Hi rdkit fiends!
The [Daylight SMARTS example page](
https://daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
gives several examples for "multiple group" smarts, including these strings:
([Cl!$(Cl~c)].[c!$(c~Cl)])
([Cl]).([c])
([Cl].[c])
[NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)]
In general, I cannot get these to be parsed by Chem.MolFromSmarts().
For example, Chem.MolFromSmarts('([Cl!$(Cl~c)].[c!$(c~Cl)])') gives me
this error message:
```
[13:01:41] SMARTS Parse Error: syntax error while parsing:
([Cl!$(Cl~c)_100].[c!$(c~Cl)_101])
[13:01:41] SMARTS Parse Error: Failed parsing SMARTS
'([Cl!$(Cl~c)_100].[c!$(c~Cl)_101])' for input: '([Cl!$(Cl~c)].[c!$(c~Cl)])'
```
My understanding of SMARTS is that the outermost parentheses in this SMARTS
string are required to force the chlorine and the aromatic carbon to be
somewhere in the same covalently connected fragment. E.g. this pattern
*should* hit benzyl chloride ClCc1ccccc1 but should *not* hit the
hydrochloride salt of aniline Cl.Nc1ccccc1.
What am I getting wrong? Is there a way to write rdkit-parsable SMARTS
that achieves this? (I want to filter our molecules that contain more than
one of certain moieties, while allowing molecules that have one (or zero)
such moieties. But salts or covalently disconnected fragments that each
contain one instance of the moiety should be fine.)
Details on my setup:
- RDKit Version: 2019.09.3
- Operating system: macOS 10.15.2
- Python version (if relevant): 3.6
- Are you using conda? yes
- If you are using conda, which channel did you install the rdkit from?
`conda-forge`
- If you are not using conda: how did you install the RDKit?
Curt
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