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RDKit hangs indefinitely when parsing not so big molblock #6434

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eloyfelix opened this issue Jun 2, 2023 · 3 comments · Fixed by #6531
Closed

RDKit hangs indefinitely when parsing not so big molblock #6434

eloyfelix opened this issue Jun 2, 2023 · 3 comments · Fixed by #6531
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bug
Milestone
2023_03_3

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@eloyfelix
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eloyfelix commented Jun 2, 2023 •
edited

Describe the bug

I had US06235754-20010522-C00041.MOL (from USPTO bulk downloads) molecule more than 10 minutes waiting to be parsed until I cancelled.
If the sanitization is turned False and Chem.Sanitize is applied afterwards everything seems to work.

To Reproduce

molfile = """
  ChemDraw12010010062D

 30 32  0  0  0  0  0  0  0  0999 V2000
   -0.6432    2.4695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6432    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484    4.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535    2.4695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484    1.7183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5540    1.7183    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.6573    4.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6573    6.2254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4131    7.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0939    7.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2582    4.7230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577    2.4695    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5587    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6432   -6.7793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6432   -5.2770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -4.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535   -5.2770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535   -6.7793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -7.5305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5540   -7.5305    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.6573   -4.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577   -5.2770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6573   -3.0235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4131   -1.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0939   -1.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2582   -4.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577   -6.7793    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    4.5587   -5.2770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 12  1  0  0  0  0
  9 13  1  0  0  0  0
  9 14  1  4  0  0  0
 13 15  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 20 22  1  0  0  0  0
 17 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 25 27  1  0  0  0  0
 24 28  1  0  0  0  0
 24 29  1  4  0  0  0
 28 30  2  0  0  0  0
M  END"""

from rdkit import Chem
mol = Chem.MolFromMolBlock(molfile)

What was a bit surprising for me is that disabling the sanitization and sanitazing afterwards seems to make things right. I thought both ways of sanitizing were equivalent.

molfile = """
  ChemDraw12010010062D

 30 32  0  0  0  0  0  0  0  0999 V2000
   -0.6432    2.4695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6432    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484    4.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535    2.4695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484    1.7183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5540    1.7183    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.6573    4.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6573    6.2254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4131    7.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0939    7.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2582    4.7230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577    2.4695    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5587    3.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6432   -6.7793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6432   -5.2770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -4.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535   -5.2770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2535   -6.7793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -7.5305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5540   -7.5305    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.6573   -4.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577   -5.2770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6573   -3.0235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4131   -1.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0939   -1.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2582   -4.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9577   -6.7793    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    4.5587   -5.2770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 12  1  0  0  0  0
  9 13  1  0  0  0  0
  9 14  1  4  0  0  0
 13 15  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 20 22  1  0  0  0  0
 17 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 25 27  1  0  0  0  0
 24 28  1  0  0  0  0
 24 29  1  4  0  0  0
 28 30  2  0  0  0  0
M  END"""

from rdkit import Chem
mol = Chem.MolFromMolBlock(molfile, sanitize=False)
Chem.SanitizeMol(mol)

Expected behavior
It parses the molecule or fails to parse it.

Configuration (please complete the following information):

  • RDKit version: 2023.03.1
  • OS: Ubuntu 20.04
  • Python version (if relevant): 3.11
  • If you are not using conda: how did you install the RDKit? pip install rdkit
@eloyfelix eloyfelix added the bug label Jun 2, 2023
@eloyfelix eloyfelix changed the title RDKit indefinetely hangs when parsing not so big molblock RDKit hangs indefinitely when parsing not so big molblock Jun 2, 2023
@klaasMensaert
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klaasMensaert commented Jul 10, 2023 •
edited by bp-kelley

Same here for the following molecule:

    molfile = """    
    Marvin  07050610402D          

 16 15  0  0  0  0            999 V2000
    7.6621   -4.0706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9496   -4.4831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2183   -4.0706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5058   -4.4831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6621   -3.2456    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3746   -4.4831    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.5058   -5.3269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7933   -4.0706    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.9496   -5.3269    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7933   -1.5768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2183   -3.2456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9328   -2.8331    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5058   -2.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7913   -3.2268    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5058   -1.9893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2203   -1.5768    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  6  1  1  0  0  0  0
  5  1  2  0  0  0  0
  3  2  2  0  0  0  0
  2  9  1  4  0  0  0
  4  3  1  0  0  0  0
 11  3  1  0  0  0  0
  8  4  1  0  0  0  0
  7  4  2  0  0  0  0
 13 11  2  0  0  0  0
 15 13  1  0  0  0  0
 10 15  2  0  0  0  0
 11 12  1  4  0  0  0
 13 14  1  4  0  0  0
 15 16  1  0  0  0  0
M  CHG  2   6  -1   8  -1
M  END
"""

@klaasMensaert
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klaasMensaert commented Jul 10, 2023 •
edited

It hangs for me with version 2023.03.2 and 2023.03.1, but not with 2022.9.5
OS: Ubuntu 20.04.6 LTS and CentOS Linux release 7.9.2009 (tested on both)
Python version (if relevant): 3.8
If you are not using conda: how did you install the RDKit? pycharm

@bp-kelley
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I've confirmed this, it looks like the bug was added to the legacy chirality detection. The fix, for now, is to use the new chirality perception:

Chem.SetUseLegacyStereoPerception(True)

@bp-kelley bp-kelley mentioned this issue Jul 10, 2023
Merged
@greglandrum greglandrum added this to the 2023_03_3 milestone Jul 13, 2023
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Minimal update to fix hang in the legacy stereo checker bp-kelley/rdkit
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