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gen3D creates invalid structures for some molecules. #2146

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tdudgeon opened this issue Mar 27, 2020 · 4 comments
Closed
1 task

gen3D creates invalid structures for some molecules. #2146

tdudgeon opened this issue Mar 27, 2020 · 4 comments

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@tdudgeon
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tdudgeon commented Mar 27, 2020 •
edited

  • [ X ] I believe this to be a bug with Open Babel
  • This is a feature request

Environment Information

Open Babel version: 3.0.0
Operating system and version: Fedora 30

Expected Behavior

Valid 3D molfile file should be created. Coordinates should be 'reasonable'.

Actual Behavior

CTAB blocks are either invalid (containing '-nan' instead of coordinates) and with all or some coordinates at 0.000, or creates structures that are unreasonable.

Steps to Reproduce

Problem 1

$ echo 'Cc1ccsc1C1(O)CCOC1' | obabel -i smi -o mol --gen3D

 OpenBabel03272011373D

 18 19  0  0  1  0  0  0  0  0999 V2000
    2.6191   -0.3198    0.0013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2344   -0.0253    0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5696    1.2219    0.0050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7972    1.2233   -0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4123   -0.3511    0.0038 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2903   -1.0407   -0.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0541   -3.3907    0.0869 C   0  0  3  0  0  0  0  0  0  0  0  0
    0.5536   -2.5620   -0.2560 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1818   -2.6278   -1.5272 C   0  0  0  0  0  2  0  0  0  0  0  0
    0.5536   -2.5620   -0.2560 C   0  0  0  0  0  2  0  0  0  0  0  0
    0.5536   -2.5620   -0.2560 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5536   -2.5620   -0.2560 C   0  0  0  0  0  2  0  0  0  0  0  0
    3.1478    0.6161    0.0046 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8965   -0.8795   -0.8720 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8905   -0.8791    0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1181    2.0974    0.0068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3761    2.0734   -0.0078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9774   -2.4581    0.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 13  1  0  0  0  0
  1 14  1  0  0  0  0
  1 15  1  0  0  0  0
  2  3  1  0  0  0  0
  2  6  2  0  0  0  0
  3  4  2  0  0  0  0
  3 16  1  0  0  0  0
  4  5  1  0  0  0  0
  4 17  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 12  1  0  0  0  0
  8 18  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
1 molecule converted

Valid CTAB is created but molecule is distorted when viewer in 3D

Problem 2

$ echo 'OC1CCOC1Cc1ccsc1' | obabel -i smi -o mol --gen3D
==============================
*** Open Babel Warning  in Build
  There exists NaN in calculated coordinates.

 OpenBabel03272011403D

 12 13  0  0  1  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  3  0  0  3  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  2  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 C   0  0  3  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  2  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  0  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan S   0  0  0  0  0  0  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  2  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
1 molecule converted

Invalid output with -nan as coordiantes and other atoms all being at 0.0000

Problem 3

echo 'OC1COC(Cc2ccsc2)C1' | obabel -i smi -o mol --gen3D
==============================
*** Open Babel Warning  in Build
  There exists NaN in calculated coordinates.

 OpenBabel03272011423D

 12 13  0  0  1  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  3  0  0  3  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  2  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 C   0  0  3  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  2  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  0  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan S   0  0  0  0  0  0  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2 12  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5 12  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  2  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
1 molecule converted

same problem

Problem 4

$ echo 'OC1(Cc2ccsc2)CCOC1' | obabel -i smi -o mol --gen3D
==============================
*** Open Babel Warning  in Build
  There exists NaN in calculated coordinates.

 OpenBabel03272011433D

 12 13  0  0  1  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  2  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  0  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
      -nan      -nan      -nan S   0  0  0  0  0  0  0  0  0  0  0  0
      -nan      -nan      -nan C   0  0  0  0  0  3  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  2  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 C   0  0  0  0  0  2  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  9  1  0  0  0  0
  2 12  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
1 molecule converted

same problem

Problem 5

$ echo 'NC1[C@@H]2C[C@@H]2[C@H]2C[C@@H]12' | obabel -i smi -o mol --gen3D
==============================
*** Open Babel Warning  in CorrectStereoAtoms
  Could not correct 2 stereocenter(s) in this molecule ()
  with Atom Ids as follows: 2 4
Warning: Stereochemistry is wrong, using the distance geometry method instead

 OpenBabel03272011433D

 19 21  0  0  1  0  0  0  0  0999 V2000
    0.0000   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  2  8  1  0  0  0  0
  2 11  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3 12  1  1  0  0  0
  4  5  1  0  0  0  0
  4 13  1  0  0  0  0
  4 14  1  0  0  0  0
  5  6  1  0  0  0  0
  5 15  1  1  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6 16  1  1  0  0  0
  7  8  1  0  0  0  0
  7 17  1  0  0  0  0
  7 18  1  0  0  0  0
  8 19  1  1  0  0  0
M  END
1 molecule converted

Complains about the stereochemistry, and then dumps all atoms at 0.0000
@hjjvandam
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Actually, this bug seems to be a duplicate of #2141. Sometimes it seems OpenBabel will crash when it hits this problem, sometimes it outputs junk coordinates. A more detailed discussion of the underlying cause can be found at #2144.

@ghutchis
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ghutchis commented Apr 3, 2020

This should now be solved by #2150 - can you please confirm by building master?

@timvdm
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timvdm commented Apr 5, 2020

Regarding problem 5: The pull request below correctly handles this case.

#2158

@ghutchis
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ghutchis commented May 7, 2020

This is fixed. I'm adding these SMILES to the coordinate generation unit test.

@ghutchis ghutchis closed this as completed May 7, 2020
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4 participants
@ghutchis @timvdm @tdudgeon @hjjvandam