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Backmerge: #2433 - Issues with Saving and Opening Structures with Multi-Tailed Arrow in CDX and CDXML Formats #2521

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merged 5 commits into from
Oct 9, 2024
Merged

Backmerge: #2433 - Issues with Saving and Opening Structures with Multi-Tailed Arrow in CDX and CDXML Formats #2521

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fe0a3ee
cdxml fix
even1024 Oct 7, 2024
7bf41b1
cdxml fix
even1024 Oct 7, 2024
365ea29
cdxml fix
even1024 Oct 7, 2024
7726ea2
cdxml fix
even1024 Oct 8, 2024
8d24ad2
cdxml fix
even1024 Oct 8, 2024
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11 changes: 11 additions & 0 deletions api/tests/integration/ref/formats/rdf_to_cdxml.py.out
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
*** 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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Original file line number Diff line number Diff line change
@@ -0,0 +1,59 @@
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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Original file line number Diff line number Diff line change
@@ -0,0 +1,155 @@
$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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