Re: [Rdkit-discuss] improving substructure search behavior with real molecules

Thu, 01 Mar 2012 03:47:30 -0800


Here's a less obvious one:
| OCO      | [CH]    | Yes   |

I would argue that this one is correct because "C[H]" is a
substructure of "OC([H])([H])O"


I always thought that by not specifying a 'count', it defaults to a count of 1 (~ the SMARTS manual at the Daylight site: http://www.daylight.com/daycgi_tutorials/depictmatch.cgi ).
Wouldn't that mean that [CH] should not match OCO? I checked it at the Daylight site with their depict tool, and these are their defs:

| OCO     | C      | Yes |
| OCO     | [CH0]  | No  |
| OCO     | [CH1]  | No  |
| OCO     | [CH2]  | Yes |



Cheers,
Hans





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On 01 Mar 2012, at 12:06, Greg Landrum wrote:

On Thu, Mar 1, 2012 at 4:49 AM, JP <[email protected]> wrote:

How are Hs handled ?  Are implicit and explicit Hs handled in the same way?

E.g.
Does molecule CCC (defined without Hs) match query [CH3][CH2][CH3] (or
[CH3]) ?  (Do you take in consideration implicit Hs?)
Does molecule [CH3][CH2][CH3] match query CCC ? (This should match as you
can find CCC in the molecule).

Good point, more clarity is needed there. How about this as a proposal:

| OCO      | C       | Yes   |
| OCO      | [CH2]   | Yes   |
| OCO      | [CH3]   | No    |
| O[CH2]O  | C       | Yes   |
| O[CH2]O  | [CH2]   | Yes   |

Here's a less obvious one:
| OCO      | [CH]    | Yes   |

I would argue that this one is correct because "C[H]" is a
substructure of "OC([H])([H])O"

-greg

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