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Bad ring finding in a complex fused ring #526

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greglandrum opened this issue Jun 19, 2015 · 0 comments
Closed

Bad ring finding in a complex fused ring #526

greglandrum opened this issue Jun 19, 2015 · 0 comments
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@greglandrum
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Reported by @sriniker

This was the minimal reproducible I could find:

In [76]:

subm = Chem.MolFromSmiles('NN1C2C3[C@@H]4[C@@H]1C1[C@H]2N([C@H]3[C@@H]1N4N1C(=O)C2=C(C=CC=C2)C1=O)N1C(=O)C2=C(C=CC=C2)C1=O')
subm1 = Chem.MolFromMolBlock("""foo
  Mrv0541 06181507362D          

 34 42  0  0  0  0            999 V2000
   -0.1591   -0.3923    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1440   -0.3923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3989    0.3923    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7314    0.8773    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0640    0.3923    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3190   -0.3923    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6514   -0.8773    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9841   -0.3923    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2390    0.3923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5715    0.8773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0959    0.3923    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7314    1.7023    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0640    2.1871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2793    1.9322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3190    2.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9064    3.6862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3190    4.4007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1440    4.4007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5564    3.6862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1440    2.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3989    2.1871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1835    1.9322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6514   -1.7023    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3190   -2.1871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1035   -1.9322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0640   -2.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4764   -3.6862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0640   -4.4007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2390   -4.4007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8264   -3.6862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2390   -2.9718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9841   -2.1871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1994   -1.9322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8806    0.6472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1 11  1  1  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  3  4  1  1  0  0  0
  3 10  1  0  0  0  0
  5  4  1  6  0  0  0
  4 12  1  0  0  0  0
  5  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7 23  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 34  1  0  0  0  0
 12 13  1  0  0  0  0
 12 21  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 20  2  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  1  0  0  0  0
 21 22  2  0  0  0  0
 23 24  1  0  0  0  0
 23 32  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 31  2  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
M  END
""")
print(len(subm.GetRingInfo().AtomRings()),len(subm1.GetRingInfo().AtomRings()))
print(Chem.MolToSmiles(subm,True) == Chem.MolToSmiles(subm1,True))
print(subm.HasSubstructMatch(subm1),subm1.HasSubstructMatch(subm))
(8, 10)
True
(False, True)
@greglandrum greglandrum added this to the 2015_09_1 milestone Jun 19, 2015
sriniker pushed a commit to sriniker/rdkit that referenced this issue Oct 20, 2015
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