Commit 793d14fc authored by FAGES Francois's avatar FAGES Francois

desole bug introduit par le changement des options sur check_multistability avec A+B=>C

parent c1a10d14
# make jupyter will make biocham without checking unitary tests (avoiding potential problems of access to BioModels in sbml.plt)
ADDITIONAL_MODULES= \
modules/sbml/sbml_utils.pl \
modules/partialfrac/partialfraction.pl \
......
......@@ -425,7 +425,7 @@ add_edge_to_multistability_graph(VertexAId, VertexBId, Species_Sorted, Reactions
%%%%% Generate the influence graph with the reactions as labels
multistability_graph :-
biocham_command,
doc("Creates the influence graph of the current model as by \\command{influence_graph/1} but with the arcs labelled with the reactions they originate from. This is used for \\command{check_multistability/0}."),
doc("Creates the influence graph of the current model as by \\command{influence_graph/1} but with the arcs labelled with the reactions they originate from. This is used for command \\command{check_multistability/0}."),
option(force_graph, yesno, ForceMultistabilityGraph, 'Force the creation of the graph'),
all_items([kind: graph], AllGraphs),
(
......
......@@ -8,7 +8,7 @@
:- doc('
The existence of oscillations and multiple non-degenerate steady states in the differential dynamics of a reaction or influence model
can be checked very efficiently by checking \\emph{necessary conditions} for those properties
in the multistability graph of the model (see \\command{multistability_graph/0}), namely the existence of respectively negative and positive circuits in that graph \\cite{BFS18jtb}. Some refined tests are optional.
in the multistability graph of the model (see \\command{multistability_graph/0}), namely the existence of respectively negative and positive circuits in that graph \\cite{BFS18jtb}. Some more computationally expensive conditions are optional.
').
:- initial(option(test_permutations: no)).
......@@ -20,9 +20,9 @@ in the multistability graph of the model (see \\command{multistability_graph/0})
check_multistability :-
biocham_command,
doc('Checks the possibility of multistability in the continuous semantics of the current model by reducing the multistability graph and searching positive feedback loops which is a necessary condition for the existence of multiple non-degenerate (i.e. with no variable equal 0) steady states.'),
doc('Checks the possibility of multistability in the continuous semantics of the current model. This commands checks a necessary condition for the existence of multiple non-degenerate (i.e. with no variable equal to 0) steady states.'),
option(test_transpositions, yesno, _TestTranspo, 'Lazy test of all possible swappings between two species only'),
option(test_permutations, yesno, _TestSwaps, 'Lazy test of all possible permutations between species (This option highly increases computation time)'),
option(test_permutations, yesno, _TestSwaps, 'Lazy test of all possible permutations between species. This option may highly increase the computation time.'),
check_multistability_graph.
:- doc('\\begin{example}').
......
......@@ -3,7 +3,7 @@
[
% Commands
% check_directory/1,
check_oscilations/0
check_oscillations/0
% Public API
]
).
......@@ -16,7 +16,7 @@
create_associated_arcs_oscilations(InArcs, OutArcs) :-
create_associated_arcs_oscillations(InArcs, OutArcs) :-
forall(
member([VertexAId, VertexMid, SpeciesIn_Sorted, ReactionsIn_Sorted, SignIn],InArcs),
forall(
......@@ -110,7 +110,7 @@ remove_vertex(VertexId) :-
)
),
% create_associated_arcs(InArcs, OutArcs),
create_associated_arcs_oscilations(InArcs, OutArcs),
create_associated_arcs_oscillations(InArcs, OutArcs),
delete_vertex([VertexName]).
......@@ -133,9 +133,9 @@ check_acyclicity :-
multistability:get_number_of_nodes(N),
check_acyclicity(N).
check_oscilations :-
check_oscillations :-
biocham_command,
doc('Check the periodic behaviour of the current model'),
doc('Checks a necessary condition for the periodic behaviour of the current model.'),
multistability:multistability_graph,
get_time(Start_time),
(check_acyclicity
......@@ -176,7 +176,7 @@ check_directory(Path) :-
delete_file(FileToExport)
),
(
check_oscilations
check_oscillations
)
).
......@@ -186,6 +186,6 @@ check_directory(Path) :-
% load_reactions_from_ode("10.ode"),
% delete_file("10.ode"),
% reset_profiler,
% profile(check_oscilations, [cumulative(true)]),
% profile(check_oscillations, [cumulative(true)]),
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