Index

A

activation_p() (pythoncyc.PGDB.PGDB method) adjacent_genes_p() (pythoncyc.PGDB.PGDB method) all_cofactors() (pythoncyc.PGDB.PGDB method) all_direct_forms_of_protein() (pythoncyc.PGDB.PGDB method) all_enzymes() (pythoncyc.PGDB.PGDB method) all_forms_of_protein() (pythoncyc.PGDB.PGDB method) all_genetic_regulation_proteins() (pythoncyc.PGDB.PGDB method) all_modulators() (pythoncyc.PGDB.PGDB method) all_operons() (pythoncyc.PGDB.PGDB method) all_orgids() (in module pythoncyc) all_pathways() (pythoncyc.PGDB.PGDB method)

all_products_of_gene() (pythoncyc.PGDB.PGDB method) all_protein_complexes() (pythoncyc.PGDB.PGDB method) all_reactions() (pythoncyc.PGDB.PGDB method) all_rxns() (pythoncyc.PGDB.PGDB method) all_sigma_factors() (pythoncyc.PGDB.PGDB method) all_substrates() (pythoncyc.PGDB.PGDB method) all_transcription_factors() (pythoncyc.PGDB.PGDB method) all_transported_chemicals() (pythoncyc.PGDB.PGDB method) all_transporters() (pythoncyc.PGDB.PGDB method) all_transporters_across() (pythoncyc.PGDB.PGDB method) autocatalytic_reactions_of_enzyme() (pythoncyc.PGDB.PGDB method)

B

base_components_of_protein() (pythoncyc.PGDB.PGDB method) binding_site_promoters() (pythoncyc.PGDB.PGDB method) binding_site_to_regulators() (pythoncyc.PGDB.PGDB method) binding_site_transcription_units() (pythoncyc.PGDB.PGDB method)

binding_sites_affecting_gene() (pythoncyc.PGDB.PGDB method) biovelo() (in module pythoncyc) bv() (in module pythoncyc)

C

chromosome_of_gene() (pythoncyc.PGDB.PGDB method) chromosome_of_object() (pythoncyc.PGDB.PGDB method) chromosome_of_operon() (pythoncyc.PGDB.PGDB method) cofactors_and_pgroups_of_enzrxn() (pythoncyc.PGDB.PGDB method) compartment_of_rxn() (pythoncyc.PGDB.PGDB method) compartments_of_reaction() (pythoncyc.PGDB.PGDB method) complex_p() (pythoncyc.PGDB.PGDB method) compounds_of_pathway() (pythoncyc.PGDB.PGDB method)

containers_of() (pythoncyc.PGDB.PGDB method) containing_chromosome() (pythoncyc.PGDB.PGDB method) containing_tus() (pythoncyc.PGDB.PGDB method) convertArgToLisp() (in module pythoncyc.PGDB) convertLispIdtoPythonId() (in module pythoncyc.PToolsFrame) cotranscribed_genes() (pythoncyc.PGDB.PGDB method) create_frame_objects() (pythoncyc.PGDB.PGDB method)

D

deactivated_or_inhibited_by_compound() (pythoncyc.PGDB.PGDB method) direct_activators() (pythoncyc.PGDB.PGDB method) direct_inhibitors() (pythoncyc.PGDB.PGDB method)

direct_regulators() (pythoncyc.PGDB.PGDB method) dna_binding_site_p() (pythoncyc.PGDB.PGDB method) DNA_binding_sites_of_protein() (pythoncyc.PGDB.PGDB method)

E

enzrxn_activators() (pythoncyc.PGDB.PGDB method) enzrxn_inhibitors() (pythoncyc.PGDB.PGDB method) enzyme_activity_name() (pythoncyc.PGDB.PGDB method) enzyme_p() (pythoncyc.PGDB.PGDB method)

enzymes_of_gene() (pythoncyc.PGDB.PGDB method) enzymes_of_pathway() (pythoncyc.PGDB.PGDB method) enzymes_of_reaction() (pythoncyc.PGDB.PGDB method)

F

full_enzyme_name() (pythoncyc.PGDB.PGDB method)

G

gene_clusters() (pythoncyc.PGDB.PGDB method) gene_p() (pythoncyc.PGDB.PGDB method) gene_transcription_units() (pythoncyc.PGDB.PGDB method) genes_in_same_operon() (pythoncyc.PGDB.PGDB method) genes_of_pathway() (pythoncyc.PGDB.PGDB method) genes_of_protein() (pythoncyc.PGDB.PGDB method) genes_of_proteins() (pythoncyc.PGDB.PGDB method) genes_of_reaction() (pythoncyc.PGDB.PGDB method) genes_regulated_by_gene() (pythoncyc.PGDB.PGDB method) genes_regulated_by_protein() (pythoncyc.PGDB.PGDB method) genes_regulating_gene() (pythoncyc.PGDB.PGDB method) get_class_all_instances() (pythoncyc.PGDB.PGDB method)

get_class_all_subs() (pythoncyc.PGDB.PGDB method) get_class_data() (pythoncyc.PGDB.PGDB method) get_frame_data() (pythoncyc.PToolsFrame.PFrame method) get_frame_objects() (pythoncyc.PGDB.PGDB method) get_frame_slot_value() (pythoncyc.PToolsFrame.PFrame method) get_major_classes() (pythoncyc.PGDB.PGDB method) get_name_string() (pythoncyc.PGDB.PGDB method) get_predecessors() (pythoncyc.PGDB.PGDB method) get_slot_value() (pythoncyc.PGDB.PGDB method) get_slot_values() (pythoncyc.PGDB.PGDB method) get_successors() (pythoncyc.PGDB.PGDB method)

H

homomultimeric_containers_of() (pythoncyc.PGDB.PGDB method)

I

inhibition_p() (pythoncyc.PGDB.PGDB method) is_a_class_name() (pythoncyc.PGDB.PGDB method)

is_an_instance_name() (pythoncyc.PGDB.PGDB method)

L

leader_peptide_p() (pythoncyc.PGDB.PGDB method)

M

may_be_frameid() (in module pythoncyc.PGDB) mkey() (in module pythoncyc.PGDB) modified_and_unmodified_forms() (pythoncyc.PGDB.PGDB method)

modified_containers() (pythoncyc.PGDB.PGDB method) modified_forms() (pythoncyc.PGDB.PGDB method) monomers_of_protein() (pythoncyc.PGDB.PGDB method)

N

neighboring_genes_p() (pythoncyc.PGDB.PGDB method) next_gene_on_replicon() (pythoncyc.PGDB.PGDB method)

noncontiguous_pathway_p() (pythoncyc.PGDB.PGDB method) nonspecific_forms_of_rxn() (pythoncyc.PGDB.PGDB method)

O

operon_of_gene() (pythoncyc.PGDB.PGDB method)

P

pathway_allows_enzrxn() (pythoncyc.PGDB.PGDB method) pathway_components() (pythoncyc.PGDB.PGDB method) pathway_hole_p() (pythoncyc.PGDB.PGDB method) pathways_of_compound() (pythoncyc.PGDB.PGDB method) pathways_of_enzrxn() (pythoncyc.PGDB.PGDB method) pathways_of_gene() (pythoncyc.PGDB.PGDB method) PFrame (class in pythoncyc.PToolsFrame) PGDB (class in pythoncyc.PGDB) phantom_gene_p() (pythoncyc.PGDB.PGDB method) polypeptide_or_homomultimer_p() (pythoncyc.PGDB.PGDB method) prepareFnCall() (in module pythoncyc.PGDB) previous_gene_on_replicon() (pythoncyc.PGDB.PGDB method) promoter_binding_sites() (pythoncyc.PGDB.PGDB method) protein_coding_gene() (pythoncyc.PGDB.PGDB method)

protein_in_compartment_p() (pythoncyc.PGDB.PGDB method) protein_or_rna_containers_of() (pythoncyc.PGDB.PGDB method) protein_p() (pythoncyc.PGDB.PGDB method) pseudo_gene_p() (pythoncyc.PGDB.PGDB method) PToolsError put_slot_value() (pythoncyc.PGDB.PGDB method) put_slot_values() (pythoncyc.PGDB.PGDB method) pythoncyc (module) pythoncyc.config (module) pythoncyc.PGDB (module) pythoncyc.PTools (module) pythoncyc.PToolsFrame (module) PythonCycError

R

reaction_reactants_and_products() (pythoncyc.PGDB.PGDB method) reaction_type() (pythoncyc.PGDB.PGDB method) reactions_of_compound() (pythoncyc.PGDB.PGDB method) reactions_of_enzyme() (pythoncyc.PGDB.PGDB method) reactions_of_gene() (pythoncyc.PGDB.PGDB method) reactions_of_protein() (pythoncyc.PGDB.PGDB method) recvAll() (in module pythoncyc.PTools) recvFixedLength() (in module pythoncyc.PTools) recvTimeOut() (in module pythoncyc.PTools) reduce_modified_proteins() (pythoncyc.PGDB.PGDB method) regulation_frame_transcription_units() (pythoncyc.PGDB.PGDB method) regulator_of_type() (pythoncyc.PGDB.PGDB method) regulator_proteins_of_transcription_unit() (pythoncyc.PGDB.PGDB method)

regulators_of_gene_transcription() (pythoncyc.PGDB.PGDB method) regulators_of_operon_transcription() (pythoncyc.PGDB.PGDB method) regulon_of_protein() (pythoncyc.PGDB.PGDB method) rna_coding_gene() (pythoncyc.PGDB.PGDB method) run_fba() (in module pythoncyc) (pythoncyc.PGDB.PGDB method) rxn_in_compartment_p() (pythoncyc.PGDB.PGDB method) rxn_present_p() (pythoncyc.PGDB.PGDB method) rxn_specific_form_of_rxn_p() (pythoncyc.PGDB.PGDB method) rxn_w_isozymes_p() (pythoncyc.PGDB.PGDB method) rxn_without_sequenced_enzyme_p() (pythoncyc.PGDB.PGDB method) rxns_adjacent_in_pwy_p() (pythoncyc.PGDB.PGDB method) rxns_catalyzed_by_complex() (pythoncyc.PGDB.PGDB method) rxns_w_isozymes() (pythoncyc.PGDB.PGDB method)

S

save_pgdb() (pythoncyc.PGDB.PGDB method) select_organism() (in module pythoncyc) sendAll() (in module pythoncyc.PTools) sendPgdbFnCall() (pythoncyc.PGDB.PGDB method) sendPgdbFnCallBool() (pythoncyc.PGDB.PGDB method) sendPgdbFnCallList() (pythoncyc.PGDB.PGDB method) sendPgdbQuery() (pythoncyc.PGDB.PGDB method) sendQueryToPTools() (in module pythoncyc.PTools) set_debug_off() (in module pythoncyc.config) set_debug_on() (in module pythoncyc.config)

set_host_name() (in module pythoncyc.config) set_host_port() (in module pythoncyc.config) small_molecule_cplxes_of_prot() (pythoncyc.PGDB.PGDB method) so() (in module pythoncyc) species_of_protein() (pythoncyc.PGDB.PGDB method) specific_forms_of_rxn() (pythoncyc.PGDB.PGDB method) substrate_of_generic_rxn() (pythoncyc.PGDB.PGDB method) substrates_of_pathway() (pythoncyc.PGDB.PGDB method) substrates_of_reaction() (pythoncyc.PGDB.PGDB method) Symbol (class in pythoncyc.PToolsFrame)

T

terminator_p() (pythoncyc.PGDB.PGDB method) terminators_affecting_gene() (pythoncyc.PGDB.PGDB method) tfs_bound_to_compound() (pythoncyc.PGDB.PGDB method) top_containers() (pythoncyc.PGDB.PGDB method) transcription_factor_active_forms() (pythoncyc.PGDB.PGDB method) transcription_factor_ligands() (pythoncyc.PGDB.PGDB method) transcription_factor_p() (pythoncyc.PGDB.PGDB method) transcription_unit_activation_frames() (pythoncyc.PGDB.PGDB method) transcription_unit_activators() (pythoncyc.PGDB.PGDB method) transcription_unit_all_components() (pythoncyc.PGDB.PGDB method) transcription_unit_binding_sites() (pythoncyc.PGDB.PGDB method) transcription_unit_first_gene() (pythoncyc.PGDB.PGDB method)

transcription_unit_genes() (pythoncyc.PGDB.PGDB method) transcription_unit_inhibition_frames() (pythoncyc.PGDB.PGDB method) transcription_unit_inhibitors() (pythoncyc.PGDB.PGDB method) transcription_unit_mrna_binding_sites() (pythoncyc.PGDB.PGDB method) transcription_unit_promoter() (pythoncyc.PGDB.PGDB method) transcription_unit_regulation_frames() (pythoncyc.PGDB.PGDB method) transcription_unit_terminators() (pythoncyc.PGDB.PGDB method) transcription_unit_transcription_factors() (pythoncyc.PGDB.PGDB method) transcription_units_of_promoter() (pythoncyc.PGDB.PGDB method) transcription_units_of_protein() (pythoncyc.PGDB.PGDB method) transported_chemicals() (pythoncyc.PGDB.PGDB method)

U

unmodified_form() (pythoncyc.PGDB.PGDB method) unmodified_gene_product() (pythoncyc.PGDB.PGDB method)

unmodified_gene_products() (pythoncyc.PGDB.PGDB method) unmodified_or_unbound_form() (pythoncyc.PGDB.PGDB method)

V

variants_of_pathway() (pythoncyc.PGDB.PGDB method)

vectorize_dict() (pythoncyc.PToolsFrame.PFrame method)