PyscesToolbox
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Introduction
Installation
Basic Usage
RateChar
Symca
Thermokin
Included Files
References
Module reference
PyscesToolbox
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Index
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Index
A
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B
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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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K
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L
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M
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N
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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
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W
A
abs_value (psctb.analyse._symca.ccobjects.CCoef property)
add_property() (psctb.utils.plotting._plotting.LineData method)
add_term_types() (psctb.latextools._expressions.LatexExpr method)
adjugate_matrix() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
adjust_figure() (psctb.utils.plotting._plotting.ScanFig method)
augment_fix_sting() (in module psctb.modeltools._pscmanipulate)
B
build_cc_matrix() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
build_inner_dict() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
build_outer_dict() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
C
categories_status (psctb.utils.plotting._plotting.ScanFig property)
category_names (psctb.utils.plotting._plotting.ScanFig property)
cc_dict() (in module psctb.utils.misc._misc)
cc_list() (in module psctb.utils.misc._misc)
CCBase (class in psctb.analyse._symca.ccobjects)
CCoef (class in psctb.analyse._symca.ccobjects)
cctype() (in module psctb.analyse._symca.ccobjects)
change_link_properties() (psctb.utils.model_graph._model_graph.ModelGraph method)
change_node_properties() (psctb.utils.model_graph._model_graph.ModelGraph method)
check_config() (psctb.utils.config.ConfigChecker static method)
check_for_negatives() (in module psctb.analyse._thermokin_file_tools)
check_term_format() (in module psctb.analyse._thermokin_file_tools)
column_multiply() (in module psctb.utils.misc._misc)
ConfigChecker (class in psctb.utils.config)
ConfigReader (class in psctb.utils.config)
ConfigWriter (class in psctb.utils.config)
construct_dict() (in module psctb.analyse._thermokin_file_tools)
CPattern (class in psctb.analyse._symca.ccobjects)
create_gamma_keq_reqn_data() (in module psctb.analyse._thermokin_file_tools)
create_reqn_data() (in module psctb.analyse._thermokin_file_tools)
D
Data2D (class in psctb.utils.plotting._plotting)
det_bareis() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
do_par_scan() (psctb.analyse._symca.ccobjects.CCoef method)
do_ratechar() (psctb.analyse._ratechar.RateChar method)
do_safe_state() (in module psctb.utils.misc._misc)
do_symca() (psctb.analyse._symca._symca.Symca method)
DotDict (class in psctb.utils.misc._misc)
draw_all_links() (psctb.utils.model_graph._model_graph.ModelGraph method)
DUMMY_SINK_NAMES (psctb.utils.model_graph._model_graph.ModelGraph attribute)
E
ec_dict() (in module psctb.utils.misc._misc)
ec_list() (in module psctb.utils.misc._misc)
ematrix (psctb.analyse._symca._symca.Symca property)
es_matrix (psctb.analyse._symca._symca.Symca property)
esL (psctb.analyse._symca._symca.Symca property)
expression_to_latex() (psctb.latextools._expressions.LatexExpr method)
extract_model() (in module psctb.utils.misc._misc)
F
filter_irreversible() (in module psctb.analyse._thermokin_file_tools)
find_match() (psctb.utils.config.PathFinder static method)
find_max() (in module psctb.utils.misc._misc)
find_min() (in module psctb.utils.misc._misc)
find_path_to() (psctb.utils.config.PathFinder static method)
fix_expressions() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
fix_metabolite() (in module psctb.modeltools._pscmanipulate)
fix_metabolite_ss() (in module psctb.modeltools._pscmanipulate)
flux_list() (in module psctb.utils.misc._misc)
fluxes (psctb.analyse._symca._symca.Symca property)
fluxes_dependent (psctb.analyse._symca._symca.Symca property)
fluxes_independent (psctb.analyse._symca._symca.Symca property)
FormatException
formatter_factory() (in module psctb.utils.misc._misc)
G
generic_populate() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_all_terms() (in module psctb.analyse._thermokin_file_tools)
get_binding_vc_terms() (in module psctb.analyse._thermokin_file_tools)
get_config() (psctb.utils.config.ConfigReader class method)
get_es_matrix() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_es_matrix_no_mca() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_file_path() (in module psctb.modeltools._paths)
get_filename_from_caller() (in module psctb.utils.misc._misc)
get_fix_denom() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_fix_denom_jannie() (psctb.analyse._symca.symca_toolbox.SymcaToolBox method)
get_fluxes_vector() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_fmt() (in module psctb.modeltools._paths)
get_gamma_keq_terms() (in module psctb.analyse._thermokin_file_tools)
get_ma_terms() (in module psctb.analyse._thermokin_file_tools)
get_model_name() (in module psctb.modeltools._paths)
get_nmatrix() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_num_ind_fluxes() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_num_ind_species() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_reqn_path() (in module psctb.analyse._thermokin_file_tools)
get_species_vector() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
get_st_pt_keq() (in module psctb.analyse._thermokin_file_tools)
get_state() (in module psctb.analyse._symca.ccobjects)
get_str_formulas() (in module psctb.analyse._thermokin_file_tools)
get_subs_dict() (in module psctb.analyse._thermokin_file_tools)
get_sympy_formulas() (in module psctb.analyse._thermokin_file_tools)
get_sympy_terms() (in module psctb.analyse._thermokin_file_tools)
get_term_dict() (in module psctb.analyse._thermokin_file_tools)
get_term_types_from_raw_data() (in module psctb.analyse._thermokin_file_tools)
get_terms() (in module psctb.analyse._thermokin_file_tools)
get_value() (in module psctb.utils.misc._misc)
get_value_eval() (in module psctb.utils.misc._misc)
get_value_sympy() (in module psctb.utils.misc._misc)
group_sort() (in module psctb.utils.misc._misc)
H
height (psctb.utils.model_graph._model_graph.ModelGraph property)
highlight_cc() (psctb.utils.model_graph._model_graph.ModelGraph method)
highlight_cp() (psctb.utils.model_graph._model_graph.ModelGraph method)
highlight_patterns() (psctb.analyse._symca.ccobjects.CCoef method)
html_table() (in module psctb.utils.misc._misc)
I
interact() (psctb.utils.plotting._plotting.ScanFig method)
invert() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
is_attr() (in module psctb.utils.misc._misc)
is_cc() (in module psctb.utils.misc._misc)
is_ec() (in module psctb.utils.misc._misc)
is_iterable() (in module psctb.utils.misc._misc)
is_linear() (in module psctb.utils.misc._misc)
is_mca_coef() (in module psctb.utils.misc._misc)
is_number() (in module psctb.utils.misc._misc)
is_parameter() (in module psctb.utils.misc._misc)
is_prc() (in module psctb.utils.misc._misc)
is_rc() (in module psctb.utils.misc._misc)
is_reaction() (in module psctb.utils.misc._misc)
is_species() (in module psctb.utils.misc._misc)
is_variable() (in module psctb.utils.misc._misc)
K
kmatrix (psctb.analyse._symca._symca.Symca property)
L
latex_expression (psctb.analyse._symca.ccobjects.CCBase property)
(psctb.analyse._symca.ccobjects.CCoef property)
(psctb.analyse._symca.ccobjects.CPattern property)
latex_expression_full (psctb.analyse._symca.ccobjects.CCoef property)
(psctb.analyse._symca.ccobjects.CPattern property)
latex_name (psctb.analyse._symca.ccobjects.CCBase property)
(psctb.analyse._symca.ccobjects.CCoef property)
(psctb.analyse._symca.ccobjects.CPattern property)
latex_numerator (psctb.analyse._symca.ccobjects.CCoef property)
(psctb.analyse._symca.ccobjects.CPattern property)
LatexExpr (class in psctb.latextools._expressions)
line_names (psctb.utils.plotting._plotting.ScanFig property)
LineData (class in psctb.utils.plotting._plotting)
lmatrix (psctb.analyse._symca._symca.Symca property)
load_data2d() (in module psctb.utils.plotting._plotting)
load_session() (psctb.analyse._ratechar.RateChar method)
(psctb.analyse._symca._symca.Symca method)
M
make_CC_dot_dict() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
make_inner_dict() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
make_internals_dict() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
make_path() (in module psctb.modeltools._paths)
maxima_factor() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
memoize() (in module psctb.utils.misc._misc)
MissingSection
MissingSetting
mod_ec_list() (in module psctb.utils.misc._misc)
mod_to_str() (in module psctb.modeltools._pscmanipulate)
ModelGraph (class in psctb.utils.model_graph._model_graph)
module
psctb
psctb.analyse
psctb.analyse._ratechar
psctb.analyse._symca
psctb.analyse._symca._symca
psctb.analyse._symca.ccobjects
psctb.analyse._symca.symca_toolbox
psctb.analyse._thermokin
psctb.analyse._thermokin_file_tools
psctb.latextools
psctb.latextools._expressions
psctb.modeltools
psctb.modeltools._paths
psctb.modeltools._pscmanipulate
psctb.utils
psctb.utils.config
psctb.utils.misc
psctb.utils.misc._misc
psctb.utils.model_graph
psctb.utils.model_graph._model_graph
psctb.utils.plotting
psctb.utils.plotting._plotting
N
next_suffix() (in module psctb.modeltools._paths)
nmatrix (psctb.analyse._symca._symca.Symca property)
nodes_fixed (psctb.utils.model_graph._model_graph.ModelGraph property)
num_ind_fluxes (psctb.analyse._symca._symca.Symca property)
num_ind_species (psctb.analyse._symca._symca.Symca property)
P
path_to() (psctb.analyse._symca._symca.Symca method)
PathFinder (class in psctb.utils.config)
percentage (psctb.analyse._symca.ccobjects.CPattern property)
plot() (psctb.utils.plotting._plotting.Data2D method)
(psctb.utils.plotting._plotting.SimpleData2D method)
populate_with_fake_elasticities() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
populate_with_fake_fluxes() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
populate_with_fake_ss_concentrations() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
prc_dict() (in module psctb.utils.misc._misc)
prc_list() (in module psctb.utils.misc._misc)
prc_subs (psctb.latextools._expressions.LatexExpr property)
print_f() (in module psctb.utils.misc._misc)
prod_ec_list() (in module psctb.utils.misc._misc)
psc_to_str() (in module psctb.modeltools._pscmanipulate)
psctb
module
psctb.analyse
module
psctb.analyse._ratechar
module
psctb.analyse._symca
module
psctb.analyse._symca._symca
module
psctb.analyse._symca.ccobjects
module
psctb.analyse._symca.symca_toolbox
module
psctb.analyse._thermokin
module
psctb.analyse._thermokin_file_tools
module
psctb.latextools
module
psctb.latextools._expressions
module
psctb.modeltools
module
psctb.modeltools._paths
module
psctb.modeltools._pscmanipulate
module
psctb.utils
module
psctb.utils.config
module
psctb.utils.misc
module
psctb.utils.misc._misc
module
psctb.utils.model_graph
module
psctb.utils.model_graph._model_graph
module
psctb.utils.plotting
module
psctb.utils.plotting._plotting
module
PseudoDotDict (class in psctb.utils.misc._misc)
R
RateChar (class in psctb.analyse._ratechar)
rc_dict() (in module psctb.utils.misc._misc)
rc_list() (in module psctb.utils.misc._misc)
REACTION_NODE (psctb.utils.model_graph._model_graph.ModelGraph attribute)
read_reqn_file() (in module psctb.analyse._thermokin_file_tools)
reload_config() (psctb.utils.config.ConfigReader class method)
remove_dummy_sinks() (psctb.utils.model_graph._model_graph.ModelGraph method)
remove_external_modifier_links() (psctb.utils.model_graph._model_graph.ModelGraph method)
replace_pow() (in module psctb.analyse._thermokin_file_tools)
reset_node_properties() (psctb.utils.model_graph._model_graph.ModelGraph method)
RGB_RGB_RGB_ (psctb.utils.model_graph._model_graph.ModelGraph attribute)
S
save() (psctb.utils.model_graph._model_graph.ModelGraph method)
(psctb.utils.plotting._plotting.ScanFig method)
save_data2d() (in module psctb.utils.plotting._plotting)
save_results() (psctb.analyse._ratechar.RateChar method)
(psctb.analyse._symca._symca.Symca method)
(psctb.analyse._thermokin.ThermoKin method)
(psctb.utils.plotting._plotting.Data2D method)
(psctb.utils.plotting._plotting.SimpleData2D method)
save_session() (psctb.analyse._ratechar.RateChar method)
(psctb.analyse._symca._symca.Symca method)
scale_matrix() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
scaled_k (psctb.analyse._symca._symca.Symca property)
scaled_k0 (psctb.analyse._symca._symca.Symca property)
scaled_l (psctb.analyse._symca._symca.Symca property)
scaled_l0 (psctb.analyse._symca._symca.Symca property)
ScanFig (class in psctb.utils.plotting._plotting)
scanner_range_setup() (in module psctb.utils.misc._misc)
show() (psctb.utils.model_graph._model_graph.ModelGraph method)
(psctb.utils.plotting._plotting.ScanFig method)
silence_print() (in module psctb.utils.misc._misc)
SimpleData2D (class in psctb.utils.plotting._plotting)
simplify_matrix() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
solve_dep() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
sort_terms() (in module psctb.analyse._thermokin_file_tools)
spawn_cc_objects() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
species (psctb.analyse._symca._symca.Symca property)
species_dependent (psctb.analyse._symca._symca.Symca property)
species_independent (psctb.analyse._symca._symca.Symca property)
SPECIES_NODE (psctb.utils.model_graph._model_graph.ModelGraph attribute)
split_coefficient() (in module psctb.utils.misc._misc)
ss_species_list() (in module psctb.utils.misc._misc)
st_pt_keq_from_expression() (in module psctb.analyse._thermokin_file_tools)
straight_links (psctb.utils.model_graph._model_graph.ModelGraph property)
stringify() (in module psctb.utils.misc._misc)
strip_fixed() (in module psctb.modeltools._pscmanipulate)
subs_dict (psctb.latextools._expressions.LatexExpr property)
subs_fluxes (psctb.analyse._symca._symca.Symca property)
substitute_fluxes() (psctb.analyse._symca.symca_toolbox.SymcaToolBox static method)
Symca (class in psctb.analyse._symca._symca)
SymcaToolBox (class in psctb.analyse._symca.symca_toolbox)
T
term_to_file() (in module psctb.analyse._thermokin_file_tools)
ThermoKin (class in psctb.analyse._thermokin)
tk_subs (psctb.latextools._expressions.LatexExpr property)
toggle_category() (psctb.utils.plotting._plotting.ScanFig method)
toggle_line() (psctb.utils.plotting._plotting.ScanFig method)
U
unix_to_windows_path() (in module psctb.utils.misc._misc)
update() (psctb.utils.misc._misc.DotDict method)
(psctb.utils.misc._misc.PseudoDotDict method)
V
value (psctb.analyse._symca.ccobjects.CCBase property)
W
warn_user() (psctb.utils.config.ConfigChecker static method)
which() (psctb.utils.config.PathFinder static method)
width (psctb.utils.model_graph._model_graph.ModelGraph property)
write_config() (psctb.utils.config.ConfigWriter static method)
write_reqn_file() (in module psctb.analyse._thermokin_file_tools)
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