Noel,
I'm not sure how to describe all the cases with a switch statement.
The original idea of using SMARTS came from your suggestion:
> The thing is, if I was matching a functional group, I would just use a
> SMARTS pattern. This is a general solution for 99% of cases, rather
> than having a
The presence of a class or not is an "implementation detail", as they
say. That is, the user doesn't need to know anything about that.
However, as I am currently replacing the use of SMARTS patterns for
atom typers with switch statements, I'd recommend you to avoid using
SMARTS for this in the
To avoid multiple threads, let's move this over to the opensmiles list.
On 2 March 2017 at 20:31, Andrew Dalke wrote:
> On Mar 2, 2017, at 20:34, Craig James wrote:
>> Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that
On Mar 2, 2017, at 20:34, Craig James wrote:
> Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that
> the "organic subset" are only allowed outside of brackets if they're in their
> normal lowest-valence state. Actually, now that I read it, it's
Hi Craig,
>From what you say, it sounds like this is a better discussion for the
OpenSMILES list. My intention is to match existing usage and what I
believe to be Daylight usage. Let's have this discussion over there,
and can clarify the spec either way depending on the outcome.
- Noel
On 2
Hi Noel,
On Thu, Mar 2, 2017 at 10:11 AM, Noel O'Boyle wrote:
> In the course of sorting out the handling of implicit Hs, I've found
> that the current SMILES writer writes hypervalent atoms from the
> organic subset in square brackets. E.g. Texas carbons:
>
> >obabel
Noel,
thanks for the clarification, the only reason why I was looking at the lazy
mechanism was
because of previous code.
I'm OK with the simple function, although I think there's still a need for a
dedicated
class behind which gets called to parse the different SMARTS patterns from a
data
Hi there,
In the course of sorting out the handling of implicit Hs, I've found
that the current SMILES writer writes hypervalent atoms from the
organic subset in square brackets. E.g. Texas carbons:
>obabel -:C(C)(C)(C)(C)C -osmi
[C](C)(C)(C)(C)C
or "FIF" as "F[I]F".
This is unusual behaviour
Typo: "But the guidelines are not unfortunately the existing code. "
On 2 March 2017 at 10:22, Noel O'Boyle wrote:
> Hi Stefano,
>
> Sounds good. But the guidelines are not unfortunately the existing
> guide. I'm currently in the process of rewriting/removing as much of
>
Hi Stefano,
Sounds good. But the guidelines are not unfortunately the existing
guide. I'm currently in the process of rewriting/removing as much of
the croft as possible and the Lazy Evaluation mechanism is in my
sights. It's a legacy from the original codebase. It'll be difficult
to change this
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