- Forwarded Message -
From: MARIA BRANDL m.bra...@btinternet.com
To: openbabel-discuss-ow...@lists.sourceforge.net
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
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
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
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
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. The
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):
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
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;
to this
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
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 the
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
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
On Tue, Dec 3, 2013 at 11:43 AM, Dimitri Maziuk dmaz...@bmrb.wisc.eduwrote:
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
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 see
On Tue, Dec 3, 2013 at 1:11 PM, Yoel yoe...@gmail.com 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
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
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
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
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