Better JME/MDL Query Support

[johnmay]

I'm a huge fan of J(S)ME but hit a bit of an issue when using it.

If you enable query features and export as a MOLfile then information is lost. I thought I found a work around by using the JME format but this also loses query bond information. I can't use SMARTS as I would like coordinates.

Example:

The MOLfile ideally would put the atom list in but instead just adds Q (hetero atom):

JME 2023-07-31 Fri Feb 09 10:08:44 GMT+000 2024

 13 14  0  0  0  0  0  0  0  0999 V2000
    2.4279    0.7004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2139    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.7004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2139    2.8014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4279    2.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6325    2.8014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8465    2.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0594    2.8016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2726    2.1014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0592    4.2023    0.0000 Q   0  0  0  0  0  0  0  0  0  0  0  0
    4.8465    0.7004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6325    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  2  0  0  0  0
  1 13  1  0  0  0  0
M  END

JME format preserves the info and coordinates.

13 14 C 2.43 0.70 C 1.21 0.00 C 0.00 0.70 C 0.00 2.10 C 1.21 2.80 C 2.43 2.10 C 3.63 2.80 C 4.85 2.10 C 6.06 2.80 C 7.27 2.10 F,Cl,Br,I 6.06 4.20 C 4.85 0.70 C 3.63 0.00 1 2 2 2 3 1 3 4 2 4 5 1 5 6 2 1 6 1 6 7 1 7 8 2 8 9 1 9 10 1 9 11 1 8 12 1 12 13 2 1 13 1

However if I now add a query bond in:

This is emitted as 0 in the JME format.

13 14 C 2.43 0.70 C 1.21 0.00 C 0.00 0.70 C 0.00 2.10 C 1.21 2.80 C 2.43 2.10 C 3.63 2.80 C 4.85 2.10 C 6.06 2.80 C 7.27 2.10 F,Cl,Br,I 6.06 4.20 C 4.85 0.70 C 3.63 0.00 1 2 2 2 3 1 3 4 2 4 5 1 5 6 2 1 6 1 6 7 1 7 8 2 8 9 1 9 10 0 9 11 1 8 12 1 12 13 2 1 13 1

I am happy to add support for this in the Java.