Index

A

A (src.strand.strand_graph.StrandGraph attribute) add_color() (src.strand.strand.Strand method) add_domain() (src.strand.strand.Strand method) add_edges() (src.strand.bond_graph.BondGraph method) add_product() (src.reaction.reaction.Reaction method) add_rate() (src.reaction.reaction.Reaction method)

add_rule() (src.reaction.reaction.Reaction method) adj (src.strand.bond_graph.BondGraph attribute) (src.strand.bond_graph.SubBondGraph attribute) anchored() (src.strand.strand_graph.StrandGraph method) anti_parallel() (src.strand.strand_graph.StrandGraph method) appenddom() (src.strand.bond.Bond method) available() (src.strand.strand_graph.StrandGraph method)

B

bi() (in module src.species.species_explore) Bond (class in src.strand.bond) bond (src.strand.strand.Domain attribute)

BondGraph (class in src.strand.bond_graph) bondgraph (src.strand.strand_graph.StrandGraph attribute) bondname (src.strand.strand.Domain attribute) build_bond_graph() (src.strand.strand_graph.StrandGraph method)

C

call_spanning() (src.strand.bond_graph.BondGraph method) canonicalform (src.species.species.Species attribute) check_binding() (in module src.basics.check_rules) check_bond_existence() (in module src.util.util) check_bonded() (src.strand.bond_graph.BondGraph method) (src.strand.strand_graph.StrandGraph method) check_candidate() (src.strand.strand_graph.StrandGraph method) check_complementary() (src.strand.strand_graph.StrandGraph method) check_continuity() (in module src.util.util) check_edge_in_tuplelist() (in module src.util.util) check_existence() (in module src.species.species_explore) check_existence_4way() (in module src.basics.check_rules) check_following_migration() (in module src.util.util) (src.strand.bond_graph.BondGraph method) check_hidden_all() (src.strand.strand_graph.StrandGraph method) check_hidden_prevbond() (in module src.species.species_explore) check_in_loop() (src.strand.bond_graph.BondGraph method) check_junction() (src.strand.bond_graph.BondGraph method) check_migration() (in module src.basics.check_rules)

check_pendingbond() (src.species.species.Species static method) check_same_domain() (src.strand.strand.Domain method) check_same_strand() (src.strand.strand.Strand method) check_strand_is_bonded() (src.strand.bond_graph.BondGraph method) check_switchable() (src.strand.strand_graph.StrandGraph method) check_switchable_2() (src.strand.strand_graph.StrandGraph method) check_toehold() (src.strand.strand_graph.StrandGraph method) check_unbinding() (in module src.basics.check_rules) color (src.strand.bond_graph.BondGraph attribute) (src.strand.strand.Strand attribute) (src.strand.strand_graph.StrandGraph attribute) colormap (src.species.species.Species attribute) (src.strand.bond_graph.SubBondGraph attribute) colorset (src.species.species.Species attribute) (src.strand.bond_graph.SubBondGraph attribute) comp (src.strand.strand.Domain attribute) compare() (in module src.util.util) construct_strands() (src.species.species.Species method) create_bond() (src.strand.bond_graph.BondGraph method)

D

delete_edge() (src.strand.strand_graph.StrandGraph method) delete_edges_regarding_v() (src.strand.strand_graph.StrandGraph method) delete_vertex() (src.strand.strand_graph.StrandGraph method) derive_canonical_form() (src.species.species.Species method)

derive_rootmap() (src.species.species.Species static method) dom (src.strand.bond.Bond attribute) dom2 (src.strand.bond.Bond attribute) Domain (class in src.strand.strand) domains (src.strand.strand.Strand attribute)

E

E (src.strand.bond_graph.BondGraph attribute) (src.strand.strand_graph.StrandGraph attribute)

F

find_loops() (src.strand.bond_graph.BondGraph method)

find_mediated_toehold() (src.strand.strand_graph.StrandGraph method) flip() (in module src.util.util)

G

generate_colorinfo() (in module src.species.species_explore) generate_concentrations() (in module src.basics.generate_pysbmodel) generate_model() (in module src.basics.generate_pysbmodel) generate_monomer() (in module src.basics.generate_pysbmodel) generate_multiple_species() (in module src.species.species_explore) generate_output() (src.reaction.reaction.Reaction method) (src.species.species.Species method) generate_rule() (in module src.basics.generate_pysbmodel) generate_species() (in module src.species.species_explore) get_absdist() (in module src.util.util) get_additional_info() (in module src.basics.initialize_system) get_bond() (src.strand.bond_graph.BondGraph method) get_closest_target() (in module src.util.util) get_closet_domain_to_target() (in module src.util.util)

get_combinations() (in module src.util.util) get_connect_toehold() (src.strand.strand_graph.StrandGraph method) get_connection() (src.strand.bond_graph.BondGraph method) get_direction() (src.strand.bond_graph.BondGraph method) get_domain_comp() (src.strand.strand_graph.StrandGraph method) get_domain_obj() (src.strand.strand_graph.StrandGraph method) get_domains_on_2sides() (in module src.util.util) get_edge_info() (in module src.util.util) get_free_domains() (in module src.util.util) get_kinetics() (in module src.basics.initialize_system) get_migrate_nodes() (in module src.util.util) get_outdir_simupara() (in module src.basics.initialize_system) get_reverse() (in module src.util.util) get_species() (src.strand.bond_graph.BondGraph method) get_starting_vertex() (src.species.species.Species method)

H

have_anchor() (src.strand.strand_graph.StrandGraph method)

hidden (src.strand.bond_graph.BondGraph attribute) hidden() (src.strand.strand_graph.StrandGraph method)

I

id (src.species.species.Species attribute)

initialize() (in module src.basics.initialize_system)

L

length (src.strand.strand_graph.StrandGraph attribute) lexer_site() (in module src.basics.lexical_analyzer)

lexer_strand() (in module src.basics.lexical_analyzer) loop (src.strand.bond_graph.BondGraph attribute)

M

map_colors() (src.strand.bond_graph.SubBondGraph method) merge_bonds_ignoring_nodes() (src.strand.bond_graph.BondGraph method) module src src.basics src.basics.check_rules src.basics.generate_pysbmodel src.basics.initialize_system src.basics.lexical_analyzer src.reaction src.reaction.reaction src.species src.species.species src.species.species_explore src.strand src.strand.bond src.strand.bond_graph src.strand.strand src.strand.strand_graph src.util src.util.util

mono() (in module src.species.species_explore)

N

name (src.strand.strand.Domain attribute) node1 (src.strand.bond.Bond attribute)

node2 (src.strand.bond.Bond attribute) nodes (src.species.species.Species attribute)

P

parsingseq (src.species.species.Species attribute) potential_junction() (src.strand.bond_graph.BondGraph method)

products (src.reaction.reaction.Reaction attribute) prune() (src.species.species.Species method) prune_starting_vertices() (src.species.species.Species method)

R

rate (src.reaction.reaction.Reaction attribute) reactants (src.reaction.reaction.Reaction attribute) Reaction (class in src.reaction.reaction)

reconstruct() (src.strand.strand_graph.StrandGraph method) refresh_for_pruning() (src.species.species.Species static method) rule (src.reaction.reaction.Reaction attribute)

S

same_species() (src.strand.strand_graph.StrandGraph method) search_path() (src.strand.bond_graph.BondGraph method) set_bond() (src.strand.strand.Domain method) set_id() (src.species.species.Species method) sort_by_strand() (in module src.util.util) sort_e_by_domain() (in module src.util.util) spanning() (src.strand.bond_graph.BondGraph method) Species (class in src.species.species) species (src.strand.bond_graph.BondGraph attribute) speciesnum (src.strand.bond_graph.BondGraph attribute) src module src.basics module src.basics.check_rules module src.basics.generate_pysbmodel module src.basics.initialize_system module src.basics.lexical_analyzer module src.reaction module src.reaction.reaction module

src.species module src.species.species module src.species.species_explore module src.strand module src.strand.bond module src.strand.bond_graph module src.strand.strand module src.strand.strand_graph module src.util module src.util.util module store_hidden() (src.strand.bond_graph.BondGraph method) Strand (class in src.strand.strand) StrandGraph (class in src.strand.strand_graph) strands (src.species.species.Species attribute) (src.strand.strand_graph.StrandGraph attribute) SubBondGraph (class in src.strand.bond_graph)

T

toehold (src.strand.strand.Domain attribute) (src.strand.strand_graph.StrandGraph attribute)

transform_E() (src.strand.bond.Bond method) traverse() (src.species.species.Species method)

V

V (src.strand.bond_graph.BondGraph attribute) (src.strand.strand_graph.StrandGraph attribute)

Vsub (src.strand.bond_graph.SubBondGraph attribute)