponent >

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

class GenericLocation(*args)[source]

the GenericLocation class is included as a starting point for specifying regions on Sequence objects with encoding properties other than IUPAC and potentially nonlinear structure. This class can also be used to set the orientation of a SequenceAnnotation and any associated Component when their parent ComponentDefinition is a partial design that lacks a Sequence.

  • orientation : URIProperty

    The orientation indicates how a region of double-stranded DNA represented by the parent SequenceAnnotation and its associated Component are oriented.

    The orientation may be one of the following values. By default it is set to SBOL_ORIENTATION_INLINE. Orientation URI

    libSBOL Symbol

    http://sbols.org/v2#inline

    SBOL_ORIENTATION_INLINE

    http://sbols.org/v2#reverseComplement

    SBOL_ORIENTATION_REVERSE_COMPLEMENT

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/location.h

class Identified(*args)[source]

All SBOL-defined classes are directly or indirectly derived from the Identified abstract class.

An Identified object is identified using a Uniform Resource Identifier (URI), a unique string that identifies and refers to a specific object in an SBOL document or in an online resource such as a DNA repository.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/identified.h

class Implementation(*args)[source]

An Implementation represents a real, physical instance of a synthetic biological construct which may be associated with a laboratory sample. An Implementation may be linked back to its original design (either a ModuleDefinition or ComponentDefinition) using the wasDerivedFrom property inherited from the Identified superclass.

  • built : URIProperty

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/implementation.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class ImplementationProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class IntProperty(*args)[source]

IntProperty objects are used to contain integers.

They can be used as member objects inside custom SBOL Extension classes.

  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/properties.h

get()[source]

get() -> int

Get the integer value.

An integer

getAll()[source]

getAll() -> std::vector< int >

class Interaction(*args)[source]

The Interaction class provides more detailed descriptionof how the FunctionalComponents are intended to work together. For example, this class can be used to represent different forms of genetic regulation (e.g., transcriptional activation or repression), processes from the central dogma of biology (e.g. transcription and translation), and other basic molecular interactions (e.g., non-covalent binding or enzymatic phosphorylation).

  • types : URIProperty

    The types property is a REQUIRED set of URIs that describes the behavior represented by an Interaction.

    The types property MUST contain one or more URIs that MUST identify terms from appropriate ontologies. It is RECOMMENDED that at least one of the URIs contained by the types property refer to a term from the occurring entity branch of the Systems Biology Ontology (SBO). (See http://www.ebi.ac.uk/sbo/main/) The following table provides a list of possible SBO terms for the types property and their corresponding URIs. Type

    URI for SBO Term

    LibSBOL symbol

    Biochemical Reaction

    http://identifiers.org/biomodels.sbo/SBO:0000176

    SBO_BIOCHEMICAL_REACTION

    Inhibition

    http://identifiers.org/biomodels.sbo/SBO:0000169

    SBO_INHIBITION

    Stimulation

    http://identifiers.org/biomodels.sbo/SBO:0000170

    SBO_STIMULATION

    Genetic Production

    http://identifiers.org/biomodels.sbo/SBO:0000589

    SBO_GENETIC_PRODUCTION

    Non-Covalent Binding

    http://identifiers.org/biomodels.sbo/SBO:0000177

    SBO_NONCOVALENT_BINDING

    Degradation

    http://identifiers.org/biomodels.sbo/SBO:0000179

    SBO_DEGRADATION

    Control

    http://identifiers.org/biomodels.sbo/SBO:0000168

    SBO_CONTROL

  • participations : OwnedObject< Participation >

    The participations property is an OPTIONAL and MAY contain a set of Participation objects, each of which identifies the roles that its referenced FunctionalComponent plays in the Interaction. Even though an Interaction generally contains at least one Participation, the case of zero Participation objects is allowed because it is plausible that a designer might want to specify that an Interaction will exist, even if its participants have not yet been determined.

  • functionalComponents : OwnedObject< FunctionalComponent >

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/interaction.h

class InteractionProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Location(*args)[source]

The Location class specifies the strand orientation of a Component and can be further extended by the Range, Cut, and GenericLocation classes.

  • orientation : URIProperty

    The orientation indicates how a region of double-stranded DNA represented by the parent SequenceAnnotation and its associated Component are oriented.

    The orientation may be one of the following values. By default it is set to SBOL_ORIENTATION_INLINE. Orientation URI

    libSBOL Symbol

    http://sbols.org/v2#inline

    SBOL_ORIENTATION_INLINE

    http://sbols.org/v2#reverseComplement

    SBOL_ORIENTATION_REVERSE_COMPLEMENT

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/location.h

class LocationProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class MapsTo(*args)[source]

The purpose of the MapsTo class is to make identity relationships between different ComponentInstances in functional and structural hierarchies more clear. For example, a MapsTo object may be used to connect outputs and inputs between different low-level ModuleDefinitions contained in a higher level Module Definition. A MapsTo object may also be used to override a generic Component in a low-level ModuleDefinition with an explicit Component in a high-level ModuleDefinition, for example mapping a generic gene to an explicit component with a name and sequence.

  • refinement : URIProperty

    Each MapsTo object MUST specify the relationship between its local and remote ComponentInstance objects using one of the REQUIRED refinement URIs provided in the table below.

    Refinement URI

    libSBOL Symbol

    Description

    http://sbols.org/v2#useRemote

    SBOL_REFINEMENT_USE_REMOTE

    All references to the local ComponentInstance MUST dereference to the remote ComponentInstance instead.

    http://sbols.org/v2#useLocal

    SBOL_REFINEMENT_USE_LOCAL

    In the context of the ComponentDefinition or ModuleDefinition that contains the owner of the MapsTo, all references to the remote ComponentInstance MUST dereference to the local ComponentInstance instead.

    http://sbols.org/v2#verifyIdentical

    SBOL_REFINEMENT_VERIFY_IDENTICAL

    The definition properties of the local and remoteComponentInstance objects MUST refer to the same ComponentDefinition.

    http://sbols.org/v2#merge

    SBOL_REFINEMENT_MERGE_DESCRIPTION

    In the context of the ComponentDefinition or ModuleDefinition that contains the owner of the MapsTo, all references to the local ComponentInstance or the remote ComponentInstance MUST dereference to both objects.

  • local : ReferencedObject

    The identity of the lower level ComponentInstance.

  • remote : ReferencedObject

    The identity of the higher level ComponentInstance.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/mapsto.h

class MapsToProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Model(*args)[source]

The purpose of the Model class is to serve as a placeholder for an external computational model and provide additional meta-data to enable better reasoning about the contents of this model.

In this way, there is minimal duplication of standardization efforts and users of SBOL can formalize the function of a ModuleDefinition in the language of their choice.

  • source : URIProperty

    The source property is REQUIRED and MUST contain a URI reference to the source file for a model.

  • language : URIProperty

    The language property is REQUIRED and MUST contain a URI that specifies the language in which the model is implemented.

    It is RECOMMENDED that this URI refer to a term from the EMBRACE Data and Methods (EDAM) ontology. The Table below provides a list of terms from this ontology and their URIs. If the language property of a Model is well- described by one these terms, then it MUST contain the URI for this term as its value. Model Language

    URI for EDAM Term

    libSBOL Symbol

    SBML

    http://identifiers.org/edam/format_2585

    EDAM_SBML

    CellML

    http://identifiers.org/edam/format_3240

    EDAM_CELLML

    BioPAX

    http://identifiers.org/edam/format_3156

    EDAM_BIOPAX

  • framework : URIProperty

    Model Language

    URI for SBO Term

    libSBOL Symbol

    Continuous

    http://identifiers.org/biomodels.sbo/SBO:0000062

    SBO_CONTINUOUS

    Discrete

    http://identifiers.org/biomodels.sbo/SBO:0000063

    SBO_DISCRETE

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/model.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class ModelProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Module(*args)[source]

The Module class represents a submodule of a ModuleDefinition within a hierarchical design.

  • definition : ReferencedObject

    The definition property is a REQUIRED URI that refers to the ModuleDefinition for the Module.

  • mapsTos : OwnedObject< MapsTo >

    The mapsTos property is an OPTIONAL set of MapsTo objects that refer to and link ComponentInstance objects together within the heterarchy of Module, ModuleDefinition, ComponentInstance, and ComponentDefinition objects.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/module.h

class ModuleDefinition(*args)[source]

The ModuleDefinition class represents a grouping of structural and functional entities in a biological design. The primary usage of this class is to assert the molecular interactions and abstract function of its child entities.

  • roles : URIProperty

    The roles property is an OPTIONAL set of URIs that clarifies the intended function of a ModuleDefinition. These URIs might identify descriptive biological roles, such as metabolic pathway and signaling cascade, but they can also identify identify logical roles, such as inverter or AND gate, or other abstract roles for describing the function of design. Interpretation of the meaning of such roles currently depends on the software tools that read and write them.

  • modules : OwnedObject< Module >

    The modules property is OPTIONAL and MAY specify a set of Module objects contained by the ModuleDefinition. While the ModuleDefinition class is analogous to a specification sheet for a system of interacting biological elements, the Module class represents the occurrence of a particular subsystem within the system. Hence, this class allows a system design to include multiple instances of a subsystem, all defined by reference to the same ModuleDefinition. For example, consider the ModuleDefinition for a network of two-input repressor devices in which the particular repressors have not been chosen yet. This ModuleDefinition could contain multiple Module objects that refer to the same ModuleDefinition of an abstract two- input repressor device. Note that the set of relations between Module and ModuleDefinition objects is strictly acyclic.

  • interactions : OwnedObject< Interaction >

    The interactions property is OPTIONAL and MAY specify a set of Interaction objects within the ModuleDefinition. The Interaction class provides an abstract, machine-readable representation of entity behavior within a ModuleDefinition. Each Interaction contains Participation objects that indicate the roles of the FunctionalComponent objects involved in the Interaction.

  • functionalComponents : OwnedObject< FunctionalComponent >

    The functionalComponents property is OPTIONAL and MAY specify a set of FunctionalComponent objects contained by the ModuleDefinition. Just as a Module represents an instance of a subsystem in the overall system represented by a ModuleDefinition, a FunctionalComponent represents an instance of a structural entity (represented by a ComponentDefinition) in the system. This concept allows a ModuleDefinition to assert different interactions for separate copies of the same structural entity if needed. For example, a ModuleDefinition might contain multiple FunctionalComponent objects that refer to the same promoter ComponentDefinition, but assert different interactions for these promoter copies based on their separate positions in another ComponentDefinition that represents the structure of the entire system.

  • models : ReferencedObject

    The models property is OPTIONAL and MAY specify a set of URI references to Model objects. Model objects are placeholders that link ModuleDefinition objects to computational models of any format. A ModuleDefinition object can link to more than one Model since each might encode system behavior in a different way or at a different level of detail.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/moduledefinition.h

assemble(*args)[source]

assemble(list_of_modules)

Assemble a high-level ModuleDefinition from lower-level submodules.

Autoconstructs Module objects in the process.

  • list_of_modules :
    A list of pointers to the submodule ModuleDefinitions
connect(output, input)[source]

connect(output, input)

Connects the output of a sub-Module with the input of another sub-Module.

Auto-constructs MapsTo objects.

  • output :
    A FunctionalComponent configured as a Module output (see setOutput)
  • input :
    A FunctionalComponent configured as a Module input (see setInput)
copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

override(highlevel, lowlevel)[source]

override(highlevel, lowlevel)

Overrides a low-level component in an abstract sub-Module with a high-level component in a parent ModuleDefinition, for example when overriding an abstract template Module with explicit components.

  • highlevel :
    A high-level FunctionalComponent
  • lowlevel :
    A low-level FunctionalComponent in a nested sub-Module
setInput(*args)[source]

setInput(input)

Configures a FunctionalComponent as an input for a Module.

Useful for bottom-up assembly of Modules and sub-Modules

  • input :
    The FunctionalComponent that will be configured
setOutput(*args)[source]

setOutput(output)

Configures a FunctionalComponent as an output for a Module.

Useful for bottom-up assembly of Modules and sub-Modules.

  • output :
    The FunctionalComponent that will be configured
class ModuleDefinitionProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class ModuleProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class OwnedActivity(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedAgent(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedAnalysis(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedAssociation(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedAttachment(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedBuild(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedCollection(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedCombinatorialDerivation(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedComponent(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedComponentDefinition(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedDesign(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedFunctionalComponent(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedImplementation(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedInteraction(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedLocation(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedMapsTo(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedModel(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedModule(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedModuleDefinition(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedParticipation(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedPlan(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedSampleRoster(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedSequence(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedSequenceAnnotation(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedSequenceConstraint(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedTest(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedUsage(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class OwnedVariableComponent(*args)[source]

A container property that contains child objects.

Creates a composition out of two or more classes. In the SBOL specification, compositional relationships are indicated in class diagrams by arrows with black diamonds. A compositional relationship means that deleting the parent object will delete the child objects, and adding the parent object to a Document will also add the child object. Owned objects are stored in arbitrary order.

  • SBOLClass :
    The type of child SBOL object contained by this Property
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(sbol_obj)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
clear()[source]

clear()

Remove all children objects from the parent and destroy them.

create(uri)[source]

create(uri) -> Test &

createCut(uri)[source]

create(uri) -> Test &

createGenericLocation(uri)[source]

create(uri) -> Test &

createRange(uri)[source]

create(uri) -> Test &

define(definition_object)[source]

define(definition_object) -> SBOLClass &

Autoconstructs a child object and attaches it to the parent object.

Additionally, it sets the definition property of the child object, for example, in the case of creating Components, FunctionalComponents, and Modules. The new object will be constructed with default values specified in the constructor for this type of object. If SBOLCompliance is enabled, the child object’s identity will be constructed using the supplied displayId argument. Otherwise, the user should supply a full URI.

  • SBOLClass :
    The type of SBOL object that will be created
  • definition_object :
    The returned object will reference the definition_object in its definition property.

A reference to the child object check uniqueness of URI in Document

find(uri)[source]

find(uri) -> bool

  • uri :
    The full uniform resource identifier of the object to search for in this property

A boolean indicating whether found or not

get(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getAll()[source]

getAll() -> std::vector< SBOLClass * >

Get all the objects contained in the property.

A vector of pointers to the objects

getCut(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getGenericLocation(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

getRange(*args)[source]

get(uri=”“) -> SBOLSubClass &

Get the child object.

  • SBOLClass :
    The type of the child object
  • SBOLSubClass :
    A derived class of SBOLClass. Use this type specialization when adding multiple types of SBOLObjects to a container.
  • uri :
    The specific URI for a child object if this OwnedObject property contains multiple objects,

A reference to the child object Returns a child object from the OwnedObject property. If no URI is specified, the first object in this OwnedObject property is returned.

remove(*args)[source]

remove(index=0)

Remove an object from the list of objects and destroy it.

  • index :
    A numerical index for the object.
set(sbol_obj)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
class PartShop(url)[source]

A class which provides an API front-end for online bioparts repositories.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/partshop.h

addSynBioHubAnnotations(doc)[source]

addSynBioHubAnnotations(doc)

attachFile(topleveluri, filename)[source]

attachFile(topleveluri, filename)

Upload and attach a file to a TopLevel object in a PartShop.

  • top_level_uri :
    The identity of the object to which the file will be attached
  • file_name :
    A path to the file attachment
countCollection()[source]

count() -> int

Return the count of objects contained in a PartShop.

  • SBOLClass :
    The type of SBOL object, usually a ComponentDefinition
countComponentDefinition()[source]

count() -> int

Return the count of objects contained in a PartShop.

  • SBOLClass :
    The type of SBOL object, usually a ComponentDefinition
downloadAttachment(*args)[source]

downloadAttachment(attachment_uri, path=”.”)

Download a file attached to a TopLevel object in an online repository.

  • attachment_uri :
    The full URI of the attached object
  • path :
    The target path to which the file will be downloaded
getURL()[source]

getURL() -> std::string

Returns the network address of the PartShop.

The URL of the online repository

login(*args)[source]

login(email, password=”“)

In order to submit to a PartShop, you must login first.

Register on SynBioHub to obtain account credentials.

  • email :
    The email associated with the user’s SynBioHub account
  • password :
    The user’s password
pull(*args)[source]

pull(uri, doc, recursive)

pullCollection(uri, doc, recursive=True)[source]

pull(uri, doc, recursive)

pullComponentDefinition(uri, doc, recursive=True)[source]

pull(uri, doc, recursive)

pullSequence(uri, doc, recursive=True)[source]

pull(uri, doc, recursive)

search(*args)[source]

search(q) -> SearchResponse &

Perform an ADVANCED search using a SearchQuery object.

  • search_query :
    A map of string key-value pairs. Keys are objectType, sbolTag, collection, dcterms:tag, namespace/tag, offset, limit.

Search metadata A vector of maps with key-value pairs.

searchCount(*args)[source]

searchCount(q) -> int

Returns the number of search records matching the given criteria for an ADVANCED search.

  • search_query :
    A map of string key-value pairs. See SearchQuery for required and optional criteria.

An integer count.

searchRootCollections()[source]

searchRootCollections() -> std::string

Returns all Collections that are not members of any other Collections.

  • doc :
    A Document to add the Collections to
searchSubCollections(uri)[source]

searchSubCollections(uri) -> std::string

Returns all Collections that are members of the Collection specified by its URI.

  • uri :
    The URI of a Collection of Collections
  • doc :
    A Document to add the subcollections to
submit(*args)[source]

submit(doc, collection=”“, overwrite=0) -> std::string

Submit an SBOL Document to SynBioHub.

  • doc :
    The Document to submit
  • collection :
    The URI of an SBOL Collection to which the Document contents will be uploaded
  • overwrite :
    An integer code: 0(default) - do not overwrite, 1 - overwrite, 2 - merge
class Participation(*args)[source]

Each Participation represents how a particular FunctionalComponent behaves in its parent Interaction.

  • roles : URIProperty

    The roles property is an OPTIONAL set of URIs that describes the behavior of a Participation (and by extension its referenced FunctionalComponent) in the context of its parent Interaction.

    The roles property MAY contain one or more URIs that MUST identify terms from appropriate ontologies. It is RECOMMENDED that at least one of the URIs contained by the types property refer to a term from the participant role branch of the SBO. The table below provides a list of possible SBO terms for the roles property and their corresponding URIs. Role

    Systems Biology Ontology Term

    LibSBOL Symbol

    Inhibitor

    http://identifiers.org/biomodels.sbo/SBO:0000020

    SBO_INHIBITOR

    Stimulator

    http://identifiers.org/biomodels.sbo/SBO:0000459

    SBO_STIMULATOR

    Reactant

    http://identifiers.org/biomodels.sbo/SBO:0000010

    SBO_REACTANT

    Product

    http://identifiers.org/biomodels.sbo/SBO:0000011

    SBO_PRODUCT

    Ligand

    http://identifiers.org/biomodels.sbo/SBO:0000280

    SBO_LIGAND

    Non-covalent Complex

    http://identifiers.org/biomodels.sbo/SBO:0000253

    SBO_NONCOVALENT_COMPLEX

    If a Participation is well described by one of the terms from this table then its roles property MUST contain the URI that identifies this term. Lastly, if the roles property of a Participation contains multiple URIs, then they MUST identify non-conflicting terms. For example, the SBO terms stimulator and inhibitor would conflict.

  • participant : ReferencedObject

    The participant property MUST specify precisely one FunctionalComponent object that plays the designated role in its parent Interaction object.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/participation.h

define(*args)[source]

define(species, role=”“)

class ParticipationProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Plan(*args)[source]

Examples of agents are person, organisation or software. These agents should be annotated with additional information, such as software version, needed to be able to run the same software again.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/provo.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class PlanProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class Range(*args)[source]

A Range object specifies a region via discrete, inclusive start and end positions that correspond to indices for characters in the elements String of a Sequence. Note that the index of the first location is 1, as is typical practice in biology, rather than 0, as is typical practice in computer science.

  • start : IntProperty

    Specifies the inclusive starting position of a sequence region. It must be 1 or greater.

  • end : IntProperty

    Specifies the inclusive end position of a sequence region. It must be equal to or greater than the start.

  • orientation : URIProperty

    The orientation indicates how a region of double-stranded DNA represented by the parent SequenceAnnotation and its associated Component are oriented.

    The orientation may be one of the following values. By default it is set to SBOL_ORIENTATION_INLINE. Orientation URI

    libSBOL Symbol

    http://sbols.org/v2#inline

    SBOL_ORIENTATION_INLINE

    http://sbols.org/v2#reverseComplement

    SBOL_ORIENTATION_REVERSE_COMPLEMENT

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/location.h

adjoins(comparand)[source]

adjoins(comparand) -> int

Indicate if these Ranges represent adjacent intervals.

Another Range object

1 if these Ranges adjoin or border each other, 0 if they are separated by an intervening Range

contains(comparand)[source]

contains(comparand) -> int

Calculates how many bases of the comparand are contained by this Range.

Another Range object

The number of bases which are contained (equivalent to the length of the comparand), or 0 if it is not contained.

follows(comparand)[source]

follows(comparand) -> int

Calculates how many bases separate these Ranges Another Range object.

The number of bases by which this Range follows the comparand, or 0 if it does not follow

length()[source]

length() -> int

Returns the length of a Range.

overlaps(comparand)[source]

overlaps(comparand) -> int

Calculates how many bases separate this Range from the comparand.

Another Range object

The number of bases by which the Ranges overlap. If they overlap, this is always a positive number regardless of direction. If they do not overlap, returns zero

precedes(comparand)[source]

precedes(comparand) -> int

Calculates how many bases separate these Ranges Another Range object.

The number of bases by which this Range precedes the comparand, or 0 if it does not precede

class ReferencedObject(*args)[source]

A reference to another SBOL object Contains a Uniform Resource Identifier (URI) that refers to an an associated object.

The object it points to may be another resource in this Document or an external reference, for example to an object in an external repository or database. In the SBOL specification, association by reference is indicated in class diagrams by arrows with open (white) diamonds.

  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

add(*args)[source]

add(obj)

Append a URI reference of an object to the property store.

  • The :
    referenced object
addReference(uri)[source]

addReference(uri)

create(uri)[source]

create(uri) -> std::string

Creates a new SBOL object corresponding to the RDF type specified in the Property definition.

Creates another SBOL object derived from TopLevel and adds it to the Document.

  • uri :
    A Uniform Resource Identifier (URI) for the new object, or a displayId if operating in SBOL-compliant mode (library default)

The full URI of the created object

  • uri :
    In “open world” mode, this is a full URI and the same as the returned URI. If the default namespace for libSBOL has been configured, then this argument should simply be a local identifier. If SBOL-compliance is enabled, this argument should be the intended displayId of the new object. A full URI is automatically generated and returned.

The full URI of the created object.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
setReference(uri)[source]

setReference(uri)

class SBOLObject(*args)[source]

An SBOLObject converts a C++ class data structure into an RDF triple store and contains methods for serializing and parsing RDF triples.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/object.h

addPropertyValue(property_uri, val)[source]

addPropertyValue(property_uri, val)

Append a value to a user-defined annotation property.

Either a literal or URI value

apply(callback_fn, user_data)[source]

apply(callback_fn, user_data)

cast(python_class)[source]

cast() -> SBOLClass &

compare(comparand)[source]

compare(comparand) -> int

Compare two SBOL objects or Documents.

The behavior is currently undefined for objects with custom annotations or extension classes.

  • comparand :
    A pointer to the object being compared to this one.

1 if the objects are identical, 0 if they are different

find(uri)[source]

find(uri) -> SBOLObject *

Search this object recursively to see if an object or any child object with URI already exists.

  • uri :
    The URI to search for.

A pointer to theobject with this URI if it exists, NULL otherwise

find_property(uri)[source]

find_property(uri) -> SBOLObject *

Search this object recursively to see if it contains a member property with the given RDF type.

  • uri :
    The RDF type of the property to search for.

A pointer to the object that contains a member property with the specified RDF type, NULL otherwise

find_property_value(*args)[source]

find_property_value(uri, value, matches={}) -> std::vector< SBOLObject * >

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

  • uri :
    The RDF type of the property to search for.
  • value :
    The property value to match

A vector containing all objects found that contain a member property with the specified RDF type

find_reference(uri)[source]

find_reference(uri) -> std::vector< SBOLObject * >

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

  • uri :
    A URI, either an ontology term or an object reference, to search for

A vector containing all objects found that contain the URI in a property value

getAnnotation(property_uri)[source]

getAnnotation(property_uri) -> std::string

Get the value of a custom annotation property by its URI.

Synonymous with getPropertyValue

  • property_uri :
    The URI for the property

The value of the property or SBOL_ERROR_NOT_FOUND

getClassName(type)[source]

getClassName(type) -> std::string

Parses a local class name from the RDF-type of this SBOL Object

getProperties()[source]

getProperties() -> std::vector< std::string >

Gets URIs for all properties contained by this object.

This includes SBOL core properties as well as custom annotations. Use this to find custom extension data in an SBOL file.

A vector of URIs that identify the properties contained in this object

getPropertyValue(property_uri)[source]

getPropertyValue(property_uri) -> std::string

Get the value of a custom annotation property by its URI.

  • property_uri :
    The URI for the property

The value of the property or SBOL_ERROR_NOT_FOUND

getPropertyValues(property_uri)[source]

getPropertyValues(property_uri) -> std::vector< std::string >

Get all values of a custom annotation property by its URI.

  • property_uri :
    The URI for the property

A vector of property values or SBOL_ERROR_NOT_FOUND

getTypeURI()[source]

getTypeURI() -> rdf_type

The uniform resource identifier that describes the RDF-type of this SBOL Object

setAnnotation(property_uri, val)[source]

setAnnotation(property_uri, val)

Set the value for a user-defined annotation property.

Synonymous with setPropertyValue If the value is a URI, it should be surrounded by angle brackets, else it will be interpreted as a literal value

setPropertyValue(property_uri, val)[source]

setPropertyValue(property_uri, val)

Set and overwrite the value for a user-defined annotation property.

Either a literal or URI value

update_uri()[source]

update_uri()

class SampleRoster(*args)[source]

A SampleRoster is a container used to group Builds that are included in an experiment together. A SampleRoster can be used to generate a Test in a Design- Build-Test-Learn workflow.

  • samples : ReferencedObject

    References to Builds which were tested in an experiment.

  • members : URIProperty

    The members property of a Collection is OPTIONAL and MAY contain a set of URI references to zero or more TopLevel objects.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/dbtl.h

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

class SampleRosterProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class SearchQuery(*args)[source]

A SearchQuery object is used to configure advanced searches for bioparts in a PartShop. Advanced searches are useful for matching values across multiple fields, or to specify multiple values in a single field.

  • objectType : URIProperty

    Set this property to indicate the type of SBOL object to search for. Set to SBOL_COMPONENT_DEFINITION by default.

  • limit : IntProperty

    Set this property to specify the total number of records to retrieve from a search request. By default 25 records are retrieved.

  • offset : IntProperty

    When the number of search hits exceeds the limit, the offset property can be used to retrieve more records.

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/partshop.h

class SearchResponse[source]

A SearchResponse is a container of search records returned by a search request.

  • records : std::vector< sbol::Identified *>

  • python_iter : std::vector< Identified * >::iterator

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/partshop.h

end()[source]

end() -> iterator

extend(response)[source]

extend(response)

Adds more search records to an existing SearchResponse.

  • response :
    A SearchResponse object
class Sequence(*args)[source]

The primary structure (eg, nucleotide or amino acid sequence) of a ComponentDefinition object.

  • elements : TextProperty

    The elements property is a REQUIRED String of characters that represents the constituents of a biological or chemical molecule. For example, these characters could represent the nucleotide bases of a molecule of DNA, the amino acid residues of a protein, or the atoms and chemical bonds of a small molecule.

  • encoding : URIProperty

    The encoding property is REQUIRED and has a data type of URI.

    This property MUST indicate how the elements property of a Sequence MUST be formed and interpreted. For example, the elements property of a Sequence with an IUPAC DNA encoding property MUST contain characters that represent nucleotide bases, such as a, t, c, and g. The elements property of a Sequence with a Simplified Molecular-Input Line-Entry System (SMILES) encoding, on the other hand, MUST contain characters that represent atoms and chemical bonds, such as C, N, O, and =. It is RECOMMENDED that the encoding property contains a URI from the table below. The terms in the table are organized by the type of ComponentDefinition that typically refer to a Sequence with such an encoding. When the encoding of a Sequence is well described by one of the URIs in the table, it MUST contain that URI. ComponentDefinition type

    Encoding

    libSBOL Symbol

    URI

    DNA, RNA

    IUPAC DNA, RNA

    SBOL_ENCODING_IUPAC

    http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html

    Protein

    IUPAC Protein

    SBOL_ENCODING_IUPAC_PROTEIN

    http://www.chem.qmul.ac.uk/iupac/AminoAcid/

    Small Molecule

    SMILES

    SBOL_ENCODING_SMILES

    http://www.opensmiles.org/opensmiles.html

  • attachments : ReferencedObject

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/sequence.h

assemble(*args)[source]

assemble(composite_sequence=”“) -> std::string

Calculates the complete sequence of a high-level Component from the sequence of its subcomponents.

Pior to assembling the the complete sequence, you must assemble a template design by calling ComponentDefinition::assemble for the ComponentDefinition that references this Sequence.

  • composite_sequence :
    Typically no value for the composite sequence should be specified by the user. This parameter is used to hold the composite sequence as it is passed to function calls at a higher-level of the recursion stack.
compile()[source]

compile() -> std::string

Synonomous with Sequence::assemble. Calculates the complete sequence of a high- level Component from the sequence of its subcomponents. Prior to assembling the the complete sequence, you must assemble a template design by calling ComponentDefinition::assemble for the ComponentDefinition that references this Sequence.

copy(*args)[source]

copy(ns=”“, version=”“) -> SBOLClass &

length()[source]

length() -> int

The length of the primary sequence in the elements property

synthesize(clone_id)[source]

synthesize(clone_id) -> ComponentDefinition &

  • clone_id :
    A URI for the build, or displayId if working in SBOLCompliant mode.
class SequenceAnnotation(*args)[source]

The SequenceAnnotation class describes one or more regions of interest on the Sequence objects referred to by its parent ComponentDefinition. In addition, SequenceAnnotation objects can describe the substructure of their parent ComponentDefinition through association with the Component objects contained by this ComponentDefinition.

  • component : ReferencedObject

    The component property is OPTIONAL and has a data type of URI. This URI MUST refer to a Component that is contained by the same parent ComponentDefinition that contains the SequenceAnnotation. In this way, the properties of the SequenceAnnotation, such as its description and locations, are associated with part of the substructure of its parent ComponentDefinition.

  • locations : OwnedObject< Location >

    The locations property is a REQUIRED set of one or more Location objects that indicate which elements of a Sequence are described by the SequenceAnnotation.

    Allowing multiple Location objects on a single SequenceAnnotation is intended to enable representation of discontinuous regions (for example, a Component encoded across a set of exons with interspersed introns). As such, the Location objects of a single SequenceAnnotation SHOULD NOT specify overlapping regions, since it is not clear what this would mean. There is no such concern with different SequenceAnnotation objects, however, which can freely overlap in Location (for example, specifying overlapping linkers for sequence assembly).

  • roles : URIProperty

    Alternatively to describing substructure, a SequenceAnnotation can be utilized to identify a feature, such as a GenBank feature, of a specified Sequence.

    In this use case, the SequenceAnnotation MUST NOT have a component property, but instead it would have a roles property. The roles property comprises an OPTIONAL set of zero or more URIs describing the specified sequence feature being annotated. If provided, these role URIs MUST identify terms from appropriate ontologies. Roles are not restricted to describing biological function; they may annotate Sequences function in any domain for which an ontology exists. It is RECOMMENDED that these role URIs identify terms that are compatible with the type properties of this SequenceAnnotations parent ComponentDefinition. For example, a role of a SequenceAnnotation which belongs to a ComponentDefinition of type DNA might refer to terms from the Sequence Ontology. See documentation for ComponentDefinition for a table of recommended ontology terms.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/sequenceannotation.h

contains(*args)[source]

contains(comparand_list) -> std::vector< SequenceAnnotation * >

extract(start_reference=1)[source]

extract(start_reference=1) -> ComponentDefinition &

Convert a SequenceAnnotation to a subcomponent.

A ComponentDefinition representing the subcomponent

follows(*args)[source]

follows(comparand_list) -> std::vector< SequenceAnnotation * >

length()[source]

length() -> int

The length of a SequenceAnnotation in base coordinates.

overlaps(*args)[source]

overlaps(comparand_list) -> std::vector< SequenceAnnotation * >

precedes(*args)[source]

precedes(comparand_list) -> std::vector< SequenceAnnotation * >

class SequenceAnnotationProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class SequenceConstraint(*args)[source]

The SequenceConstraint class can be used to assert restrictions on the relative, sequence-based positions of pairs of Component objects contained by the same parent ComponentDefinition. The primary purpose of this class is to enable the specification of partially designed ComponentDefinition objects, for which the precise positions or orientations of their contained Component objects are not yet fully determined.

  • subject : ReferencedObject

    The subject property is REQUIRED and MUST contain a URI that refers to a Component contained by the same parent ComponentDefinition that contains the SequenceConstraint.

  • object : ReferencedObject

    The object property is REQUIRED and MUST contain a URI that refers to a Component contained by the same parent ComponentDefinition that contains the SequenceConstraint. This Component MUST NOT be the same Component that the SequenceConstraint refers to via its subject property.

  • restriction : URIProperty

    The restriction property is REQUIRED and has a data type of URI.

    This property MUST indicate the type of structural restriction on the relative, sequence-based positions or orientations of the subject and object Component objects. The URI value of this property SHOULD come from the RECOMMENDED URIs in the following table. libSBOL Symbol

    Description

    SBOL_RESTRICTION_PRECEDES

    The position of the subject Component MUST precede that of the object Component.

    If each one is associated with a SequenceAnnotation, then the

    SequenceAnnotation associated with the subject Component MUST specify a region that starts before the region specified by the SequenceAnnotation associated with the object Component.

    SBOL_RESTRICTION_SAME_ORIENTATION_AS

    The subject and object Component objects MUST have the same orientation. If each one is associated with a SequenceAnnotation, then the orientation URIs of the Location objects of the first SequenceAnnotation MUST be among those of the second SequenceAnnotation, and vice versa.

    SBOL_RESTRICTION_OPPOSITE_ORIENTATION_AS

    The subject and object Component objects MUST have opposite orientations. If each one is associated with a SequenceAnnotation, then the orientation URIs of the Location objects of one SequenceAnnotation MUST NOT be among those of the other SequenceAnnotation.

  • persistentIdentity : URIProperty

    The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

  • displayId : TextProperty

    The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

  • version : VersionProperty

    If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters . and - and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

  • wasDerivedFrom : URIProperty

    The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain A was derived from B and B was derived from A is cyclical.

  • wasGeneratedBy : ReferencedObject

    An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

  • name : TextProperty

    The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the objects displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

  • description : TextProperty

    The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

  • identity : URIProperty

    The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified objects identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/sequenceconstraint.h

class SequenceConstraintProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.
validate(arg=None)[source]

validate(arg=NULL)

write()[source]

write()

class SequenceProperty(*args)[source]

Member properties of all SBOL objects are defined using a Property object.

The Property class provides a generic interface for accessing SBOL objects. At a low level, the Property class converts SBOL data structures into RDF triples.

  • The :
    SBOL specification currently supports string, URI, and integer literal values.
  • python_iter : std::vector< std::string >::iterator

C++ includes: /Users/bbartley/Dev/git/libSBOL/source/property.h

add(new_value)[source]

add(new_value)

Appends the new value to a list of values, for properties that allow it.

  • new_value :
    A new string which will be added to a list of values.
addValidationRule(*args)[source]

addValidationRule(rule)

clear()[source]

clear()

Clear all property values.

copy(target_property)[source]

copy(target_property)

Copy property values to a target object’s property fields.

find(query)[source]

find(query) -> bool

Check if a value in this property matches the query.

getLowerBound()[source]

getLowerBound() -> char

getOwner()[source]

getOwner() -> SBOLObject &

getTypeURI()[source]

getTypeURI() -> rdf_type

getUpperBound()[source]

getUpperBound() -> char

remove(index=0)[source]

remove(index=0)

Remove a property value.

set(*args)[source]

set(new_value)

Basic setter for SBOL IntProperty, but can be used with TextProperty as well.

  • new_value :
    A new integer value for the property, which is converted to a raw string during serialization.