file with .sdf of MOFs failed to calculate fingerprint and descriptors by Padelpy (verasion 0.1.11)

[shenglisa]

[shenglisa]

excuesme, recently i have calculated the fingerprints and descriptors of MOFs by Padelpy (verasion 0.1.11), but it occured errors , as shown below(Traceback (most recent call last):
File "test.py", line 57, in
padeldescriptor(mol_dir = path, d_file = output_name, fingerprints=True, retainorder=True, detectaromaticity=False, threads=4)
File "/home/lisa/.local/lib/python3.8/site-packages/padelpy/wrapper.py", line 157, in padeldescriptor
raise RuntimeError('PaDEL-Descriptor encountered an error: {}'.format(
RuntimeError: PaDEL-Descriptor encountered an error: 7月 16, 2022 1:56:08 下午 libpadeldescriptor.CDK_Fingerprint run
严重: Fingerprinter error
org.openscience.cdk.exception.CDKException: org.openscience.cdk.exception.CDKException: Timeout for AllringsFinder exceeded
at org.openscience.cdk.smiles.smarts.SMARTSQueryTool.initializeMolecule(SMARTSQueryTool.java:363)
at org.openscience.cdk.smiles.smarts.SMARTSQueryTool.matches(SMARTSQueryTool.java:214)
at org.openscience.cdk.smiles.smarts.SMARTSQueryTool.matches(SMARTSQueryTool.java:189)
at org.openscience.cdk.fingerprint.PubchemFingerprinter$CountSubstructures.countSubstructure(PubchemFingerprinter.java:312)
at org.openscience.cdk.fingerprint.PubchemFingerprinter.countSubstructures(PubchemFingerprinter.java:1099)
at org.openscience.cdk.fingerprint.PubchemFingerprinter._generateFp(PubchemFingerprinter.java:323)
at org.openscience.cdk.fingerprint.PubchemFingerprinter.generateFp(PubchemFingerprinter.java:330)
at org.openscience.cdk.fingerprint.PubchemFingerprinter.getFingerprint(PubchemFingerprinter.java:122)
at libpadeldescriptor.CDK_Fingerprint.run(Unknown Source)
at libpadeldescriptor.libPaDELDescriptorWorker.DoJob(Unknown Source)
at libpadeljobs.Worker.run(Worker.java:46)
Caused by: org.openscience.cdk.exception.CDKException: Timeout for AllringsFinder exceeded
at org.openscience.cdk.ringsearch.AllRingsFinder.checkTimeout(AllRingsFinder.java:414)
at org.openscience.cdk.ringsearch.AllRingsFinder.remove(AllRingsFinder.java:275)
at org.openscience.cdk.ringsearch.AllRingsFinder.doSearch(AllRingsFinder.java:202)
at org.openscience.cdk.ringsearch.AllRingsFinder.findAllRingsInIsolatedRingSystem(AllRingsFinder.java:174)
at org.openscience.cdk.ringsearch.AllRingsFinder.findAllRings(AllRingsFinder.java:136)
at org.openscience.cdk.ringsearch.AllRingsFinder.findAllRings(AllRingsFinder.java:117)
at org.openscience.cdk.smiles.smarts.SMARTSQueryTool.initializeMolecule(SMARTSQueryTool.java:360)
... 10 more)

Below is the SDF file of MOF, could u tell me why?

ABEXOW_clean
OpenBabel07132219403D

144158 0 0 1 0 0 0 0 0999 V2000
9.5087 7.9092 12.6259 Pr 0 0 0 0 0 0 0 0 0 0 0 0
4.2081 5.7270 16.7951 Pr 0 0 0 0 0 0 0 0 0 0 0 0
1.4993 4.0928 2.8894 Pr 0 0 0 0 0 0 0 0 0 0 0 0
6.7999 6.2750 7.0586 Pr 0 0 0 0 0 0 0 0 0 0 0 0
7.0033 1.9082 12.6259 Pr 0 0 0 0 0 0 0 0 0 0 0 0
1.2959 11.7280 16.7951 Pr 0 0 2 0 0 0 0 0 0 0 0 0
4.0047 10.0938 2.8894 Pr 0 0 0 0 0 0 0 0 0 0 0 0
9.7121 0.2740 7.0586 Pr 0 0 2 0 0 0 0 0 0 0 0 0
7.1673 6.0970 14.7333 H 0 0 0 0 0 0 0 0 0 0 0 0
8.4618 9.1287 17.8353 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4266 7.2204 14.7936 H 0 0 0 0 0 0 0 0 0 0 0 0
10.9420 2.9381 14.5755 H 0 0 0 0 0 15 0 0 0 0 0 0
3.8407 5.9050 4.9968 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5462 2.8733 8.0988 H 0 0 0 0 0 0 0 0 0 0 0 0
9.5814 4.7816 5.0571 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0660 9.0639 4.8390 H 0 0 0 0 0 15 0 0 0 0 0 0
9.3447 0.0960 14.7333 H 0 0 0 0 0 0 0 0 0 0 0 0
8.0502 3.1277 17.8353 H 0 0 0 0 0 0 0 0 0 0 0 0
4.0774 1.2194 14.7936 H 0 0 0 0 0 0 0 0 0 0 0 0
5.5700 8.9391 14.5755 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6633 11.9060 4.9968 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9578 8.8743 8.0988 H 0 0 0 0 0 0 0 0 0 0 0 0
6.9306 10.7826 5.0571 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4380 3.0629 4.8390 H 0 0 0 0 0 0 0 0 0 0 0 0
7.4040 6.7547 15.3467 C 0 0 0 0 0 3 0 0 0 0 0 0
7.0044 7.8061 17.3271 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1734 8.5406 17.1752 C 0 0 0 0 0 0 0 0 0 0 0 0
8.8879 8.3690 16.0185 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0591 9.2595 15.6621 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0896 8.0329 18.5110 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1195 6.3431 14.7644 C 0 0 0 0 0 3 0 0 0 0 0 0
1.3881 4.1563 15.3291 C 0 0 1 0 0 3 0 0 0 0 0 0
0.2290 3.8178 14.6417 C 0 0 0 0 0 1 0 0 0 0 0 0
10.5545 4.8632 14.0692 C 0 0 0 0 0 3 0 0 0 0 0 0
9.2401 4.6268 13.3293 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2390 3.0833 16.0107 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5479 4.6028 0.3466 C 0 0 0 0 0 1 0 0 0 0 0 0
2.2027 5.2269 19.3523 C 0 0 0 0 0 1 0 0 0 0 0 0
3.6040 5.2473 5.6102 C 0 0 0 0 0 3 0 0 0 0 0 0
4.0036 4.1959 7.5906 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8346 3.4614 7.4387 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1201 3.6330 6.2820 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9489 2.7425 5.9256 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9184 3.9691 8.7745 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8885 5.6589 5.0279 C 0 0 0 0 0 3 0 0 0 0 0 0
9.6199 7.8457 5.5926 C 0 0 1 0 0 3 0 0 0 0 0 0
10.7790 8.1842 4.9052 C 0 0 0 0 0 1 0 0 0 0 0 0
0.4535 7.1388 4.3327 C 0 0 0 0 0 3 0 0 0 0 0 0
1.7679 7.3752 3.5928 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7690 8.9187 6.2742 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4601 7.3992 10.0831 C 0 0 0 0 0 0 0 0 0 0 0 0
8.8053 6.7751 9.6158 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1080 0.7537 15.3467 C 0 0 0 0 0 3 0 0 0 0 0 0
9.5076 1.8051 17.3271 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3386 2.5396 17.1752 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6241 2.3680 16.0185 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4529 3.2585 15.6621 C 0 0 2 0 0 3 0 0 0 0 0 0
10.4224 2.0319 18.5110 C 0 0 0 0 0 3 0 0 0 0 0 0
4.3845 0.3421 14.7644 C 0 0 0 0 0 3 0 0 0 0 0 0
4.1159 10.1573 15.3291 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2750 9.8188 14.6417 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9575 10.8642 14.0692 C 0 0 0 0 0 3 0 0 0 0 0 0
7.2719 10.6278 13.3293 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2650 9.0843 16.0107 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9561 10.6038 0.3466 C 0 0 0 0 0 1 0 0 0 0 0 0
3.3013 11.2279 19.3523 C 0 0 0 0 0 1 0 0 0 0 0 0
1.9000 11.2483 5.6102 C 0 0 0 0 0 3 0 0 0 0 0 0
1.5004 10.1969 7.5906 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6694 9.4624 7.4387 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3839 9.6340 6.2820 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5551 8.7435 5.9256 C 0 0 2 0 0 3 0 0 0 0 0 0
0.5856 9.9701 8.7745 C 0 0 0 0 0 3 0 0 0 0 0 0
6.6235 11.6599 5.0279 C 0 0 0 0 0 3 0 0 0 0 0 0
6.8921 1.8447 5.5926 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7330 2.1832 4.9052 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0505 1.1378 4.3327 C 0 0 0 0 0 3 0 0 0 0 0 0
3.7361 1.3742 3.5928 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7430 2.9177 6.2742 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0519 1.3982 10.0831 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7067 0.7741 9.6158 C 0 0 0 0 0 0 0 0 0 0 0 0
8.5048 7.4712 15.0896 N 0 0 0 0 0 0 0 0 0 0 0 0
6.6180 6.9120 16.4138 N 0 0 0 0 0 0 0 0 0 0 0 0
11.0036 6.1138 14.0809 N 0 0 0 0 0 1 0 0 0 0 0 0
1.8350 5.4309 15.4070 N 0 0 0 0 0 0 0 0 0 0 0 0
2.5032 4.5308 5.3531 N 0 0 0 0 0 0 0 0 0 0 0 0
4.3900 5.0900 6.6773 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0044 5.8882 4.3444 N 0 0 0 0 0 1 0 0 0 0 0 0
9.1730 6.5711 5.6705 N 0 0 0 0 0 0 0 0 0 0 0 0
8.0072 1.4702 15.0896 N 0 0 0 0 0 0 0 0 0 0 0 0
9.8940 0.9110 16.4138 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5084 0.1128 14.0809 N 0 0 0 0 0 0 0 0 0 0 0 0
3.6690 11.4319 15.4070 N 0 0 0 0 0 2 0 0 0 0 0 0
3.0008 10.5318 5.3531 N 0 0 0 0 0 0 0 0 0 0 0 0
1.1140 11.0910 6.6773 N 0 0 0 0 0 0 0 0 0 0 0 0
5.4996 11.8892 4.3444 N 0 0 0 0 0 0 0 0 0 0 0 0
7.3390 0.5701 5.6705 N 0 0 0 0 0 2 0 0 0 0 0 0
10.5159 9.1539 14.4957 O 0 0 0 0 0 0 0 0 0 0 0 0
10.4477 10.0637 16.5482 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0450 7.3044 18.5558 O 0 0 0 0 0 0 0 0 0 0 0 0
6.4309 8.8803 19.3133 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7117 5.5881 12.7198 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7470 3.4674 13.4539 O 0 0 0 0 0 0 0 0 0 0 0 0
3.2969 3.4398 16.5579 O 0 0 0 0 0 0 0 0 0 0 0 0
1.8251 1.9059 15.9270 O 0 0 0 0 0 0 0 0 0 0 0 0
4.4891 4.5740 18.9803 O 0 0 0 0 0 1 0 0 0 0 0 0
3.5886 4.1743 1.5208 O 0 0 0 0 0 0 0 0 0 0 0 0
2.2456 5.8726 18.2735 O 0 0 0 0 0 0 0 0 0 0 0 0
1.2175 5.0576 0.6173 O 0 0 0 0 0 1 0 0 0 0 0 0
0.4921 2.8481 4.7592 O 0 0 0 0 0 0 0 0 0 0 0 0
0.5603 1.9383 6.8117 O 0 0 0 0 0 0 0 0 0 0 0 0
5.9630 4.6976 8.8193 O 0 0 0 0 0 0 0 0 0 0 0 0
4.5771 3.1217 9.5768 O 0 0 0 0 0 0 0 0 0 0 0 0
2.2963 6.4139 2.9833 O 0 0 0 0 0 0 0 0 0 0 0 0
2.2610 8.5346 3.7174 O 0 0 0 0 0 0 0 0 0 0 0 0
7.7111 8.5622 6.8214 O 0 0 0 0 0 0 0 0 0 0 0 0
9.1829 10.0961 6.1905 O 0 0 0 0 0 0 0 0 0 0 0 0
6.5189 7.4280 9.2438 O 0 0 0 0 0 0 0 0 0 0 0 0
7.4194 7.8277 11.2573 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7624 6.1294 8.5370 O 0 0 0 0 0 0 0 0 0 0 0 0
9.7905 6.9444 10.3538 O 0 0 0 0 0 0 0 0 0 0 0 0
5.9961 3.1529 14.4957 O 0 0 0 0 0 0 0 0 0 0 0 0
6.0643 4.0627 16.5482 O 0 0 0 0 0 0 0 0 0 0 0 0
0.4590 1.3034 18.5558 O 0 0 0 0 0 15 0 0 0 0 0 0
10.0811 2.8793 19.3133 O 0 0 0 0 0 0 0 0 0 0 0 0
7.8003 11.5891 12.7198 O 0 0 0 0 0 0 0 0 0 0 0 0
7.7650 9.4684 13.4539 O 0 0 0 0 0 0 0 0 0 0 0 0
2.2071 9.4408 16.5579 O 0 0 0 0 0 0 0 0 0 0 0 0
3.6789 7.9069 15.9270 O 0 0 0 0 0 0 0 0 0 0 0 0
1.0149 10.5750 18.9803 O 0 0 0 0 0 1 0 0 0 0 0 0
1.9154 10.1753 1.5208 O 0 0 0 0 0 0 0 0 0 0 0 0
3.2584 11.8736 18.2735 O 0 0 0 0 0 0 0 0 0 0 0 0
4.2865 11.0586 0.6173 O 0 0 0 0 0 1 0 0 0 0 0 0
5.0119 8.8491 4.7592 O 0 0 0 0 0 0 0 0 0 0 0 0
4.9437 7.9393 6.8117 O 0 0 0 0 0 0 0 0 0 0 0 0
10.5490 10.6986 8.8193 O 0 0 0 0 0 15 0 0 0 0 0 0
0.9269 9.1227 9.5768 O 0 0 0 0 0 0 0 0 0 0 0 0
3.2077 0.4129 2.9833 O 0 0 0 0 0 0 0 0 0 0 0 0
3.2430 2.5336 3.7174 O 0 0 0 0 0 0 0 0 0 0 0 0
8.8009 2.5612 6.8214 O 0 0 0 0 0 0 0 0 0 0 0 0
7.3291 4.0951 6.1905 O 0 0 0 0 0 0 0 0 0 0 0 0
9.9931 1.4270 9.2438 O 0 0 0 0 0 0 0 0 0 0 0 0
9.0926 1.8267 11.2573 O 0 0 0 0 0 0 0 0 0 0 0 0
7.7496 0.1284 8.5370 O 0 0 0 0 0 0 0 0 0 0 0 0
6.7215 0.9434 10.3538 O 0 0 0 0 0 0 0 0 0 0 0 0
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35102 1 0 0 0 0
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142 5 1 0 0 0 0
143 80 1 0 0 0 0
144 5 1 0 0 0 0
M END
$$$$

[tjkessler]

Hi @shenglisa,

I've never seen an error like that before, I'll have to punt the question to someone else. I can tell you, however, that this error originates in PaDEL-Descriptor's source code, not the PaDELPy wrapper.

Best,
Travis