2:42 AM
To: Lee-Ping Wang
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] SVG draws unwanted extra hydrogens
Dear Lee-Ping,
I do my 2D structure diagram generation [1] from 3D coordinates like this:
import openbabel as ob
molecule = ob.OBMol()
# load
.jm.mul...@gmail.com]
> Sent: Friday, September 26, 2014 3:03 AM
> Cc: openbabel-discuss@lists.sourceforge.net
> Subject: Re: [Open Babel] SVG draws unwanted extra hydrogens
>
> Hi,
>
>
> For carbon monoxyde, try this smile: [C-]#[O+]
>
> Regards,
> Pascal
>
Muller [mailto:pascal.jm.mul...@gmail.com]
Sent: Friday, September 26, 2014 3:03 AM
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] SVG draws unwanted extra hydrogens
Hi,
For carbon monoxyde, try this smile: [C-]#[O+]
Regards,
Pascal
coords.xyz
Description
Hi,
For carbon monoxyde, try this smile: [C-]#[O+]
Regards,
Pascal
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Are you Audit
The H atoms are drawn intentionally. See the docs for the 'a' option:
a draw all carbon atoms
So propane would display as H3C-CH2-CH3
What you want is an additional option that draws the C's but not the
H's. I don't have time now to do development, but it should be pretty
easy to see where o
You can put brackets around the carbon in carbon monoxide and not get the
hydrogen. Otherwise, smiles specifies that carbon must have 4 bonds, so you
need a hydrogen to fill the fourth bond.
Note, you'll probably now have a little dot next to the carbon. I have no
idea how to get rid of that.
On
Sorry for the extra email; I'm attaching the original .xyz file that I am
trying to represent in the 2D image.
- Original Message -
From: "Lee-Ping Wang"
To: openbabel-discuss@lists.sourceforge.net
Sent: Thursday, September 25, 2014 8:34:41 PM
Subject: SVG draws unwanted extra hydrogens
