Index

A

add_cadbiom_names_to_entities() (in module biopax2cadbiom.biopax_converter) add_conditions_to_reactions() (in module biopax2cadbiom.biopax_converter) add_controllers_to_reactions() (in module biopax2cadbiom.biopax_converter) add_locations_to_entities() (in module biopax2cadbiom.biopax_converter) add_modifications_features_to_entities() (in module biopax2cadbiom.biopax_converter) add_reactions_and_controllers_to_entities() (in module biopax2cadbiom.biopax_converter)

add_unique_cadbiom_name_to_entities() (in module biopax2cadbiom.biopax_converter) add_xref() (biopax2cadbiom.classes.Location method) (biopax2cadbiom.classes.PhysicalEntity method) add_xrefs_to_entities() (in module biopax2cadbiom.biopax_converter) assign_missing_names() (in module biopax2cadbiom.biopax_converter) auto_add_prefixes() (in module biopax2cadbiom.sparql_wrapper)

B

biopax2cadbiom.biopax_converter (module) biopax2cadbiom.cadbiom_writer (module) biopax2cadbiom.classes (module) biopax2cadbiom.namespaces (module)

biopax2cadbiom.sparql_biopaxQueries (module) biopax2cadbiom.sparql_wrapper (module) build_cadbiom_name() (in module biopax2cadbiom.biopax_converter) build_dynamical_system() (in module tests.test_cases) build_json_data() (in module biopax2cadbiom.cadbiom_writer)

C

classes_and_classes_complexes() (in module tests.test_functions) clean_name() (in module biopax2cadbiom.biopax_converter) clean_test_env() (in module tests.test_cases) compute_locations_names() (in module biopax2cadbiom.biopax_converter)

Control (class in biopax2cadbiom.classes) controlType (biopax2cadbiom.classes.Control attribute) create_cadbiom_model() (in module biopax2cadbiom.cadbiom_writer) createControlFromEntityOnBothSides() (in module biopax2cadbiom.biopax_converter)

D

detect_members_used() (in module biopax2cadbiom.biopax_converter)

develop_complexes() (in module biopax2cadbiom.biopax_converter) developComplexEntity() (in module biopax2cadbiom.biopax_converter)

E

entityType (biopax2cadbiom.classes.PhysicalEntity attribute)

F

filter_controls() (in module biopax2cadbiom.biopax_converter) filter_entities() (in module biopax2cadbiom.biopax_converter) filter_reactions() (in module biopax2cadbiom.biopax_converter) find_unique_synonyms() (in module biopax2cadbiom.biopax_converter)

fixture_me() (in module tests.test_cases) format_condition() (in module biopax2cadbiom.cadbiom_writer) format_events_and_conditions() (in module biopax2cadbiom.cadbiom_writer) func() (in module tests.test_cases) (in module tests.test_queries)

G

GenericBioPAXEntity (class in biopax2cadbiom.classes) GenericBioPAXInteraction (class in biopax2cadbiom.classes) get_biopax_controls() (in module biopax2cadbiom.sparql_biopaxQueries) get_biopax_locations() (in module biopax2cadbiom.sparql_biopaxQueries) get_biopax_modificationfeatures() (in module biopax2cadbiom.sparql_biopaxQueries) get_biopax_parent_pathways() (in module biopax2cadbiom.sparql_biopaxQueries) get_biopax_pathways() (in module biopax2cadbiom.sparql_biopaxQueries) get_biopax_physicalentities() (in module biopax2cadbiom.sparql_biopaxQueries) get_biopax_reactions() (in module biopax2cadbiom.sparql_biopaxQueries) get_biopax_xrefs() (in module biopax2cadbiom.sparql_biopaxQueries)

get_cadbiom_names() (in module biopax2cadbiom.biopax_converter) get_control_group_condition() (in module biopax2cadbiom.biopax_converter) get_default_blocks() (in module tests.test_cases) get_events_transitions() (in module tests.test_cases) get_graphs_from_triplestore() (in module biopax2cadbiom.sparql_biopaxQueries) get_info_from_triplestore() (in module biopax2cadbiom.sparql_biopaxQueries) get_names_of_missing_physical_entities() (in module biopax2cadbiom.cadbiom_writer) get_pathways_entities() (in module biopax2cadbiom.biopax_converter) get_RDF_prefixes() (in module biopax2cadbiom.namespaces) get_subgraphs_from_triplestore() (in module biopax2cadbiom.sparql_biopaxQueries) get_transitions() (in module biopax2cadbiom.biopax_converter)

I

interactionType (biopax2cadbiom.classes.GenericBioPAXInteraction attribute)

is_class (biopax2cadbiom.classes.PhysicalEntity attribute) is_complex (biopax2cadbiom.classes.PhysicalEntity attribute)

L

load_blacklisted_entities() (in module biopax2cadbiom.biopax_converter)

load_sparql_endpoint() (in module biopax2cadbiom.sparql_wrapper) Location (class in biopax2cadbiom.classes)

M

main() (in module biopax2cadbiom.biopax_converter)

merge_duplicated_entities() (in module biopax2cadbiom.biopax_converter) modificationFeatures (biopax2cadbiom.classes.PhysicalEntity attribute)

O

order_results() (in module biopax2cadbiom.sparql_wrapper)

P

PhysicalEntity (class in biopax2cadbiom.classes)

R

Reaction (class in biopax2cadbiom.classes)

remove_scc_from_model() (in module biopax2cadbiom.cadbiom_writer)

S

short_uri (biopax2cadbiom.classes.GenericBioPAXEntity attribute) shortening_modifications() (in module biopax2cadbiom.biopax_converter)

simulated_physical_entities() (in module tests.test_functions) sort_callback() (in module biopax2cadbiom.biopax_converter) sparql_query() (in module biopax2cadbiom.sparql_wrapper)

T

t_bad_model() (in module tests.test_cases) t_model() (in module tests.test_cases) t_modification_features() (in module tests.test_queries) test_cavia() (in module tests.test_cases) test_cricetulus() (in module tests.test_cases) test_cricetulusWithoutSmallMolecules() (in module tests.test_cases) test_crithidia() (in module tests.test_cases) test_escherichia() (in module tests.test_cases) test_get_classes_from_reactants() (in module tests.test_functions) test_homarus() (in module tests.test_cases) test_merge_entities() (in module tests.test_functions) test_mycobacterium() (in module tests.test_cases) test_sort_of_entities() (in module tests.test_functions) test_test_control_1() (in module tests.test_cases) test_test_control_2() (in module tests.test_cases) test_triticum() (in module tests.test_cases) test_vigna() (in module tests.test_cases) test_virtualCase1() (in module tests.test_cases) test_virtualCase10() (in module tests.test_cases) test_virtualCase10b() (in module tests.test_cases) test_virtualCase10c() (in module tests.test_cases) test_virtualCase11() (in module tests.test_cases) test_virtualCase14() (in module tests.test_cases) test_virtualCase14b() (in module tests.test_cases)

test_virtualCase14c() (in module tests.test_cases) test_virtualCase17() (in module tests.test_cases) test_virtualCase18() (in module tests.test_cases) test_virtualCase19() (in module tests.test_cases) test_virtualCase1_2b() (in module tests.test_cases) test_virtualCase2() (in module tests.test_cases) test_virtualCase20() (in module tests.test_cases) test_virtualCase3() (in module tests.test_cases) test_virtualCase4() (in module tests.test_cases) test_virtualCase5() (in module tests.test_cases) test_virtualCase6() (in module tests.test_cases) test_virtualCase6a() (in module tests.test_cases) test_virtualCase6b() (in module tests.test_cases) test_virtualCase7() (in module tests.test_cases) (in module tests.test_queries) test_virtualCase8() (in module tests.test_cases) (in module tests.test_queries) test_virtualCase9() (in module tests.test_cases) test_virtualCase9b() (in module tests.test_cases) test_xrefs_query() (in module tests.test_queries) tests.test_cases (module) tests.test_functions (module) tests.test_queries (module) transfer_class_attributes_on_child_entities() (in module biopax2cadbiom.biopax_converter)