Rendering of MDL functional groups (from MOLFile)

[tomyan112]

The structure in my .mol file

After import, the COO⁻ cannot be displayed

[MikeWilliams-UK]

At present we don't support input of functional groups from molfiles.

Can you post the MOLfile so that we can examine it to evaluate the possibility of doing so.

[tomyan112]

Alanine.zip

Alanine.mol
  ChemDraw02162014592D

  7  6  0  0  0  0  0  0  0  0999 V2000
    0.0000   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -0.2055    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.2055    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7120    1.0305    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7120    1.0305    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  5  6  2  0      
  5  7  1  0      
  1  5  1  0      
  1  2  1  0      
  1  3  1  0      
  1  4  1  0      
M  CHG  2   2   1   7  -1
M  STY  1   1 SUP
M  SLB  1   1   1
M  SAL   1  3   5   6   7
M  SBL   1  1   3
M  SMT   1 COO-
M  SBV   1   3    0.0000   -0.8250
M  END

[MikeWilliams-UK]

@deadlyvices what's your take on this?

[MikeWilliams-UK]

I have had a quick look at the CTAB of the MOLfile and the two O atoms are clearly present. Without reference to the MDL spec I can't tell for certain (as on my phone) but I think the line with the COO at the end may be the function group.
The problem we may have is if we do not have a definition for "COO" which from memory we don't how would we arbitrarily translate such groups!