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Actelion / openchemlib

Open source Java-based chemistry library
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SMARTS Conversion to MOL removes mapping for hydrogen #33

Open Artoria2e5 opened 5 years ago

Artoria2e5 commented 5 years ago

This breaks the [CH2:1]=[CH:2][CH:3]=[CH:4][CH2:5][H:6]>>[H:6][CH2:1][CH:2]=[CH:3][CH:4]=[CH2:5] test case from http://www.daylight.com/meetings/summerschool01/course/basics/smirks.html.

Input:

[CH2:1]=[CH:2][CH:3]=[CH:4][CH2:5][H:6]

Output:

Actelion Java MolfileCreator 1.0

  5  4  0  0  0  0  0  0  0  0999 V2000
    3.4641   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
    2.5981   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
    1.7321   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
    0.8660   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  4  0  0
    0.0000   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  3  0  0  0
  4  5  1  0  0  0  0
M  END
thsa commented 5 years ago

thanks, this should be fixed with the next nightly update, Thomas

On Mon, Nov 12, 2018 at 2:31 AM Mingye Wang notifications@github.com wrote:

Input:

[CH2:1]=[CH:2][CH:3]=[CH:4][CH2:5][H:6]

Output:

Actelion Java MolfileCreator 1.0

5 4 0 0 0 0 0 0 0 0999 V2000 3.4641 -0.5000 -0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 2.5981 -0.0000 -0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 1.7321 -0.5000 -0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0 0.8660 -0.0000 -0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0 0.0000 -0.5000 -0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 3 0 0 0 4 5 1 0 0 0 0 M END

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