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biocham
Commits
e47e8ae3
Commit
e47e8ae3
authored
Oct 16, 2015
by
Thierry Martinez
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Merge branch 'master' of
git+ssh://scm.gforge.inria.fr/gitroot/biocham/biocham
parents
6df70cc5
30a0329e
Changes
5
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5 changed files
with
159 additions
and
30 deletions
+159
-30
conservation_laws.pl
conservation_laws.pl
+90
-13
conservation_laws.plt
conservation_laws.plt
+43
-15
kinetics.pl
kinetics.pl
+3
-1
ode.pl
ode.pl
+1
-1
simplify_arithmetic.pl
simplify_arithmetic.pl
+22
-0
No files found.
conservation_laws.pl
View file @
e47e8ae3
...
...
@@ -25,31 +25,31 @@ add_conservation(Conservation) :-
caption might not be correct.'
),
doc
(
'When added, the conservation law will be checked against the r
ules (i.e.
purely from stoichiometry), if that fails against the kinetics. Since
these checks are not complete, even a failure will be accepted with a
warning.'
'When added, the conservation law will be checked against the r
eactions
(i.e. purely from stoichiometry), if that fails against the kinetics.
Since these checks are not complete, even a failure will be accepted with
a
warning.'
),
solution_to_list
(
Conservation
,
C
),
add_item
(
conservation
,
C
).
solution_to_conservation
(
Conservation
,
C
),
add_item
(
conservation
,
[],
Conservation
,
Id
),
set_annotation
(
Id
,
conservation_list
,
C
).
delete_conservation
(
Conservation
)
:-
biocham_command
,
type
(
Conservation
,
solution
),
doc
(
'removes the given mass conservation law.'
),
solution_to_list
(
Conservation
,
C
),
find_item
([
model
:
current_model
,
id
:
Id
,
type
:
conservation
,
item
:
C
]),
find_item
(
[
model
:
current_model
,
id
:
Id
,
type
:
conservation
,
item
:
Conservation
]),
delete_item
(
Id
).
delete_conservations
:-
biocham_command
,
doc
(
'removes all mass conservation laws.'
),
\
+
(
forall
(
item
([
model
:
current_model
,
kind
:
conservation
,
id
:
Id
]),
delete_item
(
Id
),
fail
delete_item
(
Id
)
).
...
...
@@ -62,10 +62,17 @@ list_conservations :-
check_conservations
:-
biocham_command
,
doc
(
'checks all conservation laws against r
ule
s, and if necessary kinetics
'checks all conservation laws against r
eaction
s, and if necessary kinetics
(see also \\command{add_conservation/1}).'
),
true
.
compute_ode
,
forall
(
(
item
([
model
:
current_model
,
kind
:
conservation
,
id
:
Id
]),
get_annotation
(
Id
,
conservation_list
,
C
)
),
check_conservation
(
C
)
).
search_conservations
:-
...
...
@@ -85,4 +92,74 @@ search_conservations(Integer) :-
true
.
%%% End of public API
solution_to_conservation
(
Solution
,
Conservation
)
:-
devdoc
(
'transforms a solution to a factorized list of coeff*object'
),
reaction_editor
:
solution_to_list
(
Solution
,
List
),
reaction_editor
:
simplify_solution
(
List
,
Conservation
).
check_conservation
(
C
)
:-
(
check_conserv_reactions
(
C
)
->
message
(
'~w checked from reactions'
,
[
C
])
;
message
(
'~w not checked from reactions'
,
[
C
]),
check_conserv_num
(
C
)
->
message
(
'~w checked from kinetics'
,
[
C
])
;
message
(
'~w not checked from kinetics either, but trusted anyway'
,
[
C
]),
throw
(
error
(
unchecked_conservation_law
(
C
)))
).
check_conserv_reactions
(
C
)
:-
forall
(
(
item
([
model
:
current_model
,
kind
:
reaction
,
item
:
Item
]),
reaction
(
Item
,
_Kinetics
,
Reactants
,
Products
)
),
(
scalar_conservation
(
Reactants
,
C
,
Moiety
),
scalar_conservation
(
Products
,
C
,
Moiety
)
)
).
check_conserv_num
(
C
)
:-
get_weighted_ode
(
C
,
WeightedSum
),
simplify
(
WeightedSum
,
Sum
),
write
(
Sum
),
nl
,
Sum
==
0
.
get_weighted_ode
([],
0
).
get_weighted_ode
([
K
*
M
|
L
],
K
*
O
+
S
)
:-
ode
(
M
,
O
),
get_weighted_ode
(
L
,
S
).
scalar_conservation
([],
_
,
0
).
scalar_conservation
([
K
*
M
|
L
],
C
,
Total
)
:-
(
member
(
I
*
M
,
C
)
->
true
;
I
=
0
),
scalar_conservation
(
L
,
C
,
T1
),
Total
is
I
*
K
+
T1
.
message
(
M
,
O
)
:-
format
(
M
,
O
),
nl
.
% vi: set ts=2 sts=2 sw=2
conservation_laws.plt
View file @
e47e8ae3
...
...
@@ -9,10 +9,11 @@ test(
[
setup(models:clear_model),
cleanup(models:clear_model),
true(Conservations == [[1*'a-a', 2*'a']])
forall(member(Input, ['a-a' + 2*'a', 'b', 'a' + 'b'])),
true(Conservations == [Input])
]
) :-
command(add_conservation(
a-a + 2*a
)),
command(add_conservation(
Input
)),
all_items([model: current_model, kind: conservation], Conservations).
%%% FIXME should test that conservations are properly used for numerical
...
...
@@ -21,9 +22,9 @@ test(
test(
'delete_conservation deletes the correct conservation',
[
setup(
(models:clear_model, add_some_conservations)
),
setup(
set_some_conservations
),
cleanup(models:clear_model),
true(Conservations == [
[1*'a-a', 2*'a'], [1*'c-c', 2*'c']])
true(Conservations == [
'a-a'+2*a,'c-c'+2*c])
]
) :-
command(delete_conservation(b-b + 2*b)),
...
...
@@ -33,7 +34,7 @@ test(
test(
'delete_conservations deletes all conservations',
[
setup(
(models:clear_model, add_some_conservations)
),
setup(
set_some_conservations
),
cleanup(models:clear_model),
true(Conservations == [])
]
...
...
@@ -42,18 +43,44 @@ test(
all_items([model: current_model, kind: conservation], Conservations).
test(
'list_conservations lists all conservations',
[
setup(set_some_conservations),
cleanup(models:clear_model),
true(Conservations ==
'[0] a-a+2*a\n[1] b-b+2*b\n[2] c-c+2*c\n')
]
) :-
with_output_to(atom(Conservations), command(list_conservations)).
test(
'check_conservations is ok with trivial P-invariants',
[
setup(models:clear_model),
cleanup(models:clear_model),
blocked(not_implemented)
cleanup(models:clear_model)
]
) :-
% not written 'a => b' to allow flycheck by separate compilation…
command(add_reaction('=>'(a, b))),
command(add_reaction('=>'(b, a))),
command(add_conservation(a + b)),
command(check_conservations).
with_output_to(atom(_), command(check_conservations)).
test(
'check_conservations is ok with kinetically conserved moieties',
[
setup(models:clear_model),
cleanup(models:clear_model)
]
) :-
% writing with 'command' produces a parsing error on k…
add_reaction('for'(k*[a], '=>'(a, b))),
add_reaction('for'(k*[a], '=>'(a, 2*a))),
command(add_conservation(a)),
with_output_to(atom(_), command(check_conservations)).
test(
...
...
@@ -61,20 +88,21 @@ test(
[
setup(models:clear_model),
cleanup(models:clear_model),
error(unproven_conservation_law([1*'a', 2*'b'])),
fixme(not_implemented)
throws(error(unchecked_conservation_law([1*'a', 2*'b'])))
]
) :-
% not written 'a => b' to allow flycheck by separate compilation…
command(add_reaction('=>'(2*a, b))),
command(add_reaction('=>'(a, b))),
command(add_conservation(a + 2*b)),
command(check_conservations
).
with_output_to(atom(_), command(check_conservations)
).
add_some_conservations :-
command(add_conservation(a-a + 2*a)),
command(add_conservation(b-b + 2*b)),
command(add_conservation(c-c + 2*c)).
set_some_conservations :-
models:clear_model,
command(add_conservation(a-a + 2*a)),
command(add_conservation(b-b + 2*b)),
command(add_conservation(c-c + 2*c)).
:- end_tests(conservation_laws).
...
...
kinetics.pl
View file @
e47e8ae3
...
...
@@ -10,6 +10,8 @@ kinetics(Kinetics, Reactants, Expression) :-
Kinetics
=
'MA'
(
Coefficient
)
->
mass_action
(
Coefficient
,
Reactants
,
Expression
)
;
Expression
=
Kinetics
).
...
...
@@ -21,5 +23,5 @@ mass_action(Coefficient, Reactants, Expression) :-
concentration_product
([],
1
).
concentration_product
([
Coefficient
*
Reactant
|
Reactants
],
Product
)
:-
Product
=
Coefficient
*
[
Reactant
]
*
ProductTail
,
Product
=
[
Reactant
]
^
Coefficient
*
ProductTail
,
concentration_product
(
Reactants
,
ProductTail
).
ode.pl
View file @
e47e8ae3
...
...
@@ -58,7 +58,7 @@ add_molecule(Coefficient * Molecule, Kinetics) :-
;
Expression
=
0
),
asserta
(
ode
(
Molecule
,
Expression
+
Kinetics
/
Coefficient
)).
asserta
(
ode
(
Molecule
,
Expression
+
Coefficient
*
Kinetics
)).
print_ode
:-
...
...
simplify_arithmetic.pl
View file @
e47e8ae3
...
...
@@ -118,6 +118,17 @@ simplify_addition(A, Value * B, Result) :-
ValueOpp
is
-
Value
,
Result
=
A
-
ValueOpp
*
B
.
simplify_addition
(
-
A
,
B
,
C
)
:-
!,
simplify_difference
(
B
,
A
,
C
).
simplify_addition
(
A
,
-
B
,
C
)
:-
!,
simplify_difference
(
A
,
B
,
C
).
simplify_addition
(
A
,
A
,
2
*
A
)
:-
!.
simplify_addition
(
A
,
B
,
A
+
B
).
...
...
@@ -148,6 +159,17 @@ simplify_difference(A, Value * B, Result) :-
ValueOpp
is
-
Value
,
Result
=
A
+
ValueOpp
*
B
.
simplify_difference
(
A
,
A
,
0
)
:-
!.
simplify_difference
(
A
,
-
B
,
C
)
:-
!,
simplify_addition
(
A
,
B
,
C
).
simplify_difference
(
-
A
,
B
,
-
C
)
:-
!,
simplify_addition
(
A
,
B
,
C
).
simplify_difference
(
A
,
B
,
A
-
B
).
...
...
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