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#2805 Saving of 3:3 reaction to SDF v2000 causes exception: Convert error! core: <reaction> is not a base molecule #2842

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merged 7 commits into from
Apr 11, 2025
Merged

#2805 Saving of 3:3 reaction to SDF v2000 causes exception: Convert error! core: <reaction> is not a base molecule #2842

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428a4f9
rdf to sdf
even1024 Apr 4, 2025
7b37a4d
rdf to sdf
even1024 Apr 4, 2025
f5eba56
rdf to sdf
even1024 Apr 8, 2025
d4074ba
tests
even1024 Apr 10, 2025
52622da
tests
even1024 Apr 10, 2025
c3daf07
tests
even1024 Apr 10, 2025
9a13f71
tests
even1024 Apr 10, 2025
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5 changes: 5 additions & 0 deletions api/tests/integration/ref/formats/ket_to_sdf.py.out
View file
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Original file line number Diff line number Diff line change
@@ -1,2 +1,7 @@
*** KET to SDF ***
acd2d_err3.sdf:SUCCEED
multi.sdf:SUCCEED
pathway1.sdf:SUCCEED
pathway2.sdf:SUCCEED
pathway3.sdf:SUCCEED
qreaction.sdf:SUCCEED
14 changes: 14 additions & 0 deletions api/tests/integration/ref/formats/reactions_to_cdxml.py.out
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
*** KET to CDXML ***
multi.cdxml:SUCCEED
pathway1.cdxml:SUCCEED
pathway10.cdxml:SUCCEED
pathway11.cdxml:SUCCEED
pathway12.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
37 changes: 37 additions & 0 deletions api/tests/integration/tests/formats/ket_to_sdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,3 +57,40 @@ def find_diff(a, b):
else:
print(filename + ".sdf:FAILED")
print(diff)

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

files = ["pathway1", "pathway2", "pathway3", "multi", "qreaction"]

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

buffer = indigo.writeBuffer()
sdfSaver = indigo.createSaver(buffer, "sdf")
for mol in ket.iterateMolecules():
sdfSaver.append(mol.clone())
sdfSaver.close()
sdf = buffer.toString()
# with open(os.path.join(ref_path, filename) + ".sdf", "w") as file:
# file.write(sdf)

with open(os.path.join(ref_path, filename) + ".sdf", "r") as file:
sdf_ref = file.read()
diff = find_diff(sdf_ref, sdf)
if not diff:
print(filename + ".sdf:SUCCEED")
else:
print(filename + ".sdf:FAILED")
print(diff)
200 changes: 200 additions & 0 deletions api/tests/integration/tests/formats/reactions/qreaction.ket
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Original file line number Diff line number Diff line change
@@ -0,0 +1,200 @@
{
"root": {
"nodes": [
{
"$ref": "mol0"
},
{
"$ref": "mol1"
},
{
"type": "arrow",
"data": {
"mode": "open-angle",
"pos": [
{
"x": 13.15,
"y": -8.3,
"z": 0
},
{
"x": 15.725121356363621,
"y": -8.3,
"z": 0
}
]
}
}
],
"connections": [],
"templates": []
},
"mol0": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [
12.08220745473898,
-8.79754874346472,
0
]
},
{
"label": "C",
"location": [
12.078504114664911,
-7.8024512565352815,
0
]
},
{
"label": "C",
"location": [
11.070294802067824,
-8.784637098341616,
0
]
},
{
"label": "A",
"location": [
11.067792545261023,
-7.8024512565352815,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
0,
1
]
},
{
"type": 1,
"atoms": [
1,
3
]
},
{
"type": 1,
"atoms": [
3,
2
]
},
{
"type": 1,
"atoms": [
2,
0
]
}
]
},
"mol1": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [
16.758987298340656,
-7.82499266647844,
0
]
},
{
"label": "C",
"location": [
16.758987298340656,
-8.825007333521562,
0
]
},
{
"label": "A",
"location": [
17.625,
-9.325014667043124,
0
]
},
{
"label": "C",
"location": [
18.491012701659344,
-8.825007333521562,
0
]
},
{
"label": "C",
"location": [
18.491012701659344,
-7.82499266647844,
0
]
},
{
"type": "atom-list",
"elements": [
"C"
],
"notList": true,
"location": [
17.625,
-7.324985332956879,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
5,
0
]
},
{
"type": 1,
"atoms": [
0,
1
]
},
{
"type": 1,
"atoms": [
1,
2
]
},
{
"type": 1,
"atoms": [
2,
3
]
},
{
"type": 1,
"atoms": [
3,
4
]
},
{
"type": 1,
"atoms": [
4,
5
]
}
]
}
}
11 changes: 6 additions & 5 deletions ...integration/tests/formats/rdf_to_cdxml.py → ...ation/tests/formats/reactions_to_cdxml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@ def find_diff(a, b):
indigo = Indigo()
indigo.setOption("ignore-stereochemistry-errors", True)

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

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

files = [
Expand All @@ -35,20 +35,21 @@ def find_diff(a, b):
"pathway10",
"pathway11",
"pathway12",
"multi",
]

files.sort()
for filename in files:
try:
ket = indigo.loadReactionFromFile(
os.path.join(root, filename + ".rdf")
os.path.join(root, filename + ".ket")
)
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"), "w") as file:
file.write(cdxml_text)

with open(os.path.join(ref_path, filename) + ".cdxml", "r") as file:
cdxml_ref = file.read()
Expand Down
93 changes: 93 additions & 0 deletions api/tests/integration/tests/formats/ref/multi.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,93 @@

-INDIGO-01000000002D

4 4 0 0 0 0 0 0 0 0999 V2000
3.5322 -4.1225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5285 -3.1275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5203 -4.1096 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5178 -3.1275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 4 1 0 0 0 0
3 4 1 0 0 0 0
M END
$$$$

-INDIGO-01000000002D

3 3 0 0 0 0 0 0 0 0999 V2000
5.2744 -4.0825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2756 -4.0825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7751 -3.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 3 1 0 0 0 0
M END
$$$$

-INDIGO-01000000002D

3 2 0 0 0 0 0 0 0 0999 V2000
0.4000 -2.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1000 -3.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4000 -4.4321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
$$$$

-INDIGO-01000000002D

7 7 0 0 0 0 0 0 0 0999 V2000
10.8545 -3.1186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.6384 -2.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.6114 -2.7236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.0455 -3.6194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8600 -4.1258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.6121 -4.5264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.6384 -4.7490 0.0000 C 0 0 0 0 0 0 0 0 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 6 1 0 0 0 0
1 5 1 0 0 0 0
5 7 1 0 0 0 0
6 7 1 0 0 0 0
M END
$$$$

-INDIGO-01000000002D

6 6 0 0 0 0 0 0 0 0999 V2000
15.5090 -2.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.5090 -3.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.3750 -4.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.2410 -3.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.2410 -2.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.3750 -2.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 6 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
M END
$$$$

-INDIGO-01000000002D

6 6 0 0 0 0 0 0 0 0999 V2000
22.5598 -3.0501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
24.2902 -3.0496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.4266 -2.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
24.2902 -4.0505 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.5598 -4.0550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.4288 -4.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
4 2 2 0 0 0 0
1 5 1 0 0 0 0
2 3 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
M END
$$$$
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