> Note that an output format is not used but something still has to be there.
> Writing the functionality as an output format -ocount as suggested by Noel
> would be clearer but I didn't find it easy to do.
I suspect the op will be slightly faster than an output format due to overhead.
-Geoff
On 08/21/2013 10:41 AM, Chris Morley wrote:
> obabel 10dataset.sdf -onul --count
...
> Note that an output format is not used but something still has to be
> there. Writing the functionality as an output format -ocount as
> suggested by Noel would be clearer but I didn't find it easy to do.
Off
On 17/08/2013 20:09, Chris Swain wrote:
Is there a way to simply count the number of molecules in a file?
There is an API command OBConversion::NumInputObjects() which works with
most multi-molecule formats (although it looks faulty for mol2). It is
currently not exposed in the obabel interfa
Hello,
For sets that are not extremly big (as it could get quite long), I'd
suggest converting to smiles and counting the lines:
obabel input.mol2 -o smi | wc -l
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/8/20 Dimitri Maziuk
> On 08/20/2013 12:32 PM, Noe
On 08/20/2013 12:32 PM, Noel O'Boyle wrote:
> I usually use grep too, but I understand what you're saying - it's a
> common task we should automate (e.g. "-ocount"). In the meanwhile, you
> could speed it up quite a bit by turning off some of the perception,
> i.e. -aT (read title only).
python:
c
I usually use grep too, but I understand what you're saying - it's a
common task we should automate (e.g. "-ocount"). In the meanwhile, you
could speed it up quite a bit by turning off some of the perception,
i.e. -aT (read title only).
- Noel
On 18 August 2013 07:35, Chris Swain wrote:
> Hi,
>
Hi,
Thanks for the suggestions
At the moment I use
/usr/local/bin/obabel '/Users/swain/Desktop/acetophenones.sdf' -onul -v 'F'
2>&1 |cut -d " " -f1
Which does work but I was wondering if there was a command I was missing
Cheers
Chris
On 18 Aug 2013, at 03:13, "S.L. Chan" wrote:
> If
If it is for an SD file and if you are on unix, you could do
fgrep -c "M END"
or
fgrep -c ''
Just check that the last line is also '', otherwise you
may have to add 1.
If it is for a mol2 file, you could do
fgrep -c "@ATOM"
If you are on Windows, open a DOS prompt and substit
