-
Notifications
You must be signed in to change notification settings - Fork 0
/
ExprGenerator.py
executable file
·105 lines (89 loc) · 3.14 KB
/
ExprGenerator.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
import numpy as np
def gen_ame(s, k, m, i_rules, c_rules, states):
#s, k, m, i_rules, c_rules, states = ame_basis_tuple
assert(k >= 0)
assert(np.sum(m) == k)
assert(s.isalpha())
assert(states == sorted(states))
m_id = str(list(m)).replace(', ','_').replace('[', '_').replace(']', '')
line = 'dt_x["{s}_{k}_{m_id}"] = 0'.format(s=s, k=k, m_id=m_id)
for rule in i_rules:
consume, product, rate = rule
if product != s:
continue
line += '+({r}*x["{c}_{k}_{m_id}"])'.format(c=consume, r=rate, m_id=m_id, k=k)
for rule in i_rules:
consume, product, rate = rule
if consume != s:
continue
line += '-({r}*x["{s}_{k}_{m_id}"])'.format(s=s, r=rate, m_id=m_id, k=k)
for rule in c_rules:
consume1 = rule[0][0]
consume2 = rule[0][1]
product1 = rule[1][0]
product2 = rule[1][1]
rate = rule[2]
if product1 != s:
continue
m_rj2 = m[states.index(consume2)]
line += '+({r}*x["{c1}_{k}_{m_id}"]*{m_rj2})'.format(c1=consume1, r=rate, m_id=m_id, k=k, m_rj2=m_rj2)
for rule in c_rules:
consume1 = rule[0][0]
consume2 = rule[0][1]
product1 = rule[1][0]
product2 = rule[1][1]
rate = rule[2]
if consume1 != s:
continue
m_rj2 = m[states.index(consume2)]
line += '-({r}*x["{s}_{k}_{m_id}"]*{m_rj2})'.format(s=s, r=rate, m_id=m_id, k=k, m_rj2=m_rj2)
for s1 in states:
for s2 in states:
if s1 == s2:
continue
beta = 'beta_{s}_{s1}_to_{s}_{s2}'.format(s=s, s1=s1,s2=s2)
m_ngbr = list()
for i in range(len(m)):
if states[i] == s1:
m_ngbr.append(m[i]+1)
elif states[i] == s2:
m_ngbr.append(m[i]-1)
else:
m_ngbr.append(m[i])
m_ngbr_id = str(list(m_ngbr)).replace(', ','_').replace('[', '_').replace(']', '')
x_ngbr = 'x["{s}_{k}_{m_ngbr_id}"]'.format(s=s, k=k, m_ngbr_id = m_ngbr_id)
m_ngbr_s1 = m_ngbr[states.index(s1)]
x_ngbr = '0.0' if '-1' in x_ngbr else x_ngbr
line += '+({beta}*{x_ngbr}*{m_ngbr_s1})'.format(beta=beta, x_ngbr = x_ngbr, m_ngbr_s1 = m_ngbr_s1)
for s1 in states:
for s2 in states:
if s1 == s2:
continue
beta = 'beta_{s}_{s1}_to_{s}_{s2}'.format(s=s, s1=s1,s2=s2)
m_s1 = m[states.index(s1)]
#print(m, states, 's1', s1, 's1count', m_s1)
line += '-({beta}*x["{s}_{k}_{m_id}"]*{m_s1})'.format(beta=beta, s = s, k = k, m_id = m_id, m_s1 = m_s1)
#print(line)
return line
def gen_beta(states_tuple):
state, s1, s2 = states_tuple
beta = 'beta_{s}_{s1}_to_{s}_{s2} = 1.0/({edge_count})*({agg_rate})'
edge_count = "edges('{s}','{s1}')"
agg_rate = "rates('{s}','{s1}','{s2}')"
edge_count = edge_count.format(s=state, s1 = s1, s2 = s2)
agg_rate = agg_rate.format(s=state, s1 = s1, s2 = s2)
beta = beta.format(s=state, s1 = s1, s2 = s2, edge_count = edge_count, agg_rate = agg_rate)
return beta
def delte_unused_betas(odes, beta_exprs):
used_betas = list()
seperators = " ,;,+,-,=,),(,*,/,**".split(',')
for ode in odes:
ode_formula = ode[0]
for ch in seperators:
ode_formula = ode_formula.replace(ch, ' '+ch+' ')
tokens = ode_formula.split(' ')
tokens = [t.strip() for t in tokens if 'beta_' in t]
for t in tokens:
used_betas.append(t)
beta_exprs = [beta for beta in beta_exprs if beta.split('=')[0].strip() in used_betas]
return beta_exprs