Oh and to ‘blank’ atoms..

ferrocene
  Mrv0541 01051417472D          

 13 12  0  0  0  0            999 V2000
    1.6500   -0.0000    0.0000     0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -0.0000    0.0000 Fe  0  2  0  0  0  0  0  0  0  0  0  0
    4.9500    0.0000    0.0000     0  0  0  0  0  0  0  0  0  0  0  0

Really nice to handle :-)

J

On 2 Jan 2014, at 20:29, Cyrus Harmon <ch-cdk@bobobeach.com> wrote:

Hi CDK list,

I came across this posting from a couple of years ago, but didn’t see a good answer. Any suggestions on how to represent bonds with a variable attachment point in CDK?

thanks,

Cyrus

Jules Kerssemakers Mon, 04 Oct 2010 08:03:51 -0700

Hello CDK-colleagues,

A question has been nagging me lately: how would one represent
partially known attachment information, also commonly referred to as
'variable attachment', in the CDK and/or a save-to-disk-format?
I'm talking about cases like "We know this benzoic acid has a chlorine
group, but we don't know if it's ortho-, meta- or para-".
The drawing convention for ring systems is to draw a bond to the
center of the ring. I'm not sure if there's a convention for non-ring
variable attachment. I'm wondering how this would work in the CDK and
if there are any good serialisation formats for this.


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