Error filtering by functional group

[felipeZ]

Given the following candidates:

,smiles
0,CN1C=NC2=C1C(=O)N(C(=O)N2C)C
1,OC(=O)C1CNC2C3C4CC2C1N34
2,C1=CC=CC=C1
3,OC(=O)C1CNC2COC1(C2)C#C
4,CCO
5,CCCCCCCCC=CCCCCCCCC(=O)O
6,CC(=O)O
7,O=C(O)Cc1ccccc1
8,CC(C(=O)O)O
9,CC12C3C(=O)OCC14CC=C(C4)C32

When applying the filter:

filters:
  include_functional_groups:
    - "C(=O)O[H]"

It returns the carboxylic acids and the esthers:

'O=C(O)C1CNC2C3CC4C2N4C13'
'C#CC12CC(CO1)NCC2C(=O)O'
 'CCCCCCCCC=CCCCCCCCC(=O)O' 
'CC(=O)O' 'O=C(O)Cc1ccccc1'
 'CC(O)C(=O)O'
 'CC12C3C(=O)OCC14CC=C(C4)C32'

[BvB93]

The issue here is that rdkit Mol.MolFromSmiles method will automatically remove the explicit hydrogen with its default sanitization setting.
This is how I manager to fix the issue in CAT: https://github.com/nlesc-nano/CAT/blob/e14032d5e4e1e1d680e155c25baa7392eebdfb5e/CAT/attachment/ligand_anchoring.py#L153-L162

[BvB93]

Shall I make a PR?

[felipeZ]

@BvB93 I am going to change to smarts. I think that smiles are not good enough, but I am still checking how it works

[BvB93]

I think Mol.FromSmarts does parse explicit hydrogens by default.
Just be aware that there are some subtle differences between SMILES and SMARTS, e.g. with aromatic systems.

[felipeZ]

I think Mol.FromSmarts does parse explicit hydrogens by default.
Just be aware that there are some subtle differences between SMILES and SMARTS, e.g. with aromatic systems.

Yes, but smiles may not be enough for filter. I am still thinking about what system to choose

[felipeZ]

@BvB93 I think that I am going to use your method but I still need to check for other functional groups :)

[BvB93]

For reference the various rdkit sanitization flags:
https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html?rdkit.Chem.rdmolops.SanitizeFlags#rdkit.Chem.rdmolops.SanitizeFlags

[BvB93]

I suspect this can be closed now with the merging of #19.

[felipeZ]

Thanks @BvB93 for the feedback while solving this issue!