On 2021-04-25 14:09, Peter Jarowski wrote:
Hi David:
I would suggest you avoid inchi entirely for this as it has its own
rules regarding canonical protonation state and connectivity (tautomer).
Stick with SMILES. There is no benefit to inchi unless you are
concerned with clashing because you have a very large database.
SMILES will represent your molecule as you want, you can use explicite
hydrogens if you need to as well.
Thanks for the suggestion, but:
% obabel -osmi -isdf perfluorotridecanoic-acid.sdf
FC(F)(C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)O
3018355
% obabel -osmi -isdf perfluorotridecanoate.sdf
FC(F)(C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)O
Identical. With the -xt h flag I get no string whatsoever.
% obabel -osmi -xt h -isdf perfluorotridecanoic-acid.sdf
3018355
If I drop the smiles string for the charged compound into Pubchem I get
the acid back, so there is still information missing.
Maybe I'm still doing something wrong. The position of the hydrogens is
crucial because the identifiers are coupled to quantum chemistry
calculations.
Best,
Peter
On Sun, 25 Apr 2021 at 12:52, David van der Spoel
<david.vandersp...@icm.uu.se <mailto:david.vandersp...@icm.uu.se>> wrote:
Hi,
I would like to generate an Inchi fro my compound but without adding
hydrogens. Is there a flag for that?
Here is an example for an acid and its deprotonated form that
yields the
same InChi:
% obabel -oinchi -isdf perfluorotridecanoic-acid.sdf
InChI=1S/C13HF25O2/c14-2(15,1(39)40)3(16,17)4(18,19)5(20,21)6(22,23)7(24,25)8(26,27)9(28,29)10(30,31)11(32,33)12(34,35)13(36,37)38/h(H,39,40)
% obabel -oinchi -isdf perfluorotridecanoate.sdf
InChI=1S/C13HF25O2/c14-2(15,1(39)40)3(16,17)4(18,19)5(20,21)6(22,23)7(24,25)8(26,27)9(28,29)10(30,31)11(32,33)12(34,35)13(36,37)38/h(H,39,40)
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