Kekulize bonds when converting sdf to mol2

[and-tos]

Is there an option to kekulize aromatic bonds when converting from SDF to mol2?

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[nbehrnd]

It does not seem possible with openbabel (version 3.1.1).

For one, there is no explicit option mentioned in the manual. From the section about SMILES one could infer -k would be a suitable flag to use to modify the output. But no, it isn't:

$ obabel -:"c1ccncc1" -h --gen3d -xk -omol2
@<TRIPOS>MOLECULE
*****
 11 11 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1 C           1.4330    0.0516    0.0010 C.ar    1  UNL1       -0.0589
      2 C           0.6880    1.2260    0.0015 C.ar    1  UNL1       -0.0436
      3 C          -0.6942    1.1256    0.0022 C.ar    1  UNL1        0.0276
      4 N          -1.3624   -0.0485    0.0055 N.ar    1  UNL1       -0.2633
      5 C          -0.6120   -1.1719    0.0069 C.ar    1  UNL1        0.0276
      6 C           0.7738   -1.1733    0.0033 C.ar    1  UNL1       -0.0436
      7 H           2.5185    0.0904   -0.0011 H       1  UNL1        0.0618
      8 H           1.1715    2.1963    0.0013 H       1  UNL1        0.0633
      9 H          -1.3198    2.0134    0.0001 H       1  UNL1        0.0829
     10 H          -1.1726   -2.1023    0.0114 H       1  UNL1        0.0829
     11 H           1.3254   -2.1063    0.0027 H       1  UNL1        0.0633
@<TRIPOS>BOND
     1     1     2   ar
     2     2     3   ar
     3     3     4   ar
     4     4     5   ar
     5     5     6   ar
     6     1     6   ar
     7     1     7    1
     8     2     8    1
     9     3     9    1
    10     5    10    1
    11     6    11    1
1 molecule converted

On then may think to create a .xyz file without any bond order described and to let openbabel "reassign" bonds. But no, this bypass does not exist. Again about the molecule of pyridine:

$ obabel -:"c1ccncc1" -h --gen3d -O pyridine.xyz
1 molecule converted
$ obabel pyridine.xyz -omol2
@<TRIPOS>MOLECULE
pyridine.xyz
 11 11 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1 C           1.4330    0.0516    0.0010 C.ar    1  UNL1       -0.0589
      2 C           0.6880    1.2260    0.0015 C.ar    1  UNL1       -0.0436
      3 C          -0.6942    1.1256    0.0022 C.ar    1  UNL1        0.0276
      4 N          -1.3624   -0.0485    0.0055 N.ar    1  UNL1       -0.2633
      5 C          -0.6120   -1.1719    0.0069 C.ar    1  UNL1        0.0276
      6 C           0.7738   -1.1733    0.0033 C.ar    1  UNL1       -0.0436
      7 H           2.5185    0.0904   -0.0011 H       1  UNL1        0.0618
      8 H           1.1715    2.1963    0.0013 H       1  UNL1        0.0633
      9 H          -1.3198    2.0134    0.0001 H       1  UNL1        0.0829
     10 H          -1.1726   -2.1023    0.0115 H       1  UNL1        0.0829
     11 H           1.3254   -2.1063    0.0027 H       1  UNL1        0.0633
@<TRIPOS>BOND
     1     7     1    1
     2     9     3    1
     3     1     2   ar
     4     1     6   ar
     5     8     2    1
     6     2     3   ar
     7     3     4   ar
     8    11     6    1
     9     6     5   ar
    10     4     5   ar
    11     5    10    1
1 molecule converted

-- and the same output with an additional -xk flag.