Hi Noel,
this is a test file with 10 molecules only. memory consumption of the
java.exe is 20-25 mb, so not a problem. Moving the builder outside of the
loop does not help with the issue. I also moved the OBConformerScore outside
of the loop. But does not help either.
--
View this message in co
It does to me in the sense that I am think of assigning R and S - not
other labels - in a correct manner according to the CIP rules. Why do
I want to do that and not @/@@? Well because that how we do it. @/@@
it is useful for database search etc but we don’t use it in the
classroom or in the semina
Hi Yoel,
On Tue, Dec 3, 2013 at 7:44 PM, Yoel wrote:
> Hum! I’m pretty confident with what I know but the issue here is that
> you answer isn’t contributing to clarifying the question. The question
> is how to we determine the chirality of a centre regardless of how you
> may choose to represent
I meant I didn’t* see anyone that couldn’t do it
On 3 December 2013 23:36, Yoel wrote:
> Indeed it is hard but I have to STRONGLY disagree that we chemists
> assign R and S configuration in any other way that by applying the CIP
> rules… and for those molecules that are more complex we usually ta
Indeed it is hard but I have to STRONGLY disagree that we chemists
assign R and S configuration in any other way that by applying the CIP
rules… and for those molecules that are more complex we usually take
more time. Neither during my PhD years or my postgrad years I saw any
organic chemist that c
> inevitable will come down to applying the CIP rules. Do you disagree with
> that?
No, I disagree. Yes, there are implementations of the CIP rules in code.
Generally these are used when generating IUPAC names, and that's about it.
If I take a structure to a colleague to synthesize, I only need
Hum! I’m pretty confident with what I know but the issue here is that
you answer isn’t contributing to clarifying the question. The question
is how to we determine the chirality of a centre regardless of how you
may choose to represent it at a later point. And this problem
inevitable will come down
On Tue, Dec 3, 2013 at 1:11 PM, Yoel wrote:
> Craig,
>
> Thanks a lot for this. I do not know the smile notation in details
> however as a chemist I’m pretty sure I understand chirality. If I
> understood your article I see that explains how chirality is
> represented in smile notations but I sti
On 12/03/2013 03:11 PM, Yoel wrote:
> Craig,
>
> Thanks a lot for this. I do not know the smile notation in details
> however as a chemist I’m pretty sure I understand chirality. If I
> understood your article I see that explains how chirality is
> represented in smile notations but I still don’t
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
Craig,
Thanks a lot for this. I do not know the smile notation in details
however as a chemist I’m pretty sure I understand chirality. If I
understood your article I see that explains how chirality is
represented in smile notations but I still don’t see how do you know
what chirality to represent
> 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.
On Tue, Dec 3, 2013 at 11:43 AM, Dimitri Maziuk wrote:
> On 12/03/2013 01:28 PM, Yoel wrote:
> > Dimitri,
> >
> > In this case you do know which way you are looking. For brevity let's
> > consider a tetrahedral carbon atom with four different substituents...
> the
> > first thing you do is to assi
I find you one of the most interesting paper I know regarding this topic
http://pubs.acs.org/doi/abs/10.1021/ci990090v
The principle author P. Matos has several other papers on implementing CIP
algorithms
I have never tackle this problem myself but she is quite convinced that the
CIP are a most
It shouldn't be any different to CIP since those are the rules I was talking
about however I was being super short! There very interesting research
papers on the topic that I came across quite sometime ago. I am sure that
with time I could get one for you.
However, the local connectivity should be
On 12/03/2013 01:28 PM, Yoel wrote:
> Dimitri,
>
> In this case you do know which way you are looking. For brevity let's
> consider a tetrahedral carbon atom with four different substituents... the
> first thing you do is to assign them priorities based on there atomic
> numbers then you place th
Dimitri,
In this case you do know which way you are looking. For brevity let's
consider a tetrahedral carbon atom with four different substituents... the
first thing you do is to assign them priorities based on there atomic
numbers then you place the smallest priority backward... this gives you t
Thank Noel,
I found the docs pretty clear. My problem isn’t with open babel
directly but with understanding how to, for example, use standard out
to write my object using the java bindings…
the lit example:
converting this "std::cout <<
facade.GetTetrahedralStereo(atom->GetId()) << std::endl;"
t
On 12/03/2013 12:54 PM, Noel O'Boyle wrote:
> We don't support generation of R and S labels. However, we do store
> the stereochemistry. It's all stored in that config object. Clockwise
> and Anticlockwise are with respect to the stereo refs in the config.
> It should be clear enough from the docs
We don't support generation of R and S labels. However, we do store
the stereochemistry. It's all stored in that config object. Clockwise
and Anticlockwise are with respect to the stereo refs in the config.
It should be clear enough from the docs (googling "openbabel
stereochemistry"): http://openb
I still haven't been able to print the winding property but obviously if it
turns out that the algorithm can't properly find the clockwise and
anticlockwise values then it is not useful unless ALA is the an exceptional
error.
--
View this message in context:
http://forums.openbabel.org/stereo-c
On 12/03/2013 12:19 PM, Yoel wrote:
> Is it right that you don't support R and S? I'm new to openbabel like two
> days old only but I have already seen that
> "facade.GetTetrahedralStereo(atom.GetId())" will return OBTetrahedralConfig
> (java) wich contain a Config structure/object with a winding p
Is it right that you don't support R and S? I'm new to openbabel like two
days old only but I have already seen that
"facade.GetTetrahedralStereo(atom.GetId())" will return OBTetrahedralConfig
(java) wich contain a Config structure/object with a winding property that
has two possible values: clockw
> 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
How many molecules are in mols.smi? Have you looked at task manager to
see memory usage while running this?
You should move the initialisation of OBBuilder outside the loop. I
have a feeling you are eating up memory by creating this multple
times.
- Noel
On 3 December 2013 06:43, Joos Kiener wr
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
- Forwarded Message -
From: MARIA BRANDL
To: "openbabel-discuss-ow...@lists.sourceforge.net"
Sent: Monday, 2 December 2013, 14:09
Subject: small molecule restraints in mmcif format
Dear open-babel discuss mailing list,
I submitted a question concerning the introduction of a new
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