mordred-descriptor / mordred

a molecular descriptor calculator
http://mordred-descriptor.github.io/documentation/master/
BSD 3-Clause "New" or "Revised" License
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Sanitization error: Can't kekulize mol in some molecule #67

Closed philopon closed 5 years ago

philopon commented 5 years ago

description

mol = Chem.MolFromMolFile('failure.mol')
failure on Chem.RemoveHs(Chem.AddHs(mol))
17508650-00-02
     RDKit          3D

 25 27  0  0  0  0  0  0  0  0999 V2000
    2.7422    1.3925    0.0418 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1417   -2.7068   -0.2424 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2063    1.2990   -0.0894 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4086   -2.5151    0.0042 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8451   -0.3680    0.1294 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2659   -0.6707   -0.1055 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5377   -1.1901   -0.1007 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0780    1.3802   -0.0268 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.0636   -1.3267    0.0586 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1595    0.6893   -0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4063   -0.2273   -0.0273 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1599   -1.4835   -0.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8726   -0.4632   -0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1239    0.7290   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0874   -0.7300   -0.1687 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8119    0.5768    0.0768 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3309   -1.7911   -0.0613 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6246   -1.0321    0.0375 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1846    0.2962    0.0969 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7004   -2.0796   -0.0417 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5082    1.6201    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6250   -2.6197   -0.1234 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8921    1.1220    0.1588 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0233   -3.1184   -0.0887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0221   -1.2670   -0.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0
  1 11  1  0
  2 12  2  0
  3 14  2  0
  4  9  1  0
  5  9  2  0
  6  7  1  0
  6 10  1  0
  6 12  1  0
  7 11  2  0
  8 10  2  0
  8 14  1  0
  9 18  1  0
 11 13  1  0
 12 15  1  0
 13 16  2  0
 13 17  1  0
 14 15  1  0
 16 19  1  0
 17 20  2  0
 18 19  2  0
 18 20  1  0
 16 21  1  0
 17 22  1  0
 19 23  1  0
 20 24  1  0
 15 25  1  0
M  CHG  3   4  -1   9   1  15  -1
M  END

environment

OS/distribution

MacOS 10.14.1

conda or pip

pip

python version

Python 3.6.7 :: Anaconda, Inc.