I have a library of ~1000 compounds as SMILES strings with an appended name
code and a property. For example:
c1ccc(c2ccccc2)cc1 0001 -2.52
Where "0001" is the name code and "-2.52" is a physicochemical property of
the molecule.
I would like to convert these strings to a concatenated SDF file, where
each entry would be akin to the following:
=====
0001
OpenBabel02272214483D
22 23 0 0 0 0 0 0 0 0999 V2000
1.4317 -0.2725 0.0379 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5308 -1.3294 -0.0416 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8440 -1.0780 -0.1205 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3552 0.2331 -0.1102 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8126 0.5061 -0.1900 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7619 -0.3658 0.3754 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1347 -0.1008 0.3061 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.5930 1.0523 -0.3227 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.6798 1.9331 -0.8908 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3094 1.6572 -0.8317 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4177 1.2799 -0.0177 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9584 1.0330 0.0475 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4994 -0.4674 0.0916 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8945 -2.3535 -0.0457 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5134 -1.9313 -0.2025 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.4437 -1.2662 0.8961 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.8433 -0.7956 0.7492 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.6576 1.2635 -0.3694 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.0288 2.8364 -1.3842 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.6294 2.3598 -1.3084 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7493 2.3157 0.0178 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6546 1.8659 0.1080 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 12 2 0 0 0 0
1 13 1 0 0 0 0
2 3 2 0 0 0 0
2 14 1 0 0 0 0
3 4 1 0 0 0 0
3 15 1 0 0 0 0
4 5 1 0 0 0 0
4 11 2 0 0 0 0
5 6 1 0 0 0 0
5 10 2 0 0 0 0
6 7 2 0 0 0 0
6 16 1 0 0 0 0
7 8 1 0 0 0 0
7 17 1 0 0 0 0
8 9 2 0 0 0 0
8 18 1 0 0 0 0
9 10 1 0 0 0 0
9 19 1 0 0 0 0
10 20 1 0 0 0 0
11 12 1 0 0 0 0
11 21 1 0 0 0 0
12 22 1 0 0 0 0
M END
> <NO.>
1
> <logX>
-2.52
$$$$
=====
Thanks for your assistance!
Best regards,
Rudy
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