Hi Lionel,
the success or failure of the SMILES searches depends on the fact that
you specify the exact formal charge as present in the database molecule,
which in turn depends on whether (and how) it was set in the input
molecule when it was loaded in the database, whereas the SMART searches
based on the element only will succeed no matter which the formal charge
is, as it does not take into account the formal charge at all.
Best,
p.
On 11/30/17 13:21, Lionel Colliandre wrote:
Hi all,
For the question of molecules that cannot be searched, I finally found
a solution in treating my queries as smarts:
SELECT id FROM rdk.mols WHERE m@>*mol_from_smarts*('[Zn]');
All the presented queries gives the expected results, even if I am not
sure what is changing when I treat the query from smiles to smarts
i.e. the query are valid smiles.
Lionel
2- for a lot of compounds, the ctab is valid and I can convert them
into mol and obtain the smile in the rdk.mols table. However I cannot
found them when I search part of the smile.
**First for molecules with metals :
m1 = [Mn+2].[Zn+2]...
m2 = [Ag+].[Na+]...
m3 = [Ca+2]....
m4 = [Na+].c1ccc([B-](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
m5 = [V+2]=O
m6 = [Rh+]...
m7 = [Cu].[Zn]
m8 = [Fe+2]...
For a database containing those molecules, these searches give:
[Mn] or [Mn+2] => 0 results (bad)
[Zn] => 0 (bad) but [Zn+2] => m1 (ok)
[Ag] or [Ag+] => m2 (ok)
[Na] => 0 (bad) why Ag is founded and not Na in the same molecule ?
but [Na+] => m2 + m4 (ok)
[Ca] => 0 (bad) but [Ca+2] => m3 (ok)
[B] or [B-] => 0 (bad)
[V] or [V+2] => 0 (bad)
[Rh] or [Rh+] => m6 (ok)
[Cu] => m7 (ok) but [Zn] => 0 (bad)
[Fe] => m8 (ok) but [Fe+2] => 0 (bad)
I cannot find a logic, sometime the atom is found and not the ion,
sometime is the invert, sometime in the same molecule one can be
found and not the other. Has someone an explanation?
** second for N3
m9 = [N-]=[N+]=[N-]
the following search gives:
[N-] or [N+] => 0 (bad)
[N-]=N => m9 (ok)
[N-]=[N+] => 0 (bad)
[N-]=[N+]=N => m9 (ok)
[N-]=[N+]=[N-] => m9 (ok)
Once again I cannot find a logic. Has someone an explanation?
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