Index

A

add_feature() (in module sbol_utilities.component) add_interaction() (in module sbol_utilities.component)

all_in_role() (in module sbol_utilities.component) association_relationship (in module sbol_utilities.graph_sbol)

B

backbone() (in module sbol_utilities.component) BASIC_PARTS_COLLECTION (in module sbol_utilities.excel_to_sbol) BIO_STRAND_FORWARD (GenBankSBOL3Converter attribute)

BIO_STRAND_REVERSE (GenBankSBOL3Converter attribute) build_reference_cache() (in module sbol_utilities.helper_functions) by_roles() (in module sbol_utilities.component) by_types() (in module sbol_utilities.component)

C

cached_references() (in module sbol_utilities.helper_functions) calculate_sequences() (in module sbol_utilities.calculate_sequences) cd_assigment_to_display_id() (in module sbol_utilities.expand_combinatorial_derivations) cd_variable_values() (CombinatorialDerivationExpander method) cds() (in module sbol_utilities.component) ChildNotFound collection_values() (CombinatorialDerivationExpander method) CombinatorialDerivationExpander (class in sbol_utilities.expand_combinatorial_derivations) command_line_converter() (in module sbol_utilities.conversion) COMP_ROLES (GenBankSBOL3Converter attribute) COMP_TYPES (GenBankSBOL3Converter attribute) COMPLEXITY_SCORE_NAMESPACE (in module sbol_utilities.calculate_complexity_scores) COMPOSITE_PARTS_COLLECTION (in module sbol_utilities.excel_to_sbol) composition_relationship (in module sbol_utilities.graph_sbol) compute_sequence() (in module sbol_utilities.calculate_sequences) constitutive() (in module sbol_utilities.component) constraint_dict (in module sbol_utilities.excel_to_sbol)

constraint_pattern (in module sbol_utilities.excel_to_sbol) contained_components() (in module sbol_utilities.component) contains() (in module sbol_utilities.component) convert2to3() (in module sbol_utilities.conversion) convert3to2() (in module sbol_utilities.conversion) convert_from_fasta() (in module sbol_utilities.conversion) convert_from_genbank() (in module sbol_utilities.conversion) convert_genbank_to_sbol3() (GenBankSBOL3Converter method) convert_identities2to3() (in module sbol_utilities.conversion) convert_sbol3_to_genbank() (GenBankSBOL3Converter method) convert_to_fasta() (in module sbol_utilities.conversion) convert_to_genbank() (in module sbol_utilities.conversion) copy_collection_and_dependencies() (in module sbol_utilities.workarounds) copy_component_and_dependencies() (in module sbol_utilities.workarounds) copy_toplevel_and_dependencies() (in module sbol_utilities.workarounds) create_gb2so_role_mappings() (GenBankSBOL3Converter method) CUSTOM_REFERENCE_NS (GenBankSBOL3Converter.CustomReferenceProperty attribute) CUSTOM_STRUCTURED_COMMENT_NS (GenBankSBOL3Converter.CustomStructuredCommentProperty attribute)

D

DEFAULT_GB_SEQ_VERSION (GenBankSBOL3Converter attribute) DEFAULT_GB_TERM (GenBankSBOL3Converter attribute) DEFAULT_SO_TERM (GenBankSBOL3Converter attribute)

derivation_to_collection() (CombinatorialDerivationExpander method) design_file_type() (in module sbol_utilities.helper_functions) dna_component_with_sequence() (in module sbol_utilities.component) doc_diff() (in module sbol_utilities.sbol_diff)

E

ed_protein() (in module sbol_utilities.component) ed_restriction_enzyme() (in module sbol_utilities.component) ed_simple_chemical() (in module sbol_utilities.component) engineered_region() (in module sbol_utilities.component)

ensure_singleton_feature() (in module sbol_utilities.component) ensure_singleton_system() (in module sbol_utilities.component) excel_to_sbol() (in module sbol_utilities.excel_to_sbol) expand_configuration() (in module sbol_utilities.excel_to_sbol) expand_derivations() (in module sbol_utilities.expand_combinatorial_derivations)

F

fasta2sbol() (in module sbol_utilities.conversion) file_diff() (in module sbol_utilities.sbol_diff) filter_top_level() (in module sbol_utilities.helper_functions) FINAL_PRODUCTS_COLLECTION (in module sbol_utilities.excel_to_sbol)

find_child() (in module sbol_utilities.helper_functions) find_top_level() (in module sbol_utilities.helper_functions) flatten() (in module sbol_utilities.helper_functions) from_json() (IDTAccountAccessor static method) functional_component() (in module sbol_utilities.component)

G

gb2so_map (GenBankSBOL3Converter attribute) GB2SO_MAPPINGS_CSV (GenBankSBOL3Converter attribute) genbank2sbol() (in module sbol_utilities.conversion) GENBANK_EXTRA_PROPERTY_NS (GenBankSBOL3Converter.ComponentGenBankExtension attribute) GENBANK_FEATURE_QUALIFIER_NS (GenBankSBOL3Converter.FeatureGenBankExtension attribute) GENBANK_LOCATION_POSITION (GenBankSBOL3Converter attribute) GENBANK_RANGE_NS (GenBankSBOL3Converter.LocationGenBankExtension attribute) GenBankSBOL3Converter (class in sbol_utilities.sbol3_genbank_conversion) GenBankSBOL3Converter.ComponentGenBankExtension (class in sbol_utilities.sbol3_genbank_conversion) GenBankSBOL3Converter.CustomReferenceProperty (class in sbol_utilities.sbol3_genbank_conversion) GenBankSBOL3Converter.CustomStructuredCommentProperty (class in sbol_utilities.sbol3_genbank_conversion)

GenBankSBOL3Converter.FeatureGenBankExtension (class in sbol_utilities.sbol3_genbank_conversion) GenBankSBOL3Converter.LocationGenBankExtension (class in sbol_utilities.sbol3_genbank_conversion) gene() (in module sbol_utilities.component) GENETIC_DESIGN_FILE_TYPES (in module sbol_utilities.helper_functions) get_complexity_score() (in module sbol_utilities.calculate_complexity_scores) get_complexity_scores() (in module sbol_utilities.calculate_complexity_scores) get_parent (in module sbol_utilities.workarounds) get_parent() (in module sbol_utilities.workarounds) get_sequence_complexity() (IDTAccountAccessor method) get_sequence_scores() (IDTAccountAccessor method) get_toplevel() (in module sbol_utilities.workarounds) graph_sbol() (in module sbol_utilities.graph_sbol)

I

id_sort() (in module sbol_utilities.helper_functions) idt_calculate_complexity_scores() (in module sbol_utilities.calculate_complexity_scores) idt_calculate_sequence_complexity_scores() (in module sbol_utilities.calculate_complexity_scores) IDTAccountAccessor (class in sbol_utilities.calculate_complexity_scores) in_role() (in module sbol_utilities.component)

is_circular() (in module sbol_utilities.helper_functions) is_dna_part() (in module sbol_utilities.component) is_library() (in module sbol_utilities.expand_combinatorial_derivations) is_plasmid() (in module sbol_utilities.helper_functions) is_RC() (in module sbol_utilities.excel_to_sbol)

L

LINEAR_PRODUCTS_COLLECTION (in module sbol_utilities.excel_to_sbol)

M

main() (in module sbol_utilities.calculate_complexity_scores) (in module sbol_utilities.calculate_sequences) (in module sbol_utilities.conversion) (in module sbol_utilities.excel_to_sbol) (in module sbol_utilities.expand_combinatorial_derivations) (in module sbol_utilities.graph_sbol) (in module sbol_utilities.sbol_diff) make_combinatorial_derivation() (in module sbol_utilities.excel_to_sbol) make_composite_component() (in module sbol_utilities.excel_to_sbol) make_composite_part() (in module sbol_utilities.excel_to_sbol) make_constraint() (in module sbol_utilities.excel_to_sbol) media() (in module sbol_utilities.component) module sbol_utilities sbol_utilities.calculate_complexity_scores sbol_utilities.calculate_sequences sbol_utilities.component sbol_utilities.conversion sbol_utilities.excel_to_sbol sbol_utilities.expand_combinatorial_derivations sbol_utilities.graph_sbol sbol_utilities.helper_functions sbol_utilities.sbol3_genbank_conversion sbol_utilities.sbol_diff sbol_utilities.sequence sbol_utilities.workarounds

mrna() (in module sbol_utilities.component)

O

operator() (in module sbol_utilities.component) order() (in module sbol_utilities.component)

order_subcomponents() (in module sbol_utilities.calculate_sequences) outgoing_links() (in module sbol_utilities.helper_functions)

P

part_in_backbone() (in module sbol_utilities.component) part_names() (in module sbol_utilities.excel_to_sbol) part_specifications() (in module sbol_utilities.excel_to_sbol)

partname_to_part() (in module sbol_utilities.excel_to_sbol) promoter() (in module sbol_utilities.component) protein_component_with_sequence() (in module sbol_utilities.component) protein_stability_element() (in module sbol_utilities.component)

R

rbs() (in module sbol_utilities.component) read_metadata() (in module sbol_utilities.excel_to_sbol) ready_to_resolve() (in module sbol_utilities.calculate_sequences) regulate() (in module sbol_utilities.component) replace_feature() (in module sbol_utilities.workarounds)

REPORT_ACTIVITY_TYPE (in module sbol_utilities.calculate_complexity_scores) resolved_dna_component() (in module sbol_utilities.calculate_sequences) reverse_complement_pattern (in module sbol_utilities.excel_to_sbol) rna_component_with_sequence() (in module sbol_utilities.component) root_combinatorial_derivations() (in module sbol_utilities.expand_combinatorial_derivations) row_to_basic_part() (in module sbol_utilities.excel_to_sbol)

S

sbol2fasta() (in module sbol_utilities.conversion) sbol2genbank() (in module sbol_utilities.conversion) sbol2to3() (in module sbol_utilities.conversion) SBOL3PassiveVisitor (class in sbol_utilities.helper_functions) sbol3to2() (in module sbol_utilities.conversion) SBOL_LOCATION_POSITION (GenBankSBOL3Converter attribute) sbol_utilities module sbol_utilities.calculate_complexity_scores module sbol_utilities.calculate_sequences module sbol_utilities.component module sbol_utilities.conversion module sbol_utilities.excel_to_sbol module sbol_utilities.expand_combinatorial_derivations module sbol_utilities.graph_sbol module

sbol_utilities.helper_functions module sbol_utilities.sbol3_genbank_conversion module sbol_utilities.sbol_diff module sbol_utilities.sequence module sbol_utilities.workarounds module SBOLGRAPH (in module sbol_utilities.conversion) SBOLObjectNotFound SCORE_TIMEOUT (IDTAccountAccessor attribute) SEQUENCE_ENCODING (GenBankSBOL3Converter attribute) so2gb_map (GenBankSBOL3Converter attribute) SO2GB_MAPPINGS_CSV (GenBankSBOL3Converter attribute) sort_owned_objects() (in module sbol_utilities.workarounds) strain() (in module sbol_utilities.component) string_to_display_id() (in module sbol_utilities.workarounds) strip_filetype_suffix() (in module sbol_utilities.helper_functions) strip_RC() (in module sbol_utilities.excel_to_sbol) strip_sbol2_version() (in module sbol_utilities.helper_functions)

T

terminator() (in module sbol_utilities.component) TEST_NAMESPACE (GenBankSBOL3Converter attribute) toplevel_named() (in module sbol_utilities.helper_functions) TopLevelNotFound

transcription_factor() (in module sbol_utilities.component) type_to_standard_extension (in module sbol_utilities.workarounds) tyto_lookup_with_caching() (in module sbol_utilities.workarounds) tyto_normalize_term() (in module sbol_utilities.workarounds)

U

unambiguous_dna_sequence() (in module sbol_utilities.sequence) unambiguous_protein_sequence() (in module sbol_utilities.sequence)

unambiguous_rna_sequence() (in module sbol_utilities.sequence) unresolved_subparts() (in module sbol_utilities.excel_to_sbol) url_to_identity() (in module sbol_utilities.helper_functions)

V

visit_activity() (SBOL3PassiveVisitor method) visit_agent() (SBOL3PassiveVisitor method) visit_association() (SBOL3PassiveVisitor method) visit_attachment() (SBOL3PassiveVisitor method) visit_binary_prefix() (SBOL3PassiveVisitor method) visit_collection() (SBOL3PassiveVisitor method) visit_combinatorial_derivation() (SBOL3PassiveVisitor method) visit_component() (SBOL3PassiveVisitor method) visit_component_reference() (SBOL3PassiveVisitor method) visit_constraint() (SBOL3PassiveVisitor method) visit_cut() (SBOL3PassiveVisitor method) visit_document() (SBOL3PassiveVisitor method) visit_entire_sequence() (SBOL3PassiveVisitor method) visit_experiment() (SBOL3PassiveVisitor method) visit_experimental_data() (SBOL3PassiveVisitor method) visit_externally_defined() (SBOL3PassiveVisitor method) visit_implementation() (SBOL3PassiveVisitor method) visit_interaction() (SBOL3PassiveVisitor method)

visit_interface() (SBOL3PassiveVisitor method) visit_local_sub_component() (SBOL3PassiveVisitor method) visit_measure() (SBOL3PassiveVisitor method) visit_model() (SBOL3PassiveVisitor method) visit_participation() (SBOL3PassiveVisitor method) visit_plan() (SBOL3PassiveVisitor method) visit_prefixed_unit() (SBOL3PassiveVisitor method) visit_range() (SBOL3PassiveVisitor method) visit_sequence() (SBOL3PassiveVisitor method) visit_sequence_feature() (SBOL3PassiveVisitor method) visit_si_prefix() (SBOL3PassiveVisitor method) visit_singular_unit() (SBOL3PassiveVisitor method) visit_sub_component() (SBOL3PassiveVisitor method) visit_unit_division() (SBOL3PassiveVisitor method) visit_unit_exponentiation() (SBOL3PassiveVisitor method) visit_unit_multiplication() (SBOL3PassiveVisitor method) visit_usage() (SBOL3PassiveVisitor method) visit_variable_feature() (SBOL3PassiveVisitor method)