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#2665, #2664, #2662 - SMILES/SMARTS reaction layout issues (#2666)
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@even1024
even1024 authored Dec 2, 2024
1 parent d62efc0 commit dfa8f2f
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Showing 15 changed files with 917 additions and 133 deletions.
4 changes: 4 additions & 0 deletions api/tests/integration/ref/formats/reactions_to_ket.py.out
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
*** SMARTS to KET ***
2662-arrow-size.ket:SUCCEED
2664-catalyst-margin.ket:SUCCEED
2665-incomplete-reaction.ket:SUCCEED
70 changes: 35 additions & 35 deletions api/tests/integration/ref/formats/rxn_no_layout.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -37,39 +37,39 @@
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Expand All @@ -80,12 +80,12 @@
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Expand Down Expand Up @@ -414,7 +414,7 @@
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Expand All @@ -428,7 +428,7 @@
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Expand All @@ -442,7 +442,7 @@
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Expand All @@ -451,7 +451,7 @@
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Expand All @@ -473,15 +473,15 @@
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Expand All @@ -503,87 +503,87 @@
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Expand Down Expand Up @@ -675,87 +675,87 @@
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55 changes: 55 additions & 0 deletions api/tests/integration/tests/formats/reactions_to_ket.py
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Original file line number Diff line number Diff line change
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import difflib
import os
import sys


def find_diff(a, b):
return "\n".join(difflib.unified_diff(a.splitlines(), b.splitlines()))


sys.path.append(
os.path.normpath(
os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
)
)
from env_indigo import * # noqa

indigo = Indigo()
indigo.setOption("json-saving-pretty", True)
indigo.setOption("ignore-stereochemistry-errors", True)

print("*** SMARTS to KET ***")

ref_path = joinPathPy("ref/", __file__)

tests = [
(
"[#6]1(-[#6])-[#6](-[#8])=[#6]-[#6](-[#16])=[#6](-[#7])-[#6]=1>>[#6]1(-Br)-[#6](-[#6])=[#6]-[#6](-I)=[#6](-[#8])-[#6]=1",
"2662-arrow-size",
),
("[#15]1-[#6]=[#6]-[#6]=[#6]-1>Br.Br>[#8]", "2664-catalyst-margin"),
("C1=OC=CC=C1>C1N=CC=C1>", "2665-incomplete-reaction"),
]

for test in tests:
try:
reaction = indigo.loadReaction(test[0])
except:
try:
reaction = indigo.loadQueryReaction(test[0])
except:
print("bad reaction data")

# with open(os.path.join(ref_path, test[1]) + ".ket", "w") as file:
# file.write(reaction.json())

with open(os.path.join(ref_path, test[1]) + ".ket", "r") as file:
ket_ref = file.read()

ket = reaction.json()
diff = find_diff(ket_ref, ket)
if not diff:
print(test[1] + ".ket:SUCCEED")
else:
print(test[1] + ".ket:FAILED")
print(diff)
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