Hi all,
I am trying to do some substructure queries using the RDKit PostgreSQL
cartridge. Specifically, my queries substructure inputs are CTAB (not
SMARTS) so I would like to use qmol_from_ctab. However, I have some
problems with making valid query molecules with a few CTABs.
In this query, I try to use a CTAB to make a query to search for aryl
boronate acid/ester. I can make an equivalent query using SMARTS but the
CTAB is not valid.
As far as I am aware, there's no warning message when using the SQL
functions, so I use MolFromMolBlock from python and get "non-ring atom 0
marked aromatic" so I correct the aromatic bond type to double bond and the
CTAB can be read in (but that's not the query I want). I am guessing that
there may be additional validity checks / sanitization steps when executing
qmol_from_ctab vs qmol_from_smarts? As far as I can see, there’s no flag in
qmol_from_ctab.
I describe the general problem below but also attach the ipynb (if it is
useful) that uses psycopg2 to do the SQL , leaving out the database
connection credentials.
Many thanks,
Susan
__________________________________
For example, I want to match an aromatic boronic acid:
sm1 = 'OB(O)c1ccccc1'
But the following CTAB isn’t valid. MolFromFromBlock returns non-ring atom
marked aromatic error so I suspect it’s to do with that. Also changing the
bond marked aromatic ‘4’ to a double bond ‘2’ makes the ctab valid.
ctab_og = """Boronate acid/ester(aryl)
SciTegic12012112112D
5 4 0 0 0 0 999 V2000
1.7243 -2.7324 0.0000 A 0 0
2.7559 -2.1456 0.0000 C 0 0
3.7808 -2.7324 0.0000 B 0 0
4.8057 -2.1456 0.0000 O 0 0
3.7808 -3.9190 0.0000 O 0 0
1 2 4 0 0 1 0
2 3 1 0
3 4 1 0
3 5 1 0
M END
> <Name>
Boronate acid/ester(aryl)
"""
ctab_fixed = """Boronate acid/ester(aryl)
SciTegic12012112112D
5 4 0 0 0 0 999 V2000
1.7243 -2.7324 0.0000 A 0 0
2.7559 -2.1456 0.0000 C 0 0
3.7808 -2.7324 0.0000 B 0 0
4.8057 -2.1456 0.0000 O 0 0
3.7808 -3.9190 0.0000 O 0 0
1 2 2 0 0 1 0
2 3 1 0
3 4 1 0
3 5 1 0
M END
> <Name>
Boronate acid/ester(aryl)
"""
select is_valid_ctab('{ctab_og}')
Returns False
select is_valid_ctab('{ctab_fixed}')
Returns True
However, I can make a qmol using SMARTS match sm1. Is there of making the
query CTAB valid so we don’t have to use SMARTS?
select mol_from_smiles('{sm1}') @> qmol_from_ctab('{ctab_fixed}')
Returns False
select mol_from_smiles('{sm1}') @> qmol_from_smarts('{alt_smarts}')
Returns True
211209_problematic_ctab_example1_for_rdkit_mailing_list.ipynb
Description: application/ipynb
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