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Backmerge: #2433 - Issues with Saving and Opening Structures with Mul…
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…ti-Tailed Arrow in CDX and CDXML Formats (#2521)
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@even1024
even1024 authored Oct 9, 2024
1 parent b36c635 commit c58e07c
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11 changes: 11 additions & 0 deletions api/tests/integration/ref/formats/rdf_to_cdxml.py.out
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*** RDF to CDXML ***
pathway1.cdxml:SUCCEED
pathway10.cdxml:SUCCEED
pathway2.cdxml:SUCCEED
pathway3.cdxml:SUCCEED
pathway4.cdxml:SUCCEED
pathway5.cdxml:SUCCEED
pathway6.cdxml:SUCCEED
pathway7.cdxml:SUCCEED
pathway8.cdxml:SUCCEED
pathway9.cdxml:SUCCEED
59 changes: 59 additions & 0 deletions api/tests/integration/tests/formats/rdf_to_cdxml.py
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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("ignore-stereochemistry-errors", True)

print("*** RDF to CDXML ***")

root = joinPathPy("reactions/rdf/", __file__)
ref_path = joinPathPy("ref/", __file__)

files = [
"pathway1",
"pathway2",
"pathway3",
"pathway4",
"pathway5",
"pathway6",
"pathway7",
"pathway8",
"pathway9",
"pathway10",
]

files.sort()
for filename in files:
try:
ket = indigo.loadReactionFromFile(
os.path.join(root, filename + ".rdf")
)
except IndigoException as e:
print(" %s" % (getIndigoExceptionText(e)))

cdxml_text = ket.cdxml()
# with open(os.path.join(ref_path, filename + ".cdxml"), "w") as file:
# file.write(cdxml_text)

with open(os.path.join(ref_path, filename) + ".cdxml", "r") as file:
cdxml_ref = file.read()

diff = find_diff(cdxml_ref, cdxml_text)
if not diff:
print(filename + ".cdxml:SUCCEED")
else:
print(filename + ".cdxml:FAILED")
print(diff)
155 changes: 155 additions & 0 deletions api/tests/integration/tests/formats/reactions/rdf/pathway1.rdf
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$RDFILE 1
$RFMT
$RXN

-INDIGO- 0808240900

2 1
$MOL

-INDIGO-08082409002D

6 6 0 0 0 0 0 0 0 0999 V2000
0.0560 -6.4789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7863 -6.4784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9228 -5.9788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7863 -7.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0560 -7.4839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9250 -7.9789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
4 2 2 0 0 0 0
2 3 1 0 0 0 0
M END
$MOL

-INDIGO-08082409002D

5 5 0 0 0 0 0 0 0 0999 V2000
6.2577 -6.2569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7581 -7.7970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0674 -6.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7574 -7.7970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4480 -6.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
5 4 2 0 0 0 0
4 2 1 0 0 0 0
2 3 2 0 0 0 0
3 1 1 0 0 0 0
M END
$MOL

-INDIGO-08082409002D

7 7 0 0 0 0 0 0 0 0999 V2000
12.1705 -6.6231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1705 -7.6231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.0365 -8.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.9026 -7.6231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.9026 -6.6231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.0365 -6.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7686 -6.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6 1 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
M END

$RFMT
$RXN

-INDIGO- 0809241137

3 1
$MOL

-INDIGO-08092411372D

7 7 0 0 0 0 0 0 0 0999 V2000
11.6489 -9.0554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.6489 -10.0554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5149 -10.5554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.3810 -10.0554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.3810 -9.0554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5149 -8.5554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.2470 -8.5554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6 1 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
M END
$MOL

-INDIGO-08092411372D

7 7 0 0 0 0 0 0 0 0999 V2000
19.5343 -8.8815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.0347 -10.4216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.3439 -9.4753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.0339 -10.4216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.7246 -9.4753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.5343 -7.8815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.5343 -7.8815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
5 4 2 0 0 0 0
4 2 1 0 0 0 0
2 3 2 0 0 0 0
3 1 1 0 0 0 0
1 6 2 0 0 0 0
6 7 1 0 0 0 0
M END
$MOL

-INDIGO-08092411372D

8 8 0 0 0 0 0 0 0 0999 V2000
5.9649 -9.1617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7488 -8.5442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7218 -8.7667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1559 -9.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9704 -10.1689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7225 -10.5696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7488 -10.7921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9990 -8.9029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
1 5 1 0 0 0 0
5 7 1 0 0 0 0
7 6 1 0 0 0 0
6 4 1 0 0 0 0
4 3 1 0 0 0 0
3 2 1 0 0 0 0
1 8 1 0 0 0 0
M END
$MOL

-INDIGO-08092411372D

9 9 0 0 0 0 0 0 0 0999 V2000
26.4095 -9.2478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.1398 -9.2473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.2763 -8.7477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.1398 -10.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4095 -10.2527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.2785 -10.7477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.5435 -10.7527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
26.5714 -11.4548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.8469 -10.9553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
4 2 2 0 0 0 0
2 3 1 0 0 0 0
5 7 1 0 0 0 0
6 8 2 0 0 0 0
4 9 1 0 0 0 0
M END

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