Pipeline Pilot components may read molfiles in V2000 format incorrectly if they include at least one line in the atom block that ends with the atom symbol plus exact one trailing space character

DB 2021-09-09

Pipeline Pilot components may read molfiles in V2000 format incorrectly if they include at least one line in the atom block that ends with the atom symbol plus exact one trailing space character. In particular, such atoms will be parsed as pseudo atoms rather than just standard atom types. The following molfile provides an example for such specific format of the lines in the atom block:

  ACCLDraw09092111232D

  5  5  0  0  0  0  0  0  0  0999 V2000
   10.6875  -10.8395    0.0000 N 
    9.7325  -11.5334    0.0000 C 
   10.0972  -12.6562    0.0000 C 
   11.2778  -12.6562    0.0000 C 
   11.6425  -11.5334    0.0000 C 
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  1  1  0  0  0  0
M  END

As a workaround, you can remove the single trailing space, or add a second one:

  ACCLDraw09092111062D

  5  5  0  0  0  0  0  0  0  0999 V2000
   10.6875  -10.8395    0.0000 N
    9.7325  -11.5334    0.0000 C
   10.0972  -12.6562    0.0000 C
   11.2778  -12.6562    0.0000 C
   11.6425  -11.5334    0.0000 C
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  1  1  0  0  0  0
M  END

The problem also applies to BIOVIA Direct; BIOVIA Draw however is not impacted. The issue will be fixed in the BIOVIA Direct and Pipeline Pilot 2022 releases.