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Introduction
Hermite and Smith Normal Forms
Systems of ODEs
ODETranslation and Reduction of ODESystems
Chemical Reaction Networks
Examples
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Index
A
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
A
add_constraints() (desr.ode_system.ODESystem method)
addr() (in module desr.diophantine)
as_vector() (desr.chemical_reaction_network.Complex method)
auxiliaries() (desr.ode_translation.ODETranslation method)
C
ChemicalReactionNetwork (class in desr.chemical_reaction_network)
ChemicalSpecies (class in desr.chemical_reaction_network)
cholesky() (in module desr.diophantine)
comparer() (in module desr.diophantine)
Complex (class in desr.chemical_reaction_network)
constant_variables (desr.ode_system.ODESystem attribute)
constraints (desr.ode_system.ODESystem attribute)
copy() (desr.ode_system.ODESystem method)
D
default_order_variables() (desr.ode_system.ODESystem method)
degree() (in module desr.sympy_helper)
dep_var_herm_mult() (desr.ode_translation.ODETranslation method)
dep_var_inv_herm_mult() (desr.ode_translation.ODETranslation method)
derivative_dict (desr.ode_system.ODESystem attribute)
derivatives (desr.ode_system.ODESystem attribute)
desr.chemical_reaction_network (module)
desr.diophantine (module)
desr.matrix_normal_forms (module)
desr.ode_system (module)
desr.ode_translation (module)
desr.sympy_helper (module)
desr.tex_tools (module)
desr.unittests (module)
dict_as_eqns() (in module desr.sympy_helper)
diff_subs() (desr.ode_system.ODESystem method)
E
element_wise_lt() (in module desr.matrix_normal_forms)
eqn_to_tex() (in module desr.tex_tools)
eqns_to_tex() (in module desr.tex_tools)
eqns_with_variables() (in module desr.sympy_helper)
expand_matrix() (in module desr.matrix_normal_forms)
expr_to_tex() (in module desr.tex_tools)
expressions_to_variables() (in module desr.sympy_helper)
extend_from_invariants() (desr.ode_translation.ODETranslation method)
extend_rectangular_matrix() (in module desr.ode_translation)
F
first_nonzero_is_negative() (in module desr.diophantine)
from_diagram() (desr.chemical_reaction_network.ChemicalReactionNetwork class method)
from_dict() (desr.ode_system.ODESystem class method)
from_equations() (desr.ode_system.ODESystem class method)
from_ode_system() (desr.ode_translation.ODETranslation class method)
from_tex() (desr.ode_system.ODESystem class method)
G
get_pivot_row_indices() (in module desr.matrix_normal_forms)
get_solutions() (in module desr.diophantine)
gram() (in module desr.diophantine)
H
herm_form (desr.ode_translation.ODETranslation attribute)
herm_mult (desr.ode_translation.ODETranslation attribute)
herm_mult_i (desr.ode_translation.ODETranslation attribute)
herm_mult_n (desr.ode_translation.ODETranslation attribute)
hnf_col() (in module desr.matrix_normal_forms)
hnf_col_lll() (in module desr.matrix_normal_forms)
hnf_row() (in module desr.matrix_normal_forms)
hnf_row_lll() (in module desr.matrix_normal_forms)
I
indep_var (desr.ode_system.ODESystem attribute)
indep_var_index (desr.ode_system.ODESystem attribute)
initial_conditions (desr.ode_system.ODESystem attribute)
initialise_working_matrices() (in module desr.diophantine)
introot() (in module desr.diophantine)
inv_herm_mult (desr.ode_translation.ODETranslation attribute)
inv_herm_mult_d (desr.ode_translation.ODETranslation attribute)
inv_herm_mult_u (desr.ode_translation.ODETranslation attribute)
invariants() (desr.ode_translation.ODETranslation method)
is_constant() (in module desr.sympy_helper)
is_equation() (in module desr.sympy_helper)
is_hnf_col() (in module desr.matrix_normal_forms)
is_hnf_row() (in module desr.matrix_normal_forms)
is_invariant_expr() (desr.ode_translation.ODETranslation method)
is_monomial() (in module desr.sympy_helper)
is_normal_hermite_multiplier() (in module desr.matrix_normal_forms)
is_smf() (in module desr.matrix_normal_forms)
L
lcasvector() (in module desr.diophantine)
lllhermite() (in module desr.diophantine)
lnearint() (in module desr.diophantine)
M
matrix_to_tex() (in module desr.tex_tools)
maximal_scaling_matrix() (desr.ode_system.ODESystem method)
(in module desr.ode_system)
minus() (in module desr.diophantine)
monomial_to_powers() (in module desr.sympy_helper)
moving_frame() (desr.ode_translation.ODETranslation method)
multiplier_add_columns() (desr.ode_translation.ODETranslation method)
multiplier_negate_column() (desr.ode_translation.ODETranslation method)
multiplier_swap_columns() (desr.ode_translation.ODETranslation method)
multr() (in module desr.diophantine)
N
n (desr.chemical_reaction_network.ChemicalReactionNetwork attribute)
(desr.ode_translation.ODETranslation attribute)
non_constant_variables (desr.ode_system.ODESystem attribute)
nonzero() (in module desr.diophantine)
normal_hnf_col() (in module desr.matrix_normal_forms)
normal_hnf_row() (in module desr.matrix_normal_forms)
NoSolutionException
num_constants (desr.ode_system.ODESystem attribute)
O
ode_equations() (desr.chemical_reaction_network.ChemicalReactionNetwork method)
ODESystem (class in desr.ode_system)
ODETranslation (class in desr.ode_translation)
P
p (desr.chemical_reaction_network.ChemicalReactionNetwork attribute)
parse_de() (in module desr.ode_system)
power_matrix() (desr.ode_system.ODESystem method)
R
r (desr.chemical_reaction_network.ChemicalReactionNetwork attribute)
(desr.ode_translation.ODETranslation attribute)
rational_expr_to_power_matrix() (in module desr.ode_system)
rational_section() (desr.ode_translation.ODETranslation method)
ratior() (in module desr.diophantine)
Reaction (class in desr.chemical_reaction_network)
reduce_matrix() (in module desr.diophantine)
reorder_variables() (desr.ode_system.ODESystem method)
reverse_translate() (desr.ode_translation.ODETranslation method)
reverse_translate_dep_var() (desr.ode_translation.ODETranslation method)
reverse_translate_general() (desr.ode_translation.ODETranslation method)
reverse_translate_parameter() (desr.ode_translation.ODETranslation method)
rewrite_rules() (desr.ode_translation.ODETranslation method)
S
scale_action() (in module desr.ode_translation)
scaling_matrix (desr.ode_translation.ODETranslation attribute)
sign() (in module desr.diophantine)
smf() (in module desr.matrix_normal_forms)
solve() (in module desr.diophantine)
standardise_equation() (in module desr.sympy_helper)
str_eqns_to_sympy_eqns() (in module desr.sympy_helper)
str_exprs_to_sympy_eqns() (in module desr.sympy_helper)
subr() (in module desr.diophantine)
swap_rows() (in module desr.diophantine)
T
test_crn_harrington() (desr.unittests.TestChemicalReactionNetwork method)
test_crn_harrington2() (desr.unittests.TestChemicalReactionNetwork method)
test_example1() (desr.unittests.TestHermiteMethods method)
test_example_6_4_hub_lab() (desr.unittests.TestODESystemScaling method)
test_example_6_6_hub_lab() (desr.unittests.TestODESystemScaling method)
test_example_pred_prey_choosing_invariants() (desr.unittests.TestODESystemScaling method)
test_example_pred_prey_hub_lab() (desr.unittests.TestODESystemScaling method)
test_example_sage() (desr.unittests.TestHermiteMethods method)
test_normal_hermite_multiplier_example() (desr.unittests.TestHermiteMethods method)
test_reduced_michaelis_menten() (desr.unittests.TestInitialConditions method)
test_verhulst_log_growth() (desr.unittests.TestODESystemScaling method)
test_wiki_example() (desr.unittests.TestHermiteMethods method)
TestChemicalReactionNetwork (class in desr.unittests)
TestHermiteMethods (class in desr.unittests)
TestInitialConditions (class in desr.unittests)
TestODESystemScaling (class in desr.unittests)
tex_to_sympy() (in module desr.tex_tools)
to_ode_system() (desr.chemical_reaction_network.ChemicalReactionNetwork method)
to_tex() (desr.ode_system.ODESystem method)
(desr.ode_translation.ODETranslation method)
translate() (desr.ode_translation.ODETranslation method)
translate_dep_var() (desr.ode_translation.ODETranslation method)
translate_general() (desr.ode_translation.ODETranslation method)
translate_parameter() (desr.ode_translation.ODETranslation method)
translate_parameter_substitutions() (desr.ode_translation.ODETranslation method)
U
unique_array_stable() (in module desr.sympy_helper)
update_initial_conditions() (desr.ode_system.ODESystem method)
V
var_to_tex() (in module desr.tex_tools)
variables (desr.ode_system.ODESystem attribute)
variables_domain (desr.ode_translation.ODETranslation attribute)
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