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RDKit postgreSQL cartridge infinity loop #7947

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garaboncias opened this issue Oct 21, 2024 · 0 comments
Open

RDKit postgreSQL cartridge infinity loop #7947

garaboncias opened this issue Oct 21, 2024 · 0 comments
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bug

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@garaboncias
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Describe the bug
RDKit PostgreSQL cartridge get infinity loop, during molecule equality check.
It seems PostgreSQL ANALYZE function (during auto-vacuum) also get infinity loop because of these two molecule when they are stored in a table.

In this example both molecule are kind of Aluminum potassium sulfate
the second one is from pubchem, the first one probably from the same source, but an earlier version of it.
https://pubchem.ncbi.nlm.nih.gov/compound/124202421
(First molecule has some invalid bounds)

To Reproduce

select mol_from_ctab('


 24  8  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Al  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 K   0  0  0  0  0  0  0  0  0  0  0  0
 13 14  6  0
 14 15  2  0
 14 16  2  0
 14 17  6  0
 18 19  6  0
 19 20  2  0
 19 21  2  0
 19 22  6  0
M  END') = mol_from_ctab('124202421
  -OEChem-10212406482D

 52 36  0     0  0  0  0  0  0999 V2000
    0.2869    3.1160    0.0000 K   0  4  0  0  0  0  0  0  0  0  0  0
    4.4768    4.6160    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    9.2828    0.8660    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   12.9727    4.3660    0.0000 Al  0  0  0  0  0 15  0  0  0  0  0  0
    5.3429    5.1160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6108    4.1160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1488    1.3660    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4167    0.3660    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9768    5.4820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9768    3.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7828    1.7320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7828    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2828   11.2321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5369    5.6160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4768    7.4820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2828    3.7320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2227    6.8660    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5369    8.1160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4768    9.9820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2227    9.3660    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5369   10.6160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2828    8.7320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2828   13.7321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2828    6.2320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8798    4.8060    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0739    4.4260    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6857    1.0560    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8798    0.6760    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8197   11.5421    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7458   11.5421    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0739    5.9260    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.9260    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0138    7.7920    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9399    7.7920    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8197    4.0420    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7458    4.0420    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7596    7.1760    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6857    7.1760    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0739    8.4260    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    8.4260    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0138   10.2921    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9399   10.2921    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7596    9.6760    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6857    9.6760    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0739   10.9260    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   10.9260    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8197    9.0420    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7458    9.0420    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8197   14.0421    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7458   14.0421    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8197    6.5420    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7458    6.5420    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  2  9  2  0  0  0  0
  2 10  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3 11  2  0  0  0  0
  3 12  2  0  0  0  0
  5 25  1  0  0  0  0
  6 26  1  0  0  0  0
  7 27  1  0  0  0  0
  8 28  1  0  0  0  0
 13 29  1  0  0  0  0
 13 30  1  0  0  0  0
 14 31  1  0  0  0  0
 14 32  1  0  0  0  0
 15 33  1  0  0  0  0
 15 34  1  0  0  0  0
 16 35  1  0  0  0  0
 16 36  1  0  0  0  0
 17 37  1  0  0  0  0
 17 38  1  0  0  0  0
 18 39  1  0  0  0  0
 18 40  1  0  0  0  0
 19 41  1  0  0  0  0
 19 42  1  0  0  0  0
 20 43  1  0  0  0  0
 20 44  1  0  0  0  0
 21 45  1  0  0  0  0
 21 46  1  0  0  0  0
 22 47  1  0  0  0  0
 22 48  1  0  0  0  0
 23 49  1  0  0  0  0
 23 50  1  0  0  0  0
 24 51  1  0  0  0  0
 24 52  1  0  0  0  0
M  RAD  1   1   2
M  END');

Expected behavior
return false, but run endless.

Configuration (please complete the following information):

  • RDKit version: 4.4.0 and 4.6.1
  • OS: Debian and MacOS
  • Postgresql 16 and 17
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@garaboncias