On Thu, Aug 8, 2013 at 12:38 AM, Pascal Muller
wrote:
> Hi all,
>
>
> With file.smi being
> C1=CC=CC=C1 single-double
> c1c1 aro
> c1c1N
>
> obgrep C1=CC=CC=C1 file.smi
> gives no output. But in my opinion, all 3 molecules should be matched.
>
No, the query string is a SMARTS, not a SMILE
With the obabel -s option you can specify the number of matches within a
single molecule, e.g. find molecules with more than 2 benzene rings. Try
obabel -L ops s
for details.
(Maybe obgrep's c option was originally going to do this?)
Chris
On 08/08/2013 09:43, Noel O'Boyle wrote:
> Or just l
Or just look at stderr, where it prints "3 molecules converted".
- Noel
On 8 August 2013 09:43, Noel O'Boyle wrote:
> I think it would be easy to add as a general option to all filters. Chris?
>
> In the meanwhile, "wc -l" will work I guess (needs Cygwin on windows).
>
> - Noel
>
> On 8 August 2
I think it would be easy to add as a general option to all filters. Chris?
In the meanwhile, "wc -l" will work I guess (needs Cygwin on windows).
- Noel
On 8 August 2013 09:38, Pascal Muller wrote:
>
>
>
>> If obabel does it, it always does it better:
>>
>> (...)
>
>
> Ok... I need to think to
If obabel does it, it always does it better:
>
> (...)
Ok... I need to think to the -s option instead of obgrep, then.
I found the -v option (invert the matching), but is there an equivalent to
the obgrep -c option (number of matches)?
> I'm in favour of replacing all obgrep, etc. with symlink
If obabel does it, it always does it better:
C:\Users\noel>obabel -:"C1=CC=CC=C1 single-double" -:"c1c1 aro"
-:c1c1N -s c1c1 -osmi
c1c1single-double
c1c1aro
c1c1N
3 molecules converted
I'm in favour of replacing all obgrep, etc. with symlinks to obabel.
-
Hi,
>>> Usually, I use obgrep (Open Babel 2.3.2) with smiles files, but today I
> >>> tried with an sdf - and it doesn't work. There is no match, and no
> error
> >>> message (e.g.
> >>> obgrep 'C' methane.sdf
> >>> gives no output, as if there were no match.
>
Trying with a "_" in the molecule n
Hi all,
With file.smi being
C1=CC=CC=C1 single-double
c1c1 aro
c1c1N
obgrep C1=CC=CC=C1 file.smi
gives no output. But in my opinion, all 3 molecules should be matched.
I'm pretty sure this problem was already discussed, but I found only this
post
http://forums.openbabel.org/Fw-Re-substru
