Hello again,
I've fixed the issue here: https://github.com/openbabel/openbabel/pull/52
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/12 Maciek Wójcikowski
> I think, I've pin-pointed the issue in the source - OBConversion class.
> The first and last molec
I think, I've pin-pointed the issue in the source - OBConversion class. The
first and last molecule is set by SetStartAndEnd method. It's being called
only by Convert method, not by Read nor ReadFile, hence the binding dont
use -f and -l. I figure if i't called SetStartAndEnd in Read or ReadFile,
t
> This only proves, that I really want to use it. Is the proof.py script
> working correctly for anybody (attached in previous mail)? It should ouptut
> molecules no. 5-10 out of 100 in proof.sdf
No, it doesn't work.
% python proof.py | wc
100 1001300
Hmm. Chris, any idea why this
This only proves, that I really want to use it. Is the proof.py script
working correctly for anybody (attached in previous mail)? It should ouptut
molecules no. 5-10 out of 100 in proof.sdf
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/3 Chris Morley
> > O
On Dec 3, 2013, at 3:52 PM, Chris Morley wrote:
> In fact it is implemented this way for most common multi-molecule file
> formats. The molecules before the one specified by the -f option are
> skipped without being parsed. (The format's virtual SkipObjects()
> function is used.)
I stand corr
> On 2013-12-03 04:28, Maciek Wójcikowski wrote:
>> You're probably right, C also has to read therm, but other than recognizing
the beginning and the end of the molecule it wouldn't do anything
especially
kekulization and bonding etc.
>
On 03/12/2013 18:11, Geoffrey Hutchison wrote:
> Actually no.
> You're probably right, C also has to read therm, but other than recognizing
> the beginning and the end of the molecule it wouldn't do anything especially
> kekulization and bonding etc.
Actually no. Indeed this would be a useful "lazy" optimization, but is not
currently implemented this way.
Hi Dimitri,
Try to do that for 20mln molecules, I guarantee you it'll kill your
machine. The point is to skip n molecules at the beginning of the file, and
do it efficiently(aka, read only desired range on n-m molecules). You're
probably right, C also has to read therm, but other than recognizing
On 2013-12-03 04:28, Maciek Wójcikowski wrote:
> Hello,
>
> I'd like to ask, if it's somehow possible to use first [-f] and last
> [-l] options via python bindings?
last = list(mols)[-1] ? -- I haven't tried myself. I suspect even in c++
you still have to actually read them all in to get random a
Hello,
I'd like to ask, if it's somehow possible to use first [-f] and last [-l]
options via python bindings? I've looked at pybel._operations, but there is
no such option there. Setting it via OBConverter's methods AddOption() and
SetOptions() does't seem to work either. My first instinct is that
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