Index

A | B | C | D | E | F | G | H | K | L | M | N | O | P | R | S | T | U

A

AChemAbstract (class in AChemKit.sims_simple)
AChemKit.__init__ (module)
AChemKit.bucket (module)
AChemKit.properties (module)
AChemKit.properties_wnx (module)
AChemKit.randomnet (module)
AChemKit.randomnet_test (module)
AChemKit.reactionnet (module)
AChemKit.reactionnet_test (module)
AChemKit.reactionnetdot (module)
AChemKit.reactionnetdot_test (module)
AChemKit.sims_gillespie (module)
AChemKit.sims_gillespie_test (module)
AChemKit.sims_simple (module)
AChemKit.sims_simple_test (module)
AChemKit.tools (module)
AChemKit.tools.chem_pp (module)
AChemKit.tools.chem_to_dot (module)
AChemKit.tools.chem_to_pdf (module)
AChemKit.tools.log_to_chem (module)
AChemKit.utils (module)
AChemKit.utils.bag (module)
AChemKit.utils.bag_test (module)
AChemKit.utils.simpledot (module)
AChemKit.utils.utils (module)
AChemKit.utils.utils_test (module)
AChemReactionNetwork (class in AChemKit.sims_simple)
add() (AChemKit.utils.bag.Bag method)
(AChemKit.utils.bag.OrderedBag method)
(AChemKit.utils.simpledot.SimpleDot method)

B

Bag (class in AChemKit.utils.bag)
Bucket (class in AChemKit.bucket)

C

cls (AChemKit.utils.bag_test.TestBag attribute)
(AChemKit.utils.bag_test.TestFrozenBag attribute)
(AChemKit.utils.bag_test.TestOrderedBag attribute)
(AChemKit.utils.bag_test.TestOrderedFrozenBag attribute)
combinations_with_replacement() (in module AChemKit.randomnet)

D

discard() (AChemKit.utils.bag.Bag method)
(AChemKit.utils.bag.OrderedBag method)
dot (AChemKit.reactionnetdot.ReactionNetworkDot attribute)

E

Event (class in AChemKit.bucket)

F

find_cycles() (in module AChemKit.properties_wnx)
from_file() (AChemKit.bucket.Bucket class method)
(AChemKit.reactionnet.ReactionNetwork class method)
from_filename() (AChemKit.bucket.Bucket class method)
(AChemKit.reactionnet.ReactionNetwork class method)
from_string() (AChemKit.bucket.Bucket class method)
(AChemKit.reactionnet.ReactionNetwork class method)
FrozenBag (class in AChemKit.utils.bag)

G

get() (AChemKit.utils.simpledot.SimpleDot method)
get_sample() (in module AChemKit.utils.utils)
Gillespie (class in AChemKit.sims_gillespie)

H

has_catalysis_direct() (in module AChemKit.properties)
has_decomposition() (in module AChemKit.properties)
has_divergence() (in module AChemKit.properties)
has_reversible() (in module AChemKit.properties)
has_synthesis() (in module AChemKit.properties)
has_varying_rates() (in module AChemKit.properties)

K

keys() (AChemKit.utils.simpledot.SimpleDot method)

L

Linear() (in module AChemKit.randomnet)

M

MultiDiGraph_make_flow() (in module AChemKit.properties_wnx)

N

next_reaction() (AChemKit.sims_gillespie.Gillespie method)
not_conservation_mass() (in module AChemKit.properties)

O

OrderedBag (class in AChemKit.utils.bag)
OrderedFrozenBag (class in AChemKit.utils.bag)

P

plot() (AChemKit.utils.simpledot.SimpleDot method)

R

react() (AChemKit.sims_simple.AChemAbstract method)
(AChemKit.sims_simple.AChemReactionNetwork method)
reaction_to_string() (AChemKit.reactionnet.ReactionNetwork class method)
reactionnet (AChemKit.bucket.Bucket attribute)
ReactionNetwork (class in AChemKit.reactionnet)
ReactionNetwork_to_MultiDiGraph() (in module AChemKit.properties_wnx)
ReactionNetworkDot (class in AChemKit.reactionnetdot)
reactions (AChemKit.reactionnet.ReactionNetwork attribute)

S

seen (AChemKit.reactionnet.ReactionNetwork attribute)
setUp() (AChemKit.randomnet_test.TestLinear method)
(AChemKit.randomnet_test.TestUniform method)
(AChemKit.reactionnet_test.TestReactionNetwork method)
(AChemKit.reactionnet_test.TestReactionNetwork_from_string method)
(AChemKit.reactionnetdot_test.TestReactionNetworkDot method)
(AChemKit.sims_gillespie_test.TestGillespie method)
(AChemKit.sims_simple_test.TestItterative method)
(AChemKit.utils.bag_test.TestBag method)
(AChemKit.utils.bag_test.TestFrozenBag method)
(AChemKit.utils.bag_test.TestOrderedBag method)
(AChemKit.utils.bag_test.TestOrderedFrozenBag method)
SimpleDot (class in AChemKit.utils.simpledot)
simulate_gillespie() (in module AChemKit.sims_gillespie)
simulate_gillespie_iter() (in module AChemKit.sims_gillespie)
simulate_itterative() (in module AChemKit.sims_simple)
simulate_itterative_iter() (in module AChemKit.sims_simple)
simulate_stepwise() (in module AChemKit.sims_simple)
simulate_stepwise_iter() (in module AChemKit.sims_simple)
simulate_stepwise_multiprocessing() (in module AChemKit.sims_simple)
simulate_stepwise_multiprocessing_iter() (in module AChemKit.sims_simple)

T

test_add() (AChemKit.utils.bag_test.TestBag method)
test_basic() (AChemKit.sims_gillespie_test.TestGillespie method)
(AChemKit.sims_simple_test.TestItterative method)
(AChemKit.sims_simple_test.TestStepwise method)
(AChemKit.sims_simple_test.TestStepwiseMultiprocessing method)
test_dicts() (AChemKit.utils.utils_test.TestGetSample method)
test_directed() (AChemKit.randomnet_test.TestLinear method)
test_discard() (AChemKit.utils.bag_test.TestBag method)
test_eq() (AChemKit.utils.bag_test.TestFrozenBag method)
test_equal() (AChemKit.reactionnet_test.TestReactionNetwork method)
test_hash() (AChemKit.reactionnet_test.TestReactionNetwork method)
(AChemKit.utils.bag_test.TestBag method)
(AChemKit.utils.bag_test.TestFrozenBag method)
test_ints() (AChemKit.utils.utils_test.TestGetSample method)
test_iter() (AChemKit.utils.bag_test.TestFrozenBag method)
(AChemKit.utils.bag_test.TestOrderedFrozenBag method)
test_len() (AChemKit.utils.bag_test.TestFrozenBag method)
test_lists() (AChemKit.utils.utils_test.TestGetSample method)
test_maxlengt_dict() (AChemKit.randomnet_test.TestLinear method)
test_maxlengt_tuple() (AChemKit.randomnet_test.TestLinear method)
test_natoms_dict() (AChemKit.randomnet_test.TestLinear method)
test_natoms_int() (AChemKit.randomnet_test.TestLinear method)
test_natoms_tuple() (AChemKit.randomnet_test.TestLinear method)
test_nmols_dict() (AChemKit.randomnet_test.TestUniform method)
test_nmols_int() (AChemKit.randomnet_test.TestUniform method)
test_nmols_list() (AChemKit.randomnet_test.TestUniform method)
test_nmols_tuple() (AChemKit.randomnet_test.TestUniform method)
test_nprods_dict() (AChemKit.randomnet_test.TestUniform method)
test_nprods_int() (AChemKit.randomnet_test.TestUniform method)
test_nprods_list() (AChemKit.randomnet_test.TestUniform method)
test_nprods_none_dict() (AChemKit.randomnet_test.TestUniform method)
test_nprods_none_tuple() (AChemKit.randomnet_test.TestUniform method)
test_nprods_tuple() (AChemKit.randomnet_test.TestUniform method)
test_nreacts_dict() (AChemKit.randomnet_test.TestUniform method)
test_nreacts_int() (AChemKit.randomnet_test.TestUniform method)
test_nreacts_list() (AChemKit.randomnet_test.TestUniform method)
test_nreacts_tuple() (AChemKit.randomnet_test.TestUniform method)
test_pbreak_tuple() (AChemKit.randomnet_test.TestLinear method)
test_pform_tuple() (AChemKit.randomnet_test.TestLinear method)
test_rate_dict() (AChemKit.randomnet_test.TestUniform method)
test_rate_float() (AChemKit.randomnet_test.TestUniform method)
test_rate_int() (AChemKit.randomnet_test.TestUniform method)
test_rate_list() (AChemKit.randomnet_test.TestUniform method)
test_rate_tuple() (AChemKit.randomnet_test.TestUniform method)
test_rates() (AChemKit.reactionnet_test.TestReactionNetwork method)
test_reaction_to_string() (AChemKit.reactionnet_test.TestReactionNetwork method)
test_reactions() (AChemKit.reactionnet_test.TestReactionNetwork method)
test_repr() (AChemKit.utils.bag_test.TestFrozenBag method)
test_seen() (AChemKit.reactionnet_test.TestReactionNetwork method)
test_str() (AChemKit.utils.bag_test.TestFrozenBag method)
test_to_dot_str() (AChemKit.reactionnetdot_test.TestReactionNetworkDot method)
test_to_string() (AChemKit.reactionnet_test.TestReactionNetwork method)
test_undirected() (AChemKit.randomnet_test.TestLinear method)
TestBag (class in AChemKit.utils.bag_test)
TestFrozenBag (class in AChemKit.utils.bag_test)
TestGetSample (class in AChemKit.utils.utils_test)
TestGillespie (class in AChemKit.sims_gillespie_test)
TestItterative (class in AChemKit.sims_simple_test)
TestLinear (class in AChemKit.randomnet_test)
TestOrderedBag (class in AChemKit.utils.bag_test)
TestOrderedFrozenBag (class in AChemKit.utils.bag_test)
TestReactionNetwork (class in AChemKit.reactionnet_test)
TestReactionNetwork_from_string (class in AChemKit.reactionnet_test)
TestReactionNetworkDot (class in AChemKit.reactionnetdot_test)
TestStepwise (class in AChemKit.sims_simple_test)
TestStepwiseMultiprocessing (class in AChemKit.sims_simple_test)
TestUniform (class in AChemKit.randomnet_test)
to_dot() (AChemKit.reactionnetdot.ReactionNetworkDot method)

U

Uniform() (in module AChemKit.randomnet)