Geoffrey Hutchison schrieb:
> If you look at the specification, most of these are marked as "ignored when
> read", query, reaction, or unused. I've definitely seen non-standard SD files
> with fewer fields.
Yes, but as far as I can see, Symyx Programs always set those fields to
zero, which wor
> According to Openbabel's wiki this format is following the specification of
> Symyx CTFile at http://www.symyx.com/downloads/public/ctfile/ctfile.jsp. But
> I have observed it does not.
I perhaps should adjust the wiki to point out that the CTFile specification has
changed repeatedly. I haven
Yes.
On Mon, 2009-11-16 at 10:13 -0800, Vinay M wrote:
> Hi Everyone,
> Can i convert large database of compounds which are
> in smiles to SDF.
>
> Thanks
>
>
>
>
> __
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Hi Everyone,
Can i convert large database of compounds which are in smiles
to SDF.
Thanks
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Dear Andrei,
My apologies for not replying sooner -- you're much more likely to get a fast
response on Open Babel issues if you e-mail through the mailing list.
The reason there isn't a direct "OBLogP" solution is because all descriptors
have changed. The code would be something like this in C+
Andreas Maunz wrote:
> Hi list,
>
> this is strictly speaking not an OB question: How can I match a SMARTS
> pattern with optional branch?
> Example: My compound is "C-C(-O)=C-C". The SMARTS expressions are
> s1="[#6]-[#6](-[#8])=[#6]" matches, as well as s2="[#6]-[#6]=[#6]".
> Since s2 is contain
Thanks for the replies. I guess it's time for a new query language with
capabilities beyond SMARTS.
I found at least a "workaround" with SMARTS: one can mandatory demand
the part "before" the branching point and then attach two versions, with
and without the branch using OR.
Consider these example
On Mon, Nov 16, 2009 at 8:52 AM, Andrew Dalke wrote:
> On Nov 16, 2009, at 1:46 PM, Andreas Maunz wrote:
>
> > Is there a way to combine s1 and s2 into a single SMARTS expression?
>
> Sadly, no. I seem to recall other molecular structure query languages
> which are a bit more capable and which mig
On Nov 16, 2009, at 1:46 PM, Andreas Maunz wrote:
> this is strictly speaking not an OB question: How can I match a SMARTS
> pattern with optional branch?
SMARTS matches each atom and bond term to an atom and bond. It does
not support optional terms.
> Is there a way to combine s1 and s2 into a
Hi list,
this is strictly speaking not an OB question: How can I match a SMARTS
pattern with optional branch?
Example: My compound is "C-C(-O)=C-C". The SMARTS expressions are
s1="[#6]-[#6](-[#8])=[#6]" matches, as well as s2="[#6]-[#6]=[#6]".
Since s2 is contained in s1 in terms of subgraphs, I w
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