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michaelAddition.py
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include("common.py")
def gen_michael_addition(inverse=False):
rules = []
# The reaction is supposed to go S1 + S2 <=> P
# define substrates as
substrate_1 = [
[
'node [ id 1 label "C" ]',
'node [ id 2 label "C" ]',
'node [ id 3 label "C" ]',
'node [ id 4 label "O" ]',
'edge [ source 2 target 3 label "-" ]',
'edge [ source 3 target 4 label "=" ]'
],
[
'node [ id 1 label "C" ]',
'node [ id 2 label "C" ]',
'node [ id 3 label "C" ]',
'node [ id 4 label "O" ]',
'edge [ source 2 target 3 label "-" ]',
'edge [ source 3 target 4 label "=" ]'
],
[
'node [ id 1 label "C" ]',
'node [ id 2 label "C" ]',
'node [ id 3 label "C" ]',
'node [ id 4 label "N" ]',
'edge [ source 2 target 3 label "-" ]',
'edge [ source 3 target 4 label "#" ]'
],
[
'node [ id 1 label "C" ]',
'node [ id 2 label "C" ]',
'node [ id 3 label "C" ]',
'node [ id 4 label "N" ]',
'edge [ source 2 target 3 label "-" ]',
'edge [ source 3 target 4 label "#" ]'
]
]
substrate_2 = [
[
'node [ id 11 label "H" ]',
'node [ id 12 label "N" ]',
'node [ id 13 label "*" ]',
'node [ id 14 label "*" ]',
'edge [ source 12 target 13 label "-" ]',
'edge [ source 12 target 14 label "-" ]'
],
[
'node [ id 11 label "H" ]',
'node [ id 12 label "S" ]',
'node [ id 13 label "*" ]',
'edge [ source 12 target 13 label "-" ]'
],
[
'node [ id 11 label "H" ]',
'node [ id 12 label "C" ]',
'node [ id 13 label "*" ]',
'node [ id 14 label "*" ]',
'edge [ source 12 target 13 label "-" ]',
'edge [ source 12 target 14 label "-" ]'
]
]
for s1 in range(len(substrate_1)):
for s2 in range(len(substrate_2)):
if s1 % 2 == 1 and inverse == True: # breaking of C#C should be irreversible
break
rule = RuleGen(f"Michael Addition {s1},{s2}, {'(reverse)' if inverse==True else ''}")
rule.context.extend(substrate_1[s1])
rule.context.extend(substrate_2[s2])
if inverse == False:
rule.left.extend([
'edge [ source 11 target 12 label "-" ]'
])
# well in the substrate_1 list, item 1 has C=C, 2 has C#C, 3 has C=C and 4 again has C#C
# so i need to treat them differently
if s1 % 2 == 0: # these have C=C
rule.left.append('edge [ source 1 target 2 label "=" ]') # break the C=C
rule.right.append('edge [ source 1 target 2 label "-" ]') # form C-C
else:
rule.left.append('edge [ source 1 target 2 label "#" ]') # break C#C
rule.right.append('edge [ source 1 target 2 label "=" ]')
rule.right.extend([
'edge [ source 12 target 1 label "-" ]', # addition
'edge [ source 11 target 2 label "-" ]' # connect the hydrogen
])
else:
rule.right.extend([
'edge [ source 11 target 12 label "-" ]'
])
# well in the substrate_1 list, item 1 has C=C, 2 has C#C, 3 has C=C and 4 again has C#C
# so i need to treat them differently
if s1 % 2 == 0: # these have C=C
rule.left.append('edge [ source 1 target 2 label "-" ]')
rule.right.append('edge [ source 1 target 2 label "=" ]')
else:
rule.left.append('edge [ source 1 target 2 label "=" ]')
rule.right.append('edge [ source 1 target 2 label "#" ]')
rule.left.extend([
'edge [ source 12 target 1 label "-" ]',
'edge [ source 11 target 2 label "-" ]'
])
# Add constraints
if s1 % 2 == 0: # if there's a C=C formation involved, don't invert if enols are a possibility
rule.constraints.extend([
'constrainAdj [',
'\tid 1 op "=" count 0',
'\tnodeLabels [ label "O" ]',
'\tedgeLabels [ label "-" ]',
']',
'constrainAdj [',
'\tid 2 op "=" count 0',
'\tnodeLabels [ label "O" ]',
'\tedgeLabels [ label "-" ]',
']'
])
if s2 == 0:
rule.constraints.extend([
'constrainAdj [',
'\tid 1 op "=" count 0', # avoid forming diamine or aminols
'\tnodeLabels [ label "O" label "N" ]',
'\tedgeLabels [ label "-" ]',
']',
'constrainAdj [',
'\tid 13 op "=" count 0',
'\tnodeLabels [ label "O" ]',
'\tedgeLabels [ label "=" ]',
']',
'constrainAdj [',
'\tid 14 op "=" count 0',
'\tnodeLabels [ label "O" ]',
'\tedgeLabels [ label "=" ]',
']',
'constrainAdj [',
'\tid 12 op "=" count 0',
'\tnodeLabels [ label "O" label "N" label "S" ]',
'\tedgeLabels [ label "-" ]',
']'
])
elif s2 == 1:
rule.constraints.extend([
'constrainAdj [',
'\tid 13 op "=" count 0',
'\tnodeLabels [ label "O" ]',
'\tedgeLabels [ label "=" ]',
']',
])
elif s2 == 2:
rule.constraints.extend([
'constrainAdj [',
'\tid 13 op "=" count 0',
'\tnodeLabels [ label "O" label "N" ]',
'\tedgeLabels [ label "=" label "#" ]',
']',
])
rules.append(rule)
return [r.loadRule() for r in rules]
michael_addition = gen_michael_addition()
michael_addition_inv = gen_michael_addition(inverse=True)
'''def michaelAddition34Gen():
r = RuleGen("Michael Addition ")
r.left.extend([
'# RC=C-',
'edge [ source 1 target 3 label "=" ]',
])
r.context.extend([
'# RC=C-',
'node [ id 0 label "H" ]',
'node [ id 1 label "C" ]',
'node [ id 3 label "C" ]',
'node [ id 4 label "H" ]',
'node [ id 5 label "C" ]',
'edge [ source 0 target 1 label "-" ]',
'edge [ source 3 target 4 label "-" ]',
'edge [ source 3 target 5 label "-" ]',
])
r.right.extend([
'# RC=C-',
'edge [ source 1 target 3 label "-" ]',
])
rBase = r
for i in range(1, 5):
rNum = rBase.clone()
rNum.name += " %d" % i
for r in attach_H_C(rNum, 1, 2):
if i == 1 or i == 3:
r.context.extend([
'node [ id 6 label "O" ]',
'edge [ source 5 target 6 label "=" ]'
])
elif i == 2 or i == 4:
r.context.extend([
'node [ id 6 label "N" ]',
'edge [ source 5 target 6 label "#" ]'
])
else: assert False
if i < 3:
r.left.extend([
'# Nu',
'edge [ source 100 target 200 label "-" ]',
])
r.context.extend([
'# Nu',
'node [ id 100 label "H" ]',
])
r.right.extend([
'# Nu',
'edge [ source 1 target 200 label "-" ]',
'edge [ source 3 target 100 label "-" ]',
])
for r in attach_Nu(r, 200):
yield r.loadRule()
else:
r.left.extend([
'# -EWG',
'edge [ source 102 target 103 label "-" ]',
])
r.context.extend([
'# -EWG',
'node [ id 100 label "O" ]',
'node [ id 101 label "C" ]',
'node [ id 102 label "C" ]',
'node [ id 103 label "H" ]',
'edge [ source 100 target 101 label "=" ]',
'edge [ source 101 target 102 label "-" ]',
])
r.right.extend([
'edge [ source 1 target 102 label "-" ]',
'edge [ source 3 target 103 label "-" ]',
])
for r in attach_H_C(r, 102, 104):
for r in attach_EWG(r, 102, 200):
yield r.loadRule()
michaelAddition34 = [a for a in michaelAddition34Gen()]'''